Identification of bioactive natural compounds as efficient inhibitors against Mycobacterium tuberculosis protein-targets: A molecular docking and molecular dynamics simulation study

Emergence of Meropenem Resistance Among Cefotaxime Non-susceptible Streptococcus pneumoniae: Evidence and Challenges

“…In addition, the number of stabilizing mutations in the transpeptidase domain of the PBPs rather than the total number of mutations contributes to decreasing drug affinity, and the same can be transferred to subsequent generations for selective/evolutionary benefits (DUET results considered evolutionary selection while designating thermodynamically stabilizing/destabilizing mutations). The identically low residuelevel RMSDs, atomic-level fluctuations, and radius of gyration in the PBPs as a result of cumulative mutations further 13 https://view-hub.org/map/?set=wuenic-coverage&group=vaccine-coverage& category=pcv ascertained that the nsSNPs did not alter the overall stability or compactness of the PBP structures (Carugo, 2018;Miryala et al, 2021). Among the three PBPs, PBP2B has a greater number of substitutions (equal number of stabilizing and destabilizing mutations) owing to the prolonged use of penicillin, resulting in balanced stability of the PBP2B TP domain.…”

“…The top-ranked complexes based on the lowest binding energies (highest affinities) were visualized using USCF Chimera (Pettersen et al, 2004) and Discovery Studio (Jejurikar and Rohane, 2021). The intermolecular interactions of the complexes were analyzed to determine the crucial residues of the target that can contribute to the drug binding (Basu et al, 2020;Miryala et al, 2021;Naha et al, 2021;Vasudevan et al, 2021).…”

Structure-based screening of natural product libraries in search of potential antiviral drug-leads as first-line treatment to COVID-19 infection

“…Due to the advancements in virology, molecular biology, and computational biology, we can now decipher the pathophysiology of many viral diseases, including COVID-19 infection [ 57 ]. Natural products have been playing an important role as complementary medicine to combat viral infections, and herbal medicines have been an excellent source for modern drug research programs for a long time [ 58 ]. Their origin, availability, safety, and cost-effectiveness make them a reliable choice alongside modern medicine [ 59 ].…”

Datasets comprising the quality validations of simulated protein-ligand complexes and SYBYL docking scores of bioactive natural compounds as inhibitors of Mycobacterium tuberculosis protein-targets

“… The docking scores can further be exploited either based on individual compounds or collective understanding of a specific class of compounds or analysis of specific chemical parameters based on individual scoring algorithms. The compounds that were not considered as per criteria presented in the main publication can further be explored similarly against other potent targets [1] . The optimised simulation parameters can readily guide researchers by providing a set of standard values that can be utilised to design simulation experiments regarding the same/similar macromolecules The simulation profiles may encourage designing of efficient therapeutic agents by providing crucial interaction dynamics values.…”