Computational modelling, molecular docking, and molecular dynamics simulation studies of Enterococcus faecalis diaminopimelate epimerase

Jyoti Chaudhary, Prashant Sharma, Nagendra Singh, Vijay Kumar Srivastava, Anupam Jyoti, Sanket Kaushik

Page No: 117-129

DOI: 10.86493/VEREDAS.2024/V14I4/08

Background: Enterococcus faecalis (E. faecalis) is an opportunistic bacterial pathogen which is resistant to a several class of antibiotics. E. faecalis, infection is increasing in numbers frequently and it is needful to find alternative approaches to fight against the pathogen. Diaminopimelate epimerase (DapF) enzyme is an essential enzyme in the Lysine biosynthesis pathway which catalyses the formation of meso-2, 6-diaminoheptanedioate from 2,6- diaminoheptanedioate. Lysine is an essential amino acid, therefore, targeting the E. faecalis Diaminopimelate epimerase (EfDapF) will help us to develop antimicrobial drugs. Material and Method: We have reported here cloning of EfDapF gene its expression, and purification along with the structural prediction of EfDapF using computational methods. We have also done molecular docking studies of EfDapF with ajmalicine. Docking studies were also validated by MD simulation studies. Results: These studies indicated the binding of ajmalicine with EfDapF. Structural studies indicated a mixed structure of EfDapF having both alpha helixes and beta sheets. Docking studies further showed that amino acid residue Ser73 for ajmalicine which is a part of phosphate‑binding loop of EfDapF plays a significant role in the formation of Hydrogen bond with the ligand. The exact position of ligand binding is deep groove, regarded as the protein’s binding cavity. Conclusion: These studies indicated reasonably good interactions of ajmalicine with EfDapF which can eventually diminish the catalytic activity of the protein.

Citations

APA: Jyoti Chaudhary, Prashant Sharma, Nagendra Singh, Vijay Kumar Srivastava, Anupam Jyoti, Sanket Kaushik (2025). Computational modelling, molecular docking, and molecular dynamics simulation studies of Enterococcus faecalis diaminopimelate epimerase. DOI: 10.86493/VEREDAS.2024/V14I4/08

AMA: Jyoti Chaudhary, Prashant Sharma, Nagendra Singh, Vijay Kumar Srivastava, Anupam Jyoti, Sanket Kaushik. Computational modelling, molecular docking, and molecular dynamics simulation studies of Enterococcus faecalis diaminopimelate epimerase. 2025. DOI: 10.86493/VEREDAS.2024/V14I4/08

Chicago: Jyoti Chaudhary, Prashant Sharma, Nagendra Singh, Vijay Kumar Srivastava, Anupam Jyoti, Sanket Kaushik. "Computational modelling, molecular docking, and molecular dynamics simulation studies of Enterococcus faecalis diaminopimelate epimerase." Published 2025. DOI: 10.86493/VEREDAS.2024/V14I4/08

IEEE: Jyoti Chaudhary, Prashant Sharma, Nagendra Singh, Vijay Kumar Srivastava, Anupam Jyoti, Sanket Kaushik, "Computational modelling, molecular docking, and molecular dynamics simulation studies of Enterococcus faecalis diaminopimelate epimerase," 2025, DOI: 10.86493/VEREDAS.2024/V14I4/08

ISNAD: Jyoti Chaudhary, Prashant Sharma, Nagendra Singh, Vijay Kumar Srivastava, Anupam Jyoti, Sanket Kaushik. "Computational modelling, molecular docking, and molecular dynamics simulation studies of Enterococcus faecalis diaminopimelate epimerase." DOI: 10.86493/VEREDAS.2024/V14I4/08

MLA: Jyoti Chaudhary, Prashant Sharma, Nagendra Singh, Vijay Kumar Srivastava, Anupam Jyoti, Sanket Kaushik. "Computational modelling, molecular docking, and molecular dynamics simulation studies of Enterococcus faecalis diaminopimelate epimerase." 2025, DOI: 10.86493/VEREDAS.2024/V14I4/08