{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:07:44Z","timestamp":1772168864545,"version":"3.50.1"},"reference-count":37,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T00:00:00Z","timestamp":1687737600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Universidad del Sin\u00fa","award":["BS-PD\/2023-03"],"award-info":[{"award-number":["BS-PD\/2023-03"]}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    <ns3:bold>Background:<\/ns3:bold>\n                    A\u00a0\n                    <ns3:italic>coronavirus<\/ns3:italic>\n                    \u00a0identified in 2019,\u00a0\n                    <ns3:italic>SARS<\/ns3:italic>\n                    -\n                    <ns3:italic>CoV<\/ns3:italic>\n                    -\n                    <ns3:italic>2<\/ns3:italic>\n                    , has\u00a0\n                    <ns3:italic>caused<\/ns3:italic>\n                    \u00a0a pandemic of respiratory\u00a0\n                    <ns3:italic>illness<\/ns3:italic>\n                    , called\u00a0\n                    <ns3:italic>COVID<\/ns3:italic>\n                    -\n                    <ns3:italic>19<\/ns3:italic>\n                    . Most people with COVID-19 experience mild to moderate symptoms and recover without the need for special treatments. The SARS\u2011CoV\u20112 RNA\u2011dependent RNA polymerase (RdRp) plays a crucial role in the viral life cycle. The active site of the RdRp is a very accessible region, so targeting this region to study the inhibition of viral replication may be an effective therapeutic approach. For this reason, this study has selected and analysed a\n                    <ns3:bold\/>\n                    series of ligands used as SARS-CoV-2 virus inhibitors, namely: the Zidovudine, Tromantadine, Pyramidine, Oseltamivir, Hydroxychoroquine, Cobicistat, Doravirine (Pifeltro), Dolutegravir, Boceprevir, Indinavir, Truvada, Trizivir, Trifluridine, Sofosbuvir \u00a0and Zalcitabine.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Methods:<\/ns3:bold>\n                    These ligands were analyzed using molecular docking, Receptor-Based Pharmacophore Modelling. On the other hand, these outcomes were supported with chemical reactivity indices defined within a conceptual density functional theory framework.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Results:<\/ns3:bold>\n                    The results show the conformations with the highest root-mean-square deviation (RMSD), have \u03c0-\u03c0 stacking interaction with residue LEU141, GLN189, GLU166 and GLY143, HIE41, among others. Also was development an electrostatic potential comparison using the global and local reactivity indices.\n                  <\/ns3:p>\n                  <ns3:p>\n                    <ns3:bold>Conclusions:<\/ns3:bold>\n                    These studies allow the identification of the main stabilizing interactions using the crystal structure of SARS\u2011CoV\u20112 RNA\u2011dependent RNA polymerase. In this order of ideas, this study provides new insights into these ligands that can be used in the design of new COVID-19 treatments. The studies allowed us to find an explanation supported in the Density Functional Theory about the chemical reactivity and the stabilization in the active site of the ligands.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.133426.1","type":"journal-article","created":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T11:25:09Z","timestamp":1687778709000},"page":"749","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Receptor-Based Pharmacophore Modelling of a series of ligands used as inhibitors of the SARS-CoV-2 virus by complementary theoretical approaches, molecular docking, and reactivity descriptors."],"prefix":"10.12688","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9159-5289","authenticated-orcid":false,"given":"Alejandro","family":"Morales-Bayuelo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jes\u00fas","family":"S\u00e1nchez-M\u00e1rquez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2023,6,26]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"jrm00063","DOI":"10.2340\/16501977-2694","article-title":"Long-term clinical outcomes in survivors of severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus outbreaks after hospitalisation or ICU admission: A systematic review and meta-analysis.","volume":"52","author":"H Ahmed","year":"2020","journal-title":"J. Rehabil. Med."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"n1412","DOI":"10.1136\/bmj.n1412","article-title":"Risk of hospital admission for patients with SARS-CoV-2 variant B.1.1.7: cohort analysis.","volume":"15","author":"T Nyberg","year":"2021 Jun","journal-title":"BMJ."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1507-1517","DOI":"10.1016\/S1473-3099(21)00290-5","article-title":"Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study.","volume":"21","author":"P Bager","year":"2021 Nov","journal-title":"Lancet Infect. Dis."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"581-590","DOI":"10.1002\/jcph.1788","article-title":"Antiretrovirals for Prophylaxis Against COVID-19: A Comprehensive Literature Review.","volume":"61","author":"G Alavian","year":"2021 May","journal-title":"J. Clin. Pharmacol."},{"key":"ref5","first-page":"1152-1155","article-title":"Randomized double-blind trial of tromantadine versus aciclovir in recurrent herpes orofacialis.","volume":"39","author":"K Ostheimer","year":"September 1989","journal-title":"Arzneimittelforschung."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"134-140","DOI":"10.1038\/s41586-022-04482-x","article-title":"Pyrimidine inhibitors synergize with nucleoside analogues to block SARS-CoV-2.","volume":"604","author":"D Schultz","year":"2022","journal-title":"Nature."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.26633\/RPSP.2020.40","article-title":"Clinical trials on drug repositioning for COVID-19 treatment.","volume":"44","author":"S Rosa","year":"2020","journal-title":"Rev. Panam. Salud Publica."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"105949","DOI":"10.1016\/j.ijantimicag.2020.105949","article-title":"Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial.","volume":"56","author":"Gautret","year":"2020","journal-title":"Int. J. Antimicrob. Agents."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"33-39","DOI":"10.1016\/S1131-3587(20)30033-9","article-title":"Tratamientos farmacol\u00f3gicos de los pacientes con COVID19: interacciones e indicaciones [Pharmacological treatments for COVID-19 patients: interactions and indications].","volume":"20","author":"M Iglesias","year":"2020","journal-title":"Revista Espa\u00f1ola de Cardiolog\u00eda Suplementos."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"422-432","DOI":"10.1080\/00498254.2018.1451667","article-title":"Characterisation of the absorption, distribution, metabolism, excretion and mass balance of doravirine, a non-nucleoside reverse transcriptase inhibitor in humans.","volume":"49","author":"R Sanchez","year":"2018 Mar 28","journal-title":"Xenobiotica."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"205-215","DOI":"10.4067\/s0716-10182020000300205","article-title":"F\u00e1rmacos prometedores y potenciales para el tratamiento de COVID-19.","volume":"37","author":"C Moneriz","year":"2020","journal-title":"Rev. Chil. Infectol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"6258-6272","DOI":"10.18632\/aging.202703","article-title":"Screening potential FDA-approved inhibitors of the SARS-CoV-2 major protease 3CLpro through high-throughput virtual screening and molecular dynamics simulation.","volume":"13","author":"W Liu","year":"2021 03 07","journal-title":"Aging."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"100531","DOI":"10.1016\/j.imu.2021.100531","article-title":"Identification of potential antivirals against SARS-CoV-2 using virtual screening method.","volume":"23","author":"M Rahman","year":"2021","journal-title":"Inform Med Unlocked."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"426-433","DOI":"10.1086\/422520","article-title":"AIDS Clinical Trials Group 320 Study Team, Impact of Indinavir on the Quality of Life in Patients with Advanced HIV Infection Treated with Zidovudine and Lamivudine.","volume":"39","author":"P Coplan","year":"1 August 2004","journal-title":"Clin. Infect. Dis."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"289-295","DOI":"10.1021\/ar010048x","article-title":"Molecular Quantum Similarity and the Fundamentals of QSAR.","volume":"35","author":"E Besal\u00fa","year":"2002","journal-title":"Acc. Chem. Res."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"D464-D474","DOI":"10.1093\/nar\/gky1004","article-title":"RCSB Protein Data Bank: Biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.","volume":"47","author":"S Burley","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"1739-1749","DOI":"10.1021\/jm0306430","article-title":"Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy.","volume":"47","author":"R Friesner","year":"2004","journal-title":"J. Med. Chem."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"6177-6196","DOI":"10.1021\/jm051256o","article-title":"Extra Precision Glide:\u2009 Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein\u2013Ligand Complexes.","volume":"49","author":"R Friesner","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"221-234","DOI":"10.1007\/s10822-013-9644-8","article-title":"Protein and ligand preparation: parameters, protocols, and influence on virtual screen- ing enrichments.","volume":"27","author":"G Madhavi Sastry","year":"2013","journal-title":"J. Comput. Aided Mol. Des."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"11225-11236","DOI":"10.1021\/ja9621760","article-title":"Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids.","volume":"118","author":"W Jorgensen","year":"1996","journal-title":"J. Am. Chem. Soc."},{"key":"ref21","first-page":"4509","article-title":"Europ.","volume":"45","author":"A Morales-Bayuelo","year":"2010","journal-title":"J. Med. Chem."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"2637-2642","DOI":"10.1002\/qua.23284","article-title":"Quantum molecular similarity analysis and quantitative definition of catecholamines with respect to biogenic monoamines associated: Scale alpha and beta of quantitative convergence.","volume":"112","author":"A Morales-Bayuelo","year":"2012","journal-title":"Int. J. Quantum Chem."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"2681-2687","DOI":"10.1002\/qua.23288","article-title":"Theoretical study of the chemical reactivity and molecular quantum similarity in a series of derivatives of 2-adamantyl-thiazolidine-4-one using density functional theory and the topo-geometrical superposition approach.","volume":"112","author":"A Morales-Bayuelo","year":"2012","journal-title":"Int. J. Quantum Chem."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"223-239","DOI":"10.1142\/S0219633612500150","article-title":"H\u00dcCKEL TREATMENT OF PYRROLE AND PENTALENE AS A FUNCTION OF CYCLOPENTADIENYL USING LOCAL QUANTUM SIMILARITY INDEX (LQSI) AND THE TOPO-GEOMETRICAL SUPERPOSITION APPROACH (TGSA).","volume":"11","author":"A Morales-Bayuelo","year":"2012","journal-title":"J. Theo. Comp. Chem."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"125-143","DOI":"10.1007\/s10910-012-0069-8","article-title":"Topological model to quantify the global reactivity indexes as local in Diels\u2013Alder reactions, using density function theory (DFT) and local quantum similarity (LQS).","volume":"51","author":"A Morales-Bayuelo","year":"2013","journal-title":"J. Math. Chem."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1-10","DOI":"10.1155\/2014\/585394","article-title":"Theoretical Calculations and Modeling for the Molecular Polarization of Furan and Thiophene under the Action of an Electric Field Using Quantum Similarity.","volume":"2014","author":"A Morales-Bayuelo","year":"2014","journal-title":"J. Quant. Chem."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1-12","DOI":"10.1155\/2014\/850163","article-title":"Topological Model on the Inductive Effect in Alkyl Halides Using Local Quantum Similarity and Reactivity Descriptors in the Density Functional Theory.","volume":"2014","author":"A Morales-Bayuelo","year":"2014","journal-title":"J. Quant. Chem."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1-19","DOI":"10.1155\/2014\/239845","article-title":"Understanding the Polar Character Trend in a Series of Diels-Alder Reactions Using Molecular Quantum Similarity and Chemical Reactivity Descriptors.","volume":"2014","author":"A Morales-Bayuelo","year":"2014","journal-title":"J. Quant. Chem."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"7512-7516","DOI":"10.1021\/ja00364a005","article-title":"Absolute hardness: companion parameter to absolute electronegativity.","volume":"105","author":"R Parr","year":"1983","journal-title":"J. Am. Chem. Soc."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1793-1874","DOI":"10.1021\/cr990029p","article-title":"Conceptual density functional theory.","volume":"103","author":"P Geerlings","year":"2003","journal-title":"Chem. Rev."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"2065-2091","DOI":"10.1021\/cr040109f","article-title":"Electrophilicity index.","volume":"106","author":"P Chattaraj","year":"2006","journal-title":"Chem. Rev."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1922-1924","DOI":"10.1021\/ja983494x","article-title":"Electrophilicity Index.","volume":"121","author":"R Parr","year":"1999","journal-title":"J. Am. Chem. Soc."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"2544-2551","DOI":"10.1063\/1.1305879","article-title":"On the condensed Fukui function.","volume":"113","author":"P Fuentealba","year":"2000","journal-title":"J. Chem. Phys."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"5648-5652","DOI":"10.1063\/1.464913","article-title":"Density-functional thermochemistry. III The role of exact exchange.","volume":"98","author":"A Becke","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"4700-4711","DOI":"10.1021\/acs.jpca.0c01342","article-title":"On Electronegativity, Hardness, and Reactivity Descriptors: A New Property-Oriented Basis Set.","volume":"124","author":"J S\u00e1nchez-M\u00e1rquez","year":"2020","journal-title":"J. Chem. Phys. A."},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.7910\/DVN\/IA8EOB","article-title":"Data for Receptor-Based Pharmacophore Modelling of a series of ligands used as inhibitors of the SARS-CoV-2 virus by complementary theoretical approaches, molecular docking, and reactivity descriptors.","volume":"V1","author":"A Morales-Bayuelo","year":"2023","journal-title":"Harvard Dataverse."},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.6084\/m9.figshare.22670167.v1","article-title":"Supporting Information.docx. figshare. 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The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}