Bacterial M10 metallopeptidase as a medicinal target - coordination chemistry of possible metal-based inhibition

Determination of the role of specific amino acids in the binding of Zn(II), Ni(II), and Cu(II) to the active site of the M10 family metallopeptidase

Metallopeptidases are a group of metal-dependent enzymes that hydrolyze peptide bonds. These enzymes found in Streptococcus pneumoniae assist the pathogen in infecting the host by breaking down host tissues and extracellular matrix proteins. Considering metallopeptidases' significant role in bacterial virulence, inhibiting this enzyme represents a promising avenue for research. These enzymes are characterized by the presence of Zn(II) in the active site, proper coordination of which is essential for their catalytic function. This work aims to determine the significance of the specific amino acids in the metal binding domain of metallopeptidase from S. pneumoniae. For this purpose, we investigated the coordination chemistry of Zn(II), Ni(II), and Cu(II) ions with point-mutated peptide models of the metal-binding domain. Mutations were introduced at His-2 (L1) and Glu-1. Studies have shown that at pH 7.14 (pH of infected lungs by S. pneumoniae), point mutation on glutamic acid caused only minor effects on the binding of Zn(II) and Ni(II), while significantly improving Cu(II) binding. The stability of copper complexes is greater with the mutant Glu-1 → Gln-1 than with the original domain due to a hydrogen bonding network created by the Gln backbone with its side chain. Substituting histidine resulted in a significant reduction in metal binding for all metal ions, highlighting the crucial role of His-2 in metal coordination. Introduced mutations at neutral pH did not significantly affect the secondary structure of metal complexes. However, at alkaline pH, the peptides showed a higher percentage of antiparallel β-sheet structures upon the addition of Cu(II), Ni(II) and Zn(II).

Key biological processes and essential genes for Proteus mirabilis biofilm development inhibition by protocatechuic acid

Proteus mirabilis is an opportunistic pathogen linked to human urinary tract infections, and is potentially present as a foodborne pathogen within poultry products, including broiler chickens. This report outlines the inhibitory impacts of protocatechuic acid (PCA) on P. mirabilis isolated from a broiler slaughterhouse in China as well as its biofilm. This investigation encompasses assays related to motility and adhesion, bacterial metabolic activity, extracellular polymer (EPS) production, and scavenging capacity. The findings demonstrated that PCA reduced biofilm formation by 61 %. Transcriptomics findings identified that PCA limited the expression of genes like PstS that promote adhesin formation, rbsA and RcsB that alter bacterial chemotaxis, lipopolysaccharide synthesis genes LpxA and EptB, and cell wall synthesis genes MurF and MrdA, and affects the Regulator of Capsule Synthesis (RCS) two-component modulation system. Weighted gene co-expression network analysis (WGCNA) was conducted to identify the core genes. Furthermore, the binding sites of PCA to cytochrome oxidases cydA and cydB, two subunits of ATP synthase atpI and atpH, and ftsZ, which regulate bacterial division, were predicted via molecular docking. Metabolome analysis determined that PCA critically influenced coenzyme A biosynthesis, nucleotide metabolism, alanine, aspartic acid, and glutamate metabolic pathways of P. mirabilis. Therefore, PCA impacts metabolism within bacteria via various pathways, limiting the levels of extracellular polymer and bacterial viability to hinder biofilm formation. Additionally, we prepared an antibacterial plastic film containing protocatechuic acid using PVA as the monomer and CNC as the reinforcing agent. We examined the mechanical and antibacterial properties of this film. When used to wrap chicken, it reduced the total number of colonies, slowed the deterioration of chicken, and maintained the freshness of chicken. In conclusion, the information outlined in this study complements our comprehension of P. mirabilis inhibition by PCA and provides clues for the reduction of foodborne infections associated with P. mirabilis.

Copper Forms a PPII Helix-Like Structure with the Catalytic Domains of Bacterial Zinc Metalloproteases

The rapid spread of antibiotic-resistant bacteria continuously raises concerns about the future ineffectiveness of current antimicrobial treatments against infectious diseases. To address this problem, new therapeutic strategies and antimicrobial drugs with unique modes of action are urgently needed. Inhibition of metalloproteases, bacterial virulence factors, is a promising target for the development of antibacterial treatments. In this study, the interaction among Zn(II), Cu(II), and the metal-binding domains of two metalloproteases, AprA (Pseudomonas aureginosa) and CpaA (Acinetobacter baumanii), was investigated. The objective was to determine the coordination sphere of Zn(II) with a peptide model of two zinc-dependent metalloproteases. Additionally, the study explored the formation of Cu(II) complexes with the domains, as Cu(II) has been shown to inhibit metalloproteases. The third aim was to understand the role of nonbinding amino acids in stabilizing the metal complexes formed by these proteases. This work identified specific coordination patterns (HExxHxxxxxH) for both Zn(II) and Cu(II) complexes, with AprA and CpaA exhibiting a higher affinity for Cu(II) compared to Zn(II). The study also found that the CpaA domain has greater stability for both Zn(II) and Cu(II) complexes compared to AprA. The nonbinding amino acids of CpaA surrounding the metal ion contribute to the increased thermodynamic stability of the metal-peptide complex through various intramolecular interactions. These interactions can also influence the secondary structures of the peptides. The presence of certain amino acids, such as tyrosine, arginine, and glutamic acid, and their interactions contribute to the stability and, only in the case of Cu(II) complexes, the formation of a rare protein structure called a left-handed polyproline II helix (PPII), which is known to play a role in the stability and function of various proteins. These findings provide valuable insights into the coordination chemistry of bacterial metalloproteases and expand our understanding of potential mechanisms for inhibiting these enzymes.