In silico structural and mechanical insights into bedaquiline resistance associated with high-grade non-synonymous mutations in atpE, mmpR5, and pepQ

• Published in: Journal of biomolecular structure & dynamics 2024-12, Vol.42 (20), p.10937-10949
• Main Authors: Chakraborty, Gourav, Nath I.V, Ambily, Sharma, Mukta, Sheth, Jigar, Kori, Mahima, Tiwari, Avlokita, Patra, Niladri
• Format: Article
• Language: English
• Subjects: Antitubercular Agents - pharmacology; AtpE; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; bedaquiline; Computer Simulation; Diarylquinolines - pharmacology; Drug Resistance, Bacterial - genetics; in silico; MmpR5; Models, Molecular; Molecular Dynamics Simulation; Mutation; Mycobacetrium tuberculosis; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - genetics; PepQ; Polymorphism, Single Nucleotide; Protein Binding; single nucleotide polymorphism
• ISSN: 0739-1102; 1538-0254; 1538-0254
• DOI: 10.1080/07391102.2023.2259486

Clinical resistance against bedaquiline (BDQ) remains intractable to anti-tuberculosis therapies since its introduction to the market over a decade ago. Herein, we investigated the structural and mechanical aspects of BDQ resistance in AtpE, MmpR5, and PepQ. The known target-specific resistant single non-synonymous mutations were refined to high-grade candidates. Thus, 7 (AtpE), 5 (MmpR5), and 1 (PepQ) single nucleotide polymorphisms (SNPs) and one insertion frameshift mutation in MmpR5 were recreated at the molecular level, and these phenotypic models were then directed to stringent dynamics to define time-scaled changes. The AtpE variants destabilized the structure; mainly, L59V, E61D, and I66M were detrimental to the complex fitness, while L74V and L114P boosted the BDQ binding to MmpR5. The first three and last two alterations gave rise to loss- and gain-of-function to AtpE and MmpR5, respectively. Hence, these five mutants are functionally relevant and therapeutically targetable hotspots of BDQ resistance. There were no noticeable changes in PepQ data analysis. The present study revealed that MmpR5 mutations confer BDQ resistance, whereas AtpE and PepQ SNPs display low susceptibility. These results were tallied with the published findings, which testified to the pursued method's reliability and accuracy. We hope these data and inferences could be helpful for the futuristic design of novel TB drugs. Communicated by Ramaswamy H. Sarma