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

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.

Unique alterations in penicillin-binding protein 2B of multidrug-resistant Streptococcus pneumoniae from Korea / 감염

BACKGROUND: Pneumococcal resistance became a global issue during the past decades. Korea is reported to be the hottest spot in the world with regard to the prevalence of penicillin and multidrug resistance. Previous molecular epidemiologic studies strongly suggested that antibiotic-resistant pneumococci from Korea are genetically related. To investigate the molecular characteristics of multidrug-resistant (MDR) pneumococcal isolates in Korea, we performed the DNA sequencing of the gene encoding penicillin-binding protein (PBP) 2B. METHODS: A total of 9 invasive MDR strains which were collected from 1990 to 1995 in various parts of Korea and one internationally epidemic Spanish 23F clone were analyzed. The 1.5 kb transpeptidase-encoding region (TER) of PBP 2B gene was amplified and directly sequenced using ABI PRISM Big Dye Terminator cycle sequencing kit (Perkin Elmer). Sequence data were compared with that of a penicillin-susceptible R6 strain. RESULTS: Alterations in nucleotide sequence (5.4-7.8%) and amino acids (3.0-4.3%) of the PBP 2B gene were relatively uniform among 9 Korean MDR strains. Most alterations in nucleotides (86-94%) and amino acids (86-100%) were noted in the hypervariable region between 408 and 993 bp. All 9 strains possessed 14 common alterations in amino acids, among which Asn-276-->Lys, Arg-285-->Cys and Ser-305-->Phe substitutions were unique to Korean MDR strains. CONCLUSION: Sequence analysis of invasive MDR strains showed that a limited number of amino acid substitutions were noted in the wild-type Korean MDR strains in the transpeptidase domain of the PBP 2B gene. Data strongly suggest the possibility of the spread of a few epidemic clones of resistant pneumococci within Korea, which could partly explain the rapid increase of pneumococcal resistance.