Repurposing FDA-approved drugs as HIV-1 integrase inhibitors: an in silico investigation

Abstract

The Human Immunodeficiency Virus (HIV) infection is a global pandemic that has claimed 33 million lives to-date. One of the most efficacious treatments for naïve or pretreated HIV patients is the HIV integrase strand transfer inhibitors (INSTIs). However, given that HIV treatment is life-long, the emergence of HIV strains resistant to INSTIs is an imminent challenge. In this work, we showed two best regression QSAR models that were constructed using a boosted Random Forest algorithm (r² = 0.998, q²_10CV = 0.721, q²_{external_test} = 0.754) and a boosted K* algorithm (r² = 0.987, q²_10CV = 0.721, q²_{external_test} = 0.758) to predict the pIC₅₀ values of INSTIs. Subsequently, the regression QSAR models were deployed against the Drugbank database for drug repositioning. The top-ranked compounds were further evaluated for their target engagement activity using molecular docking studies and accelerated Molecular Dynamics simulation. Lastly, their potential as INSTIs were also evaluated from our literature search. Our study offers the first example of a large-scale regression QSAR modelling effort for discovering highly active INSTIs to combat HIV infection.

Communicated by Ramaswamy H. Sarma

Keywords:

• Drug repositioning
• HIV-1 integrase
• virtual screening
• molecular dynamics
• machine learning

Disclosure statement

No potential conflict of interest was reported by the author(s).

Author contributions

X.C. and L.N.K. conceived the study, guided the experimental design and drafted the manuscript. C.H. conducted the QSAR modelling and data collection. T.R. conducted molecular docking studies. H.S.S. and Y.W.K. provided input on data analysis. All authors helped by providing suggestions and ideas for improving the study, and reviewed and approved the submitted manuscript.

Additional information

Funding

This work is kindly supported by the Swinburne Strategic Research Grant (SSRG2-5624) by Swinburne University of Technology (Sarawak Campus) awarded to X.C.