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Molecular Dynamics Simulations of Novel Potential Inhibitors for Penicillin Binding Protein 2B of the Resistant 5204 Strain of Streptococcus pneumoniae

[ Vol. 13 , Issue. 3 ]

Author(s):

Suvaiyarasan Suvaithenamudhan and Subbiah Parthasarathy   Pages 234 - 248 ( 15 )

Abstract:


Background: Top five best hit compounds (ZINC59376795, ZINC60175365, ZINC36922620, ZINC39550705 and ZINC36953975) were obtained through our high throughput virtual screening (HTVS) analysis with resistant 5204-PBP2B (5204 Penicillin Binding Protein 2B) and sensitive R6-PBP2B (R6 Penicillin Binding Protein 2B) proteins of Streptococcus pneumoniae. Objective: To gain insight in molecular docking and dynamics simulations of these top five best hit compounds with both resistant 5204-PBP2B and sensitive R6-PBP2B targets.

Methods: We have employed Glide XP docking and molecular dynamics simulations of these five best hit compounds with 5204-PBP2B and R6-PBP2B targets. The stability analysis has been carried out through DFT, prime-MM/GBSA binding free energy, RMSD, RMSF and Principal Component Analysis.

Results: The reference drug, penicillin G forms stable complex with sensitive R6-PBP2B protein. Similar stability is observed for the mutant resistant 5204-PBP2B with the top scoring compound ZINC592376795 which implies that this compound may act as an effective potential inhibitor. The compound ZINC59376795 forms a total of five hydrogen bonds with resistant 5204-PBP2B protein of which three are with mutated residues. Similarly, the other four compounds including penicillin G also form hydrogen bonds with mutated residue. The MD simulations and stability analysis of the complexes of wild and mutant forms are evaluated for a trajectory period of 16ns and further MD simulations of ZINC59376795 with resistant 5204-PBP2B and sensitive R6-PBP2B confirmed the stability for 50 ns.

Conclusion: These results suggest that the top five best hit compounds are found to be a promising gateway for the further development of anti-pneumococcal therapeutics.

Keywords:

Glide docking, molecular dynamics simulation, penicillin G, penicillin binding protein 2B, Streptococcus pneumoniae, resistant 5204 strain, sensitive R6 strain.

Affiliation:

Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli – 620 024, Tamil Nadu, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli – 620 024, Tamil Nadu

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