{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T13:22:25Z","timestamp":1783516945430,"version":"3.55.0"},"reference-count":50,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T00:00:00Z","timestamp":1782345600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Background: Antiretroviral resistance-associated mutations, within the broader context of HIV-1 genetic variability, represent a growing challenge for HIV-1 control, highlighting the need for continuous molecular surveillance and mechanistic understanding of drug resistance. This study aimed to characterize mutations in the pol gene associated with resistance to protease inhibitors and to explore their structural implications. Methods: Viral RNA was extracted from plasma samples of HIV-positive patients, and a 266 bp fragment of the HIV-1 pol gene was amplified by RT-PCR and sequenced using the Sanger method. Sequences showing \u226598% homology were aligned and analyzed using MEGA v11 and the Stanford HIV Drug Resistance Database to identify resistance-associated mutations, while viral subtypes were determined using COMET, jpHMM-HIV, and STAR tools. Amino acid sequences were used for structural modeling with AlphaFold, followed by molecular docking with Nelfinavir using the CB-Dock2 server. Results: Four samples exhibited resistance-associated profiles, including high-level, intermediate, and low-level resistance, with one isolate showing high-level resistance to multiple protease inhibitors. Structural analyses revealed that Nelfinavir preferentially binds to alternative hydrophobic cavities rather than the canonical catalytic site, lacking direct interactions with the Asp25\/Asp25\u2032 dyad. Conclusions: These findings suggest a structural mechanism of resistance based on non-canonical ligand binding that may impair effective protease inhibition.<\/jats:p>","DOI":"10.3390\/v18070701","type":"journal-article","created":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T14:27:52Z","timestamp":1783434472000},"page":"701","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Non-Canonical Binding of Nelfinavir in HIV-1 Protease Variants Reveals Structural Mechanisms of Antiretroviral Resistance"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6282-6762","authenticated-orcid":false,"given":"Christian","family":"Cadena-Cruz","sequence":"first","affiliation":[{"name":"Programa de Bacteriolog\u00eda, Universidad Libre Seccional Barranquilla, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7637-5106","authenticated-orcid":false,"given":"Marcio","family":"De Avila-Arias","sequence":"additional","affiliation":[{"name":"Grupo GIBAC (Grupo de Investigaci\u00f3n B\u00e1sicas y Cl\u00ednicas), Fundaci\u00f3n Universitaria San Mart\u00edn (FUSM), Puerto Colombia 081007, Colombia"},{"name":"Grupo de Investigaci\u00f3n en Biomedicina, Facultad de Ciencias B\u00e1sicas Biom\u00e9dicas, Universidad Metropolitana, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3746-5277","authenticated-orcid":false,"given":"Fabio","family":"Guzm\u00e1n","sequence":"additional","affiliation":[{"name":"Programa de Microbiolog\u00eda, Universidad Libre Seccional Barranquilla, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana","family":"P\u00e9rez","sequence":"additional","affiliation":[{"name":"Independent Researcher, Barranquilla 080020, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1126-1144","authenticated-orcid":false,"given":"Mar\u00eda Angelica","family":"Zuluaga","sequence":"additional","affiliation":[{"name":"Independent Researcher, Barranquilla 080020, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7567-6409","authenticated-orcid":false,"given":"Elkin","family":"Navarro Quiroz","sequence":"additional","affiliation":[{"name":"Facultad de Ciencias B\u00e1sicas y Biom\u00e9dicas, Universidad Sim\u00f3n Bol\u00edvar, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9642-3048","authenticated-orcid":false,"given":"Alejandro","family":"Angulo","sequence":"additional","affiliation":[{"name":"Independent Researcher, Barranquilla 080020, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-7966-2942","authenticated-orcid":false,"given":"Luz Elena Prieto","family":"Garcerant","sequence":"additional","affiliation":[{"name":"Especializaci\u00f3n en Medicina Interna, Universidad Libre Seccional Barranquilla, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hector Rodr\u00edguez","family":"Rojas","sequence":"additional","affiliation":[{"name":"Especializaci\u00f3n en Medicina Interna, Universidad Libre Seccional Barranquilla, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dinno Alberto Fern\u00e1ndez","family":"Chica","sequence":"additional","affiliation":[{"name":"Especializaci\u00f3n en Medicina Interna, Universidad Libre Seccional Barranquilla, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillermo","family":"Cervantes","sequence":"additional","affiliation":[{"name":"Independent Researcher, Barranquilla 080020, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7240-7462","authenticated-orcid":false,"given":"Jose Luis","family":"Villarreal-Camacho","sequence":"additional","affiliation":[{"name":"Programa de Medicina, Universidad Libre Seccional Barranquilla, Barranquilla 081007, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"S94","DOI":"10.1002\/eji.200737441","article-title":"A History of AIDS: Looking Back to See Ahead","volume":"37","author":"Greene","year":"2007","journal-title":"Eur. 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