Understanding the structural basis of the binding specificity of c-di-AMP to M. smegmatis RecA using computational biology approach.

Mycobacterium tuberculosis RecA (MtRecA), a protein involved in DNA repair, homologous recombination and SOS pathway, contributes to the development of multidrug resistance. ATP binding-site in RecA has been a drug target to disable RecA dependent DNA repair. For the first time, experiments have shown the existence and binding of c-di-AMP to a novel allosteric site in the C-terminal-Domain (CTD) of Mycobacterium smegmatis RecA (MsRecA), a close homolog of MtRecA. In addition, it was observed that the c-di-AMP was not binding to Escherichia coli RecA (EcRecA). This article analyses the possible interactions of the three RecA homologs with the various c-di-AMP conformations to gain insights into the structural basis of the natural preference of c-di-AMP to MsRecA and not to EcRecA, using the structural biology tools. The comparative analysis, based on amino acid composition, homology, motifs, residue types, docking, molecular dynamics simulations and binding free energy calculations, indeed, conclusively indicates strong binding of c-di-AMP to MsRecA. Having very similar results as MsRecA, it is highly plausible for c-di-AMP to strongly bind MtRecA as well. These insights from the in-silico studies adds a new therapeutic approach against TB through design and development of novel allosteric inhibitors for the first time against MtRecA.Communicated by Ramaswamy H. Sarma.

Investigation of Severe Plastic Deformation Effects on Magnesium RZ5 Alloy Sheets Using a Modified Multi-Pass Equal Channel Angular Pressing (ECAP) Technique.

The present study investigates the effects of multiple passes of equal channel angular pressing (ECAP) on magnesium alloy sheets with the assistance of an Inconel plunger along with a die setup having a channel angle of 120° and corner angle of 10° operating at a temperature of 200 °C followed by the required heat treatment processes. The microstructural analysis of the sheet samples at various stages of the multi-pass hot ECAP has shown evidence of ultrafine grain refinement (UFG) due to the occurrence of severe plastic deformation. X-ray diffraction analysis has also exhibited the presence of phases like MgZn and CeZn3 which is supposedly responsible for the enhancement of the mechanical properties. As a result, the room temperature tensile and compressive strengths have improved by 6.12% and 6.63%, respectively, after the second pass, and 11.56% and 15.64%, respectively, after the fourth pass of ECAP. Additionally, the hardness of the sheets has increased by 6.49% and 16.64% after the second and fourth pass of hot ECAP, respectively, mainly attributed to the drastic decrease in grain size from 164 µm to 12 µm within four ECAP passes, all these with a negligible change in ductility. This success in the thermomechanical processing of Mg-RZ5 alloy sheets using a die channel angle of 120° with a minimal number of passes of hot ECAP under a controlled equivalent strain, further opens doors for incorporating optimizations and/or additional aspects so as to achieve even better grain refinements, and consequently, mechanical strength improvements thereby catering to the industrial needs of aerospace and construction areas.

Appraisal of Pancreatic Lipase Inhibitory Potential of Ziziphus oenoplia (L.)Mill. Leaves by In Vitro and In Silico Approaches.

Pancreatic lipase is one of the crucial lipolytic enzymes of the gut that actively facilitates the digestion and absorption of the dietary triglycerides and cholesteryl esters. Although it has been deemed as one of the most reliable targets for the treatment of obesity and/or dyslipidemia, to date, orlistat is the only known FDA-approved, effective, oral pancreatic lipase inhibitor available for clinical use apart from the centrally acting antiobesity agents. However, it is known to be associated with adverse gastrointestinal and renal complications. In this study, we attempted to assess the antioxidant and porcine pancreatic lipase inhibitory potentials of Ziziphus oenoplia (L.)Mill. leaves through a systematic combination of in vitro and in silico approaches. Among the four different extracts including petroleum ether extract, ethyl acetate extract, ethanolic extract, and aqueous extract obtained through successive solvent extraction, the ethyl acetate extract has outperformed the other extracts and orderly displayed competent peroxide scavenging (IC50 value: 267.30 µg/mL) and porcine pancreatic lipase inhibitory (IC50 value: 444.44 µg/mL) potentials compared to the selected reference compounds: ascorbic acid (IC50 value: 251.50 µg/mL) and orlistat (IC50 value: 502.51 µg/mL) in the selected in vitro assay models. In addition, based on the molecular docking simulations of the six essential phytoconstituents of the leaves of Ziziphus oenoplia (L.)Mill. and their respective chemical analogues against the crystal structure of pancreatic lipase-colipase complex (PDB ID: 1LPB), four best-ranked molecules (PubChem CIDs: 15515703, 132582306, 11260294, and 44440845) have been proposed. Further, among these, the interaction potentials of the two top-ranked molecules (PubChem CIDs: 132582306 and 15515703) were analyzed through molecular dynamics (MD) simulations at a trajectory of 100 ns. Finally, absorption, distribution, metabolism, excretion, and toxicity (ADMET) parameters were theoretically predicted for all of the molecules using Swiss ADME and ADMET lab2.0. In conclusion, Ziziphus oenoplia (L.)Mill. leaves could become a prominent source for various potent bioactive compounds that may serve as prospective leads for the development of clinically cognizable pancreatic lipase inhibitors, provided their pharmacokinetic and in particular toxicity properties are thoroughly optimized.

Molecular docking analysis reveals differential binding affinities of multiple classes of selective inhibitors towards cancer-associated KRAS mutants.

KRAS is the most frequently mutated oncogene in solid cancers, and inhibitors that specifically target the KRAS-G12C mutant were recently approved for clinical use. The limited availability of experimental data pertaining to the sensitivity of KRAS-non-G12C mutants towards RAS inhibitors made it difficult to predict the response of KRAS-mutated cancers towards RAS-targeted therapies. The current study aims at evaluating sensitivity profiles of KRAS-non-G12C mutations towards clinically approved sotorasib and adagrasib, and experimental RAS inhibitors based on binding energies derived through molecular docking analysis. Computationally predicted sensitivities of KRAS mutants conformed with the available but limited experimental data, thus validating the usefulness of molecular docking approach in predicting clinical response towards RAS inhibitor treatment. Our results indicate differential sensitivity of KRAS mutants towards both clinical and experimental therapeutics; while certain mutants exhibited broad cross-resistance to most inhibitors, some mutants showed resistance towards specific inhibitors. These results thus suggest the potential of emergence of more resistance mutations in future towards RAS-targeted therapy and points to an urgent need to develop novel classes of inhibitors that are able to overcome both primary and secondary drug resistance. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03407-9.

Targeting the DENV NS2B-NS3 protease with active antiviral phytocompounds: structure-based virtual screening, molecular docking and molecular dynamics simulation studies.

Dengue fever has been a global health concern. Mitigation is a challenging problem due to non-availability of workable treatments. The most difficult objective is to design a perfect anti-dengue agent capable of inhibiting infections caused by all four serotypes. Various tactics have been employed in the past to discover dengue antivirals, including screening of chemical compounds against dengue virus enzymes. The objective of the current study is to investigate phytocompounds as anti-dengue remedies that target the non-structural 2B and non-structural 3 protease (NS2B-NS3pro), a possible therapeutic target for dengue fever. Initially, 300 + antiviral phytocompounds were collected from Duke's phytochemical and ethnobotanical database and 30 phytocompounds with anti-dengue properties were identified from previously reported studies, which were virtually screened against NS2B-NS3pro using molecular docking and toxicity evaluation. The top five most screened ligands were naringin, hesperidin, gossypol, maslinic acid and rhodiolin with binding affinities of - 8.7 kcal/mol, - 8.5 kcal/mol, - 8.5 kcal/mol, - 8.5 kcal/mol and - 8.1 kcal/mol, respectively. The finest docked compounds complexed with NS2B-NS3pro were subjected for molecular dynamics (MD) simulations and binding free energy estimations through molecular mechanics generalized born surface area-based calculations. The results of the study are intriguing in the context of computer-aided screening and the binding affinities of the phytocompounds, proposing maslinic acid (MAS) as a potent bioactive antiviral for the development of phytocompound-based anti-dengue agent.

Estimated sensitivity profiles of lung cancer specific uncommon BRAF mutants towards experimental and clinically approved kinase inhibitors.

Current experimental and clinical data are inadequate to conclusively predict the oncogenicity of uncommon BRAF mutants and their sensitivity towards kinase inhibitors. Therefore, the present study aims at estimating sensitivity profiles of uncommon lung cancer specific BRAF mutations towards clinically approved as well as experimental therapeutics based on computationally derived direct binding energies. Based on the data derived from cBioportal, BRAF mutants displayed significant mutual exclusivity with KRAS and EGFR mutants indicating them as potential drivers in lung cancer. Predicted sensitivity of BRAF-V600E conformed to published experimental and clinical data thus validating the usefulness of computational approach. The BRAF-V600K displayed higher sensitivity to most inhibitors as compared to that of the BRAF-V600E. All the uncommon mutants displayed higher sensitivity than both the wild type and BRAF-V600E towards PLX 8394 and LSN3074753. While V600K, G469R and N581S displayed favorable sensitivity profiles to most inhibitors, V600L/M, G466A/E/V and G469A/V displayed resistance profiles to a variable degree. Notably, molecular dynamic (MD) simulation revealed that increased number of interactions caused enhanced sensitivity of G469R and N581S towards sorafenib. RAF kinase inhibitors were further classified into two groups as per their selectivity (Group I: BRAF-V600E-selective and Group II: CRAF-selective) based on which potential mutation-wise combinations of RAF kinase inhibitors were proposed to overcome resistance. Based on computational inhibitor sensitivity profiles, appropriate treatment strategies may be devised to prevent or overcome secondary drug resistance in lung cancer patients with uncommon mutations.