{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T19:28:59Z","timestamp":1790278139786,"version":"4.1.0"},"reference-count":46,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,2,20]],"date-time":"2023-02-20T00:00:00Z","timestamp":1676851200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001409","name":"Department of Science and Technology","doi-asserted-by":"publisher","award":["DST\/ICD\/BRICS\/Call-3\/HIV protease\/2019"],"award-info":[{"award-number":["DST\/ICD\/BRICS\/Call-3\/HIV protease\/2019"]}],"id":[{"id":"10.13039\/501100001409","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Acquired immunodeficiency syndrome (AIDS) is one of the most challenging infectious diseases to treat on a global scale. Understanding the mechanisms underlying the development of drug resistance is necessary for novel therapeutics. HIV subtype C is known to harbor mutations at critical positions of HIV aspartic protease compared to HIV subtype B, which affects the binding affinity. Recently, a novel double-insertion mutation at codon 38 (L38HL) was characterized in HIV subtype C protease, whose effects on the interaction with protease inhibitors are hitherto unknown. In this study, the potential of L38HL double-insertion in HIV subtype C protease to induce a drug resistance phenotype towards the protease inhibitor, Saquinavir (SQV), was probed using various computational techniques, such as molecular dynamics simulations, binding free energy calculations, local conformational changes and principal component analysis. The results indicate that the L38HL mutation exhibits an increase in flexibility at the hinge and flap regions with a decrease in the binding affinity of SQV in comparison with wild-type HIV protease C. Further, we observed a wide opening at the binding site in the L38HL variant due to an alteration in flap dynamics, leading to a decrease in interactions with the binding site of the mutant protease. It is supported by an altered direction of motion of flap residues in the L38HL variant compared with the wild-type. These results provide deep insights into understanding the potential drug resistance phenotype in infected individuals.<\/jats:p>","DOI":"10.3390\/genes14020533","type":"journal-article","created":{"date-parts":[[2023,2,21]],"date-time":"2023-02-21T02:30:35Z","timestamp":1676946635000},"page":"533","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Understanding Drug Resistance of Wild-Type and L38HL Insertion Mutant of HIV-1 C Protease to Saquinavir"],"prefix":"10.3390","volume":"14","author":[{"given":"Sankaran","family":"Venkatachalam","sequence":"first","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nisha","family":"Murlidharan","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5404-3266","authenticated-orcid":false,"given":"Sowmya R.","family":"Krishnan","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4622-2496","authenticated-orcid":false,"given":"C.","family":"Ramakrishnan","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mpho","family":"Setshedi","sequence":"additional","affiliation":[{"name":"Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramesh","family":"Pandian","sequence":"additional","affiliation":[{"name":"Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2557-7768","authenticated-orcid":false,"given":"Debmalya","family":"Barh","sequence":"additional","affiliation":[{"name":"Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil"},{"name":"Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8554-1660","authenticated-orcid":false,"given":"Sandeep","family":"Tiwari","sequence":"additional","affiliation":[{"name":"Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil"},{"name":"Institute of Biology, Federal University of Bahia, Salvador, BA 40110-909, Brazil"},{"name":"Institute of Health Sciences, Federal University of Bahia, Salvador, BA 40110-909, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4775-2280","authenticated-orcid":false,"given":"Vasco","family":"Azevedo","sequence":"additional","affiliation":[{"name":"Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1781-2115","authenticated-orcid":false,"given":"Yasien","family":"Sayed","sequence":"additional","affiliation":[{"name":"Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1776-4096","authenticated-orcid":false,"given":"M. Michael","family":"Gromiha","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,2,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"690647","DOI":"10.3389\/fmicb.2021.690647","article-title":"Global and Regional Estimates for Subtype-Specific Therapeutic and Prophylactic HIV-1 Vaccines: A Modeling Study","volume":"12","author":"Elangovan","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1097\/COH.0000000000000534","article-title":"HIV subtype diversity worldwide","volume":"14","author":"Bbosa","year":"2019","journal-title":"Curr. Opin. HIV AIDS"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Giovanetti, M., Ciccozzi, M., Parolin, C., and Borsetti, A. (2020). Molecular Epidemiology of HIV-1 in African Countries: A Comprehensive Overview. Pathogens, 9.","DOI":"10.3390\/pathogens9121072"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1515\/hsz-2014-0162","article-title":"Non-B HIV-1 subtypes in sub-Saharan Africa: Impact of subtype on protease inhibitor efficacy","volume":"395","author":"Naicker","year":"2014","journal-title":"Biol. Chem."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e166","DOI":"10.1016\/S2352-3018(16)00023-0","article-title":"Virological failure in patients with HIV-1 subtype C receiving antiretroviral therapy: An analysis of a prospective national cohort in Sweden","volume":"3","author":"Svedhem","year":"2016","journal-title":"Lancet HIV"},{"key":"ref_6","first-page":"165","article-title":"Protease inhibition in African subtypes of HIV-1","volume":"5","author":"Vega","year":"2003","journal-title":"AIDS Rev."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"11476","DOI":"10.1128\/JVI.00726-08","article-title":"Active-site mutations in the South african human immunodeficiency virus type 1 subtype C protease have a significant impact on clinical inhibitor binding: Kinetic and thermodynamic study","volume":"82","author":"Mosebi","year":"2008","journal-title":"J. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Eche, S., Kumar, A., Sonela, N., and Gordon, M.L. (2021). Acquired HIV-1 Protease Conformational Flexibility Associated with Lopinavir Failure May Shape the Outcome of Darunavir Therapy after Antiretroviral Therapy Switch. Biomolecules, 11.","DOI":"10.3390\/biom11040489"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5441","DOI":"10.1128\/jvi.71.7.5441-5448.1997","article-title":"Sequence and drug susceptibility of subtype C reverse transcriptase from human immunodeficiency virus type 1 seroconverters in Zimbabwe","volume":"71","author":"Shafer","year":"1997","journal-title":"J. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Mendoza, Y., Bello, G., Castillo Mewa, J., Mart\u00ednez, A.A., Gonz\u00e1lez, C., Garc\u00eda-Morales, C., Avila-R\u00edos, S., Reyes-Ter\u00e1n, G., and Pascale, J.M. (2014). Molecular epidemiology of HIV-1 in Panama: Origin of non-B subtypes in samples collected from 2007 to 2013. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0085153"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Foster, G.M., Ambrose, J.C., Hu\u00e9, S., Delpech, V.C., Fearnhill, E., Abecasis, A.B., Leign Brown, A.J., and Geretti, A.M. (2014). Novel HIV-1 recombinants spreading across multiple risk groups in the United Kingdom: The identification and phylogeography of Circulating Recombinant Form (CRF) 50_A1D. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0083337"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1370","DOI":"10.1080\/07391102.2012.736774","article-title":"Structural insights into the South African HIV-1 subtype C protease: Impact of hinge region dynamics and flap flexibility in drug resistance","volume":"31","author":"Naicker","year":"2013","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1111\/cbdd.12063","article-title":"Comparison of the Molecular Dynamics and Calculated Binding Free Energies for Nine FDA-Approved HIV-1 PR Drugs Against Subtype B and C-SA HIV PR","volume":"81","author":"Ahmed","year":"2013","journal-title":"Chem. Biol. Drug. Des."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"11956","DOI":"10.1021\/ja504096m","article-title":"Drug Resistance Conferred by Mutations Outside the Active Site through Alterations in the Dynamic and Structural Ensemble of HIV-1 Protease","volume":"136","author":"Ragland","year":"2014","journal-title":"J. Am. Chem. Soc."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Obasa, A.E., Ambikan, A.T., Gupta, S., Neogi, U., and Jacobs, G.B. (2021). Increased acquired protease inhibitor drug resistance mutations in minor HIV-1 quasispecies from infected patients suspected of failing on national second-line therapy in South Africa. BMC Infect. Dis., 21.","DOI":"10.1186\/s12879-021-05905-2"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"438","DOI":"10.3389\/fmicb.2020.00438","article-title":"Drug Resistance Mutations Against Protease, Reverse Transcriptase and Integrase Inhibitors in People Living With HIV-1 Receiving Boosted Protease Inhibitors in South Africa","volume":"11","author":"Obasa","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1089\/aid.2019.0012","article-title":"Low Frequency of Protease Inhibitor Resistance Mutations and Insertions in HIV-1 Subtype C Protease Inhibitor-Na\u00efve Sequences","volume":"35","author":"Ledwaba","year":"2019","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.1080\/07391102.2016.1185380","article-title":"Homology model, molecular dynamics simulation and novel pyrazole analogs design of Candida albicans CYP450 lanosterol 14 \u03b1-demethylase, a target enzyme for antifungal therapy","volume":"35","author":"Jacob","year":"2017","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1007\/978-1-4939-9869-2_17","article-title":"Molecular Dynamics Simulation of Proteins","volume":"2073","author":"Collier","year":"2020","journal-title":"Methods Mol. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.compbiolchem.2018.06.005","article-title":"Docking techniques in pharmacology: How much promising?","volume":"76","author":"Gupta","year":"2018","journal-title":"Comput. Biol. Chem."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1002\/prot.21123","article-title":"Comparison of multiple Amber force fields and development of improved protein backbone parameters","volume":"65","author":"Hornak","year":"2006","journal-title":"Proteins"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","article-title":"The Amber biomolecular simulation programs","volume":"26","author":"Case","year":"2005","journal-title":"J. Comput. Chem."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1021\/ja00392a016","article-title":"Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water","volume":"103","author":"Jorgensen","year":"1981","journal-title":"J. Am. Chem. Soc."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An N\u22c5log(N) method for Ewald sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular dynamics with coupling to an external bath","volume":"81","author":"Berendsen","year":"1984","journal-title":"J. Chem. Phys."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0021-9991(77)90098-5","article-title":"Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes","volume":"23","author":"Ryckaert","year":"1977","journal-title":"J. Comput. Phys."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"3976","DOI":"10.1016\/j.ejmech.2011.05.071","article-title":"Synthesis and structural studies of pentacycloundecane-based HIV-1 PR inhibitors: A hybrid 2D NMR and docking\/QM\/MM\/MD approach","volume":"46","author":"Makatini","year":"2011","journal-title":"Eur. J. Med. Chem."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1016\/j.bmcl.2011.02.105","article-title":"Pentacycloundecane-based inhibitors of wild-type C-South African HIV-protease","volume":"21","author":"Makatini","year":"2011","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Kasahara, K., Fukuda, I., and Nakamura, H. (2014). A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer\u2013DNA Complex. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0112419"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1080\/073911012010525020","article-title":"Dynamic and Structural Changes in the Minimally Restructuring EcoRI Bound to a Minimally Mutated DNA Chain","volume":"29","author":"Ramakrishnan","year":"2012","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1021\/ar000033j","article-title":"Calculating Structures and Free Energies of Complex Molecules:\u2009 Combining Molecular Mechanics and Continuum Models","volume":"33","author":"Kollman","year":"2000","journal-title":"Acc. Chem. Res."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1002\/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E","article-title":"Theory and applications of the generalized Born solvation model in macromolecular simulations","volume":"56","author":"Tsui","year":"2001","journal-title":"Biopolymers"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1002\/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A","article-title":"Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)","volume":"20","author":"Weiser","year":"1999","journal-title":"J. Comput. Chem."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"107931","DOI":"10.1016\/j.jmgm.2021.107931","article-title":"Cantilever-centric mechanism of cooperative non-active site mutations in HIV protease: Implications for flap dynamics","volume":"106","author":"Sherry","year":"2021","journal-title":"J. Mol. Graph. Model"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"4464","DOI":"10.1039\/C9CP06657H","article-title":"Revealing the binding and drug resistance mechanism of amprenavir, indinavir, ritonavir, and nelfinavir complexed with HIV-1 protease due to double mutations G48T\/L89M by molecular dynamics simulations and free energy analyses","volume":"22","author":"Wang","year":"2020","journal-title":"Phys. Chem. Chem. Phys."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Weber, I.T., Wang, Y.-F., and Harrison, R.W. (2021). HIV Protease: Historical Perspective and Current Research. Viruses, 13.","DOI":"10.3390\/v13050839"},{"key":"ref_38","first-page":"95","article-title":"HIV protease inhibitors: A review of molecular selectivity and toxicity","volume":"7","author":"Lv","year":"2015","journal-title":"HIV AIDS"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1080\/1062936X.2021.1979647","article-title":"Decoding molecular mechanism underlying binding of drugs to HIV-1 protease with molecular dynamics simulations and MM-GBSA calculations","volume":"32","author":"Yu","year":"2021","journal-title":"SAR QSAR Environ. Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1515\/hsz-2017-0107","article-title":"I36T\u2191T mutation in South African subtype C (C-SA) HIV-1 protease significantly alters protease-drug interactions","volume":"398","author":"Maseko","year":"2017","journal-title":"Biol. Chem."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1089\/aid.1996.12.1329","article-title":"Full-length sequence of an ethiopian human immunodeficiency virus type 1 (HIV-1) isolate of genetic subtype C","volume":"12","author":"Salminen","year":"1996","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"12890","DOI":"10.1128\/JVI.76.24.12890-12899.2002","article-title":"Early evolution of the human immunodeficiency virus type 1 subtype C epidemic in rural Malawi","volume":"76","author":"McCormack","year":"2002","journal-title":"J. Virol."},{"key":"ref_43","first-page":"83","article-title":"Update on HIV-1 diversity in Africa: A decade in review","volume":"14","author":"Lihana","year":"2012","journal-title":"AIDS Rev."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"5869","DOI":"10.1128\/JVI.02325-07","article-title":"Ninety-nine is not enough: Molecular characterization of inhibitor-resistant human immunodeficiency virus type 1 protease mutants with insertions in the flap region","volume":"82","author":"Brynda","year":"2008","journal-title":"J. Virol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1097\/01.aids.0000196179.11293.fc","article-title":"Clinical validation of atazanavir\/ritonavir genotypic resistance score in protease inhibitor-experienced patients","volume":"20","author":"Vora","year":"2006","journal-title":"AIDS"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"45121","DOI":"10.1039\/C7RA09691G","article-title":"Structural insights into HIV-1 protease flap opening processes and key intermediates","volume":"7","author":"Yu","year":"2017","journal-title":"RSC Adv."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/14\/2\/533\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:37:32Z","timestamp":1760121452000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/14\/2\/533"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,20]]},"references-count":46,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2023,2]]}},"alternative-id":["genes14020533"],"URL":"https:\/\/doi.org\/10.3390\/genes14020533","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,20]]}}}