Weak spots inhibition in the Mycobacterium tuberculosis antigen 85C target for antitubercular drug design through selective irreversible covalent inhibitor-SER124

Abstract

Mycobacterium tuberculosis (Mtb) encoded secreted antigen 85 enzymes (Ag85A/Ag85B/Ag85C) play that critical roles in the virulence, survival and drug-resistant TB of the pathogen. Ag85 proteins are potential antitubercular drug targets because they are essential in the catalytic synthesis of trehalose moieties and mycolic acid attachment to the Mtb cell wall. Recently, experimental protocols led to the discovery of a selective covalent Ag85 inhibitor, b-isomer monocyclic enolphosphorus Cycliphostin (CyC 8b) compound, which targets the Ag85 serine 124 to exhibit a promising therapeutic activity. For the first time, our study unravelled the structural features among Mtb Ag85C homologs and motions and dynamics of Ag85C when the CyC 8b bound covalently and in open model conformations to the protein using bioinformatics tools and integrated Molecular dynamics simulations. Comparative Ag85C sequence analysis revealed conserved regions; 70% active site, 90% Adeniyi loop L1 and 50% loop L2, which acts as a switch between open and closed conformations. The average C-a atoms RMSD (2.05 Å) and RMSF (0.9 Å) revealed instability and high induced flexibility in the CyC 8b covalent-bound compared to the apo and open model systems, which displayed more stability and lower fluctuations. DSSP showed structural transitions of a-helices to bend and loops to 3 10-helices in the bound systems. SASA of CyC 8b covalent bound showed active site hydrophobic residues exposure to huge solvent. Therefore, these findings present the potential opportunity hotspots in Ag85C protein that would aid the structure-based design of novel chemical entities capable of resulting in potent antitubercular drugs.

An Allosteric Inhibitory Potential of Triterpenes from Combretum racemosum on the Structural and Functional Dynamics of Plasmodium falciparum Lactate Dehydrogenase Binding Landscape

“…From the trajectory snapshots of the 300 ns MD simulations, the analysis of distance (D) was determined for Apo and MA‐bound systems to gain further insights into the inhibitory potency of MA on the dynamical conformation and movements of pf LDH. Measuring D between the side chains of two different interacting residues is a commonly used metric for describing proteins’ curling and twisting motions [30] . Thus, the distance between loop residues MET175 and LEU177 around the active site, responsible for the opened and closed structure conformations, was considered in this study.…”

“…Gradual heating of the systems was conducted beginning from 0 to 300 K for 50 ps, which was to enable the maintenance of a fixed volume and number of atoms considering a canonical ensemble (NVT). The shake algorithm was used to reduce the hydrogen bond constraint by applying one bar pressure used by the Barendsen‐Barostat [29,30] . The total duration for running the MD simulations was 300 ns with a time scale of 2 fs using a Langevin thermostat, at 300 K, and 1 bar constant pressure.…”

“…The molecular mechanics/generalised‐born surface area (MM/GBSA) method calculated the protein system's binding free energy (BFE) [35] . With the aid of the MM/GBSA technique, the BFE was utilised to estimate the binding affinities within the docked receptor‐ligand systems to gain insights into their binding landscape [30] . The calculated energies utilised over 300 000 snapshots from the 300 ns trajectories.…”

“…The shake algorithm was used to reduce the hydrogen bond constraint by applying one bar pressure used by the Barendsen-Barostat. [29,30] The total duration for running the MD simulations was 300 ns with a time scale of 2 fs using a Langevin thermostat, at 300 K, and 1 bar constant pressure. The coordinates of the Apo-pfLDH and bound-pfLDH complexes were saved every 1 ps, and the CJTRAJ and PTRAJ module in AMBER 18/GPU was used to analyse the trajectories.…”

“…[35] With the aid of the MM/ GBSA technique, the BFE was utilised to estimate the binding affinities within the docked receptor-ligand systems to gain insights into their binding landscape. [30] The calculated energies utilised over 300 000 snapshots from the 300 ns trajectories. The MM/ GBSA protocol requires complete removal of the used solvent and replacement by a dielectric continuum.…”