Understanding the structural basis of the binding specificity of c-di-AMP to M. smegmatis RecA using computational biology approach

Abstract

Mycobacterium tuberculosis RecA (MtRecA), a protein involved in DNA repair, homologous recombination and SOS pathway, contributes to the development of multidrug resistance. ATP binding-site in RecA has been a drug target to disable RecA dependent DNA repair. For the first time, experiments have shown the existence and binding of c-di-AMP to a novel allosteric site in the C-terminal-Domain (CTD) of Mycobacterium smegmatis RecA (MsRecA), a close homolog of MtRecA. In addition, it was observed that the c-di-AMP was not binding to Escherichia coli RecA (EcRecA). This article analyses the possible interactions of the three RecA homologs with the various c-di-AMP conformations to gain insights into the structural basis of the natural preference of c-di-AMP to MsRecA and not to EcRecA, using the structural biology tools. The comparative analysis, based on amino acid composition, homology, motifs, residue types, docking, molecular dynamics simulations and binding free energy calculations, indeed, conclusively indicates strong binding of c-di-AMP to MsRecA. Having very similar results as MsRecA, it is highly plausible for c-di-AMP to strongly bind MtRecA as well. These insights from the in-silico studies adds a new therapeutic approach against TB through design and development of novel allosteric inhibitors for the first time against MtRecA.

Communicated by Ramaswamy H. Sarma

Keywords:

• RecA
• tuberculosis
• c-di-AMP
• C-terminal domain
• allostery
• docking
• drug target

Acknowledgements

BVLS acknowledges the Core Research Grant (CRG), Science and Engineering Research Board (SERB), India. The authors like to acknowledge Dr. Krishna Murari Sinha, Dr. Srinivas B, Dr. Manikandan for the discussions and suggesting modifications to the MS.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Ethical approval

This report does not include any of the author’s experiments on humans or animals.

Authors contribution

Conceptualization: BVLS. Investigation: BVLS. Methodology: Docking Studies: PSS, AD, JJ, KSSV, PSK. Natural Conformers: SK, KSSV. Simulations: PSS, KSSV. Supervision: BVLS. Validation: BVLS. Writing—original draft: BVLS, AD, JJ Writing—review & editing: BVLS, PSS, PSK.

Additional information

Funding

This research received external funding from the Science and Engineering Research Board (SERB), India. The grant number is (CRG/2018/003276).