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Python-based QSAR modeling protocol for antioxidant activity: a case-study using a library of di(hetero)cyclic amines or amides

2025-09-16Journal article Open access
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datacite.subject.fosEngenharia e Tecnologia::Engenharia Eletrotécnica, Eletrónica e Informática
datacite.subject.sdg04:Educação de Qualidade
datacite.subject.sdg09:Indústria, Inovação e Infraestruturas
dc.contributor.authorMateus, Cristiano
dc.contributor.authorAbreu, Rui M. V.
dc.contributor.authorAbreu, Rui M.V.
dc.contributor.authorMateus, Cristiano
dc.date.accessioned2026-01-08T14:59:07Z
dc.date.available2026-01-08T14:59:07Z
dc.date.issued2025-09-16
dc.description.abstractConstructing a QSAR model involves several critical steps, including chemical structure preparation, molecular descriptor calculation and selection, and model development and validation. This study presents a comprehensive methodology for preparing QSAR models using freely open-source software tools. A detailed, stepby- step protocol outlines the entire process, from compound library preparation to statistical validation. As a case study, we developed a QSAR model to predict the antioxidant activity, specifically radical scavenging activity, of 70 di(hetero)aryl amine and amide compounds. Molecular descriptors (12,072 total) were calculated using the OCHEM platform, and PyQSAR built-in tools were used for descriptor selection and model construction. Four key descriptors (B06[C-O], Eig04_AEA(dm), JGI2, and J_Dz(p)) were selected to develop a MLR model with strong statistical performance (Q2CV = 0.8676, RSRCV = 0.3518). Internal validation showed strong predictive stability, while external validation demonstrated the model’s generalizability with a Q2EXT > 0.5. This study not only demonstrates the application of a freely open-source QSAR approach but also contributes to ongoing efforts in identifying and designing potent antioxidant agents with potential therapeutic applications. All relevant files and the detailed protocol are provided, allowing other researchers to replicate the antioxidant QSAR model and apply the methodology to develop QSAR models for other compound libraries and biological activities.por
dc.description.sponsorshipThis work was supported by national funds through FCT/MCTES (PIDDAC): CIMO, UIDB/00690/2020 ( h t t p s : / / d o i . org / 1 0 . 5 4 4 9 9 / U I D B / 0 0 6 9 0 / 2 0 2 0 ) and UIDP/00690/2020 (https://doi.org/10.54499/UIDP/00690/2020); and SusTEC, LA/P/0007/2020 (https://doi.org/10.54499/LA/P/0007/2020).
dc.identifier.citationMateus, Cristiano; Abreu, Rui M.V. (2025). Python-based QSAR modeling protocol for antioxidant activity: a case-study using a library of di(hetero)cyclic amines or amides. Discover Chemistry. ISSN 3005-1193. 2:1, p. 1-17
dc.identifier.doi10.1007/s44371-025-00290-0
dc.identifier.issn3005-1193
dc.identifier.urihttp://hdl.handle.net/10198/35376
dc.language.isoeng
dc.peerreviewedyes
dc.publisherSpringer
dc.relationMountain Research Center
dc.relationAssociate Laboratory for Sustainability and Tecnology in Mountain Regions
dc.relationMountain Research Center
dc.relation.ispartofDiscover Chemistry
dc.relation.ispartofseries1; 17
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectQSAR modeling
dc.subjectMolecular descriptors
dc.subjectMethodology
dc.subjectAntioxidant activity
dc.subjectDi(hetero)aryl amines and amides
dc.titlePython-based QSAR modeling protocol for antioxidant activity: a case-study using a library of di(hetero)cyclic amines or amides
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleMountain Research Center
oaire.awardTitleAssociate Laboratory for Sustainability and Tecnology in Mountain Regions
oaire.awardTitleMountain Research Center
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F00690%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/LA%2FP%2F0007%2F2020/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F00690%2F2020/PT
oaire.citation.issue1
oaire.citation.titleDiscover Chemistry
oaire.citation.volume2
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream6817 - DCRRNI ID
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
person.familyNameAbreu
person.familyNameMateus
person.givenNameRui M.V.
person.givenNameCristiano
person.identifier.ciencia-id0F19-0DE2-12A2
person.identifier.ciencia-id5018-C0F7-7A81
person.identifier.orcid0000-0002-7745-8015
person.identifier.orcid0000-0003-0757-9548
person.identifier.scopus-author-id7003290613
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
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relation.isAuthorOfPublication24929dd6-ef8d-4534-8010-603dd86acebf
relation.isAuthorOfPublication.latestForDiscoverycadb03a4-5e60-4745-b35f-fc3a97c071bc
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