Structure-based virtual screening to identify inhibitors against Staphylococcus aureus MurD enzyme

Identification of potential inhibitors against Escherichia coli Mur D enzyme to combat rising drug resistance: an in-silico approach

Indiscriminate use of anti-microbial agents has resulted in the inception, frequency, and spread of antibiotic resistance among targeted bacterial pathogens and the commensal flora. Mur enzymes, playing a crucial role in cell-wall synthesis, are one of the most appropriate targets for developing novel inhibitors against antibiotic-resistant bacterial pathogens. In the present study, in-silico high-throughput virtual (HTVS) and Standard-Precision (SP) screening was carried out with 0.3 million compounds from several small-molecule libraries against the E. coli Mur D enzyme (PDB ID 2UUP). The docked complexes were further subjected to extra-precision (XP) docking calculations, and highest Glide-score compound was further subjected to molecular simulation studies. The top six virtual hits (S1-S6) displayed a glide score (G-score) within the range of -9.013 to -7.126 kcal/mol and compound S1 was found to have the highest stable interactions with the Mur D enzyme (2UUP) of E. coli. The stability of compound S1 with the Mur D (2UUP) complex was validated by a 100-ns molecular dynamics simulation. Binding free energy calculation by the MM-GBSA strategy of the S1-2UUP (Mur D) complex established van der Waals, hydrogen bonding, lipophilic, and Coulomb energy terms as significant favorable contributors for ligand binding. The final lead molecules were subjected to ADMET predictions to study their pharmacokinetic properties and displayed promising results, except for certain modifications required to improve QPlogHERG values. So, the compounds screened against the Mur D enzyme can be further studied as preparatory points for in-vivo studies to develop potential drugs. HIGHLIGHTSE.coli is a common cause of urinary tract infections.E.coli MurD enzyme is a suitable target for drug development.Novel inhibitors against E.coli MurD enzyme were identified.Molecular dynamics studies identified in-silico potential of identified compound.ADMET predictions and Lipinski's rule of five studies showed promising results.Communicated by Ramaswamy H. Sarma.

Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches

Introduction

The rapid emergence of antibiotic resistance among various bacterial pathogens has been one of the major concerns of health organizations across the world. In this context, for the development of novel inhibitors against antibiotic-resistant bacterial pathogens, UDP-N-Acetylmuramoyl-L-Alanine-D-Glutamate Ligase (MurD) enzyme represents one of the most apposite targets.

Body

The present review focuses on updated advancements on MurD-targeted inhibitors in recent years along with genetic regulation, structural and functional characteristics of the MurD enzyme from various bacterial pathogens. A concise account of various crystal structures of MurD enzyme, submitted into Protein Data Bank is also discussed.

Discussion

MurD, an ATP dependent cytoplasmic enzyme is an important target for drug discovery. The genetic organization of MurD enzyme is well elucidated and many crystal structures of MurD enzyme are submitted into Protein Data bank. Various inhibitors against MurD enzyme have been developed so far with an increase in the use of in-silico methods in the recent past. But cell permeability barriers and conformational changes of MurD enzyme during catalytic reaction need to be addressed for effective drug development. So, a combination of in-silico methods along with experimental work is proposed to counter the catalytic machinery of MurD enzyme.

Identification of lactoferrin-derived peptides as potential inhibitors against the main protease of SARS-CoV-2

COVID-19 is a global health emergency that causes serious concerns. A global effort is underway to identify drugs for the treatment of COVID-19. One possible solution to the present problem is to develop drugs that can inhibit SARS-CoV-2 main protease (M^pro), a coronavirus protein that been considered as one among many drug targets. In this work, lactoferrin from Bos taurus L. was in silico hydrolyzed. The bioactivity, water solubility, and ADMET properties of the generated peptides were predicted using various online tools. The molecular interactions between M^pro and the peptides were studied using molecular docking and molecular dynamic simulation. The results demonstrated that peptide GSRY was predicted to have better physicochemical properties, and the value of '-C DOCKER interaction energy' between peptide GSRY and M^pro was 80.8505 kcal/mol. The interaction between the peptide GSRY and the native ligand N3 co-crystallized with M^pro had overlapped amino acids, i.e., HIS163, GlY143, GLU166, GLN189 and MET165. Molecular dynamic simulation revealed that M^pro/GSRY complexes were stable. Collectively, the peptide GSRY may be a potential candidate drug against M^pro of SARS-CoV-2.

Proteomic and Metabolomic Analyses Provide Insights into the Mechanism on Arginine Metabolism Regulated by tRNA Modification Enzymes GidA and MnmE of Streptococcus suis

GidA and MnmE, two important tRNA modification enzymes, are contributed to the addition of the carboxymethylaminomethyl (cmnm) group onto wobble uridine of tRNA. GidA-MnmE modification pathway is evolutionarily conserved among Bacteria and Eukarya, which is crucial in efficient and accurate protein translation. However, its function remains poorly elucidated in zoonotic Streptococcus suis (SS). Here, a gidA and mnmE double knock-out (DKO) strain was constructed to systematically decode regulatory characteristics of GidA-MnmE pathway via proteomic. TMT labelled proteomics analysis identified that many proteins associated with cell divison and growth, fatty acid biosynthesis, virulence, especially arginine deiminase system (ADS) responsible for arginine metabolism were down-regulated in DKO mutant compared with the wild-type (WT) SC19. Accordingly, phenotypic experiments showed that the DKO strain displayed decreased in arginine consumption and ammonia production, deficient growth, and attenuated pathogenicity. Moreover, targeted metabolomic analysis identified that arginine was accumulated in DKO mutant as well. Therefore, these data provide molecular mechanisms for GidA-MnmE modification pathway in regulation of arginine metabolism, cell growth and pathogenicity of SS. Through proteomic and metabolomic analysis, we have identified arginine metabolism that is the links between a framework of protein level and the metabolic level of GidA-MnmE modification pathway perturbation.

Synthesis, molecular docking, binding free energy calculation and molecular dynamics simulation studies of benzothiazol-2-ylcarbamodithioates as Staphylococcus aureus MurD inhibitors

A new series of benzothiazol-2-ylcarbamodithioate functional compounds 5a-f has been designed, synthesized and characterized by spectral data. These compounds were screened for their in vitro antibacterial activity against strains of Staphylococcus aureus (NCIM 5021, NCIM 5022 and methicillin-resistant isolate 43300), Bacillus subtilis (NCIM 2545), Escherichia coli (NCIM 2567), Klebsiella pneumoniae (NCIM 2706) and Psudomonas aeruginosa (NCIM 2036). Compounds 5a and 5d exhibited significant activity against all the tested bacterial strains. Specifically, compounds 5a and 5d showed potent activity against K. pneumoniae (NCIM 2706), while compound 5a also displayed potent activity against S. aureus (NCIM 5021). Compound 5d showed minimum IC₅₀ value of 13.37 μM against S. aureus MurD enzyme. Further, the binding interactions of compounds 5a-f in the catalytic pocket have been investigated using the extra-precision molecular docking and binding free energy calculation by MM-GBSA approach. A 30 ns molecular dynamics simulation of 5d/modeled S. aureus MurD enzyme was performed to determine the stability of the predicted binding conformation.