ROLE OF HETEROCYCLIC SCAFFOLDS IN MODERN DRUG DESIGN: STRUCTURE–ACTIVITY RELATIONSHIPS, THERAPEUTIC APPLICATIONS AND EMERGING COMPUTATIONAL APPROACHES

Heterocyclic scaffolds are central structural elements in medicinal chemistry because incorporationofnitrogen,oxygen orsulfurintoaringcan altermolecularshape, electronicdistribution,ionisation,hydrogen-bondingcapacity,lipophilicityand metabolicbehaviour.Thesefeaturesallowmedicinalchemiststotunetarget recognitionanddrug-likepropertieswhileretainingacompactandsynthetically modifiable framework. Nitrogen-containing heterocycles are particularly prominent in approvedsmall-moleculemedicines;aninfluentialanalysisofUSFDA-approved pharmaceuticalsreportedthat59% ofuniquesmall-moleculedrugsinitsdataset contained at least one nitrogen heterocycle [1]. A later analysis of 321 unique smallmolecule drugs approved during 2013–2023 reported that 82% contained at least one nitrogen heterocycle[12].These valuesarisefrom differentapprovalperiodsand datasetsandshouldnotbeinterpretedasauniversalordirectlycomparable prevalenceestimate.Thepresentnarrativereviewdiscussesthecontributionof heterocyclic scaffolds to modern drug design, with emphasis on scaffold selection, structure–activityrelationships(SAR),representativetherapeuticapplications, physicochemicaloptimisationandcomputationalapproaches.Five-andsixmemberedmonocyclicrings,fusedsystemsandsaturatedheterocyclesare considered,includingimidazole,triazole,pyridine,pyrimidine,indole,quinoline, piperidineandmorpholinemotifs.Selectedmarketeddrugsillustratehow heterocycles can act as recognition elements, tune basicity and solubility, or serve as bioisostericreplacements.Thereview alsoexaminestheintegrationofmolecular docking,ligand-basedmodelling,virtualscreeningandmachine-learningmethods intoheterocycle-focuseddiscovery.Importantly,aheterocyclicringdoesnot independentlyguaranteepotency,selectivityorfavourablepharmacokinetics;its value depends on substitution pattern, three-dimensional context, target biology and whole-moleculeproperties.Currentchallengesincludepromiscuousbinding, metabolic liabilities, solubility limitations, synthetic accessibility, selectivity and overreliance on computational scores. A rational workflow combining medicinal-chemistry design,experimentaltestinganditerativeoptimisationisthereforeessentialfor translating heterocyclic hits into safe and effective drug candidates.

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Publication Details

Journal
ChemRxiv
Published
2026-11-01
DOI
https://doi.org/10.26434/chemrxiv.15011456/v1
Primary Topic
Computational Drug Discovery Methods
Type
preprint
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preprint

ROLE OF HETEROCYCLIC SCAFFOLDS IN MODERN DRUG DESIGN: STRUCTURE–ACTIVITY RELATIONSHIPS, THERAPEUTIC APPLICATIONS AND EMERGING COMPUTATIONAL APPROACHES

Brijesh Kumar, Brijesh Jaiswal, Anchal Shukla
ChemRxiv
Computational Drug Discovery Methods
preprint

ROLE OF HETEROCYCLIC SCAFFOLDS IN MODERN DRUG DESIGN: STRUCTURE–ACTIVITY RELATIONSHIPS, THERAPEUTIC APPLICATIONS AND EMERGING COMPUTATIONAL APPROACHES

Brijesh Kumar, Brijesh Jaiswal, Anchal Shukla
preprint en

Abstract

Heterocyclic scaffolds are central structural elements in medicinal chemistry because incorporationofnitrogen,oxygen orsulfurintoaringcan altermolecularshape, electronicdistribution,ionisation,hydrogen-bondingcapacity,lipophilicityand metabolicbehaviour.Thesefeaturesallowmedicinalchemiststotunetarget recognitionanddrug-likepropertieswhileretainingacompactandsynthetically modifiable framework. Nitrogen-containing heterocycles are particularly prominent in approvedsmall-moleculemedicines;aninfluentialanalysisofUSFDA-approved pharmaceuticalsreportedthat59% ofuniquesmall-moleculedrugsinitsdataset contained at least one nitrogen heterocycle [1]. A later analysis of 321 unique smallmolecule drugs approved during 2013–2023 reported that 82% contained at least one nitrogen heterocycle[12].These valuesarisefrom differentapprovalperiodsand datasetsandshouldnotbeinterpretedasauniversalordirectlycomparable prevalenceestimate.Thepresentnarrativereviewdiscussesthecontributionof heterocyclic scaffolds to modern drug design, with emphasis on scaffold selection, structure–activityrelationships(SAR),representativetherapeuticapplications, physicochemicaloptimisationandcomputationalapproaches.Five-andsixmemberedmonocyclicrings,fusedsystemsandsaturatedheterocyclesare considered,includingimidazole,triazole,pyridine,pyrimidine,indole,quinoline, piperidineandmorpholinemotifs.Selectedmarketeddrugsillustratehow heterocycles can act as recognition elements, tune basicity and solubility, or serve as bioisostericreplacements.Thereview alsoexaminestheintegrationofmolecular docking,ligand-basedmodelling,virtualscreeningandmachine-learningmethods intoheterocycle-focuseddiscovery.Importantly,aheterocyclicringdoesnot independentlyguaranteepotency,selectivityorfavourablepharmacokinetics;its value depends on substitution pattern, three-dimensional context, target biology and whole-moleculeproperties.Currentchallengesincludepromiscuousbinding, metabolic liabilities, solubility limitations, synthetic accessibility, selectivity and overreliance on computational scores. A rational workflow combining medicinal-chemistry design,experimentaltestinganditerativeoptimisationisthereforeessentialfor translating heterocyclic hits into safe and effective drug candidates.

ChemRxiv
Computational Drug Discovery Methods
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