Exploring Phytochemical Compounds: A Computational Study for HIV-1 Reverse Transcriptase Inhibition

IF 0.5 4区生物学 Q4 BIOCHEMICAL RESEARCH METHODS Current Proteomics Pub Date : 2024-09-18 DOI:10.2174/0115701646316517240901091407

Jyotsna Bandi, Madhan Chunduru, Satya Tulasi Mangamuri, Anand Kumar Nelapati, Jalaja Naravula, Viswajit Mulpuru

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Abstract

Background: HIV-1 is the most virulent type, causing most AIDS cases worldwide. Therapeutics like NRTIs and NNRTIs terminate replication by terminating polymerization reactions. Natural-based therapeutics are increasingly being used to reduce side effects and combat disease. Method: The study focuses on identifying phytochemical compounds that effectively inhibit the HIV-1 reverse transcriptase process using molecular docking and molecular dynamic simulations. Result: Molecular docking results show anisomelolide has a significantly stronger binding affinity (-29.9992KJ/mol) compared to nevirapine (-13.34696 KJ/mol), forming more hydrogen bonds and hydrophilic interactions, indicating a more stable and specific binding. MD simulations further support these findings, with anisomelolide exhibiting lower RMSD and RMSF values, suggesting greater structural stability and lower flexibility. Interaction energy analysis reveals robust binding and stability for anisomelolide over time. Additionally, hydrogen bond analysis indicates more frequent and stronger interactions for anisomelolide. Conclusion: The phytochemical compound anisomelolide exhibits superior binding affinity, structural stability, and interaction dynamics, making it a promising candidate for drug development against HIV-1 RT.

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探索植物化学化合物：抑制 HIV-1 逆转录酶的计算研究

背景：HIV-1 是毒性最强的类型，导致全球大多数艾滋病病例。NRTIs 和 NNRTIs 等治疗药物通过终止聚合反应来终止复制。天然疗法正越来越多地被用于减少副作用和防治疾病。方法：研究重点是利用分子对接和分子动力学模拟，确定能有效抑制 HIV-1 逆转录酶过程的植物化学化合物。结果分子对接结果显示，与奈韦拉平（-13.34696 KJ/mol）相比，茴香内酯的结合亲和力（-29.9992KJ/mol）明显更强，形成的氢键和亲水相互作用更多，表明其结合更稳定、更特异。MD 模拟进一步证实了这些发现，阿尼索美洛内酯的 RMSD 值和 RMSF 值更低，表明其结构更稳定，灵活性更低。相互作用能分析表明，随着时间的推移，茴芹内酯的结合力更强，稳定性更高。此外，氢键分析表明，茴芹内酯的相互作用更频繁、更强烈。结论植物化学化合物茴芹内酯表现出卓越的结合亲和力、结构稳定性和相互作用动力学，使其成为开发抗 HIV-1 RT 药物的理想候选物质。

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来源期刊

Current Proteomics BIOCHEMICAL RESEARCH METHODS-BIOCHEMISTRY & MOLECULAR BIOLOGY

CiteScore

1.60

自引率

0.00%

发文量

审稿时长

>0 weeks

期刊介绍： Research in the emerging field of proteomics is growing at an extremely rapid rate. The principal aim of Current Proteomics is to publish well-timed in-depth/mini review articles in this fast-expanding area on topics relevant and significant to the development of proteomics. Current Proteomics is an essential journal for everyone involved in proteomics and related fields in both academia and industry. Current Proteomics publishes in-depth/mini review articles in all aspects of the fast-expanding field of proteomics. All areas of proteomics are covered together with the methodology, software, databases, technological advances and applications of proteomics, including functional proteomics. Diverse technologies covered include but are not limited to: Protein separation and characterization techniques 2-D gel electrophoresis and image analysis Techniques for protein expression profiling including mass spectrometry-based methods and algorithms for correlative database searching Determination of co-translational and post- translational modification of proteins Protein/peptide microarrays Biomolecular interaction analysis Analysis of protein complexes Yeast two-hybrid projects Protein-protein interaction (protein interactome) pathways and cell signaling networks Systems biology Proteome informatics (bioinformatics) Knowledge integration and management tools High-throughput protein structural studies (using mass spectrometry, nuclear magnetic resonance and X-ray crystallography) High-throughput computational methods for protein 3-D structure as well as function determination Robotics, nanotechnology, and microfluidics.