Computational study of quinoline-based thiadiazole compounds as potential antileishmanial inhibitors

Abstract

Leishmaniasis is a severe disease caused by protozoan parasites of the genus Leishmania and it is accountable for sizable morbidity and mortality worldwide.

Computational Screening for the Identification of Potential Phytochemical Inhibitors of Leishmania infantum Trypanothione Reductase

“…Interestingly, Khaldan et al also reported that their compounds exhibited similar interactions with the same protein, with the ligand forming critical interactions with Tyr 198, Ile 199, and Arg 287 of TryR. [39] Alpha-bisabolene interacted with TryR majorly via hydrophobic interactions with residues including Gly 11, Gly 13, Val 34, Asp 35, Val 36, Ala 46, Thr 51, Phe 126, Gly 127, Glu 141, Ala 159, Thr 160, Arg 290, and Ala 293, while a very similar interaction profile was maintained by beta-bisabolene. Interestingly, some of the hit compounds reported by Khaldan et al also shared interactions with Gly 13 and Val 36.…”

Quality Control of Coumarins, Furocoumarins and Polymethoxyflavones in Citrus Essential Oils: In Silico Analysis

“…where, $${\Delta {G}_{Complex\ }{\rm \ }}$$ is the total free energy of the protein–ligand complex, and $${\Delta {G}_{protein\ }}$$ and $${\Delta {G}_{ligand\ }}$$ are total free energies of the isolated protein and ligand in solvent, respectively. g_mmpbsa can also estimate the energy contribution per residue to the binding energy [38] . To decompose the binding energy, at first $${\Delta {E}_{MM\ },\ \Delta {G}_{polar\ }}$$ and $${\Delta {G}_{non-polar\ }}$$ were separately calculated for each residue and were then summed up to obtain the contribution of each residue to the binding energy.…”

“…k is the number of descriptors in the model. A leverage value (h) greater than the threshold (h*) suggests that the compound has a large influence on the model [38] …”

“…g_mmpbsa can also estimate the energy contribution per residue to the binding energy. [38] To decompose the binding energy, at first DE MM ; DG polar and DG nonÀ polar were separately calculated for each residue and were then summed up to obtain the contribution of each residue to the binding energy. Considering that g_mmpbsa only read the files of some specific GROMACS versions, the binary run input file (.tpr) required for MM-PBSA calculation through the g_mmpbsa was regenerated by GROMACS 2020.2.…”

Computational investigation of novel pyrimidine derivatives as potent FAK inhibitorsvia3D-QSAR, molecular docking, molecular dynamics simulation and retrosynthesis

“…Molecular dynamics (MD) simulation is a technique for examining the movement of atoms and molecules, which offers details on the conformational changes in protein–ligand complexes. 46 The three complexes (most active compound 36 , most suitable candidate D3 , and Defactinib as a reference drug) were used as starting structures to better understand the protein–ligand interactions stability. The CHARMM-GUI solution builder created the input files for the MD calculations using the CHARMM force field parameters for proteins.…”