Optimisation of Peptides Targeting Reverse Transcriptase HIV-1 Using QSAR, Machine Learning, and Computational Approaches

Fachrur Rizal Mahendra^1,2Indira Prakoso¹Alfa Marzelino¹Muhamad Rizqy Fadhillah^1,3,4Syukriyansyah Syukriyansyah^5,6Muhammad Marsha Azzami Hasibuan^5,7Juniza Firdha Suparningtyas¹Mikael Kristiadi¹Aprijal Ghiyas Setiawan⁸Faris Izzatur Rahman¹Anissa Nofita Sari^1,9Nauval Rajwaa Raysendria¹⁰Ilham Kurniawan¹¹Wawaimuli Arozal⁴Kusmardi Kusmardi^12,13,14*

• ¹Bioinformatic Research Center, Indonesian Institute of Bioinformatics (INBIO), Malang, Indonesia
• ²Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus,, Bogor, Indonesia
• ³Doctoral Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Central Jakarta, Indonesia
• ⁴Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Central Jakarta, Indonesia
• ⁵Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Dramaga Campus, Bogor, Indonesia
• ⁶Department of Information Systems, Faculty of Technology and Computer Science, Indraprasta PGRI University, South Jakarta, Indonesia
• ⁷Bachelor Degree of Pharmacy, Faculty of Pharmacy, Mulawarman University, Samarinda, Indonesia
• ⁸Biochemistry and Biomolecular Engineering Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
• ⁹Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Bogor, Indonesia
• ¹⁰Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
• ¹¹Faculty of Medicine, Universitas Pembangunan Nasional "Veteran" Jawa Timur, Surabaya, Indonesia
• ¹²Department of Pathological Anatomy, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
• ¹³Human Cancer Research Center, IMERI, Universitas Indonesia, Central Jakarta, Indonesia
• ¹⁴Drug Development Research Center, IMERI, Central Jakarta, Indonesia

The emergence of drug resistance and adverse side effects associated with current HIV-1 reverse transcriptase (RT) inhibitors underscores the need for novel therapeutic strategies. Peptide-based drugs offer high specificity and lower toxicity, but their development is challenged by the vast combinatorial space of possible sequences and formulation issues. This study aims to identify potent tripeptide-based inhibitors targeting HIV-1 RT through an integrated computational pipeline combining machine learning, QSAR modeling, and in silico validation techniques. From 2,197 screened tripeptides, three candidates, namely FHW, HFW, and HHW, emerged with superior predicted affinity, stability, and drug-like properties. Among them, FHW exhibited the strongest interaction with HIV-1 RT, with a binding energy of −63.50 kcal/mol using MM/GBSA, outperforming the reference drug Nevirapine. FHW peptide also shows four same residues with Nevirapine, including Leu100, Val106, Tyr181, and Tyr188 by hydrophobic contacts. DFT analysis revealed favorable electronic properties, including a low HOMO-LUMO gap (4.73 eV) and high electrophilicity index (13.60). Based on these findings, the FHW peptide demonstrates the highest electrophilicity index among the four ligands, indicating superior electrophilic character relative to Nevirapine. PerMM simulations further indicated consistently negative energy profiles for FHW during membrane translocation and reflecting favorable interactions with the lipid environment. Molecular dynamics simulations confirmed the structural stability of the FHW–RT complex over a 50 ns trajectory. Collectively, these findings identify FHW as the most promising tripeptide-based RT inhibitor with potential for development into next-generation HIV therapeutics, with HFW and HHW as alternative candidates.