Molecular modelling of quinoline derivatives as telomerase inhibitors through 3D-QSAR, molecular dynamics simulation, and molecular docking techniques

Rising mortality due to cancer has led to the development and identification of newer targets and molecules to cure the disease. Telomerase is one of the attractive targets for design of many chemotherapeutic drugs. This research highlights the designing of novel telomerase inhibitors using ligand-based (3D-QSAR) and structure-based (molecular docking and molecular dynamics simulation) approaches. For the development of the 3D-QSAR model, 37 synthetic molecules reported earlier as telomerase inhibitors were selected from diversified literature. Three different alignment methods were explored; among them, distill alignment was found to be the best method with good statistical results and was used for the generation of QSAR model. Statistically significant CoMSIA model with a correlation coefficient (r²_ncv) value of 0.974, leave one out (q²) value of 0.662 and predicted correlation coefficient (r²_pred) value of 0.560 was used for the analysis of QSAR. For the MDS study, A-chain of telomerase was stabilised for 50 ns with respect to 1-atm pressure, with an average temperature of 299.98 k and with potential energy of 1,145,336 kJ/m converged in 997 steps. Furthermore, the behaviour study of variants towards the target revealed that active variable gave better affinity without affecting amino acid sequences and dimensions of protein which was accomplished through RMSD, RMSF and Rg analysis. Results of molecular docking study supported the outcomes of QSAR contour maps as ligand showed similar interactions with surrounded amino acids which were identified in contour map analysis. The results of the comprehensive study might be proved valuable for the development of potent telomerase inhibitors.

Exploring interfacial dynamics in homodimeric S-ribosylhomocysteine lyase (LuxS) from Vibrio cholerae through molecular dynamics simulations

To the best of our knowledge, this is the first molecular dynamics simulation study on the dimeric form of the LuxS enzyme from Vibrio cholerae to evaluate its structural and dynamical properties including the dynamics of the interface formed by the two monomeric chains of the enzyme. The dynamics of the interfacial region were investigated in terms of inter-residual contacts and the associated interface area of the enzyme in its ligand-free and ligand–bound states which produced characteristics contrast in the interfacial dynamics. Moreover, the binding patterns of the two inhibitors (RHC and KRI) to the enzyme forming two different enzyme–ligand complexes were analyzed which pointed towards a varying inhibition potential of the inhibitors as also revealed by the free energies of ligand binding. It is shown that KRI is a more potent inhibitor than RHC – a substrate analogue, showing correlation with experimental data. Moreover, the role of a loop in chain B of the enzyme was found to facilitate the binding of RHC similar to that of the substrate, while KRI demonstrates a differing binding pattern. The computation of the free energy of binding for the two ligands was also carried out via thermodynamic integration which ultimately served to correlate the dynamical properties with the inhibition potential of two different ligands against the enzyme. Furthermore, this successful study provides a rational to suggest novel LuxS inhibitors which could become promising candidates to treat the diseases caused by a broad variety of bacterial species.

To the best of our knowledge, this is the first molecular dynamics simulation study on the dimeric form of the LuxS enzyme from Vibrio cholerae to evaluate its structural and dynamical properties including the dynamics of the interface formed by the two monomeric chains of the enzyme.

The Impairment of Methyl Metabolism From luxS Mutation of Streptococcus mutans

The luxS gene is present in a wide range of bacteria and is involved in many cellular processes. LuxS mutation can cause autoinducer(AI)-2 deficiency and methyl metabolism disorder. The objective of this study was to demonstrate that, in addition to AI-2-mediated quorum sensing (QS), methyl metabolism plays an important role in LuxS regulation in Streptococcus mutans. The sahH gene from Pseudomonas aeruginosa was amplified and introduced into the S. mutans luxS-null strain to complement the methyl metabolism disruption in a defective QS phenotype. The intracellular activated methyl cycle (AMC) metabolites [S-adenosylmethionine (SAM), S-adenosylhomocysteine (SAH), homocysteine (HCY), and methionine] were quantified in wild-type S. mutans and its three derivatives to determine the metabolic effects of disrupting the AMC. Biofilm mass and structure, acid tolerance, acid production, exopolysaccharide synthesis of multispecies biofilms and the transcriptional level of related genes were determined. The results indicated that SAH and SAM were relatively higher in S. mutans luxS-null strain and S. mutans luxS null strain with plasmid pIB169 when cultured overnight, and HCY was significantly higher in S. mutans UA159. Consistent with the transcriptional profile, luxS deletion-mediated impairment of biofilm formation and acid tolerance was restored to wild-type levels using transgenic SahH. These results also suggest that methionine methyl metabolism contributes to LuxS regulation in S. mutans to a significant degree.