Structure-based identification of novel scaffolds as potential HIV-1 entry inhibitors involving CCR5

Abstract

C-C chemokine receptor 5 (CCR5), which is part of the chemokine receptor family, is a member of the G protein-coupled receptor superfamily. The interactions of CCR5 with HIV-1 during viral entry position it as an effective therapeutic target for designing potent antiviral therapies. The small-molecule Maraviroc was approved by the FDA as a CCR5 drug in 2007, while clinical trials failure has characterised many of the other CCR5 inhibitors. Thus, the continual identification of potential CCR5 inhibitors is, therefore, warranted. In this study, a structure-based discovery approach has been utilised to screen and retrieved novel potential CCR5 inhibitors from the Asinex antiviral compound (∼ 8,722) database. Explicit lipid-bilayer molecular dynamics simulation, in silico physicochemical and pharmacokinetic analyses, were further performed for the top compounds. A total of 23 structurally diverse compounds with binding scores higher than Maraviroc were selected. Subsequent molecular dynamics (MD) simulations analysis of the top four compounds LAS 51495192, BDB 26405401, BDB 26419079, and LAS 34154543, maintained stability at the CCR5 binding site. Furthermore, these compounds made pertinent interactions with CCR5 residues critical for the HIV-1 gp120-V3 loop binding such as Trp86, Tyr89, Phe109, Tyr108, Glu283 and Tyr251. Additionally, the predicted in silico physicochemical and pharmacokinetic descriptors of the selected compounds were within the acceptable range for drug-likeness. The results suggest positive indications that the identified molecules may represent promising CCR5 entry inhibitors. Further structural optimisations and biochemical testing of the proposed compounds may assist in the discovery of effective HIV-1 therapy.

Communicated by Ramaswamy H. Sarma

Keywords:

• C-C chemokine receptor 5
• Maraviroc
• structure-based drug design
• MD simulations
• ADMET

Acknowledgements

The authors would like to acknowledge the Centre for High-Performance Computing (CHPC), Cape Town, South Africa, for providing access to Schrödinger Maestro v12 molecular modelling suite.

Disclosure statement

The authors declare no conflicts of interest in this work.

Ethics approval and consent to participate

Not applicable

Human and animal rights

No humans and animals were used in the study.

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Authors contribution

P. Appiah-Kubi: Conceptualisation and study design, screening and simulation experiment, data analysis, and manuscript writing. E.A. Iwuchukwu: Data analysis, manuscript writing. M.E.S Soliman: Supervision.

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Additional information

Funding

None.