Institution: University of the Western Cape

Project Affiliation:

Abstract

HIV/AIDS is a global viral disease with reports suggesting the virus to be a threat with about 38.4 million people living with it in 2021. Human immunodeficiency virus (HIV) infection diagnostic tests have evolved over the past decades since the development of the first enzyme immunoassay, western blot, and later the rapid lateral flow assays (LFAs). These tests use antibodies which are costly, have low sensitivity, selectivity, and stability. Aptamers are deemed superior to antibodies, and they have great potential to replace the antibodies in the LFAs.
In this study, briefly, intensive literature mining coupled with in silico approaches were carried out to study the HIV genome and to identify a potential HIV biomarker present in the patient’s serum after few days of HIV exposure. A library pool consisting of random DNA aptamer sequences were also selected by in silico approaches, where they were prepared by Autodock/MGL Tools version 1.5.7. A potential HIV biomarker p24 (a capsid protein detected between the first two weeks after infection), and aptamer 3D structures will then be subjected to molecular docking (virtual screen) via Autodock VinaXB stand-alone package, where several potential aptamers will be selected based on their docking scores. The potential aptamers will be subjected to stability tests using M-fold web server version 2.3, where additional nucleotides will be added to both ends of the potential aptamers to create stable rigid structures. The stable structures will then be subjected to molecular docking via HADDOCK web-based software version 2.4, to generate protein-aptamer complexes, which will be subjected to molecular dynamics (MD) simulations using GROMACS 2019 package to determine structural stability. From the MD simulations, only few potential aptamers will be selected based on the root mean square deviation (RMSD) of the protein backbone, fluctuations (RMSF) of the amino acids, radius of gyration (RyG), number of hydrogen (H) bonds, non-bonded interaction energy and binding free energy (MMPBSA).
The selected potential aptamers will be synthesized and characterized via microscale thermophoresis (MST) to validate their binding kinetics to a recombinant p24 protein to facilitate HIV diagnosis. Such a test would allow for a short diagnostic turnaround time, and hence expedite treatment.

KEY WORDS: Biomarker, diagnosis, molecular dynamic simulation; binding energy; lateral flow assay; microscale thermophoresis.

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