Cancer: From Genomics to Pharmaceutics

242 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPY2. NanocarriersThere are different types of nanocarriers and some of them are described below.2.1. LiposomesAn aqueous core is encircled by one or more layers of phospholipids and cholesterol, whichtogether form a lipid bilayer and result in a liposome (Figure 1) (6). A team led by Banghamdeveloped liposomes in 1965 for the first time (7, 8). The US Food and Drug Administration(FDA) authorized the use of doxorubicin (Doxil) in a liposomal formulation in 1995 to treatKaposi sarcoma associated with AIDS (9). As nanocarriers for drug delivery, liposomes alsoprovide a number of other benefits. Liposomes shield the drug from deteriorating due todegradation and stop it from being unintentionally released into the environment, which mayreduce the rate of drug release (10-13). The lipid bilayer is stabilized by certain lipid species,such as rigid saturated lipids and cholesterol, to fend off attacks from plasma proteins andlessen drug leakage (12,13). Many researches have recently concentrated on changing thedrug-releasing mechanisms of liposomes. For instance, several stimuli such as hyperthermia(14), magnetism (15-17), enzymes (18,19), ultrasound (20,21), or light (22,23) can causethe release of drugs from liposomes. Furthermore, nucleic acid delivery via ligand-mediatedtargeting may be paired with drug-releasing liposomes (24-27).By conjugating targeting moieties, namely peptides, monoclonal antibodies orsmall-molecule ligands, with liposomes, tumor cells may be actively targeted. (28) Theendocytosis-mediated cellular liposome absorption boosts the efficiency of the drug. Thetherapeutic window is increased by liposome-mediated intracellular and organelle targeting.Figure 1: LiposomeRecent advances in liposome technology have led to the creation of stimuli-sensitiveliposomal systems (these stimuli being redox, pH, temperature and enzymatic changes) thathave improved anticancer effectiveness (29, 30). Circulating and tissue-specific systems maybe created by changing the lipid content, size, and surface charge of liposomes. Liposomaldrug delivery has difficult limits in terms of industrial reproducibility, stability and scalability,Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 243yet they are nevertheless regarded as novel technologies. The enhanced permeation andretention (EPR) effect contributes to intratumor liposome accumulation (31).2.2. Polymer-based nanocarriersColloidal particles with diameters ranging from 1 to 100 nm are known as polymericnanoparticles (PNPs). The PNP structure is made of polymers of natural or synthetic originsthat are biodegradable and biocompatible (Figure 2). While PNPs and liposomes have verysimilar form and size characteristics, they also have greater in vivo and in vitro stability, arelatively high cargo capacity, and improved targeting capabilities (32, 33). PNPs have beenmade using biodegradable polymers such as polyamides (albumin, gelatin, etc.), polyesters(Poly(lactide-co-glycolide)-PLGA, Poly(caprolactone-PCL), polyanhydrides, polyurethanes,and polyphosphazenes (34).Figure 2: Polymeric nanoparticleThese are the first-generation PNPs, which target tumor cells passively. The developmentof a new generation of PNPs for carrier-mediated drug targeting to cancer cells is aresult of improvements in pharmaceutical research and development (35). By coveringPNPs with polymers that particularly bind to the overexpressed receptors on cancercells, second-generation nanoparticles were created, whereas third-generation PNPs havecell-specific ligands for targeted delivery, which allow active targeting to the tumor location.The most significant key material properties that influence the in vivo performance ofnanocarriers are their entrapment efficiency, zeta potential, particle size, and drug releaseprofile (36). By adjusting the formulation characteristics (polymer type, solubility, molecularweight, excipient type, drug ratio, etc.) and manufacturing process (homogenization speed,temperature, etc.), it is possible to tune the distinctive qualities of these PNPs (37). Dependingon the formulation design, several processes, including drug diffusion, erosion, hydrolysis,and the enzymatic degradation of the polymer matrix, can be used to regulate the pace atwhich anticancer drugs are released.There have been many researches on polymeric nanoparticles, micelles, dendrimers,nanosponges, nanogels, and nanofibers (38,39). Only one albumin-based nanoparticle,Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

244 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPYprotein-bound paclitaxel (Abraxane®) (40, 41), has received FDA approval for clinicalusage in the treatment of breast cancer, non-small cell lung cancer, and pancreatic cancer.Paclitaxel-containing albumin nanoparticles have positively altered the pharmacokineticformulation of the drug increasing its water solubility and decreasing its dose-limiting toxicity(42).2.3. Polymeric micellesSelf-assembling colloidal nanocarriers with a hydrophilic corona and a hydrophobiccore are called polymeric micelles (Figure 3). They are produced when amphiphilic blockcopolymers self-assemble in aqueous mediums at concentrations above the critical micelleconcentration (43). A synergistic anticancer action can be produced by solubilizing one ormore drugs in the micellar core (44, 45). By adding targeting molecules to the micellar corona(46), polymeric micelles may be directed toward the tumor site. In 2007 the FDA authorizedGenexol-PM, a primary paclitaxel-loaded mPEG-PLA polymeric micelle (47, 48). It has beendemonstrated to lessen the severity of toxic effects like hyperlipidemia, peripheral neuropathyand hypersensitivity reactions, and is loaded with a free-Taxol formulation.Figure 3: MicelleHydrophilic polymers including chitosan, poly(oxazolines), dextran and poly(ethyleneglycol), as well as hydrophobic ones like polyesters, phosphatidyl ethanolamines andpoly(amino acids) make up micelle-forming copolymers (49). Furthermore, micellarstructures can be created by drug-conjugated polymers, altering the drug release profile(50, 51). Owing to their small particle size (≺100 nm), micelles are particularly appealingdrug delivery methods for cancer treatment because they are able to exhibit the EPR effectand thus can allow for tumor-selective targeting. Moreover, they are susceptible to cues inthe tumor microenvironment like hypoxia, enzymes and pH (52, 53). The pH-dependentdegradable linkers (e.g. hydrazones) or the pH-sensitive polymers (e.g. polyhistidines andpoly-?-aminoesters) of micelle-forming polymers may cause micellar deconstruction andtrigger the encapsulated cargo’s release as a response to low tumoral pH.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 2452.4. DendrimersDendrimers are globular macromolecules that have complex spherical structures and rangein size from 1 to 100 nm (53, 54). A central core, branches dubbed “generations”, repeatunits containing at least one branch junction, and several terminal functional groups are theircharacteristics (55, 56) (Figure 4).Figure 4: DendrimerDendrimers generate organic or inorganic hybrid nanoparticles that have the ability tostabilize and self-assemble. For use as drug carriers (57, 58) and target-specific carriers,dendrimers can be coupled to nanoparticles (59, 60), carbon nanotubes (61-63) and liposomes(57, 64, 65) to modulate their solubility (58, 66, 67).2.5. Inorganic NanomaterialsA variety of inorganic nanoparticles (these including quantum dots, superparamagneticiron oxides, gold nanoparticles, carbon nanotubes, and other nanoclusters or non-metallic andmetallic nanoparticles) improve tumor imaging and increase the efficiency of radiotherapy(68, 69). The size of some of these inorganic nanoparticles (10-100 nm) allows them topass through capillaries and be absorbed by various organs. Others are more substantialand need passive targeting by delivery to particular disease sites. Moreover, multifunctionalnanodevices are being developed to target cancer for treatment (70-72).3. Passive TargetingIt has been determined that approximately 17% of deaths in the world in 2020 are causedby cancer (73). In order to develop an approach to treatment in cancer, where there is a lotof loss and death rates increase on a daily basis, it is necessary to understand cancer cellsand their structure. It is known that treatments used in traditional cancer treatment destroyhealthy cells along with cancer cells (74). When the cancer cells and normal cells werecompared in the studies, it was seen that the structure and environment of both cells weredifferent. In recent years, approaches to producing drugs based on these differences havestarted to be implemented. The main difference in these two cell structures is that cancerCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

246 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPYcells have increased angiogenesis and cellular permeation, increased intracellular pH, andmoderate hyperthermia (75). These structural changes in and around cells are called the EPReffect (Figure 5).Leaky blood vessels and poor lymphatic drainage are among the common characteristicsof tumors. One would expect free-roaming drugs to diffuse in a nonspecific way, thoughunlike them nanocarriers have the ability to escape into the tumor tissues through the leakyvessels. This occurs due to the EPR effect. Another common characteristic is caused by therapid and defective formation of new blood vessels from the already existing ones (a processthat is known as angiogenesis), causing an increased permeability of blood vessels.Figure 5: The comparison of normal and cancer cells and tissuesAdditionally, the lymphatic drainage in tumor tissues not operating normally or properlyleads to the accumulation of nanocarriers and leads them to releasing drugs in close vicinityof tumor cells (76). This leaky vascular feature and less lymphatic system around the tumortissue allow for passive targeting.In the studies, it was observed that there was no significant difference between non-targetednanocarriers and receptor-targeted nanocarriers in terms of overall tumor accumulationassessment (77, 78).In light of all this information, two main approaches are applied to ensure passive targetingand to ensure that the nanoparticles stay in the cancerous tissue for a longer time. These arethe physicochemical properties of the particle and the changes that can be made in the tumortissue, respectively.3.1. Physicochemical properties of the particlesAmong the approaches developed to turn the differences in tumor tissue into an advantagewith EPR effect; size, molecular weight, ionic charge and nanoparticle shape are the mainfactors in the properties of particles. If we look at these elements;• Nanoparticles with a particle size of 10-200 nm, especially around 100 nm, leak fromthe vessels, but cannot return to the systemic circulation since they are low in lymphaticCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 247drainage and accumulate in the area of the tumor tissue (79).• Studies have shown that the ability to accumulate in tumor tissue has an effect onthe molecular weights of these structures together with nano-sized carriers, and smallKDa molecules are discarded faster. It has been shown that molecules above 40KDa, which is the limit for renal clearance, can accumulate better (80). Studies haveshown that the residence time of NPs in the blood contributes to the accumulationof NP in the tumor tissue. In order to ensure this accumulation and reduce theexcretion from the kidneys, the size of the NP is increased with polymers such asN-(2-hydroxypropyl)methacrylamide (HPMA) and poly(ethylene glycol) (PEG) in orderto increase the MW to a certain point, thus increasing its residence time in the tissue (81).For macrophages, one of our body’s defense mechanisms, every unrecognized structurethat enters the bloodstream is seen as a threat and eliminated via phagocytosis. Theseparticulate systems prepared at nanoscale are classified as foreign by macrophagesand are tried to be destroyed. This situation is also one of the biggest obstacles fornanosystems that must remain in the bloodstream (75). Pegylation is also advantageousin this sense, as it reduces the detectability of nanoparticles by macrophages.• Ionic charge is another factor affecting the amount of accumulation of NPs in the tumortissues. Studies have shown that particles with positive ionic charge have a shorterresidence time in plasma than neutral or negative ones, and they do accumulate intumor tissues (82).• Another factor affecting the residence time of NPs in tumor tissues is the shape of theparticle. In studies, when spherical particles and rod-shaped particles are compared, ithas been observed that even though they have the same size, the excretion of rod-shapedparticles from the kidneys is lower and they accumulate more in tumor tissues (83).3.2. Making changes in tumor tissueWith this irregular blood supply in the tumor area, the blood vessels there also have lesssmooth muscle layer, compared to the blood vessels of normal tissues. This anomaly in thevascular structure has attracted the attention of scientists and it has been determined that thereare ways to increase drug accumulation by chemical or mechanical means (84).In studies conducted within these groups, it has been observed that the interaction withAngiotensin II (AT II) is less and when AT II is secreted in the body and hypertensionis present, drug accumulation in cancerous tissues is approximately 5 times higher than innormal tissues (85). Like AT II, the cancerous region is also present in different mediators thatincrease drug accumulation. These mediators help drug retention by taking advantage of thedifferentiation in vascular blood supply. Nitric oxide (NO), vascular endothelial growth factorCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

248 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPY(VEGF), peroxynitrite, bradykinin, matrix metalloproteinases (MMPs) and prostaglandins(PGs) are some of these mediators (86).It is possible to list ultrasound, radiation, hyperthermia, or photo-immunotherapy asmechanical approaches that can be used to modulate tumor vasculature and increase thepermeation of nanoparticles (84).4. Active TargetingActive targeting describes the manner of action of nanoparticles that have surfacemodification in order to contain affinity ligands that possess specificity to tissues and cellswith disease. Such nanoparticles selectively attach to targeted molecules thanks to the abilityof the ligands to bind to the surface. Though due to their limitations there haven’t beenmany nanoparticles that could reach actual clinical approval, despite managing to reach theclinical development stage. There are various limiting factors that contribute to this, likethe insufficient amount of knowledge and expertise on what happens to the nanoparticlesat the body on a cellular level, the overall difficulty in the synthesis of nanoparticles thatare both reproducible and controlled and producing them at sufficiently larger scales forcommercialization, or the absence of sufficient technology allowing for screening underbiologically relevant conditions for a large number of nanoparticle candidates that might beconsistently associated to clinical performance (87).Unlike passive targeting, active targeting actually revolves around targeting ligands (likepeptides and antibodies) that have the ability to bind only to the receptor structures which areexpressed or overexpressed and at the same time located at the targeted location (Figure6). The use of active targeting can be generalized for the purpose of enhancing therecognition and uptake of the target cell, and not improving overall accumulation of tumorcells. Galactosamine, folate and transferrin are good examples of ligands that are used on aregular basis for the active targeting of nanosized formulations (88).Active targeting contributes to the improved distribution capabilities of nanoparticlesystems through employing peripherally conjugated targeting moieties. It should be noted,however, that contrary to the belief that antibody targeting is a promising approach, it hasbeen observed that internalization is enhanced in animal models, rather than the localization oftumor cells. Although internalization results in a greater therapeutic impact with nanoparticledrug delivery systems, only a portion of the released drug ends up reaching the targetcell. For some anticancer drugs to be delivered effectively, particularly in the case of genesilencing, gene delivery, and other biotherapeutics, internalization of the nanoparticle istypically necessary (89). In order to enhance the accumulation of nanoparticles, the activetargeting mechanism makes use of extremely precise interactions between the targeting ligandand particular tissues or cells in the body. It has been demonstrated that increasing avidity bysurface-functionalizing a number of molecules or using multivalent designs can compensateCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 249Figure 6: Active targeting of cancer cellsfor poor affinity in the case of weak binding ligands (77).Active targeting has attracted a noticeably large amount of interest in the researchcommunity over the years, seemingly being easy despite being quite a complicated processto achieve with nanomaterials. It makes use of various targeting groups like aptamers,antibodies and polypeptides. The complication of active targeting stems from the sizes ofboth nanoparticles and the water-soluble polymers. They are both large enough to be ableto engage in non-specific surface interactions. A possible fix is modifying the surface of thenanoparticle in question by using an inert polymer. The latter would ideally have a minimalamount of interactions with the cells while also being able to get one or more ligands attachedat the inert layer, which would lead to the specific binding of the receptor and the ligand.Polyethylene glycol is used widely for this purpose as an ideal polymer, standing out amongstothers due to the difficulty of correctly identifying a polymer that can be truly considered inert(90).4.1. Antibodies in Active TargetingOne of the most popular types of ligands for targeted nanomedicines is an antibody,including monoclonal antibodies (mAbs) or mAb fragments. Comparing antibodies to otherligands, they have a number of distinct benefits. First off, compared to small molecule ligandslike folate or RGD peptides, antibodies have far better specificity and affinities. Second,the antibodies include a significant quantity of -??2 and -COOH groups, which serve asconjugation sites for the crosslinking of nanomedicines. Third, numerous mAbs are approvedby FDA for use in cancer treatment (like rituximab or trastuzumab), unlike the other ligandsthat lack such approval and use (91).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

250 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPYThere are a number of factors that make the active targeting with antibodies morechallenging. These include the extravasation into the tissue, binding specifically to target cellsand survival in the bloodstream. Such obstacles may prevent proper diffusion and dispersionof the targeted nanomedicines, throughout the tumor parenchyma. The increased permeabilityand retention effect is widely acknowledged to be the passive targeting mechanism by whichtargeted nanomedicines enter tumors. Also, the first tumor cells that have the nanomedicinesattached to themselves actually prevent the latter from diffusing into the tumor parenchyma.This occurrence is collectively referred to as the binding site barrier, and has led to numerousstudies being unable to display the benefits of targeted nanomedicines (91).4.2. Factors Affecting the Active Targeting ProcessThere are several factors that immensely affect the active targeting process (Figure 7).The density of the targeting molecules on the surface of the nanoparticles has an influenceon the affinity for the substrate, as increased valency might lead to cooperative effects. Thenanoparticles’ sizes and shapes also have an impact on the process, if they are sphericalparticles, since smaller particle sizes may be problematic for the functionalization of theligand after the synthesis. The charges of the surface of the nanoparticles and the ligandsalso play a role (92), being able to impose a change on the spatial display of the ligand or theconjugation yield, whereas the forces between the ligand and the surface of the nanoparticles,regardless of being attractive or repulsive, may affect the conjugation process or the structureor conformation of the final ligand. Surface hydrophobicity, on the other hand, is anotherfactor that can impact the ligand display’s architecture, and may lead to serious changes inoutcomes, as the majority of the polymeric nanoparticles possess hydrophobic cores (81).4.3. Binding of Nanoparticles to Receptors on Cancer CellsThe explanation for why ligand-modified nanoparticles specifically bind to receptorson cancer cells is based on three factors. These are the overexpression of certain antigenicreceptors on the surface of cancer cells in comparison to cells in regular tissues, the intracellulardelivery made possible by the specificity and high binding affinity of targeting ligands toreceptors, and cell-mediated endocytosis via the ligand-receptor interaction (93).The primary mechanism that active targeting revolves around is the ligand’s recognitionby the targeted substrate. Two crucial factors that need to be considered when assessing theeffectiveness of a system utilizing active targeting are the delivery capacity and the targetingspecificity. The latter is linked directly to the structure and the material of the nanoparticlethat is being used. The former, on the other hand, is established by the biodistribution of thenanoparticle (that has been ligand-functionalized). Additionally, targeting specificity is alsodetermined by the nature of interaction of cells and off-target molecules with the nanoparticlessystem and the conjugated ligand (81).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 251Figure 7: Summary of factors influencing active targetingNanoparticles used for active targeting have an intrinsic attribute; they need to be in thevicinity of their target antigen in order to be able to interact with and recognize said antigen.This is considered to be one of the main difficulties of developing nanoparticles for activetargeting. On the other hand, it should also be considered that nanoparticles with activetargeting should possess longer circulation times than normal, due to their systemic clearance,as this has an impact on how much of the nanoparticles are available for supplying the tumor.The increase in the affinity of the nanoparticles is not always capable of compensation for theclearance in a natural way, since the tumor blood flow is relatively smaller than normal (94).Aside from that, the location of the molecular targets being in the extravascular spaces of thetumors, nanoparticles also have to rely on the EPR effect in order to reach their targets. Assuch, the circulation times of the nanoparticles have to go through proper optimization for anideal active targeting process (81).4.4. Methods for Conjugation of LigandsAs previously mentioned, the avidity of nanoparticles has a direct correlation withthe density of ligands. Thus, during the designing phase of actively-targeted systems, theplacement of ligands on the nanoparticle surface becomes a crucial factor. In this regard,covalent reactions are used widely in conjugation techniques (95). Although they first seem toprovide an efficient method for irreversibly linking antibodies to nanomedicines, it should notbe forgotten that they can also alter the antibodies’ biological activities. A favorable antibodyCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

252 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPYorientation is not certain either. Additionally, the management of the effect of the covalentreactions on both the positioning of the antibodies, as well as their biological activities, can bechallenging, which might lead to diminished biological activity of antibodies or poor overallefficiency in conjugation (91).The type and characteristics of the particle has an impact on the complexity of theconjugation process of the ligands, and so different approaches are needed for organicpolymers whose side chains or terminal reactive functionalities react either prior to or duringnanoparticle production. The targeting moiety will always be retained on the surface of theparticle in accordance with the stability of the ligand-nanoparticle bond. Other design factorsshould also be considered in that regard (81, 96).4.4.1. Methods for Pre-conjugation and Post-formulation PhasesWhen done prior to the assembly of the nanoparticle formulation, the conjugation ofthe ligand to the nanoparticle material is rather simple and can be accomplished with theuse of aptamers, peptides, and small molecules (97). Given that the conjugation procedureoften includes exposure to organic solvents, it is less suitable for native proteins that possesscomplex secondary structures. Pre-conjugation offers a single-step formulation process thatimproves control over drug release and nanoparticle characteristics while lowering the risk ofadverse reactions and creating covalent connections between the ligands and nanoparticles.Additionally, this approach makes it easier to purify nanoparticles once they have been createdand permits the addition of other ligands (81).Post-formulation conjugation, in contrast to this pre-formulation method, involves directcovalent bond formation between the ligands and the prepared nanoparticles. This approach iseffective with all ligand types and may be preferable in situations where the ligand’s stability inorganic solvents is problematic, its size is excessive, or its presence alters the physicochemicalproperties of the copolymers. In certain circumstances, conjugating these ligands directlyonto the nanoparticle surface after nanoparticle production might frequently be advantageous(98).4.4.2. Synthetic MethodsSynthetic strategies are also used for conjugation. Bifunctional linkers are utilized inchemical conjugation procedures to associate the ligand with polymers or nanoparticlesthrough a sequence of chemical coupling events. By activating carboxylic groups andreacting them with nucleophilic groups on the ligand, peptidic bonds between the ligandand nanoparticle surface are typically formed (99). This is a method that is simple and at thesame time effective, both in aqueous and organic environments. However, the selectivity ofthe conjugation is dependent on the amount of reactive amine functionalities on the ligand.As such, if the ligand has more than one reactive group, the final orientation of the ligand maybe affected (68).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 253Click chemistry is another bioconjugation technique that uses heteroatom bonding in asingle step with or without catalysts. Azide groups on the surface of nanoparticles or thebackbone of polymers, for instance, will easily form a connection with alkyne groups (100)on peptides or small molecules without causing any adverse effects. This process offersextremely strong yields and is highly selective. The difficult purification process needed toget rid of the toxic catalyst and the possibility of copper having negative effects on the ligandsthemselves put a cap on copper-catalyzed click chemistry. This approach is less effective forlarger, more complicated proteins created by recombinant or bioengineering methods as wellas for tiny compounds where the additional, relatively bulky functional groups may interferewith affinity (93).4.4.3. Non-covalent MethodsNon-covalent approaches have also been developed in order to overcome the drawbacks ofsynthetic conjugation methods (91). Biotin and streptavidin’s interaction can be considereduseful in this sense. Biotin is frequently employed thanks to its small molecule size and alsothe fact that it doesn’t alter nor inhibit ligand functions. On the other hand, avidin-coatednanoparticles and biotinylated ligands are known to work well together (81). This approach,which is more flexible than the bioconjugation technique, has been used with aptamers,peptides, and antibodies (101). Additionally, it is helpful in aiding the screening of differentligands and the establishment of proof of concepts. This method’s drawback is that it typicallyisn’t suited for usage on humans and that the exogenous protein on the surface might lead toimmunogenicity (102).5. ConclusionThe human lifespan has extended and accordingly new treatment possibilities havesurfaced. As a more effective treatment approach, especially in cancer diseases, treatment withnano-based systems that can release drugs in effective concentrations in the cancerous regionhas become a topic of interest. By adjusting the particle size of these drug delivery systemsor targeting them to the cancerous tissue by active targeting with some specific strategies,it is possible to protect the patient from the side effects of the drug and to provide effectivetreatment with a lower drug concentration. Many cancer products with nano-based systemsare on the market and it is seen that liposomal products are used the most in these products. Inthe near future, it is anticipated that products including other nano-based systems discussedin this section will also be on the pharmacy shelves.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

CANCER: FROM GENOMICS TO PHARMACEUTICSREFERENCES1. Malam Y, Loizidou M, Seifalian AM. Liposomes and nanoparticles: nanosizedvehicles for drug delivery in cancer. Trends in pharmacological sciences. 2009 Nov1;30(11):592-9.2. Burgess P, Hutt PB, Farokhzad OC, Langer R, Minick S, Zale S. On firmground: IP protection of therapeutic nanoparticles. Nature biotechnology. 2010Dec;28(12):1267-70.3. Farokhzad OC, Langer R. Impact of nanotechnology on drug delivery. ACS nano. 2009Jan 27;3(1):16-20.4. Farjadian F, Ghasemi A, Gohari O, Roointan A, Karimi M, Hamblin MR.Nanopharmaceuticals and nanomedicines currently on the market: challenges andopportunities. Nanomedicine. 2019 Jan;14(1):93-126.5. Alexis F, Rhee JW, Richie JP, Radovic-Moreno AF, Langer R, Farokhzad OC. Newfrontiers in nanotechnology for cancer treatment. InUrologic Oncology: Seminars andOriginal Investigations 2008 Jan 1 (Vol. 26, No. 1, pp. 74-85). Elsevier.6. Gulati M, Grover M, Singh S, Singh M. Lipophilic drug derivatives in liposomes.International journal of pharmaceutics. 1998 May 14;165(2):129-68.7. Chang HI, Yeh MK. Clinical development of liposome-based drugs: formulation,characterization, and therapeutic efficacy. International journal of nanomedicine. 2012Dec 30:49-60.8. Bangham AD, Standish MM, Watkins JC. Diffusion of univalent ions across the lamellaeof swollen phospholipids. Journal of molecular biology. 1965 Aug 1;13(1):238-IN27.9. James ND, Coker RJ, Tomlinson D, Harris JR, Gompels M, Pinching AJ, et al. Liposomaldoxorubicin (Doxil): an effective new treatment for Kaposi’s sarcoma in AIDS. Clinicaloncology. 1994 Jan 1;6(5):294-6.10. Scherphof G, Roerdink F, Waite M, Parks J. Disintegration of phosphatidylcholineliposomes in plasma as a result of interaction with high-density lipoproteins. Biochimicaet biophysica acta. 1978 Aug 1;542(2):296-307.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 25511. Ensign LM, Cone R, Hanes J. Oral drug delivery with polymeric nanoparticles:the gastrointestinal mucus barriers. Advanced drug delivery reviews. 2012 May1;64(6):557-70.12. Allen TM, Cleland LG. Serum-induced leakage of liposome contents. Biochimica etbiophysica acta (BBA)-biomembranes. 1980 Apr 10;597(2):418-26.13. Senior J, Gregoriadis G. Is half-life of circulating liposomes determined by changes intheir permeability?. FEBS letters. 1982 Aug 16;145(1):109-14.14. Papahadjopoulos D, Jacobson K, Nir S, Isac T. Fluorescence polarization andpermeability measurements concerning the effect of temperature and cholesterol.Biochim. Biophys. Acta. 1973;311:330-48.15. Du B, Han S, Li H, Zhao F, Su X, Cao X, et al. Multi-functional liposomesshowing radiofrequency-triggered release and magnetic resonance imaging for tumormulti-mechanism therapy. Nanoscale. 2015;7(12):5411-26.16. Arie AA, Lee JK. Effect of boron doped fullerene C60 film coating on theelectrochemical characteristics of silicon thin film anodes for lithium secondary batteries.Synthetic metals. 2011 Jan 1;161(1-2):158-65.17. Dao TT, Matsushima T, Murata H. Organic nonvolatile memory transistors basedon fullerene and an electron-trapping polymer. Organic Electronics. 2012 Nov1;13(11):2709-15.18. Pak CC, Erukulla RK, Ahl PL, Janoff AS, Meers P. Elastase activated liposomal deliveryto nucleated cells. Biochimica et Biophysica Acta (BBA)-Biomembranes. 1999 Jul15;1419(2):111-26.19. Meers P. Enzyme-activated targeting of liposomes. Advanced drug delivery reviews.2001 Dec 31;53(3):265-7220. Huang SL, MacDonald RC. Acoustically active liposomes for drug encapsulation andultrasound-triggered release. Biochimica et Biophysica Acta (BBA)-Biomembranes.2004 Oct 11;1665(1-2):134-41.21. Ueno Y, Sonoda S, Suzuki R, Yokouchi M, Kawasoe Y, Tachibana K, et al. Combinationof ultrasound and bubble liposome enhance the effect of doxorubicin and inhibit murineosteosarcoma growth. Cancer biology therapy. 2011 Aug 15;12(4):270-7.22. Gerasimov OV, Boomer JA, Qualls MM, Thompson DH. Cytosolic drug deliveryusing pH-and light-sensitive liposomes. Advanced drug delivery reviews. 1999 Aug20;38(3):317-38.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

256 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPY23. Bondurant B, Mueller A, O’Brien DF. Photoinitiated destabilization of stericallystabilized liposomes. Biochimica et Biophysica Acta (BBA)-Biomembranes. 2001 Mar9;1511(1):113-22.24. Landen Jr CN, Chavez-Reyes A, Bucana C, Schmandt R, Deavers MT, Lopez-BeresteinG, et al. Therapeutic EphA2 gene targeting in vivo using neutral liposomal smallinterfering RNA delivery. Cancer research. 2005 Aug 1;65(15):6910-8.25. Miller CR, Bondurant B, McLean SD, McGovern KA, O’Brien DF. Liposomecell interactions in vitro: effect of liposome surface charge on the binding andendocytosis of conventional and sterically stabilized liposomes. Biochemistry. 1998Sep 15;37(37):12875-83.26. Wolfrum C, Shi S, Jayaprakash KN, Jayaraman M, Wang G, Pandey RK, et al.Mechanisms and optimization of in vivo delivery of lipophilic siRNAs. Naturebiotechnology. 2007 Oct;25(10):1149-57.27. Wang Z, Yu Y, Dai W, Lu J, Cui J, Wu H, et al. The use of a tumor metastasistargeting peptide to deliver doxorubicin-containing liposomes to highly metastaticcancer. Biomaterials. 2012 Nov 1;33(33):8451-60.28. Perez-Herrero E, Fern ´ andez-Medarde A. Advanced targeted therapies in cancer: Drug ´nanocarriers, the future of chemotherapy. European journal of pharmaceutics andbiopharmaceutics. 2015 Jun 1;93:52-79.29. Lee Y, Thompson DH. Stimuli-responsive liposomes for drug delivery.Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology. 2017Sep;9(5):e1450.30. Deshpande PP, Biswas S, Torchilin VP. Current trends in the use of liposomes for tumortargeting. Nanomedicine. 2013 Sep;8(9):1509-28.31. Bolkestein M, de Blois E, Koelewijn SJ, Eggermont AM, Grosveld F, de Jong M, KoningGA. Investigation of factors determining the enhanced permeability and retention effectin subcutaneous xenografts. Journal of nuclear medicine. 2016 Apr 1;57(4):601-7.32. Sailor MJ, Park JH. Hybrid nanoparticles for detection and treatment of cancer.Advanced materials. 2012 Jul 24;24(28):3779-802.33. Kuai R, Li D, Chen YE, Moon JJ, Schwendeman A. High-density lipoproteins: nature’smultifunctional nanoparticles. ACS nano. 2016 Mar 22;10(3):3015-41.34. Rao JP, Geckeler KE. Polymer nanoparticles: Preparation techniques and size-controlparameters. Progress in polymer science. 2011 Jul 1;36(7):887-913.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 25735. Agarwal S, Dominic A, Wasnik S. An overview of polymeric nanoparticles as potentialcancer therapeutics. Polymeric nanoparticles as a promising tool for anti-cancertherapeutics. 2019 Jan 1:21-34.36. Yalcin TE, Ilbasmis-Tamer S, Ibisoglu B, Ozdemir A, Ark M, Takka S. Gemcitabine ¨hydrochloride-loaded liposomes and nanoparticles: comparison of encapsulationefficiency, drug release, particle size, and cytotoxicity. Pharmaceutical developmentand technology. 2018 Jan 2;23(1):76-86.37. Soni G, Kale K, Shetty S, Gupta MK, Yadav KS. Quality by design (QbD) approachin processing polymeric nanoparticles loading anticancer drugs by high pressurehomogenizer. Heliyon. 2020 Apr 1;6(4):e03846.38. Nguyen TT, Ghosh C, Hwang SG, Tran LD, Park JS. Characteristics of curcumin-loadedpoly (lactic acid) nanofibers for wound healing. Journal of materials science. 2013Oct;48:7125-33.39. Tan S, Gan C, Li R, Ye Y, Zhang S, Wu X, et al. A novel chemosynthetic peptide with?-sheet motif efficiently kills Klebsiella pneumoniae in a mouse model. Internationaljournal of nanomedicine. 2015;10:1045.40. Miele E, Spinelli GP, Miele E, Tomao F, Tomao S. Albumin-bound formulation ofpaclitaxel (Abraxane® ABI-007) in the treatment of breast cancer. International journalof nanomedicine. 2009 Apr 20:99-105.41. Yardley DA. nab-Paclitaxel mechanisms of action and delivery. Journal of ControlledRelease. 2013 Sep 28;170(3):365-72.42. Hawkins MJ, Soon-Shiong P, Desai N. Protein nanoparticles as drug carriers in clinicalmedicine. Advanced drug delivery reviews. 2008 May 22;60(8):876-85.43. Sun TM, Du JZ, Yan LF, Mao HQ, Wang J. Self-assembled biodegradable micellarnanoparticles of amphiphilic and cationic block copolymer for siRNA delivery.Biomaterials. 2008 Nov 1;29(32):4348-55.44. Han Y, He Z, Schulz A, Bronich TK, Jordan R, Luxenhofer R, Kabanov AV. Synergisticcombinations of multiple chemotherapeutic agents in high capacity poly (2-oxazoline)micelles. Molecular pharmaceutics. 2012 Aug 6;9(8):2302-13.45. Shin HC, Alani AW, Cho H, Bae Y, Kolesar JM, Kwon GS. A 3-in-1 polymeric micellenanocontainer for poorly water-soluble drugs. Molecular pharmaceutics. 2011 Aug1;8(4):1257-65.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

258 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPY46. Jhaveri AM, Torchilin VP. Multifunctional polymeric micelles for delivery of drugs andsiRNA. Frontiers in pharmacology. 2014 Apr 25;5:77.47. Ahn HK, Jung M, Sym SJ, Shin DB, Kang SM, Kyung SY, et al. A phase II trialof Cremorphor EL-free paclitaxel (Genexol-PM) and gemcitabine in patients withadvanced non-small cell lung cancer. Cancer chemotherapy and pharmacology. 2014Aug;74:277-82.48. Park S, Healy KE. Nanoparticulate DNA packaging using terpolymers ofpoly (lysine-g-(lactide-b-ethylene glycol)). Bioconjugate chemistry. 2003 Mar19;14(2):311-9.49. Ghosh B, Biswas S. Polymeric micelles in cancer therapy: State of the art. Journal ofControlled Release. 2021 Apr 10;332:127-47.50. Danafar H, Rostamizadeh K, Davaran S, Hamidi M. Drug-conjugated PLA–PEG–PLAcopolymers: a novel approach for controlled delivery of hydrophilic drugs by micelleformation. Pharmaceutical development and technology. 2017 Nov 17;22(8):947-57.51. Wei H, Zhuo RX, Zhang XZ. Design and development of polymeric micelles withcleavable links for intracellular drug delivery. Progress in polymer Science. 2013 Mar1;38(3-4):503-35.52. Gao GH, Li Y, Lee DS. Environmental pH-sensitive polymeric micelles forcancer diagnosis and targeted therapy. Journal of Controlled Release. 2013 Aug10;169(3):180-4.53. Tomalia DA, Baker H, Dewald J, Hall M, Kallos G, Martin S, et al. A newclass of polymers: starburst-dendritic macromolecules. Polymer journal. 1985Jan;17(1):117-32.54. Buhleier E, Vogtle F, Wehner W. Cascade and nonskid-chain-like syntheses of molecularcavity topologies. Synthesis. 1978;2:155-8.55. Gillies ER, Frechet JM. Dendrimers and dendritic polymers in drug delivery. Drugdiscovery today. 2005 Jan 1;10(1):35-43.56. Kesharwani P, Jain K, Jain NK. Dendrimer as nanocarrier for drug delivery. Progress inPolymer Science. 2014 Feb 1;39(2):268-307.57. Khopade AJ, Caruso F, Tripathi P, Nagaich S, Jain NK. Effect of dendrimeron entrapment and release of bioactive from liposomes. International journal ofpharmaceutics. 2002 Jan 31;232(1-2):157-62.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 25958. Prajapati RN, Tekade RK, Gupta U, Gajbhiye V, Jain NK. Dendimer-mediatedsolubilization, formulation development and in vitro in vivo assessment of piroxicam.Molecular pharmaceutics. 2009 Jun 1;6(3):940-50.59. Karadag M, Geyik C, Demirkol DO, Ertas FN, Timur S. Modified gold surfacesby 6-(ferrocenyl) hexanethiol/dendrimer/gold nanoparticles as a platform for themediated biosensing applications. Materials Science and Engineering: C. 2013 Mar1;33(2):634-40.60. Tao X, Yang YJ, Liu S, Zheng YZ, Fu J, Chen JF. Poly (amidoamine) dendrimer-graftedporous hollow silica nanoparticles for enhanced intracellular photodynamic therapy.Acta Biomaterialia. 2013 May 1;9(5):6431-8.61. Yoshioka H, Suzuki M, Mugisawa M, Naitoh N, Sawada H. Synthesis and applicationsof novel fluorinated dendrimer-type copolymers by the use of fluoroalkanoyl peroxideas a key intermediate. Journal of colloid and interface science. 2007 Apr 1;308(1):4-10.62. Zeng YL, Huang YF, Jiang JH, Zhang XB, Tang CR, Shen GL, et al. Functionalizationof multi-walled carbon nanotubes with poly (amidoamine) dendrimer for mediator-freeglucose biosensor. Electrochemistry Communications. 2007 Jan 1;9(1):185-90.63. Tang L, Zhu Y, Yang X, Li C. An enhanced biosensor for glutamatebased on self-assembled carbon nanotubes and dendrimer-encapsulated platinumnanobiocomposites-doped polypyrrole film. Analytica chimica acta. 2007 Jul30;597(1):145-50.64. Papagiannaros A, Dimas K, Papaioannou GT, Demetzos C. Doxorubicin–PAMAMdendrimer complex attached to liposomes: cytotoxic studies against human cancercell lines. International journal of pharmaceutics. 2005 Sep 30;302(1-2):29-38.65. Purohit G, Sakthivel T, Florence AT. Interaction of cationic partial dendrimers withcharged and neutral liposomes. International Journal of Pharmaceutics. 2001 Feb19;214(1-2):71-6.66. Chauhan AS, Sridevi S, Chalasani KB, Jain AK, Jain SK, Jain NK, et al.Dendrimer-mediated transdermal delivery: enhanced bioavailability of indomethacin.Journal of controlled release. 2003 Jul 31;90(3):335-43.67. Quintana A, Raczka E, Piehler L, Lee I, Myc A, Majoros I, Patri AK, Thomas T, Mule J, ´Baker JR. Design and function of a dendrimer-based therapeutic nanodevice targeted totumor cells through the folate receptor. Pharmaceutical research. 2002 Sep;19:1310-6.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

260 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPY68. Jung HS, Han J, Lee JH, Lee JH, Choi JM, Kweon HS, et al. Enhanced NIRradiation-triggered hyperthermia by mitochondrial targeting. Journal of the AmericanChemical Society. 2015 Mar 4;137(8):3017-23.69. Chen PC, Mwakwari SC, Oyelere AK. Gold nanoparticles: from nanomedicine tonanosensing. Nanotechnology, science and applications. 2008 Nov 2:45-65.70. Janib SM, Moses AS, MacKay JA. Imaging and drug delivery using theranosticnanoparticles. Advanced drug delivery reviews. 2010 Aug 30;62(11):1052-63.71. Grossman JH, McNeil SE. Nanotechnology in cancer medicine. Physics Today. 2012Aug 1;65(8):38.72. Huang HC, Barua S, Sharma G, Dey SK, Rege K. Inorganic nanoparticles for cancerimaging and therapy. Journal of controlled Release. 2011 Nov 7;155(3):344-57.73. WHO, 2022. https://www.who.int/news-room/fact-sheets/detail/cancer. Accessed on:15.12.2022.74. Volker Schirrmacher. 2018. From chemotherapy to biological therapy: A review ofnovel concepts to reduce the side effects of systemic cancer treatment (Review). Journalof Oncology. 407-419, https://doi.org/10.3892/ijo.2018.4661.75. Shagufta Khan, Vaishali Kilor, Dilesh Singhavi, Kundan Patil, Chapter 12 - Progressin nanotechnology-based targeted cancer treatment, Editor(s): Nilesh M. Mahajan,Avneet Saini, Nishikant A. Raut, Sanjay J. Dhoble, Photophysics and Nanophysics inTherapeutics, Elsevier, 2022, 239-250.76. Peer, D., Karp, J. M., Hong, S., Farokhzad, O. C., Margalit, R., & Langer, R.(2007). Nanocarriers as an emerging platform for cancer therapy. Nano-Enabled MedicalApplications, 61-91.77. Alexis F, Pridgen E, Molnar LK, Farokhzad OC. Factors affecting the clearance andbiodistribution of polymeric nano-particles. Mol Pharm. 2008; 5:505–515. [PubMed:18672949]78. Gullotti E, Yeo Y. Extracellularly activated nanocarriers: A new paradigm of tumortargeted drug delivery. Mol Pharm. 2009; 6:1041–1051. [PubMed: 19366234]79. Lee, H., Fonge, H., Hoang, B., Reilly, R.M., Allen, C., 2010. The effect of particle sizeand molecular targeting on the intratumoral and subcellular distribution of polymericnanoparticles. Mol. Pharm. 7 (4), 1195–1208.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Yavuz Selim C¸ EL˙IK, Burcu MESUT, Yıldız OZSOY ¨ 26180. Greish K. Enhanced permeability and retention of macromolecular drugs in solid tumors:a royal gate for targeted anticancer nanomedicines. J Drug Target. 2007;15:457–464.81. Bertrand N, Wu J, Xu X, Kamaly N, Farokhzad OC. Cancer nanotechnology: theimpact of passive and active targeting in the era of modern cancer biology. Advanceddrug delivery reviews. 2014 Feb 1;66:2-5.82. Krasnici S, Werner A, Eichhorn ME, Schmitt-Sody M, Pahernik SA, Sauer B, Schulze B,Teifel M, Michaelis U, Naujoks K, Dellian M. Effect of the surface charge of liposomeson their uptake by angiogenic tumor vessels. Int J Cancer. 2003; 105:561–567. [PubMed:12712451]83. Shukla S, Ablack AL, Wen AM, Lee KL, Lewis JD, Steinmetz NF. Increased tumorhoming and tissue penetration of the filamentous plant viral nanoparticle Potato virusX. Mol Pharmaceutics. 2013; 10:33–42.84. Mohamed F. Attia, Nicolas Anton, Justine Wallyn, Ziad Omran and Thierry F.Vandamme, An overview of active and passive targeting strategies to improve thenanocarriers efficiency to tumour sites. Journal of Pharmacy and Pharmacology, 71(2019), pp. 1185–119885. Wu J, Akaike T, Maeda H. Modulation of enhanced vascular permeability in tumors by abradykinin antagonist, a cyclooxygenase inhibitor, and a nitric oxide scavenger. CancerRes. 1998;58:159–165.86. Maeda H. The enhanced permeability and retention (EPR) effect in tumor vasculature:the key role of tumor-selective macromolecular drug targeting. Adv Enzyme Regul.2001;41:189–207.87. Kamaly N, Xiao Z, Valencia PM, Radovic-Moreno AF, Farokhzad OC. Targetedpolymeric therapeutic nanoparticles: design, development and clinical translation.Chemical Society Reviews. 2012;41(7):2971-3010.88. Lammers T, Kiessling F, Hennink WE, Storm G. Drug targeting to tumors:principles, pitfalls and (pre-) clinical progress. Journal of controlled release. 2012 Jul20;161(2):175-87.89. Byrne JD, Betancourt T, Brannon-Peppas L. Active targeting schemes for nanoparticlesystems in cancer therapeutics. Advanced drug delivery reviews. 2008 Dec14;60(15):1615-26.90. Sahay G, Alakhova DY, Kabanov AV. Endocytosis of nanomedicines. Journal ofcontrolled release. 2010 Aug 3;145(3):182-95.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

262 TARGETING STRATEGIES WITH NEW DRUG DELIVERY SYSTEMS IN CANCER THERAPY91. Gao J, Feng SS, Guo Y. Antibody engineering promotes nanomedicine for cancertreatment. Nanomedicine. 2010 Oct;5(8):1141-5.92. Lu H, Stenzel MH. Multicellular tumor spheroids (MCTS) as a 3D in vitro evaluationtool of nanoparticles. Small. 2018 Mar;14(13):1702858.93. Shi M, Lu J, Shoichet MS. Organic nanoscale drug carriers coupled with ligands fortargeted drug delivery in cancer. Journal of materials chemistry. 2009;19(31):5485-98.94. Song CW. Effect of local hyperthermia on blood flow and microenvironment: a review.Cancer research. 1984 Oct;44(10 Supplement):4721s-30s.95. Heinz H, Pramanik C, Heinz O, Ding Y, Mishra RK, Marchon D, Flatt RJ,Estrela-Lopis I, Llop J, Moya S, Ziolo RF. Nanoparticle decoration with surfactants:molecular interactions, assembly, and applications. Surface Science Reports. 2017 Feb1;72(1):1-58.96. Wu J, Wu D, Mutschler MA, Chu CC. Cationic hybrid hydrogels from amino-acid-basedpoly (ester amide): fabrication, characterization, and biological properties. Advancedfunctional materials. 2012 Sep 25;22(18):3815-23.97. D Friedman A, E Claypool S, Liu R. The smart targeting of nanoparticles. Currentpharmaceutical design. 2013 Oct 1;19(35):6315-29.98. Yu MK, Park J, Jon S. Targeting strategies for multifunctional nanoparticles in cancerimaging and therapy. Theranostics. 2012;2(1):3.99. Marques AC, Costa PJ, Velho S, Amaral MH. Functionalizing nanoparticles withcancer-targeting antibodies: A comparison of strategies. Journal of Controlled Release.2020 Apr 10;320:180-200.100. Johnson JA, Finn MG, Koberstein JT, Turro NJ. Construction of linear polymers,dendrimers, networks, and other polymeric architectures by copper-catalyzedazide-alkyne cycloaddition “click” chemistry. Macromolecular rapid communications.2008 Jul 1;29(12-13):1052-72.101. Park J, Mattessich T, Jay SM, Agawu A, Saltzman WM, Fahmy TM. Enhancementof surface ligand display on PLGA nanoparticles with amphiphilic ligand conjugates.Journal of controlled release. 2011 Nov 30;156(1):109-15.102. Yumura K, Ui M, Doi H, Hamakubo T, Kodama T, Tsumoto K, et al. Mutations fordecreasing the immunogenicity and maintaining the function of core streptavidin. ProteinScience. 2013 Feb;22(2):213-21.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

CANCER: FROM GENOMICS TO PHARMACEUTICSCHAPTER 10CURRENT ADVANCES IN MEDICINAL CHEMISTRY OFANTICANCER AGENTSEfe Dogukan D ˘˙INCEL1,2, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I31PhD, ˙Istanbul University, Institute of Graduate Studies in Health Sciences, ˙Istanbul, T¨urkiye2PhD, ˙Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, ˙Istanbul, T¨urkiyeE-mail: [email protected]. Dr., ˙Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, ˙Istanbul, T¨urkiyeE-mail: [email protected]: 10.26650/B/LSB28LSB48LSB56.2024.019.010ABSTRACTCancer is a tedious mortal disease, which is the 2nd major cause of death, after cardiovascular disease. Cancer isalone responsible for 10 million deaths reported worldwide in the year 2020. Over 19 million novel cancer diagnoseshave been reported in 2021. This number is anticipated to be twenty-two million by the year 2030. Tobacco, radiation,diverse genetic mutations, and viral infections can be listed as cancer-causing factors. There are over one hundredtypes of this mortal disease. Lung cancer, prostate and colorectal cancer are the most commonly diagnosed typesof cancer in men, whereas breast cancer, cervical cancer are the most diagnosed types of cancer in females. Today,gold-standard cancer treatments include surgery, chemotherapy, radiation therapy, hormone therapy, immunotherapy,stem cell transplantations, targeted therapy, precision medicine, and biomarker testing. Within the overall treatmenttypes, chemotherapy possesses a significant potential in the treatment. However, there are diverse problems, likethe poor selectivity of the drugs, resistance formation, and cytotoxic effects on healthy human cells. The mentionedproblems indicate that the discovery of novel and safe anticancer drugs is an obligation. Herein, we report the currentadvances in medicinal chemistry of anticancer agents within the years of 2014-2023. We proposed to present theresearchers current data related to the last studies, thus helping them perform their drug research and developmentjourneys.Keywords: Medicinal Chemistry, Pharmaceutical Chemistry, Anticancer Agents, Anticancer Activity, SynthesisCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

264 CURRENT ADVANCES IN MEDICINAL CHEMISTRY OF ANTICANCER AGENTS1. IntroductionCancer is a huge health problem, affecting people from every region, social and economiclevel. Enormous efforts are being performed to overcome this mortal disease. The discoveryof novel compounds targeting anticancer treatment corresponds to one of the major areas ofmedicinal chemists (1).Arun et al. reported the discovery and anticancer activity studies ofnovel spirooxindole-pyrrolidine compounds (2). The researchers obtainedthe novel compounds through 1,3-dipolarcycloaddition of azomethineylidesgenerated from isatin and sarcosine or thioproline with the dipolarophile3-(1H-imidazol-2-yl)-2-(1H-indole-3-carbonyl)acrylonitrile under the optimised reactioncondition. Among the synthesized compounds 4j, 6b and 6h displayed significant activity66.3%, 64.8% and 66.3% at 25 ?g/ml concentration against A549 lung adenocarcinomacancer cell line (Figure 1). All the synthesized novel spirooxindole-pyrrolidine compoundswere subjected to molecular docking studies using AutoDock Tools (ADT) version 1.5.6and AutoDock version 4.2.5.1 docking program to investigate the potential binding modeof inhibitors. Anaplastic Lymphoma Kinase (ALK) receptor was chosen as the target.Compound 6b fit well in the binding site of ALK with a docking score of -8.47 kcal/mol(Figure 2). This compound fit in the binding site of ALK receptor as like as crizotinib andinteracts with six amino acids, namely, Leu-1122, Leu 1198, Met-1199, Ala-1200, Gly-1202and Asp-1203 which resulted seven hydrogen bonds with ALK receptor. The researchersunderlined that, these spirooxindole-pyrrolidine compounds can be promising therapeuticagents for A549 lung adenocarcinoma cancer cell line.Figure 1: The title compounds reported by Arun et al. (2).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Efe Dogukan D ˘˙INCEL, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I 265Figure 2: Binding mode of the most active compound 6b with ALK receptor (2)Li et al. reported the discovery of novel 4-pyrazolyl-1,8-naphthalimide derivatives (3).Compound 4i displayed cytotoxic activities against human mammary cancer cells (MCF-7 /??50: 0.51 ?M), human cervical carcinoma cells (Hela / IC50: 3.09 ?M), and human lungcancer cells (A549 / ??50: 5.14 ?M) better than the reference compound Amonafide(??50values / 1.68 ?M for MCF 7; 6.71 ?M for Hela; 13.00 ?M for A549) (Figure 3).Figure 3: Compound 4i reported by Li et al. (3).Nguyen et al. performed studies related to the discovery of novel carbazole-based thiazolederivatives (4). The title compounds were evaluated for their cytotoxic activity against threeCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

266 CURRENT ADVANCES IN MEDICINAL CHEMISTRY OF ANTICANCER AGENTScancer cell lines A549 (human lung cancer), MCF-7 (human breast cancer), and HT29 (humancolon cancer) by MTT ((3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide))assay. 4-(4-Bromophenyl)-2-(2-((9-ethyl-9H-carbazol-3-yl)methylene)hydrazinyl)thiazole(3f) and 2-(2-((9-ethyl-9H-carbazol-3-yl)methylene)hydrazinyl)-4-(4-nitrophenyl)thiazole(3g) displayed remarkable cytotoxic activity against three cancer cell line within thecompounds (Figure 4). Structure-activity relationships indicated that 4-halophenyl (3e, 3f)and 4-nitro phenyl (3g) thiazole derivatives displayed attractive activity on three cancer celllines over the other phenyl substituted thiazoles.Figure 4: Compounds 3e, 3f and 3g reported by Nguyen et al. (4).Swamy et al. reported the discovery of novel compounds bearing benzofuran scaffold(5). Compounds 5s, 5r and 17b displayed the highest anticancer activity against Ehrlichascites carcinoma cells (Figure 5). In vitro anticancer activity percentage values of 5s, 5r,textbf17b and the reference compound 5-fluorouracil at 1000 ?g/mL concentrations weredetermined as 82.2%, 83.9%, 74.2% and 86.7% respectively. Molecular docking studiesof all the synthesized compounds were performed by targeting GABA receptor-associatedprotein-like 1 cancer receptor (Figure 6). The study underlined the significance of benzofuran,aminopyrimidines and azetidinone nucleus for anticancer activity. On the basis of dockingsimulations, strong binding affinities of 5s and 5r derivatives were determined. Thestrong hydrogen bonding interactions with the backbone of benzofuran and aminopyrimidinemoieties were found to be responsible of this strong binding interactions. Interactions withAsn 82, Tyr 106, Glu 34, Asp 8, Lys 35, Tyr 106 and Asn 81 were found significant for thementioned biological activity. Moreover the ??2 group of Gln 4 interacts with the nitrogenof azetidinone ring in case of compounds 17b and 17c, and this interactions were thought tobe the reason of their anticancer activities.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Efe Dogukan D ˘˙INCEL, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I 267Figure 5: Compounds 5s, 5r and 17b reported by Swamy et al. (5).Figure 6: Binding mode of ligand 5r into its binding site of GABAA receptor-associated protein-like 1(5).Ruddarraju et al. reported the discovery of theophylline containing acetylenes andtheophylline containing 1,2,3-triazoles with variant nucleoside derivatives (6) (Figure 7).The results displayed that compounds 29 and 30 displayed remarkable cytotoxic effect on allfour cancer cells such as lung (A549), colon (HT-29), breast (MCF-7) and melanoma (A375)with ??50 values of 2.56, 2.19, 1.89, 4.89 ?M and 3.57, 2.90, 2.10, 5.81 ?M respectively.The researchers also performed molecular docking studies targeting epidermal growth factorreceptor (EGFR), human epidermal growth factor receptor 2 (HER 2), vascular endothelialgrowth factor receptor 2 (VEGFR 2), human placental aromatase cytochrome P450, caspase3, caspase 6, caspase 8 and cyclin A to illuminated the binding interactions (Figure 8).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

268 CURRENT ADVANCES IN MEDICINAL CHEMISTRY OF ANTICANCER AGENTSFigure 7: Compounds 29 and 30 reported by Ruddarraju et al. (6).Figure 8: Molecular interactions of compound 29 with active site of target protein VEGFR2 (6).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Efe Dogukan D ˘˙INCEL, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I 269Yang et al. reported the discovery of benzenesulfonamide derivatives as potenttubulin-targeting agents (7). The novel compounds displayed significant activities againstcellular proliferative and tubulin polymerization. Compound BA-3b was determined as themost potent compound with ??50 value ranging from 0.007 to 0.036 µM against seven cancercell lines, and three drug-resistant cancer cell lines (Figure 9).Figure 9: Compound BA-3b reported by Yang et al. (7).Gouda et al. reported the discovery of a novel series of pyrrolizine-5-carboxamides (8).Anticancer activity studies were performed against human breast MCF-7, lung carcinomaA549 and hepatoma Hep3B cancer cell lines. Compound 10c was determined as the mostactive against MCF-7 with ??50 value of 4.72 ?M, while compound 12b was the mostactive against A549 and Hep3B cell lines (Figure 10). Moreover, molecular docking studiestargeting COX-1/COX-2 and two kinases namely: ALK1 and Aurora kinases were performedto illuminate the binding interactions (Figure 11).Figure 10: Compound 10c and 12b reported by Gouda et al. (8).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

270 CURRENT ADVANCES IN MEDICINAL CHEMISTRY OF ANTICANCER AGENTSFigure 11: a) Comparative docking mode of compound 12b into COX1 (PDB ID:1eqg), it exhibited aGoldscore fitness of 35.92, RMSD of 2.66 ˚A, and one hydrogen bond with Arg120; b) docking mode ofcompound 12b into COX2 (PDB ID: 5kir), it revealed a Goldscore fitness of 88.15, RMSD of 0.58 ˚A,and two hydrogen bond with Tyr355 and Phe518. (8).Simon et al. reported the discovery of novel 3-benzylchroman-4-one derivatives (9). Theanticancer activity evaluations were performed against two diverse cancerous cell lines BT549(human breast carcinoma), HeLa (human cervical carcinoma), and noncancerous cell line vero(normal kidney epithelial cells). Compound 3b was determined as the most active moleculeagainst BT549 cells (??50: 20.1 ?M) and 3h against HeLa cells (??50: 20.45 ?M) (Figure 12).Moreover, 3b displayed moderate activity against HeLa cells (??50: 42.8 ?M). Additionally,molecular docking studies between the tumor suppressor protein p53 with the lead compound3h was examined (Figure 13). According to the molecular docking studies 3h was surroundedwith Leu145, Trp146, Val147, Asp148, Ser149, Thr150, Pro151, Cys220, Glu221, Pro222,Pro223, Asp228, Cys229, and Thr230 amino acids of the target. 3h formed hydrogen bondinteractions with Val147, Thr150, and Thr230. It also formed hydrophobic contacts withLeu145, Cys220, Pro222, Pro223, and Cys229 of p53 amino acid residues (Figure 13).Figure 12: Compound 3b and 3h reported by Simon et al. (9).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Efe Dogukan D ˘˙INCEL, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I 271Figure 13: Molecular interactions of 3h with p53 (9). a) Surface representation of p53 with 3h isshown. b) In silico docking results of p53 with 3h, and (c) molecular interactions of p53 crystallizedwith 7-ethyl-3-(piperidin-4-yl)-1H-indole (PDB ID: 5ab9) is shown.Sreenivasulu et al. reported the discovery of novel bis(indolyl) triazinones as Nortopsentinanalogs (10). The anticancer activities were evaluated against HeLa, MCF-7, MDA-MB-231and A549 cell lines. Compounds 17a and 17b displayed remarkable cytotoxic activity againstthe human cervical cell line (??50 values 4.6 ?M and 1.3 ?M respectively) (Figure 14). Theresearchers have also performed molecular docking studies and underlined that, the in silicosimulations studies revealed unique ?-? interactions of indole ring of compound 17b withcolchicines active site residue Tyr312 could be a valid reason behind its maximum potencywhen compared to remaining compounds in responsible of its higher activity.Figure 14: Compound 17a and 17b reported by Sreenivasulu et al. (10).Karakus¸ et al. reported the synthesis and anticancer activity evaluation ofN-(5-methyl-1,3,4-thiadiazol-2-yl)-4-[(3-substituted)ureido/thioureido]benzenesulfonamidederivatives (11) (Figure 15). The anticancer activity of the compounds was evaluated againsthuman colorectal carcinoma (HTC116) and human cervix carcinoma (HeLa) cell lines.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

272 CURRENT ADVANCES IN MEDICINAL CHEMISTRY OF ANTICANCER AGENTSCompound 4 displayed remarkable anticancer activity with ??50 values of 13.92 ± 0.22 ?Mand 37.91 ± 0.10 ?M against HeLa and HCT116, respectively.Figure 15: Compound 4 reported by Karakus¸ et al. (11).Amr et al. described the discovery of novel estrogen derivatives (12). Overall compoundsdisplayed potent in vitro and in vivo cytotoxic activities against breast cancer cell lines.Moreover all compounds were subjected to in vitro and in vivo inhibition assays for EGFRand VEGFR-2 kinases as well as p53 ubiquitination activity to obtain more details about theirmechanism of action. Compound 5a displayed the most potent biological activity withinthe synthesized compounds (Figure 16). To explain and rationalize the experimental resultsobtained, the researchers have also performed molecular docking studies targeting EGFR andVEGFR-2 (Figure 17).Figure 16: Compound 5a reported by Amr et al (12)Figure 17: Compound 5a docked into EGFR binding site of protein (1M17) (12)Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Efe Dogukan D ˘˙INCEL, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I 273Abou-Zied et al. described the design, synthesis, anticancer activity and docking studies ofnovel xanthine derivatives carrying chalcone moiety as hybrid molecules (13). The anticanceractivity studies were performed against human pancreas cell line (Panc-1), breast cancer cellline (MCF-7), colon cancer cell line (HT-29), and epithelial cancer cell line (A-549) by usingMTT assay and Doxorubicin was used as the reference compound. Compounds 10, 11, 13,14, 16, 20 and 23 displayed potent inhibition of cancer cells growth with ??50 values rangingfrom 1.0 ± 0.1 to 3.5 ± 0.4 ?M compared to Doxorubicin with ??50 ranging from 0.90 ±0.62 to 1.41 ± 0.58 ?M and that compounds 11 and 16 were the best (Figure 18). Moleculardocking studies were adopted to confirm the mechanism of action (Figure 19).Figure 18: Compounds 11 and 16 reported by Abou-Zied et al. (13)Figure 19: Superimposition of the active docked poses 10, 11, 20 and 21 inside the EGFR active site(PDB ID: 1m17) where EGFR protein is represented as a seconday structure (13)Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

274 CURRENT ADVANCES IN MEDICINAL CHEMISTRY OF ANTICANCER AGENTSIacopetta et al. described the discovery and antioxidant properties of new indole andpyrano indole derivatives (14) (Figure 20). The anticancer activity of the novel compoundshas been evaluated on breast cancer cell lines, as MCF-7 and MDA-MB231, cervical cancercells line HeLa and Ishikawa endometrial cancer cell line. Compound 7, displayed potentantitumor activity on HeLa cell line (??50: 3.6 ± 0.5), leading to cell death by apoptosis due tothe inhibition of tubulin polymerization, which demonstrated that the compound can explicateits function in similar way to Vinblastine, a well-known inhibitor of tubulin polymerization.Figure 20: Compound 7 reported by Iacopetta et al. (14)Sreenivasulu et al. reported the discovery of novel 2,5-bis(indolyl)-1,3,4-oxadiazoles,Nortopsenting analogues (Figure 21) (15). The anticancer activity studies were performedagainst A549, MDA-MB-231, MCF-7 and HeLa using MTT reduced assay. Compound 12edisplayed remarkable cytotoxic activity on MCF-7 cell line with ??50 value of 1.8 ?M andit was identified as a promising drug lead when compared to the standard drug Doxorubicin(??50 value 0.98 ?M). Compound 12h displayed better antitumor activity against three cancercell lines i.e., lung (A549), breast (MCF-7), and cervical (HeLa) with ??50 values of 3.3 ?M,2.6 ?M and 6.34 ?M respectively. The impact of the title compounds on colchicine bindingsite of tubulin polymer was carefully investigated using molecular docking studies.Figure 21: Compounds 12e and 12h reported by Sreenivasulu et al. (15)Suryanarayana et al. reported the discovery of novel dinitrophenylpyrazole bearing1,2,3-triazoles (Figure 22) (16). The anticancer activity studies were performed against breastadenocarcinoma (MCF-7), cervical carcinoma (HeLa), and human colorectal adenocarcinoma(Caco-2) via MTT assay. Compounds 9e, 9f, and 9h displayed remarkable anticancer activityagainst HeLa cell line (??50: 4.0 ?M, 5.0 ?M and 6.0 ?M) which were higher than the referencecompound Combretastatin-A4 (??50: 9.0 ?M). Moreover, compound 9h was found potentCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Efe Dogukan D ˘˙INCEL, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I 275against MCF-7 cell line with a ??50 value of 8.0 ?M. Molecular docking studies targetingbreast adenocarcinoma protein (PDB ID: 6SBO), cervical carcinoma protein (PDB ID: 2Q79),and human epithelial colorectal adenocarcinoma protein (PDB ID: 2MAW) were conductedusing blind-docking. Molecular docking studies confirmed the experimental findings andexplained the most probable interactions pattern.Figure 22: Compounds 9e, 9f and 9h reported by Suryanarayana et al. (16)Othman et al. performed a study related to discovery of novel pyrimidine andpyrazole-based compounds (Figure 23) (17). The novel compounds were assessed ascytotoxic candidates against human breast cancer cells (MCF-7) and hepatocellular carcinomacells (HepG-2). Overall compounds displayed better activity than Erlotinib, while onlycompound 4a exhibited more potency than 5-fluorouracil and 4b analogue was equipotent toit. Accordingly, kinase suppression effect of 4a and 4b was further evaluated against EGFR??,EGFR?858?, and EGFR?790?. Both pyrimidine analogues 4a and 4b displayed remarkableinhibitory activity against EGFR?? and its two mutated isoforms EGFR?858?, EGFR?790?in comparing to Erlotinib and Osimertinib as reference drugs (Figure 24). Additionally, insilico ADMET studies were performed for novel derivatives which represented their good oralabsorption, good drug-likeness properties and low toxicity risks in humans.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

276 CURRENT ADVANCES IN MEDICINAL CHEMISTRY OF ANTICANCER AGENTSFigure 23: Compounds 4a and 4b reported by Othman et al. (17)Figure 24: 2D binding views of compound 4a into active site of EGFR?? (PDB ID: 1M17) (17)El-Sayed et al. reported the discovery of novel 2,4-dichlorophenoxymethyl-basedderivatives linked to nitrogenous heterocyclic rings systems as potential CDK-2 inhibitors(Figure 25) (18). The antiproliferative activity of all newly synthesized compounds wasperformed against human HCT-116 and MCF-7 cancer cell lines. Compounds 5, 9, 13 and15 displayed potent anticancer activity. In order to clarify the hypothetical binding modesof the title compounds, molecular docking simulations was achieved within the active site ofCDK-2/cyclin A kinase (Figure 26).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Efe Dogukan D ˘˙INCEL, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I 277Figure 25: Compounds 5, 9, 13, 15 reported by El-Sayed et al. (18)Figure 26: 2D Binding views of compound 5 into the active site of CDK-2/cyclin A kinase (PDB ID:3ddq) (18)Bourzikat et al. reported the discovery of a novel class of2-phenyl-5,6,7,8-tetrahydroimidazo[1,2-b]pyridazine derivatives bearing sulfonamides(Figure 27) (19). The anticancer activities of novel molecules were evaluated against fivediverse human cancer cell lines, including A-549, Hs-683, MCF-7, SK-MEL-28 and B16-F10cell lines using 5-fluorouracil and etoposide as the reference drugs. 4e and 4f displayedsignificant activities against MCF-7 and SK-MEL-28 cancer cell lines, with ??50 valuesranging from 1 to 10 ?M. The molecular docking studies of 4e, and 4f displayed significantbinding interactions with some kinases.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

278 CURRENT ADVANCES IN MEDICINAL CHEMISTRY OF ANTICANCER AGENTSFigure 27: Compounds 4e and 4f reported by Bourzikat et al. (19)Azher et al. reported the discovery of novel 2-(phenylamino)pyrazolo[1,5-a]pyrimidineanalogues (Figure 28) (20). The anticancer activity of the novel pyrazolopyrimidinederivatives have been performed against MCF-7, PC-3, Hep-2 and WI38 cell lines. Incomparison to the effects of 5-fluorouracil, ??50 = 10.19 ± 0.42 ?M and 7.19 ± 0.47 ?M,compounds 6a-c displayed significant anticancer activities with ??50 values for MCF-7 (10.80± 0.36-19.84 ± 0.49 ?M) and Hep-2 (8.85 ± 0.24-12.76 ± 0.16 ?M).Figure 28: Compound 6c reported by Azher et al. (20)Gariganti et al. reported the discovery of novel amide derivatives derived from1,2,3-triazole-benzofuran hybrids (Figure 29) (21). Overall derivatives were evaluated fortheir anticancer activities in four human cancer cell lines i.e.; PC3 (prostate cancer), A549(lung cancer), MCF7 (breast cancer), and A2780 (ovarian cancer) by employing MTT assayusing Etoposide as the reference compound. Among the novel amide derivatives (9a, 9j),mainly 9a-c, 9i, and 9j displayed potent anticancer activity towards MCF7 (9a, 9j), A549 (9b),A2780 (9c) and PC3 (9i) human cancer cell lines respectively. Furthermore, using moleculardocking simulations with the BCL-2 (PDB ID: 4LVT), Colchicine binding site of Tubulin(PDB ID: 1SA0), Kinase domain of C-ABL (PDB ID: 1IEP), and CLK-2 (PDB ID: 6FYL)proteins, the experimentally observed biological impact of new amide derivatives (9a-j), wereinvestigated, and it was discovered that the experimental findings of the researchers wereconsistent with the computationally derived results (Figure 30).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Efe Dogukan D ˘˙INCEL, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I 279Figure 29: The title compounds reported by Gariganti et al. (21)Figure 30: a) 2D representation of the binding interactions between the colchicine-binding site ofNavitoclax-binding site of 4LVT and 9a. b) Binding interactions between 9a and the Navitoclax-bindingsite of 4LVT . (21)2. ConclusionWithin all serious diseases cancer possesses specific significance since its complexpathophysiology. The researchers have performed many studies related to synthesis anddiscovery of novel effective small molecules against diverse cancer cell lines. Moreover,many compounds have been discovered which were determined as more active than thereference compounds which are used in clinics today. These results lighted hope againstthis mortal disease. The researchers also underlined the significance of multi-disciplinaryco-operation of researchers for discovery of effective compounds. In silico studies in drugdiscovery minimize time and cost in processes. Overall reported in silico and in vitro resultsprovided data for researchers for the synthesis of more efficient and target-specific agents.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

CANCER: FROM GENOMICS TO PHARMACEUTICSHence, the drug discovery studies should be continued and supported by computer-aided drugdesign techniques.REFERENCES1. Otto T, Sicinski P. Cell cycyle proteins as promising targets in cancer therapy. Nat RevCancer 2017;17:93-115.2. Arun Y, Saranraj K, Balachandran C, Perumal PT. Novel spirooxindole-pyrrolidinecompounds: Synthesis, anticancer and molecular docking studies. Eur J Med Chem2014;74:50-64.3. Li Shenghui, Xu Shengjie, Tang Yonghe, Ding Shan, Zang Jinchao, Wang Shuxiang,Zhou Guoqiang, Zhou Chuanqi, Li Xiaoliu. Synthesis, anticancer activity, andDNA-binding properties of novel 4-pyrazolyl-1,8-naphthalimide derivatives. BioorganicMed Chem Lett 2014;24:586-590.4. Nguyen MAT, Mungara AK, Kim JA, Lee KD, Park S. Synthesis, anticancer andantioxidant activity of novel carbazole-based thiazole derivatives. Phosphorus SulfurSilicon Relat Elem 2015;190:191-199.5. Swamy PMG, Prasad YR, Ashvini HM, Giles D, Shashidhar BV, Agasimundin YS.Synthesis, anticancer and molecular docking studies of benzofuran derivatives. MedChem Res 2015;24:3437-3452.6. Ruddarraju RR, Murugulla AC, Kotla R, Tirumalasetty MCB, Wudayagiri R,Donthabakthuni S, Maroju R, Baburao K, Parasa LS. Design, synthesis, anticancer,antimicrobial activities and molecular docking studies of theophylline containingacetylenes and theophylline containing 1,2,3-triazoles with variant nucleosidederivatives. Eur J Med Chem 2016;123:379-396.7. Yang J, Yang S, Zhou S, Lu D, Ji L, Li Z, Yu S, Meng X. Synthesis, anti-cancerevaluation of benzenesulfonamide derivatives as potent tubulin-targeting agents. Eur JMed Chem 2016;122:488-496.8. Gouda AM, Abdelazeem AH, Omar HA, Abdalla AN, Abourehab AS, Ali HI.Pyrrolizines: Design, synthesis, anticancer evaluation and investigation of the potentialmechanism of action. Bioorg Med Chem 2017;25:5637-5651.9. Simon L, Salam AAA, Kumar SM, Shilpa T, Srinivasan KK, Byrappa K. Synthesis,anticancer, structural, and computational docking studies of 3-benzylchroman-4-onederivatives. Bioorganic Med Chem Lett 2017;27:5284-5290.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Efe Dogukan D ˘˙INCEL, Nuray ULUSOY GUZELDEM ¨ ˙IRC˙I 28110. Sreenivasulu R, Durgesh R, Jadav SS, Sujitha P, Kumar CG, Raju RR. Synthesis,anticancer evaluation and molecular docking studies of bis(indolyl) triazinones,Nortopsentin analogs. Chem Pap 2018;72:1369-1378.11. Karakus¸ S, Tok F, T¨urk S, Salva E, Tatar G, Taskın-Tok T,Kocyigit-Kaymakcıoglu B. Synthesis, anticancer activity and ADMETstudies of N-(5-methyl-1,3,4-thiadiazol-2-yl)-4-[(3-subtituted)ureido/thioureido]benzenesulfonamide derivatives. Phosphorus Sulfur Silicon Relat Elem2018;193:528-534.12. Amr AEGE, Elsayed EA, Al-Omar MA, Eldin HOB, Nossier ES, Abdallah MM. Design,synthesis, anticancer evaluation and molecular modeling of novel estrogen derivatives.Molecules 2019; 24: 416.13. Abou-Zied HA, Youssif BGM, Mohamed MFA, Hayallah AM, Abdel-Aziz M. Design,synthesis, anticancer activity and docking studies of novel xanthine derivatives carryingchalcone moiety as hybrid molecules. Bioorg Chem 2019; 89: 102997.14. Iacopetta D, Catalano A, Ceramella J, Barbarossa A, Carocci A, Fazio A, Torre CL,Caruso A, Ponassi M, Rosano C, Franchini C, Sinicropi MS. Synthesis, anticancer andantioxidant properties of new indole and pyranoindole derivatives. Bioorg Chem 2020;105: 104440.15. Sreenivasulu R, Tej MB, Jadav SS, Sujitha P, Kumarn CG, RajuRR. Synthesis, anticancer evaluation and molecular docking studies of2,5-bis(indolyl)-1,3,4-oxadiazoles, Nortopsenting analogues. 2020; 1208: 127875.16. Suryanarayana K, Robert AR, Kerru N, Pooventhiran T, Thomas R, Maddila S,Jonnalagadda SB. Design, synthesis, anticancer activity and molecular docking analysisof novel dinitrophenylpyrazole bearing 1,2,3-triazoles. J Mol Struct 2021; 1243: 130865.17. Othman IMM, Alamshany ZM, Tashkandi NY,Gad-Elkareem MAM, Anwar MM,Nossier ES. New pyrimidine and pyrazole-based compounds as potential EGFRinhibitors: Synthesis, anticancer, antimicrobial evaluation and computational studies.Bioorg Chem 2021; 114: 105078.18. El-Sayed AA, Nossier ES, Almehizia AA, Amr AEE. Design, synthesis, anticancerevaluation and molecular docking study of novel 2,4-dichlorophenoxymethyl-basedderivatives linked to nitrogenous heterocyclic ring systems as potential CDK-2 inhibitors.J Mol Struct 2022; 1247: 131285.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

282 CURRENT ADVANCES IN MEDICINAL CHEMISTRY OF ANTICANCER AGENTS19. Bourzikat O, Abbouchi AE, Ghammaz H, Brahmi NE, Fahime EE, Paris A, DaniellouR, Suzenet F, Guillaumet G, Kazzouli SE. Synthesis, anticancer activities and moleculardocking studies of a novel class of 2-phenyl-5,6,7,8-tetrahydroimidazo[1,2-b]pyridazinederivatives bearing sulfonamides. Molecules 2022; 27, 5238.20. Azher OA, Hossan A, Pashameah RA, Alsoliemy A, Alharbi A, Habeebullah TM,El-Metwaly NM. Synthesis, anticancer evaluation, and molecular modeling study of new2-(phenylamino)pyrazolo[1,5-a]pyrimidine analogues. Arab J Chem 2023; 16: 104437.21. Gariganti N, Loke SK, Pagadala E, Chinta P, Poola B, Chetti P, Bansal A,Ramachandran B. Design, synthesis, anticancer activity of new amide derivativesfrom 1,2,3-triazole-benzofuran hybrids: An insights from molecular docking, moleculardynamics simulation and DFT studies. J Mol Struct 2023; 1273: 134250.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

CANCER: FROM GENOMICS TO PHARMACEUTICSCHAPTER 11THE ROLE OF PHARMACOGENOMICS INCHEMOTHERAPEUTIC SUSCEPTIBILITY ANDTOXICITYOzge Sultan ZENG ¨ ˙IN1,2, Mahmoud ABUDAYYAK3, Gul¨ OZHAN ¨ 41PhD Candidate., ˙Istanbul University Institute of Graduate Studies in Health Sciences, ˙Istanbul, T¨urkiye2˙Istanbul University Faculty of Pharmacy, Department of Pharmaceutical Toxicology, ˙Istanbul, T¨urkiyeE-mail: [email protected]. Prof. Dr., ˙Istanbul University Faculty of Pharmacy, Department of Pharmaceutical Toxicology, ˙Istanbul,T¨urkiyeE-mail: [email protected]. Dr. ˙Istanbul University Faculty of Pharmacy, Department of Pharmaceutical Toxicology, ˙Istanbul, T¨urkiyeE-mail: [email protected]: 10.26650/B/LSB28LSB48LSB56.2024.019.011ABSTRACTPharmacogenetics is the study of different responses to disease susceptibility and drug response in individualsaccording to their genetic characteristics. The genetic structure can affect drug metabolism, pharmacokinetics andpharmacodynamics. Pharmacogenetics, which determines the relationship between genetics and drug response andthe differences between individuals, allows the safest and most appropriate treatment to be planned individually.This method is especially prominent when creating a treatment plan for cancer patients. Oncologic treatments oftencause serious side effects in patients and may cause treatment to be interrupted. In the light of pharmacogeneticsinformation, it can be determined which chemotherapeutic will treat the patient most effectively and safely accordingto the patient’s genetic structure. Research in recent years has contributed to the treatment planning of many patientsin the clinic. However, since it is still a developing field, many studies are still needed to resolve the link betweendrug response and genetic structure.Keywords: Pharmacogenetic, Chemotherapeutics, Polymorphisms, SNPsCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

284 THE ROLE OF PHARMACOGENOMICS IN CHEMOTHERAPEUTIC SUSCEPTIBILITY ANDTOXICITY1. Introduction1.1. Pharmacogenetics/PharmacogenomicsDrug response varies among patients due to individual factors such as gender, age, weight,lifestyle, genetics, and environmental factors like air pollution and radiation. Every human hasa genome of 3×109 base pairs of DNA and it is known that no two people can be geneticallyidentical except identical twins. Genomic variation exists in about every 300-1000 nucleotidesin the human genome and the entire human genome contains over 14 million single nucleotidepolymorphisms (SNPs) (1).Pharmacogenetics is the study of the differences in individuals and the variability indrug response and susceptibility to disorders according to their genetic characteristics (2).Pharmacogenetics can be used in treatment planning and the prevention of side effects byselecting the drug and dose according to the patient’s drug response. Due to interindividualdifferences, a drug administered at the same dose may treat one patient, while it may not affectanother patient or may even cause serious adverse effects in another patient. By identifyingthe DNA variants that cause interindividual differences, personalized effective, and safetreatment can be planned (1, 2). The U.S. Food and Drug Administration (FDA) put a list ofthe pharmacogenomic biomarkers required to be tested before the prescription of drugs thatcould be affected negatively or positively by genetic variations among the patients. Althoughthe list is updated according to recent data, there are 541 tests for different genes and mutationsrelated to the response of variable drug groups such as chemotherapy, antibiotics, psychology,neurology, and cardiology drugs. Among the biomarkers, 81 biomarkers related to 125anticancer drugs (3) at the same hand, among 241 tests recommended by the National Libraryof Medicine/National Institutes of Health (NCBI/NIH) in 2018, there were 64 biomarker testsfor 18 drugs affected by from genes variations (2, 4).Pharmacogenetic studies have recently been frequently referred to as pharmacogenomics.While pharmacogenetics investigates genes that affect drug metabolism, pharmacogenomicscovers genes in the genome that affect drug response. Pharmacogenomics examines therelationship between interindividual differences and drug response from genomic, proteomic,transcriptomic, and metabolomic perspectives (1, 5).1.2. Pharmacogenetics/Pharmacogenomics in CancerPharmacogenomics assumes a significant part in oncology therapy procedures, as theindividual genotypes significantly, positively or negatively, affect the treatment. In thelight of pharmacogenomics research, the treatment is individualized, aiming for maximumefficiency and minimum toxicities and adverse effects. For that, genetic variations suchas somatic mutations in the tumor genome or germline mutations are considered whenestablishing the treatment protocol (6, 7). Pharmacogenetic screening of cancer patients canidentify chemotherapeutics to which patients will respond and those to which they show drugCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Ozge Sultan ZENG ¨ ˙IN, Mahmoud ABUDAYYAK, G¨ul OZHAN ¨ 285resistance. Since genetic variations affect drug metabolism, both the patient’s and the tumor’sgenome are examined in the screens (1). Polymorphisms of the human genome can affect drugabsorption, distribution, metabolism, efficacy, and side effects in the patient’s body. Patientsmay not benefit from chemotherapy treatment because of their genetic structure; alternativetreatment methods can be tried on patients for whom the classical treatment protocol will notwork due to their genetic profile (7, 8).1.3. Limitations on Pharmacogenetic/Pharmacogenomic EvaluationThere are a lot of limitations that interface the pharmacogenetic tests, which are assumedto be very useful in directing patients to effective treatment, among these limitations (2, 9-12);• Since it is still a developing science, clinical studies on the relationship between genesand cancer may not have been conducted in all populations. It is impossible to generalizethe data obtained to the world population. Most of the published clinical trials are onCaucasian populations, many more studies need to be done with Chinese, Indian, andAfrican populations to make a worldwide interpretation. These limited studies are notsufficient to make a risk assessment for the general population.• The amount of published clinical trials is not sufficient and usually consists ofunreplicated data. Although randomized controlled trials are the most appropriate forpharmacogenetic/pharmacogenomic clinical trials, financial and feasibility challengeslimit the spread and multiply of studies. For example, in a study on warfarin, it wasobserved that genetic variance was not the only factor affecting drug response. Althoughdrug dose changes were recommended in people with CYP2C9 and VKORC1 geneticvariants, it was also found that the polymorphism in the patient did not lead to a toxicityphenotype. During warfarin treatment, besides the patient’s genetic profile, factors suchas diet, lifestyle, diseases, and other medications affect the drug response.• SNPs are detected in most studies and clinical trials are guided by the data. Inaddition to SNPs, copy number variation (CNV) can also be used, but their effectsare underestimated because they have not yet been adequately studied. SNPs shouldnot be directly accepted as the main genetic variation, and it should be kept in mind thatvariants such as insertions and deletions in the genome can have as much or even moreimpact on drug response and cancer risk as SNPs. Cancer risk cannot be determined byidentifying a single SNP or gene; cancer is a much more complex entity. More studiesare needed to evaluate the association between gene variations and cancer.• In studies conducted for pharmacogenetics, it is not correct to make evaluations basedonly on the genetic structure without considering individual factors; genotype andphenotype cannot be considered separately from each other. Since these studiesCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

286 THE ROLE OF PHARMACOGENOMICS IN CHEMOTHERAPEUTIC SUSCEPTIBILITY ANDTOXICITYwill affect clinical applications, genotyping should be standardized, results shouldbe properly reported and verified. With the development of genome technology,pharmacogenetics will give more direction to cancer treatment.• Another challenge physicians experience is the lack of standardized explanations ofpharmacogenetic terms. To illustrate with an example, the drug label of codeine statesthat CYP2D6 ultra-rapid metabolizers should be avoided when using codeine but doesnot provide information on how to derive the ultra-rapid metabolizer from genotypedata.• Since it is a new and developing research field, many physicians do not have sufficientknowledge about pharmacogenomics. In the study conducted by Peterson et al. (11),physicians were surveyed about pharmacogenetics/pharmacogenomics, and althoughphysicians found the studies quite valuable, they expressed that they were not surehow the findings would be used in clinical practice. Physicians frequently encounterproblems in cancer treatment such as patient non-response to treatment, lack ofalternative drugs, and severe toxicity of chemotherapeutics. By informing the physicianabout pharmacogenomic studies and informing the patient, target-oriented treatment canbe planned and contribute to overcoming these problems.• Guidelines and definitions for pharmacogenetics are still not established by thecompetent authorities. Even if biomarker information is included in drug labels, itis not possible to include information such as pharmacogenetic recommendations andhow and when to apply them to whom. There may also be differences between sourcesof pharmacogenetic information and it may be unclear which sources should be usedas the basis for clinical practice.• For pharmacogenetic information to be applied in the clinic, some official regulationsand changes should be made. Patients’ genetic structures should be legally protectedwithin the scope of their privacy and health policies should be updated. Besides that,as the field of pharmacogenetics/pharmacogenomics continues to develop rapidly, it isimportant and necessary for physicians to access up-to-date information.• For the clinical application of pharmacogenetic information, there is a need for databaseswhere physicians can access patient genotypes and find SNP-drug response associations.The Pharmacogenetics and Pharmacogenomics Knowledge Bank (PharmGKB) (12), isone of the databases serving both physicians and researchers. It compiles genotypeand clinical data with the information in the literature and presents it to theuser. PharmGKB can be searched for genes, drugs, diseases, and mechanisms.Although access to information has become easier for physicians, there is a needCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Ozge Sultan ZENG ¨ ˙IN, Mahmoud ABUDAYYAK, G¨ul OZHAN ¨ 287for guidelines to put this information into clinical practice. Another effectively activeorganization, that helps the physicians in this field, is The Clinical PharmacogeneticsImplementation Consortium (CPIC) which was established as a partnership betweenmembers and experts of the Pharmacogenomics Research Network, PharmGKB, andpharmacogenomics and medicinal labs. A strong collaboration between physicians,researchers, pharmaceutical companies, and patients is needed to promote and sustainthe application of pharmacogenetic knowledge in the clinic.• Pharmacogenetic/pharmacogenomic toxicity tests have limited applicability dueto their cost and feasibility. In fact, with the development ofpharmacogenetics/pharmacogenomics, patients can be provided with the most effectivetreatment instead of trying treatments that will not be operative, and also potentialtoxicities can be identified and prevented, reducing healthcare costs. In addition totesting costs, logistical problems like test availability and turnaround times also hinderclinical development.• In biomarker selection for pharmacogenetic research, the prevalence of the biomarkerin the population should be considered for validation and clinical application. Workingwith a rare biomarker is likely to increase the cost of testing. While patients alreadyneed to be persuaded to participate in pharmacogenetic studies, the increased cost willinevitably negatively affect patient preferences.• Although many studies have been conducted, there are still problems in theclinical application of the data. Awareness raising of patients and physicians,improvements in legislation, and more studies are needed. Advances in the field ofpharmacogenetics/pharmacogenomics have a hopeful future in the treatment of cancer.In recent years, technological advances in the field of healthcare, lead to an increase inthe biomarkers that can be identified and used in cancer treatment. Genetic markers canbe used to select the drug that will provide the most effective treatment for the patient,adjust the dose of the drug and eliminate drugs that pose a risk of serious toxicity. Byusing pharmacogenetic/pharmacogenomic tests, the number of drugs to be tested on patientsand thus the toxic effects to be seen can be reduced, saving time and money. The use ofpharmacogenetic information in chemotherapeutics with a narrow therapeutic index is veryadvantageous.Pharmacogenomics can accelerate drug discovery and development. The sensitivityor resistance of neoplastic cells to drugs can be explained by mutations in oncogenes.Understanding how somatic mutations of tumors develop has encouraged the progressionin the field of molecular targeting and targeting therapy. The use of targeted agents instead oftrying different drugs may increase the efficacy of treatment and reduce the overall cost.Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

288 THE ROLE OF PHARMACOGENOMICS IN CHEMOTHERAPEUTIC SUSCEPTIBILITY ANDTOXICITY1.4. Markers for Predictive Response to ChemotherapyFDA has approved several predictive biomarkers (3) that can be used in the improvementor monitoring of several chemotherapy drugs (Table 1). The predictive biomarkers aremainly somatic or acquired genetic variations such as nucleotide mutations. Additionally,other genetic variations are frequently seen in cancerous cells such as changes in the copiesnumbers, the epigenetic features, and the chromosomal rearrangement.Targeting of oncogenes that are essential to the proliferation, maintenance, and metastasisof cancerous cells plays a critical role in the success of chemotherapy and getting a response.As an example, the response of adenocarcinoma lung tumor with EGFR tyrosine kinasedomain mutation to gefitinib and erlotinib. The different results and reactions to the targeteddrugs play an important role in the identification of the phenotypic specifications and in theverifying of the biomarkers. For the previous example, while the deletion mutation at exon19 and the substitution mutation at exon 21 increase the sensitivity and so the effectivity oftyrosine kinase inhibitors, the T790M mutation at exon 20 increases the resistance to thosedrugs (13).The forecast of therapy success by germline biomarkers has not been as useful in clinicalpractice as expected. Tamoxifen, a widely used anticancer drug, is biotransformed to itsactive metabolite endoxifen by CYP2D6 and CYP2D6*10 polymorphism decreases CYP2D6activity. This was suggested to impair clinical outcomes in tamoxifen-treated breast cancerpatients. Subsequent analyses have reported no link between CYP2D6 polymorphisms andtamoxifen treatment outcomes. Although not included in these analyses, hormonal therapyrates and tamoxifen dose changes are other factors affecting treatment. The clinical andobservational studies showed that patients with ultrahigh CYP2D6 activity had a highertendency to develop discontinuation rates at 4 months, compared to the other groups. Theultrahigh activity of CYP2D6 enzymes that are responsible for activating tamoxifen is acceptedas a benefit of these patients, and those patients asked to be cautious about CYP2D6 inhibitors.However, the real advantage for this group is still inconceivable, especially since these patientsshow a higher tendency to give up the treatment early. Despite that, the testing for possibleCYP2D6 mutations and to detect the ultrahigh metabolizer still in the FDA recommendedbiomarker tests before starting with tamoxifen treatment, the predictive value and so theoutcomes are still unsatisfying, and there is a need for further studies and data (14).1.5. Markers for Predictive Toxicity to ChemotherapyPharmacogenetic studies have identified many chemotherapeutic agents with germlinemarkers of toxicity (Table 1). While studying the human genome, polymorphisms havebeen identified by utilizing pharmacokinetic, pharmacodynamic, pathophysiology, and tumorbiology information, and their roles in drug therapies have been investigated. Withtoday’s technology, genes with polymorphism potential can be identified using statisticsCancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Ozge Sultan ZENG ¨ ˙IN, Mahmoud ABUDAYYAK, G¨ul OZHAN ¨ 289and probability (14, 15).The different responses of ethnic groups to the same drug is a very important point thatis worthy of notice when new ‘’across the world” experimental models are developed. Forexample, it is important to know which polymorphisms are more prevalent and what is the ratioof these polymorphisms in the studied society. UGT1A1 as an example, In Caucasian peoplethe most prevalent variant is UGT1A1*28 polymorphism, however, UGT1A1*6 polymorphismis the most prevalent in East Asian nations with a ratio of about 23%, while the ratio ofUGT1A1*28 polymorphism less than 5%. This was the reason behind the approvement thetest of both UGT1A1*28 and UGT1A1*6 in Japan. This emphasized that even though theassociations between some polymorphisms and treatment outcomes are well established insome ethnic groups this could be without benefits for others, making the application of thebiomarker tests in the clinical practice polemical (14, 15).1.6. Prognostic Markers to Guide TherapyThe application of drug targeting, where the applied drugs react with specific moleculesinside the cancerous cells, increases dramatically. The targeting of anaplastic lymphomakinase (ALK) in non-small cell lung cancer patients by specific inhibitors such as Crizotinibsuccess in more than 70% of the patients. Research and clinical uses show the low efficacy ofCrizotinib seen in patients with echinoderm microtubule-associated protein-like 4 anaplasticlymphoma kinase (EML4-ALK) fusion gene. This mutation is more common in non-smokeradenocarcinoma lung cancer female patients. Knowing that EML4-ALK and EGFR mutationsare significantly exclusive of each other, in other words, the prevalence of one of thosemutations decreases the probability of having the second, helps in the selection of the clinicaltrial groups. By choosing patients negative for EGFR mutation, the number of patientswho need to be screened for EML4-ALK mutation decreased, the trials accelerated and thedevelopment of Crizotinib succeeded (14).The importance of biomarkers in choosing and developing a new drug or designing anew therapy regime could be noticed after years of using the drug/s. As an example, it wasnoticed that the addition of cetuximab and panitumumab to the therapy regime gave betterresults and increased the survival rate and success in patients with KRAS wild type. Since theretrospective studies, the validation of biomarker clinical applications may not be able to testpatient samples or information related to patients, biopsies or biological samples are missed,or the size of sample/patients is not big enough. There was a need for prospective studies toconfirm the noticed results (14).Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

290 THE ROLE OF PHARMACOGENOMICS IN CHEMOTHERAPEUTIC SUSCEPTIBILITY ANDTOXICITYTable 1: The example of pharmacogenetic biomarkers*Gene Polymorphism Molecular effect Affectedanticancer drugs Response ReferencesALKALK /EML4(CD246) (chr. 2),ALK/RANBP2 (chr.2), ALK/ATIC(chr.2), ALK/TFG (chr.3), ALK/NPM1(chr. 5),ALK/SQSTM1 (chr.5), ALK/KIF5B (chr.10), ALK/CLTC(chr. 17),ALK/TPM4 (chr.19), ALK/MSN (chr.X)Encodes a receptortyrosine kinaseAlectinib,Lorlatinib,Atezolizumab,BrentuximabVedotin, Brigatinib,Ceritinib, CrizotinibIndicated for the treatment ofpatients with ALK-positive3, 17,18ALKALK /EML4(CD246) (chr. 2),ALK/RANBP2 (chr.2), ALK/ATIC(chr.2), ALK/TFG (chr.3), ALK/NPM1(chr. 5),ALK/SQSTM1 (chr.5), ALK/KIF5B (chr.10), ALK/CLTC(chr. 17),ALK/TPM4 (chr.19), ALK/MSN (chr.X)Encodes a receptortyrosine kinaseDurvalumab,Ipilimumab,Nivolumab,Pembrolizumab,Pemetrexed,Tremelimumab-actNot for patients with ALKgenomic aberrations ormutations3, 17,18BCR-ABL1(Philadelphiachromosome)T (9;22)translocationand fusion withthe 5’ end of thebreakpoint clusterregion gene (BCR;MIM:151410).Involved ina variety ofcellular processes,including celldivision, adhesion,differentiation, andresponse to stressAsciminib,Blinatumomab,Bosutinib,Busulfan,Dasatinib, Imatinib,InotuzumabOzogamicin,Nilotinib,Omacetaxine,Ponatinib,VincristineIntended for Philadelphiachromosome-positive patients.Allele T is associated withresistance to nilotinib.Genotype CT is associatedwith an increased likelihood ofrecurrence when treated withDasatinib19-21BRAFCommonly theV600E and V600KmutationsEncodes a proteinbelonging to theRAF family ofserine/threonineprotein kinases.Important for theregulation of theMAP kinase/ERKsignaling pathwayAtezolizumab,Binimetinib,Cetuximab,Cobimetinib,Dabrafenib,Encorafenib,Nivolumab,Nivolumab andRelatlimab-rmbw,Pembrolizumab,Trametinib,VemurafenibApproved for the treatment ofpatients with a BRAF V600Eor V600K mutation. AlleleG and allele T are associatedwith increased sensitivity tothe drugs as compared to alleleA.22-24CD274 mutations in the3’-UTREncodes PD-L1,the type Itransmembraneprotein that hasimmunoglobulinV-like and C-likedomains. ˙It’sbinding withreceptors inhibitsT-cell activation andcytokine productionAtezolizumab,Avelumab,Cemiplimab-rwlc,Durvalumab,Ipilimumab,Nivolumab,Nivolumab andRelatlimab-rmbw,Pembrolizumab,Pemetrexed,Tremelimumab-actlDrug resistance 25-27EGFRThere are at least14 variants, mainlySNPs. The mostcommons are exon19 deletions, exon21 codon L858R,and codon T790MEncodes atransmembraneglycoprotein thatis accepted asa receptor formembers of theepidermal growthfactor family.Important for tprotein kinaseactivityAtezolizumab,Tremelimumab-actl,Tepotinib,Ipilimumab,Panitumumab,Cetuximab,DurvalumabDrug resistance or decrease inactivity. Differences betweenalleles regarding Cetuximaband Panitumumab activity ortoxicity (as exp. CC genotype)28-30Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.

Ozge Sultan ZENG ¨ ˙IN, Mahmoud ABUDAYYAK, G¨ul OZHAN ¨ 291Table 1: ContinuedEGFRThere are at least14 variants, mainlySNPs. The mostcommons are exon19 deletions, exon21 codon L858R,and codon T790MEncodes atransmembraneglycoprotein thatis accepted asa receptor formembers of theepidermal growthfactor family.Important for tprotein kinaseactivityDacomitinib,Erlotinib,Gefitinib, Afatinib,Mobocertinib,Nivolumab,Osimertinib,Cemiplimab-rwlc,Pembrolizumab,RamucirumabIndicated for patients havingEGFR exon 19 deletions orexon 21 (L858R) substitutionmutations or EGFRaberrations. Differencesbetween alleles regardingErlotinib activity and toxicity(as exp. allele G, GGgenotype)28-30ERBB2(HER2)Allelic variationsat amino acidpositions 654 and655 of isoformA. Ile654/Ile655amplification and/oroverexpression.Encodes a memberof the EGF receptorfamily, importantfor tyrosine kinasesactivity and itssignaling pathwaysAbemaciclib,Everolimus,Alpelisib, Olaparib,Ribociclib,TalazoparibDrugs improved forhormone receptor-positive,HER2-negative breast cancer.HER’s overexpression relatedto drug resistance31-33ERBB2(HER2)Allelic variationsat amino acidpositions 654 and655 of isoformA. Ile654/Ile655amplification and/oroverexpression.Encodes a memberof the EGF receptorfamily, importantfor tyrosine kinasesactivity and itssignaling pathwaysCapecitabine,Lapatinib,Margetuximab-cmkb,Neratinib,Palbociclib,Pembrolizumab,Pertuzumab,Trastuzumab,TucatinibUse for HER2 (encoded bygene ERBB2)-over-expressing.AG and GG genotypesassociated with increased riskof cardiotoxicity. Allele Gassociated with decreaseddrug (Trastuzumab) response31-33HLA-AMore than 6000HLA-A alleles havebeen described. atleast 24 variantswere reported inresearch related todrug activity/ safety.Encodes class Imolecules, it playsa central role inthe immune systemactivityIpilimumab,Tebentafusp-tebnOnly HLA-A*02:01 genotypepositive are accepted in thetrials.34-36HLA-BAt least 72 variantswere reported inresearch related todrug activity/safety.Common mutationsare HLA-B*58:01,HLA-B*57:01, andHLA-B*15:02.Encodes class Imolecules. It playsa central role inthe immune systemactivityAllopurinol,PazopanibPatients with HLA-B*58:01allele is at a higher risk ofallopurinol hypersensitivitysyndrome. HLA-B*57:01carriage associated withhepatotoxicity.37-39HLA-DQA1At least 6 variantswere reported inresearch related todrug activity/safety.Commonmutations areHLA-DQA1*02:01HLA-DQA1*01:02andHLA-DQA1*01:03.Encodes aheterodimer classIL molecule.Important for theimmune systemactivity especiallyin B Lymphocytes,dendritic cells, andmacrophages.LapatinibHLA-DQA1*02:01 isassociated with an increasedrisk of toxic liver disease.40-42HLA-DRB1Hundreds of DRB1alleles have beendescribed. Atleast 34 variantswere reported inresearch related todrug activity/safety.Common alleles areHLA-DRB1*04:03,HLA-DRB1*07:01,HLA-DRB1*03:01,HLA-DRB1*01:01.Encodes aheterodimer classIL molecule.Important for theimmune systemactivity especiallyin B Lymphocytes,dendritic cells, andmacrophages.LapatinibHLA-DRB1 *07:01 isassociated with an increasedrisk of toxic liver disease.HLA-DRB1 *04:03 isassociated with an increasedlikelihood of Exanthema.43-45IDH1At least 165 variantswere reported inresearch related tocancers, or drugactivity/toxicity.The commonmutations areIDH1 missensemutations at R132.Additional somaticIDH1variants(G70D, G123R,I130M, H133Q,A134D, V71I, andV178I)Metabolismof endogenouscofactorsIvosidenib,OlutasidenibIndicated for the treatmentof patients with a susceptibleIDH1 mutation46-48Cancer: from Genomics to Pharmaceutics, edited by Zeynep Karakas, et al., Istanbul University Press, 2024. ProQuest Ebook Central, http://ebookcentral.proquest.com/lib/uitm-ebooks/detail.action?docID=31789562.Created from uitm-ebooks on 2025-12-02 14:42:18. Copyright © 2024. Istanbul University Press. All rights reserved.