Evaluating the suitability of RNA intervention mechanism exerted by some flavonoid molecules against dengue virus MTase RNA capping site: a molecular docking, molecular dynamics simulation, and binding free energy study.

Dengue virus (DENV) is one of the most dangerous mosquito-borne human pathogens known to the mankind. Currently, no vaccines or standard therapy is avaliable to treate DENV infection. This makes the drug development against DENV more significant and challenging.

Evaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-α via quantum mechanics/molecular mechanics, molecular dynamics and binding free energy calculations.

The resistance to the endocrine therapy of breast cancer leads to the emergence of new class of drugs that downregulates the estrogen receptor action known as selective estrogen receptor downregulators (SERDs). The first approved SERD is fluvestrant; after this, there are several downregulators evolved and are in clinical trials, in which the brilanestrant (BRI) molecule shows nM range of binding affinity and efficacy. In the present study, to understand the binding nature of BRI molecule in the active site of ERα, the molecular docking analysis has been performed.

Investigation of activation mechanism and conformational stability of -(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxybenzamide and -(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide in the: active site of p300 histone acetyl transferase enzyme by molecular dynamics and binding free energy studies.

The CBP (CREB-binding protein) and p300 are related to transcriptional coactivator family and are involved in several post-translational modifications, in which the acetylation is an important factor because it commences the transcription process. Experimental studies report that CTPB (-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide) and CTB (-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxybenzamide) are good activators of p300 HAT enzyme, but yet, the molecular mechanism of their activation is not explored. The present study pertains to determine the intermolecular interactions, stability and binding free energy of CTB and CTPB from the molecular docking, molecular dynamics (MD) simulation and binding free energy calculation.

Probing the "fingers" domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking, molecular dynamics simulation and binding free energy calculations.

The NS5B RdRp polymerase is a prominent enzyme for the replication of Hepatitis C virus (HCV). During the HCV replication, the template RNA binding takes place in the "fingers" sub-domain of NS5B. The "fingers" domain is a new emerging allosteric site for the HCV drug development.