Skripsi

Hubungan Mutasi Atipikal V75L Protein Reverse Transcriptase HIV- 1 CRF01_AE pada Sensitivitas Tenofovir Secara In Silico = The Association of the Atypical V75L Mutation in HIV-1 CRF01_AE Reverse Transcriptase with Tenofovir Sensitivity: An In Silico Study.

Latar Belakang Resistensi terhadap obat antiretroviral menjadi tantangan utama dalam penatalaksanaan infeksi HIV-1. Subtipe HIV-1 CRF01_AE merupakan subtipe dominan di Asia Tenggara, termasuk Indonesia. Tenofovir adalah salah satu obat lini pertama dari golongan nucleotide Reverse Transcriptase inhibitor (NRTI). Meskipun mutasi primer resistansi tenofovir telah banyak diketahui, peran mutasi atipikal seperti V75L masih belum sepenuhnya dipahami. Penelitian ini bertujuan untuk menganalisis dampak mutasi V75L pada protein Reverse Transcriptase HIV-1 CRF01_AE terhadap afinitas ikatannya dengan tenofovir melalui pendekatan in silico. Metode Penelitian ini menggunakan metode molecular docking untuk memprediksi interaksi antara tenofovir (dalam bentuk aktifnya, tenofovir difosfat) dengan protein Reverse Transcriptase HIV-1 CRF01_AE. Dua struktur protein disiapkan dengan pemodelan homologi Alphafold: wild-type dan mutan V75L. Struktur protein dimodelkan dan divalidasi, kemudian dilakukan molecular docking. Analisis difokuskan pada perbandingan energi ikatan (afinitas), konstanta inhibisi, jarak atom, serta interaksi ikatan antara tenofovir dengan kedua varian protein. Hasil Hasil penambatan molekuler menunjukkan adanya penurunan afinitas ikatan tenofovir pada protein Reverse Transcriptase mutan V75L dibandingkan dengan protein wild-type. Energi ikatan pada protein mutan V75L tercatat sebesar -6.81 kkal/mol, lebih rendah (kurang negatif) dibandingkan pada protein wild-type yang sebesar -8.98 kkal/mol. Penurunan afinitas ini secara konsisten berkorelasi dengan peningkatan nilai konstanta inhibisi (Ki) sebesar 38 kali lipat pada protein mutan. Analisis interaksi menunjukkan bahwa mutasi V75L mengakibatkan hilangnya interaksi kunci pada residu asam amino lisin 65. Kesimpulan Mutasi atipikal V75L pada protein Reverse Transcriptase HIV-1 CRF01_AE terbukti menurunkan afinitas ikatan tenofovir secara in silico. Penurunan afinitas ini disebabkan oleh perubahan situs aktif enzim yang mengganggu interaksi optimal dengan obat. Temuan ini mengindikasikan bahwa mutasi V75L berpotensi berkontribusi pada penurunan sensitivitas terhadap tenofovir.
Kata Kunci: resistensi, molecular docking, NRTI, antiretroviral, alphafold


Introduction Resistance to antiretroviral drugs remains a major challenge in the management of HIV- 1 infection. The HIV-1 CRF01_AE subtype is predominant in Southeast Asia, including Indonesia. Tenofovir is one of the first-line drugs that belongs to the nucleotide reverse transcriptase inhibitor (NRTI) class. While primary mutations conferring resistance to tenofovir are well documented, the role of atypical mutations such as V75L has not been fully elucidated. This study aimed to analyze the structural and energetic impact of the V75L mutation in the reverse transcriptase protein of HIV-1 CRF01_AE on its binding affinity with tenofovir through an in silico approach. Method This study employed molecular docking to predict the interaction between tenofovir (in its active form, tenofovir diphosphate) and the HIV-1 CRF01_AE reverse transcriptase protein. Two protein structures were prepared using AlphaFold homology modeling: a wild-type and a V75L mutant. The protein structures were modeled and validated, after which molecular docking was performed. The analysis focused on comparing binding energy (affinity), inhibition constant (Ki), atomic distances and the binding interactions of tenofovir with both protein variants. Results Molecular docking showed a reduced binding affinity of tenofovir to the V75L mutant reverse transcriptase compared with the wild type. The binding energy of the mutant protein was –6.81 kcal/mol, higher (less negative) than that of the wild type at –8.98 kcal/mol. This reduction in affinity correlated with a 38-fold increase in the inhibition constant (Ki) of the mutant protein. Interaction analysis revealed that the V75L mutation resulted in the loss of a key interaction with lysine residue 65. Conclusion The atypical V75L mutation in the reverse transcriptase protein of HIV-1 CRF01_AE was found to reduce the binding affinity of tenofovir in in silico analysis. This reduction is attributed to alterations in the enzyme’s active site that disrupt optimal drug interactions. These findings suggest that the V75L mutation may contribute to decreased sensitivity to tenofovir.
Keywords: resistance, molecular docking, NRTI, antiretroviral, alphafold