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Background <p>Nef is the accessory protein of HIV required for viral replication and release of virus from the host cell.</p> Aim <p>The aim of the study is the genomic characterization, subtypes of HIV-1, amino acids substations, and identification of a&#xa0;novel peptide (Mastoparan-L peptide) for inhibition of Nef activity.</p> Methods <p>Blood samples were taken from HIV-positive patients from the Pakistan Institute of Medical Sciences (PIMS) hospital in&#xa0;Islamabad Pakistan. The samples were confirmed by Real Time-Polymerase Chain Reaction. The HIV positive samples were further processed for <i>Nef</i> gene amplification followed by nucleotide sequencing through the Sanger method. Phylogenic analysis was performed by PhyML 3.0. Moreover, amino acid substitutions were also determined. Molecular docking (HDOCK server) was performed to identify the novel peptides that inhabit the Nef gene activity.</p> Results <p>Among 26 samples, 8 samples were successfully sequenced by Sanger sequencing. Out of 8, 4 isolates belong to subtype G, 3 belong to subtype B, and 1 belongs to CRF01_AE. Our isolates PQ358732, PQ159093, PQ165302, PQ382799, and PO159091 form a&#xa0;cluster with AF061641 from Finland. Similarly, our isolates PQ159090 form a&#xa0;cluster with L15510.1 HIV-1 proviral Nef gene and our isolates PQ358731 and PQ159092 make clusters with AAA0649 sequence from South Korea and another isolate accession number L154920.1. Molecular docking revealed that all our isolates strongly bind with Mastoparan-L peptide, inhibiting the Nef activity. The highest docking score (−186.39) was observed in one of the&#xa0;isolates AKZU-IDMPL-111 with a confidence interval of&#xa0;0.6743.</p> Conclusion <p>We have successfully sequenced the Nef gene of HIV-1 circulating in Pakistan. We have identified a&#xa0;novel peptide mastoparan-L which potentially inhibits the Nef activity and&#xa0;results in minimizing HIV infection.</p>

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HIV-1 Nef Gene Characterization and Subtype Analysis in Pakistan: A Molecular Docking Approach with Mastoparan-L Peptide

  • 期刊论文

  • 发表日期：

    2025年3月4日

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  • Akmal Zubair,
  • Muhammad Ali,
  • Naseem Akhtar

摘要

Background

Nef is the accessory protein of HIV required for viral replication and release of virus from the host cell.

Aim

The aim of the study is the genomic characterization, subtypes of HIV-1, amino acids substations, and identification of a novel peptide (Mastoparan-L peptide) for inhibition of Nef activity.

Methods

Blood samples were taken from HIV-positive patients from the Pakistan Institute of Medical Sciences (PIMS) hospital in Islamabad Pakistan. The samples were confirmed by Real Time-Polymerase Chain Reaction. The HIV positive samples were further processed for Nef gene amplification followed by nucleotide sequencing through the Sanger method. Phylogenic analysis was performed by PhyML 3.0. Moreover, amino acid substitutions were also determined. Molecular docking (HDOCK server) was performed to identify the novel peptides that inhabit the Nef gene activity.

Results

Among 26 samples, 8 samples were successfully sequenced by Sanger sequencing. Out of 8, 4 isolates belong to subtype G, 3 belong to subtype B, and 1 belongs to CRF01_AE. Our isolates PQ358732, PQ159093, PQ165302, PQ382799, and PO159091 form a cluster with AF061641 from Finland. Similarly, our isolates PQ159090 form a cluster with L15510.1 HIV-1 proviral Nef gene and our isolates PQ358731 and PQ159092 make clusters with AAA0649 sequence from South Korea and another isolate accession number L154920.1. Molecular docking revealed that all our isolates strongly bind with Mastoparan-L peptide, inhibiting the Nef activity. The highest docking score (−186.39) was observed in one of the isolates AKZU-IDMPL-111 with a confidence interval of 0.6743.

Conclusion

We have successfully sequenced the Nef gene of HIV-1 circulating in Pakistan. We have identified a novel peptide mastoparan-L which potentially inhibits the Nef activity and results in minimizing HIV infection.