Investigating the role of hypothetical protein (AAB33144.1) in HIV-1 virus pathogenicity: A comparative study with FDA-Approved inhibitor compounds through In silico analysis and molecular docking

Md Imran Hossain; Anika Tabassum Asha; Md Arju Hossain; Shahin Mahmud; Kamal Chowdhury; Ramisa Binti Mohiuddin; Nazneen Nahar; Saborni Sarker; Suhaimi Napis; Md Sanower Hossain; A K M Mohiuddin

doi:10.1016/j.heliyon.2023.e23183

Investigating the role of hypothetical protein (AAB33144.1) in HIV-1 virus pathogenicity: A comparative study with FDA-Approved inhibitor compounds through In silico analysis and molecular docking

Heliyon. 2023 Dec 6;10(1):e23183. doi: 10.1016/j.heliyon.2023.e23183. eCollection 2024 Jan 15.

Affiliations

¹ Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh.
² Biology Department, Claflin University, 400 Magnolia St, Orangeburg, SC 29115, USA.
³ Department of Pharmacy, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh.
⁴ Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor D.E., Malaysia.
⁵ Centre for Sustainability of Mineral and Resource Recovery Technology (Pusat SMaRRT), Universiti Malaysia Pahang Al-Sultan Abdullah, Kuantan 26300, Malaysia.

Abstract

Aim and objective: Due to the a lot of unexplored proteins in HIV-1, this research aimed to explore the functional roles of a hypothetical protein (AAB33144.1) that might play a key role in HIV-1 pathogenicity.

Methods: The homologous protein was identified along with building and validating the 3D structure by searching several bioinformatics tools.

Results: Retroviral aspartyl protease and retropepsin like functional domains and motifs, folding pattern (cupredoxins), and subcellular localization in cytoplasmic membrane were determined as biological activity. Besides, the functional annotation revealed that the chosen hypothetical protein possessed protease-like activity. To validate our generated protein 3D structure, molecular docking was performed with five compounds where nelfinavir showed (-8.2 kcal/mol) best binding affinity against HXB2 viral protease (PDB ID: 7SJX) and main protease (PDB ID: 4EYR) protein.

Conclusions: This study suggests that the annotated hypothetical protein related to protease action, which may be useful in viral genetics and drug discovery.

Keywords: AAB33144.1; Cupridoxins; Cytoplasmic membrane; HXB2 strain; Hypothetical protein; Protease.