Rerank Score Research Articles

Computational Prediction and Analysis of Interaction of Silver Nitrate with Chitinase Enzyme

Silver nitrate is an inorganic compound with chemical formula AgNO3. Silver or silver ions have long been used in many areas due to their strong antimicrobial activity against pathogenic microbes such as bacteria, yeast, fungi and algae. Trichoderma spp. are considered as biocontrol and growth promoting agents for many crop plants due to their antagonistic properties against plant pathogens. We, in this study, checked the possible interaction between silver nitrate and Chitinase enzyme. We used Molegro virtual docker (MVD). The results obtained from docking showed us that the best pose which is derived from MolDock score for Chitinase was -49.1418 with reranking score equal to -58. 1719. It is concluded that silver nitrate and Chitinase have interaction. Obtained results showed that silver nitrate can be attached to Chitinase in Trichoderma fungi cells leading to deactivation the enzymes.

Docking Studies of Chlorogenic Acid against Aldose Redutcase by using Molgro Virtual Docker Software

Docking studies of chlorogenic acid against aldose reductase, an enzyme involved in diabetic complications, have been performed, in order to evaluate the inhibitory effects of chlorogenic acid on this enzyme. The docking studies were performed using Molgro Virtual Docker (MVD) software. From the several available alternative methods to incorporate protein flexibility in docking studies, the use of multiple crystal structures with different bound ligands was applied here, thus, of the available crystal structures of the non- mutated aldose reductase enzyme from Homo sapiens, five were selected for the final docking studies. The docking results of chlorogenic acid with selected aldose reductase crystal structures shows that it forms hydrogen bonds with at least two out of three key active site residues (Tyr48, His110 and Trp111). It also form hydrogen bonds to other active site residues, in particular Thr113. The average MolDock score and the MolDock Re-rank score for cholorogenic acid are -119.34 Kcal/mol and -114.92 Kcal/mol respectively. The docking results show that chlorogenic acid fits well in the active site of aldose reductase and interact with the residues in the active site which are crucial for their biological activity, thus, it could a potent inhibitor of aldose reductase enzyme and thus be used for prevention/treatment of diabetic complications.

Cross evaluation of different classes of alpha-adrenergic receptor antagonists to identify overlapping pharmacophoric requirements

Structurally dispersive classes of drugs targeting identical receptor binding site can serve as a source of information in the design of novel drug candidates. Their comparative cross structural features can be utilized toward optimization of receptor–ligand interactions. Five established alpha-adrenergic receptors antagonists were selected as representative compounds of their respective classes. The selected antagonists are Phenoxybenzamine, Phentolamine, Prazosin, Ergoloid Mesylate and Labetalol. A small library of 1000 molecules, 200 from each class, were submitted to molecular docking in the antagonist binding site of alpha-adrenergic receptor. The present work includes homology modeling of alpha-adrenergic receptor using SPDBV and its structure validation from Procheck. The molecule library was developed using drug likeness filters (Lipinski's rules). Flexible molecular docking was performed using MVD (Molegro Virtual Docker) after receptor and ligand preparation. The conclusive outcome of the present work is identification of antagonist binding sites of the alpha-1 (α1)-adrenergic receptor exclusively as hydrophobic due to presence of the amino acids Val 107, Val 157, Asp 106, Ile 157, Ser 158, Ser 192, Ala 189, Phe 288 and Phe 289.The amino acids identified were found crucial to identify pharmacophoric features for alpha-1 (α1)-adrenergic receptor and antagonists. Results also include identification of new molecule (PubChem ID 10289950) similar to Ergoloid Mesylate with re-rank score −113.571. The present work explains successive workflow of homology modeling, flexible molecular docking, and pharmacophoric features identification.

English

QSAR studies of thirty 2-arylbenzoxazole derivatives are carried out to probe their inhibitory activity against Cholesteryl Ester Transfer Protein (CETP). QSAR models have been obtained using multiple linear regression (MLR) analysis after manifestation of forward selection algorithm to cull significant descriptors out of descriptor’s pool. QSAR models are elected with adherent set of statistical parameters with R2=0.9431 and R2=0.9069. Validation of modeling includes method of Y-Scrambling and in addition to this, some other methods of validation. Moreover, QSAR approach of 2-arylbenzoxazoles are also attempted, supported and validated by flexible docking studies as well. The search strategies include evolutionary algorithm and edited form of Gehlhaar PLP scoring function. The same set of thirty candidates from 2-arylbenzoxazole derivatives is processed in molecular docking and their docking scores are found in agreement with QSAR studies reported. Remarkable CETP inhibitory activity is exhibited by a 2-arylbenzoxazole derivatives molecule 29C with most comprehensive set of interactions with rerank scores -102.167 and RMSD values 1.104. Hydrogen bond interactions along with hydrophobic and electrostatic interactions are mapped to confirm their potencies.

Medicinal herbs production to discourage and eliminate germs that contaminate burns: In silico study

Civilian patients with severe burns were almost local and systemic cell host immune responses concurrent depression because of complications after microbial infections. The most abundant and harmful bacterial infections are associated with opportunistic bacteria Staphylococcus aureus and Pseudomonas aeruginosa, linked to nosocomial infection with prolonged stay in a hospital. Many virulence factors excrete from both species that facilitate adherence to the burned area, localized and invasion tissue, and the emergence of antibacterial resistance. Molecular docking of molecules assimilates the interaction between a ligand and its receptor the virulence factor; this project designed to show the extent of interaction between active component extracted from black tea and mint and virulence factors (coagulase, exozyme S, the extended-spectrum of beta- lactamase and beta-lactam binding protein) using molecular docking. Aqueous extracts of black tea and mint were analyzed by GC mass and each of the bioactive components was docked against each virulence factor. Re- rank score was monitored to explain the power of interaction between ligand and receptor.Results found here that components of black tea gave more re-rank score with all virulence factors; the most active was Myricetin that needs -80.906, -80.19, -69.04, and -67.06 for PBP2 protein, exozyne S, extended-spectrum beta-lactamase, and coagulase respectively. It was noticed that Myricetin was more active against proteins excreted from P. aeruginosa than that of S. aureus. Kaempferol as a second bioactive compound that gave a positive effect regarding its re rank score -90.195 and -79.54 when docked with PBP2 and exozyme S from P.aeruginosa.Molecular docking revealed that the aqueous extract of both black tea and mint have high re-rank as inhibitory substances against different virulence factors of S.aureus and P.aeruginosa that could be a good candidate for treating burns injuries.