Biology subjects

Patrizio, P.

Publications and source records attributed to Patrizio, P..

3 recordsLinked to original sources

bioRxiv2021

Docking Molecular analysis of potential Aldosterone antagonists

BackgroundAldosterone antagonists (spironolactone, eplerenone) inhibit the action of aldosterone in the collecting duct; as such, these agents cause modest diuresis but inhibit potassium and hydrogen ion secretion. We report first time Potential Aldosterone antagonists by in Silico approach, using AutoDock Vina and AutoDock 4 (or MGL Tool), estimated with Pyrx and AM Dock Software, calculating three different important parameters: Binding Affinity (kcal/mol), estimated Ki (in nM units) and Ligand Efficiency (L.E. in kcal/mol). After a selective analysis of over 1000 drugs, processed with Pyrx (a Virtual Screening software for Computational Drug Discovery) in the Ligand Binding site pocket of the protein (ID PDB 2OAX Chain A:), we noticed high values of Binding Energy, about -13.55 kcal/mol estimated by AutoDock 4 with AM Dock Software, concluding that it could be an excellent candidate drug, compared to everyone else Aldosterone antagonists. Indeed, from the results of AutoDock Vina and AutoDock 4 (or AutoDock 4.2), implemented with Lamarckian genetic algorithm, LGA, trough AMDock Software, our results of Binding Energy are very similar to the crystallized Spironolactone in PDB 2OAX Chain A protein.

bioinformatics↗

bioRxiv2021

Development and Validation Molecular Docking Analysis of Human serum albumin (HSA)

BackgroundHAS (Human Serum Albumin) is a highly water-soluble globular plasma protein, with a relative molecular weight (g/mol) of 67 KDa, consisting of 585 amino acid residues. In this study, we have investigated the interaction of the Crystal structures complexed in human serum albumin at resolutions of 2.8 to 2.0: Camptothecin, 9-amino-camptothecin, Etoposide, Teniposide, Bicalutamide and Idarubicin, using a bioinformatic approach, estimated by Pyrx Virtual Screen Tool and AMDock (AMDock, Assisted Molecular Docking). We have analyzed a validated protocol, studying several parameters, as Binding Affinity, RMSD value, Ligand Efficiency, and Inhibition constant (Ki value). MethodsHuman Serum Albumin protein preparation was characterized with several programs, as Chimera, MGLTools 1.5.6, Swiss PDB Viewer Software to perform docking analysis by Autodock Vina estimated with Pyrx Software. ResultsIn this work, we have found crystalized camptothecin, crystalized 9-amino-camptothecin and crystalized teniposide, gave excellent results for Binding Affinity, (kcal/mol), RMSD value (A{degrees}), inhibition constant Ki value (nM): -Binding Affinity of 9-amino-camptothecin (ca.-10 kcal/mol), camptothecin (-9 kcal/mol) and teniposide (-11 kcal/mol, -RMSD Value of 9 -amino-camptothecin (ca.1.8 [A]), camptothecin (ca.2.2 [A]) and teniposide (ca. 3.6 [A]), - Ki Value: 9 -amino-camptothecin (ca 59 nM), camptothecin (ca 183 nM) and teniposide (ca 9 nM), -Ligand efficiency: of 9 -amino-camptothecin(ca -0.35 kcal/mol), camptothecin (ca -0.34 kcal/mol) and teniposide (ca -0.24 kcal/mol ConclusionsWe explored the best three crystallized ligand in Human Serum Albumin. Moreover, we observe a complete overlap, during the re-docking analysis phase, estimated by chimera Software. Therefore we have concluded that ID PDB Crystal 4L8U human serum albumin-Crystallised 9 -amino Camptothecin; ID PDB Crystal 4L9K human serum albumin-Crystallised Camptothecin and ID PDB Crystal 4L9Q human serum albumin-crystallized teniposide be used as a possible as a reference template protein to be compared with the target protein, by Docking molecular analysis.

bioinformatics↗

bioRxiv2019

Late Embryogenesis Abundant (LEA) proteins confer water stress tolerance to mammalian somatic cells

Late Embryogenesis Abundant (LEA) proteins are commonly found in organisms capable of undergoing reversible dehydration - \"anhydrobiosis\". Here, we have produced three LEA proteins: pTag-RAB17-GFP-N, Zea mays dehydrin-1dhn, expressed in the nucleo-cytoplasm; pTag-WCOR410-RFP, Tricum aestivum cold acclimation protein WCOR410, binding to cellular membranes, and pTag-LEA-BFP, Artemia franciscana LEA protein group 3 that targets the mitochondria. Somatic cells transfected with three LEA proteins were subjected to desiccation under controlled conditions, followed by rehydration, viability assessment and membrane/mitochondria functional tests were performed. Results shown that LEA protect cells from desiccation injury. Cells expressed all LEA proteins shown very high percentage of viable cells (58%) after four hour of desiccation compare to un-transfected cells (1% cell alive). Plasmalemma, cytoskeleton and mitochondria appeared unaffected in LEA-expressing cells, confirming their protective action during the entire desiccation and rehydration process. Here, we show that natural xeroprotectants (LEA proteins) transiently expressed in somatic cells confer them desiccation tolerance.

cell biology↗