Targeting multi-drug-resistant Acinetobacter baumannii: a structure-based approach to identify the promising lead candidates against glutamate racemase

Identification and prioritization of novel therapeutic candidates against glutamate racemase from Klebsiella pneumoniae

BACKGROUND

Klebsiella pneumoniae, a gram-negative bacterium in the Enterobacteriaceae family, is non-motile, encapsulated, and a major cause of nosocomial infections, particularly in intensive care units. The bacterium possesses a thick polysaccharide capsule and fimbriae, which contribute to its virulence, resistance to phagocytosis, and attachment to host cells. The bacterium has developed serious resistance to most antibiotics currently in use.

OBJECTIVE

This study aims to investigate the structural properties of MurI (glutamate racemase) from Klebsiella pneumoniae and to identify potential candidate inhibitors against the protein, which will help in the development of new strategies to combat the infections related to MDR strains of Klebsiella pneumoniae.

METHODS

The 3D structure of the protein was modelled using SWISS-MODEL, which utilizes the homology modelling technique. After refinement, the structure was subjected to virtual high throughput screening on the TACC server using Enamine AC collection. The obtained molecules were then put through various screening parameters to obtain promising lead candidates, and the selected molecules were then subjected to MD simulations. The data obtained from MD simulations was then assessed with the help of different global dynamics analyses. The protein-ligand complexes were also subjected to MM/PBSA-based binding free energy calculation using the g_mmpbsa program.

RESULTS

The screening parameters employed on the molecules obtained via virtual screening from the TACC server revealed that Z1542321346 and Z2356864560 out of four molecules have better potential to act as potential inhibitors for MurI protein. The binding free energy values, which came out to be -27.26±3.06 kcal/mol and -29.53±4.29 kcal/mol for Z1542321346 and Z2356864560 molecules, respectively, favoured these molecules in terms of inhibition potential towards targeted protein.

CONCLUSION

The investigation of MurI via computational approach and the subsequent analysis of potential inhibitors can pave the way for developing new therapeutic strategies to combat the infections and antibiotic resistance of Klebsiella pneumoniae. This study could significantly help the medical fraternity in the treatment of infections caused by this multidrug-resistant pathogen.

Screening and Identification of Natural Compounds as Potential Inhibitors of Glutamate Racemase, an Emerging Drug Target of Food Pathogen E. coli O157:H7: An In-silico Approach to Combat Increasing Drug Resistance

BACKGROUND

Shiga Toxin-Producing Escherichia coli (E. coli) O157:H7, capable of causing serious food-borne illnesses, is extensively studied and is known to be transmitted through animal reservoirs or person-to-person contact, leading to severe disease outbreaks. The emergence of antibiotic resistance in these strains, coupled with increased adverse effects of existing therapeutics, underscores the urgent need for alternative therapeutic strategies.

OBJECTIVE

This study aims to evaluate Glutamate Racemase (MurI protein) of the food-pathogenic E. coli O157:H7 (EC MurI) as a novel drug target. Furthermore, the study seeks to identify new compounds with potential inhibitory effects against this protein.

METHODS

Using computational tools, the study identified inhibitor binding sites on EC MurI and identified relevant inhibitors capable of binding to these sites. Molecular docking techniques were employed to assess potential hits, and selected compounds were further analyzed for their structural activity and binding affinity to the protein.

RESULTS

The results of the study revealed that Frigocyclinone and Deslanoside, exhibited the best binding affinity with EC-MurI. Subsequent molecular dynamic (MD) simulations of the selected complexes indicated that both compounds were stable. This suggests that Frigocyclinone and Deslanoside have the potential to serve as potent inhibitors of EC-MurI.

CONCLUSION

In summary, this study highlights the urgent need for alternative therapies against food-pathogenic E. coli, focusing on E. coli O157:H7. Evaluation of Glutamate Racemase as a drug target identified Frigocyclinone and Deslanoside as promising inhibitors. MD simulations indicated their stability, suggesting their potential as lead molecules for further research and treatment development.

Computer-assisted discovery and evaluation of potential ribosomal protein S6 kinase beta 2 inhibitors

S6K2 is an important protein in mTOR signaling pathway and cancer. To identify potential S6K2 inhibitors for mTOR pathway treatment, a virtual screening of 1,575,957 active molecules was performed using PLANET, AutoDock GPU, and AutoDock Vina, with their classification abilities compared. The MM/PB(GB)SA method was used to identify four compounds with the strongest binding energies. These compounds were further investigated using molecular dynamics (MD) simulations to understand the properties of the S6K2/ligand complex. Due to a lack of available 3D structures of S6K2, OmegaFold served as a reliable 3D predictive model with higher evaluation scores in SAVES v6.0 than AlphaFold, AlphaFold2, and RoseTTAFold2. The 150 ns MD simulation revealed that the S6K2 structure in aqueous solvation experienced compression during conformational relaxation and encountered potential energy traps of about 19.6 kJ mol-1. The virtual screening results indicated that Lys75 and Lys99 in S6K2 are key binding sites in the binding cavity. Additionally, MD simulations revealed that the ligands remained attached to the activation cavity of S6K2. Among the compounds, compound 1 induced restrictive dissociation of S6K2 in the presence of a flexible region, compound 8 achieved strong stability through hydrogen bonding with Lys99, compound 9 caused S6K2 tightening, and the binding of compound 16 was heavily influenced by hydrophobic interactions. This study suggests that these four potential inhibitors with different mechanisms of action could provide potential therapeutic options.

A prototrophic suppressor of a Vibrio fischeri D-glutamate auxotroph reveals a member of the periplasmic broad-spectrum racemase family (BsrF)

Although bacterial peptidoglycan (PG) is highly conserved, some natural variations in PG biosynthesis and structure have evolved. Understanding the mechanisms and limits of such variation will inform our understanding of antibiotic resistance, innate immunity, and the evolution of bacteria. We have explored the constraints on PG evolution by blocking essential steps in PG biosynthesis in Vibrio fischeri and then selecting mutants with restored prototrophy. Here, we attempted to select prototrophic suppressors of a D-glutamate auxotrophic murI racD mutant. No suppressors were isolated on unsupplemented lysogeny broth salts (LBS), despite plating >1011 cells, nor were any suppressors generated through mutagenesis with ethyl methanesulfonate. A single suppressor was isolated on LBS supplemented with iso-D-gln, although the iso-D-gln subsequently appeared irrelevant. This suppressor has a genomic amplification formed by the creation of a novel junction that fuses proB to a gene encoding a putative broad-spectrum racemase of V. fischeri, bsrF. An engineered bsrF allele lacking the putative secretion signal (ΔSS-bsrF) also suppressed D-glu auxotrophy, resulting in PG that was indistinguishable from the wild type. The ΔSS-bsrF allele similarly suppressed the D-alanine auxotrophy of an alr mutant and restored prototrophy to a murI alr double mutant auxotrophic for both D-ala and D-glu. The ΔSS-bsrF allele increased resistance to D-cycloserine but had no effect on sensitivity to PG-targeting antibiotics penicillin, ampicillin, or vancomycin. Our work helps define constraints on PG evolution and reveals a periplasmic broad-spectrum racemase in V. fischeri that can be co-opted for PG biosynthesis, with concomitant D-cycloserine resistance.

IMPORTANCE

D-Amino acids are used and produced by organisms across all domains of life, but often, their origins and roles are not well understood. In bacteria, D-ala and D-glu are structural components of the canonical peptidoglycan cell wall and are generated by dedicated racemases Alr and MurI, respectively. The more recent discovery of additional bacterial racemases is broadening our view and deepening our understanding of D-amino acid metabolism. Here, while exploring alternative PG biosynthetic pathways in Vibrio fischeri, we unexpectedly shed light on an unusual racemase, BsrF. Our results illustrate a novel mechanism for the evolution of antibiotic resistance and provide a new avenue for exploring the roles of non-canonical racemases and D-amino acids in bacteria.