Structure-based virtual screening, free energy of binding and molecular dynamics simulations to propose novel inhibitors of Mtb-MurB oxidoreductase enzyme

Subtractive proteomics approach to Unravel the druggable proteins of the emerging pathogen Waddlia chondrophila and drug repositioning on its MurB protein

“…Subsequently, the study was geared towards identifying drug molecules that can effectively inhibit the critical proteins of W. chondrophila. Even though from a functional perspective all six protein candidates were prominent drug targets, the rest of the study only focused on MurB for the following reasons – Due to its involvement in peptidoglycan biosynthesis, MurB a prominent target against bacteria especially against its cell wall, and various researches had taken place on this protein to discover the inhibition strategy [ 72 , 73 , 74 , 75 ]. Although putative D-alanyl-D-alanine carboxypeptidase was related to peptidoglycan biosynthesis pathway, the unsuccessful prediction of the structure led to exclusion of the protein from virtual docking study.…”

Identification of potent human carbonic anhydrase IX inhibitors: a combination of pharmacophore modeling, 3D-QSAR, virtual screening and molecular dynamics simulations

“…Consensus scoring balances out the errors associated with the use of a single scoring function (Yang et al, 2005). Therefore, the final ranking was done by the combined use of the Glide energy, Gibbs energy of binding (DG 1 bind ), along with the docking score (Nirwan et al, 2020). The stepwise filtering process used for the selection of the final hits is shown in Figure 9.…”

High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment

“…Structure-based drug design by virtual screening and molecular docking studies has become a valuable primary step in the identification of novel lead molecules for the treatment of diseases [59,60], and proven to be a very efficient tool for antiviral [61][62][63][64] and antibacterial [65,66] and antiprotozoal [67,68] drug discovery. Therefore, a virtual screening experiment was conducted to determine the interaction of natural ligands of the NPASS database within the binding pocket of putative drug targets of the virus that was calculated in terms of docking scores and MM-GBSA values.…”