<p>In silico study by molecular docking, drug discovery, and virtual screening are useful for obtaining compounds with promising biological activity. The force fields energy minimization in molecular docking is the overall process to produce better geometry estimation and ligand-receptor affinity. In this study, the divide and conquer algorithm based on the Mikowski matrix in MarvinSketch and the conjugate gradient algorithm of Open Babel were used to minimise acetone-based oxindole derivatives in indoleamine 2,3-dioxygenase 1 (IDO1). The results showed that the binding energy produced by MarvinSketch was generally better than the binding energy obtained with Open Babel. The visualization of molecular docking results indicated that the poses and hydrogen bonding, halogen bonding and π-π interactions are different between MarvinSketch, Open Babel, and no energy minimization. The results revealed that energy minimization affects the molecular docking results.</p><p> </p>
Cyclin-dependent kinase 6 (CDK6) is an important member of protein kinases, involving in many cellular pathways especialy cell cycle progression. Thus, CDK6 is a promising target in cancer therapy. This report aims to predict inhibiton of CDK6 by some complex compounds by using molecular docking and pharmacological properties analysis. Those compounds are isatinyl-2-aminobenzoylhydrazone (ISABH) and cobalt (II), nickel (II), copper (II), and zinc (II) transition metal complexes. The molecular docking against CDK6 (PDB code: 3NUP) revealed that ISABH/ISABH-transition metal complexes established ligand-protein interaction as expressed by negative binding affinity values. Drug-likeness by SwissADME indicated that ISABH and Ni-ISABH met the Lipinski’s rule of five. Both compounds also showed reasonable pharmacological criteria by admetSAR.
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