Efficacy of neuraminidase (NA) inhibitors against H1N1 strains of different geographical regions: an in silico approach

Jatrorrhizine hydrochloride potentiates the neuraminidase inhibitory effect of oseltamivir towards H7N9 influenza

By analyzing the docking result of the binding position, hydrogen bond interactions, pi–pi interaction, etc., it is likely that jatrorrhizine hydrochloride potentiates the neuraminidase inhibitory effect of oseltamivir towards H7N9 influenza.

Molecular docking analysis of new generation cephalosporins interactions with recently known SHV-variants

Extended-spectrum-β-lactamases (ESBLs), constitutes the growing class of betalactamses, these are enzymes produced by bacteria which impart resistance against advanced-generation-cephalosporins. SHV enzymes are among the most prevalent ESBLs. The mode of molecular interactions of recent SHV-variants to advanced generation cephalosporins has not been reported yet. This is the first time we are reporting the insilico study of these recent variants with new generation cephaosporins. Homology models for SHV-105, SHV-95, SHV-89, SHV-61 and SHV-48 were generated using MODELLER9v3. New generation Cephalosporins were selected to target the active site amino acid residues of these modeled SHV enzymes for predicting comparative efficacies of these inhibitors against the said enzymes on the basis of interaction energies of docking. The docked complexes were analyzed by using DISCOVERY STUDIO 2.5. In this study A237, S70, K234, R275, N132, R244 and S130 were found crucial to the correct positioning of drugs within the binding site of SHV enzymes in 11, 6, 6, 6, 5, 5 and 5 instances, respectively. On the basis of interaction energy and Ki calculations cefatoxime emerged as the most efficient among the other advanced cephalosporins against all the studied SHV variants, excluding SHV-48 where ceftazidime was found to be most effective drug. Furthermore, this study identified amino acid residues crucial to ‘SHV-Cephalosporins’ interactions and this information will be useful in designing effective and versatile drug candidates.

Interaction of CTX-M-15 enzyme with cefotaxime: a molecular modelling and docking study

Extended­spectrum β­lactamases (ESBLs) are the bacterial enzymes that make them resistant to advanced-generation cephalosporins. CTXM enzymes (the most prevalent ESBL­type) target cefotaxime. Aims of the study were:

Modelling of CTX­M enzyme from bla_CTX­M sequences of clinical Escherichia coli isolates

Docking of cefotaxime with modelled CTX­M enzymes to identify amino acid residues crucial to their interaction

To hypothesize a possible relationship between ’interaction energy of the docked enzyme­antibiotic complex‘ and ’minimum inhibitory concentration (MIC) of the antibiotic against the bacteria producing that enzyme‘.

Seven E. coli strains of clinical origin which were confirmed as PCR­positive for bla_CTX­M were selected for the study. C600 cells harboring cloned bla_CTX­M were tested for ESBL­production by double­disk­synergy test. BLAST analysis confirmed all the bla_CTX-M genes as blaCTX­M­15. Four of the 7 strains were found to be clonally related. Modelling was performed using Swiss Model Server. Discovery Studio 2.0 (Accelrys) was used to prepare Ramachandran plots for the modelled structures. Ramachandran Z­scores for modelled CTX­M enzymes from E. coli strains D8, D183, D253, D281, D282, D295 and D296 were found to be ­0.449, 0.096, 0.027, 0.043, 0.032, ­1.249 and ­1.107, respectively. Docking was performed using Hex 5.1 and the results were further confirmed by Autodock 4.0. The amino acid residues Asn 104, Asn132, Gly 227, Thr 235, Gly 236, and Ser237 were found to be responsible for positioning cefotaxime into the active site of the CTX­M­15 enzyme. It was found that cefotaxime MICs for the CTX­M­15­producers increased with the increasing negative interaction energy of the enzyme­antibiotic complex.