Computer-based identification of potential compounds from Salviae miltiorrhizae against Neirisaral adhesion A regulatory protein

Abstract

In silico studies are attracting considerable interest due to their ability to understand protein–ligand interactions at the atomic level. The main principal tools of this in silico analyses are molecular docking and molecular dynamic (MD) simulation. This paper examines how can natural compounds that are derived from Salviae miltiorrhizae to block Neisseria adhesion A Regulatory protein (NadR). In molecular docking analysis, only four compounds were found in higher binding affinity with NadR among 10 candidates (tanshinol B, tanshinol A, lithospermic acid and tournefolal were −7.61, −7.56, −8.22 and −7.81 kcal/mol, respectively, compared to −7.23 kcal/mol of native ligand). Absorption, distribution, metabolism, excretion (ADME) and toxicity properties, medicinal chemistry profile, and physicochemical features were displayed that tournefolal contains good properties to work as a safe and good anti-adhesive drug. Therefore, the complexes of these four ligands with NadR protein were subjected to 100 ns of MD simulation. RMSD, RMSF, RG and hydrogen bonding exhibited that tournefolal showed stable binding affinity and molecular interaction with NadR protein. In light of these results, there is now a need to conduct much more in vitro and in vivo studies about the efficacy of tournefolal.

Communicated by Ramaswamy H. Sarma

Keywords:

• Neisseria meningitides
• NadR
• Salvia miltiorrhiza
• molecular docking
• molecular dynamic simulation

Acknowledgments

This study was supported by the R&D project of MOST Bangladesh.

Authors’ contributions

M.O.R. and K.A. performed data analysis and drafted the manuscript. T.T.T. reviewed and edited the manuscript. M.S.R. designed and supervised the study, reviewed and edited the manuscript.

Disclosure statement

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

Data availability statement

The authors declare that all the data supporting the findings of this study are available within the paper.

Additional information

Funding

MSR acknowledges this research was supported by a grant from the R&D Project from MOST.