Evaluation of the interaction between potent small molecules against the Nipah virus Glycoprotein in Malaysia and Bangladesh strains, accompanied by the human Ephrin-B2 and Ephrin-B3 receptors; a simulation approach

Integrated Computational Biophysics approach for Drug Discovery against Nipah Virus

“…Therefore, they are characterized by the presence of multiple aromatic rings with hydroxyl groups that allow interactions with proteins through hydrogen bridges [50]. These chemical characteristics make procyanidins an attractive target for drug design approaches such as ligand-based pharmacophore modeling [51].…”

Exploring the inhibitory potential of Nigella sativa against dengue virus NS2B/NS3 protease and NS5 polymerase using computational approaches

“…The input PDB les were uploaded to iMODS with the default settings of 300 K constant temperature, 1 atm constant pressure, and 50 ns molecular dynamic simulation for each complex. 44,45 The best docked structures were validated for their protein exibility by performing molecular dynamic simulations using the CABS-ex 2.0 server and displayed as RMSF values (root mean square uctuation). Simulations in CABS-ex were conducted using default parameters, i.e., protein rigidity: 1.0, number of cycles: 50, number of cycles between trajectories: 50, temperature range: 1.40, and a random number of generator seed of 5711.…”

Drug discovery: In silico dry data can bypass biological wet data?

“…The Abhinand group proposed the alkaloid serpentinine as a candidate inhibitor, after a virtual screening on 1426 phytocompounds from Indian medicinal plants, whereas the Kalbhor group identified five compounds from three antiviral databases comprising 79,892 chemical entities. At the beginning of this year, Ebrahimi also recommended pemirolast, isoniazide, cepharantine and hypericin as candidate inhibitors (Ebrahimi & Alijanianzadeh, 2023). Beside the fact that none of these investigators tested these 'putative active compounds' in any wet test in laboratory, we should underline that hypericin is an unstable molecule and acts as an IMPS.…”

“…Traps of several kinds may arise if computational drift emerges, similarly to what was observed in the context of ‘research of new therapies against COVID19’, with countless number of papers deposited either on public archives or published in peer‐reviewed journals, simply reporting virtual screening results. Although motivated by finest intentions, these investigations did not observe best practices of CADD (Ebrahimi & Alijanianzadeh, 2023) that require knowledge and proficiency that, in turn, is only acquired through multiple rigorously designed benchmarking investigations and rigorous experimental validation (Gentile et al, 2023).…”