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In silico and in vitro study of Mycobacterium tuberculosis H37Rv uncharacterized protein (RipD): an insight on tuberculosis therapeutics

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Abstract

Tuberculosis caused by Mycobacterium tuberculosis (Mtb) is responsible for the highest global health problem, with the deaths of millions of people. With prevalence of multiple drug resistance (MDR) strains and extended therapeutic times, it is important to discover small molecule inhibitors against novel hypothetical proteins of the pathogen. In this study, a virtual screening protocol was carried out against MtbH37Rv hypothetical protein RipD (Rv1566c) for the identification of potential small molecule inhibitors. The 3D model of the protein structure binding site was used for virtual screening (VS) of inhibitors from the Pathogen Box, followed by its validation through a molecular docking study. The stability of the protein–ligand complex was assessed using a 150 ns molecular dynamics simulation. MM-PBSA and MM-GBSA are the two approaches that were used to perform the trajectory analysis and determine the binding free energies, respectively. The ligand binding was observed to be stable across the entire time frame with an approximate binding free energy of -22.9916 kcal/mol. The drug-likeness of the inhibitors along with a potential anti-tuberculosis compound was validated by ADMET prediction software. Furthermore, a CFU inhibition assay was used to validate the best hit compound’s in vitro inhibitory efficacy against a non-pathogenic Mycobacterium smegmatis MC2155 under low nutrient culture conditions. The study reported that the compound proposed in our study (Pathogen Box ID: MMV687700) will be useful for the identification of potential inhibitors against Mtb in future.

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Acknowledgements

The authors would like to acknowledge Bioinformatics and Immunology laboratory facilities of School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, for completion of the research work. The help from Mr. Somdeb Chatterjee, NII, New Delhi, is also of great importance, particularly during the MD simulation analysis. In addition, the author would like to acknowledge KIIT Deemed to be University, Odisha, India, and Ethiopia Federal Democratic Republic, National Veterinary Institute, Debre Zeit, Ethiopia, for providing the financial support to conduct the PhD research work.

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This research work is not supported by any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

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Authors and Affiliations

  1. School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha, India

    Aregitu Mekuriaw Arega, Ajit Kumar Dhal, Sasmita Nayak & Rajani Kanta Mahapatra

  2. National Veterinary Institute, Debre Zeit, Ethiopia

    Aregitu Mekuriaw Arega

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  1. Aregitu Mekuriaw Arega
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  2. Ajit Kumar Dhal
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Contributions

AM contributed to performing and analyzing the in silico and wet-lab experiments as well as writing and revision of the manuscript. AKD performed the MD simulation and analysis of the results. SN provided the chemicals, Petri-plates, and co-supervised the study. RKM conceived the project, supervised the whole study, and corrected the manuscript.

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Correspondence to Rajani Kanta Mahapatra.

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Arega, A.M., Dhal, A.K., Nayak, S. et al. In silico and in vitro study of Mycobacterium tuberculosis H37Rv uncharacterized protein (RipD): an insight on tuberculosis therapeutics. J Mol Model 28, 171 (2022). https://doi.org/10.1007/s00894-022-05148-1

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