RESUMO

Molegro Virtual Docker is a protein-ligand docking simulation program that allows us to carry out docking simulations in a fully integrated computational package. MVD has been successfully applied to hundreds of different proteins, with docking performance similar to other docking programs such as AutoDock4 and AutoDock Vina. The program MVD has four search algorithms and four native scoring functions. Considering that we may have water molecules or not in the docking simulations, we have a total of 32 docking protocols. The integration of the programs SAnDReS ( https://github.com/azevedolab/sandres ) and MVD opens the possibility to carry out a detailed statistical analysis of docking results, which adds to the native capabilities of the program MVD. In this chapter, we describe a tutorial to carry out docking simulations with MVD and how to perform a statistical analysis of the docking results with the program SAnDReS. To illustrate the integration of both programs, we describe the redocking simulation focused the cyclin-dependent kinase 2 in complex with a competitive inhibitor.

Assuntos

Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Software , Sítios de Ligação , Quinase 2 Dependente de Ciclina/química , Desenho de Fármacos , Humanos , Ligantes , Ligação Proteica , Proteínas/química , Interface Usuário-Computador

RESUMO

ABSTRACT Tuberculosis is leading cause of death among the global bacterial infections. The main causative for tuberculosis is Mycobacterium tuberculosis, which will survive in its host human being for decades in latent or chronic levels. In addition, the late multidrug resistance at a disturbing rate accompanies the appearance of tuberculosis. The quick spread of resistance to initial stage treatment medications has redirected the focus of the medical community in the creation of an array of new drug against Mycobacterium tuberculosis. The InhA protein is a component of Fatty acid synthetase (FAS) II and exhibits an NADH reliant enoyl-ACP reductase activity. InhA is a vital enzyme of M.tuberculosis in control of cell wall synthesis, which can turn out to be a great focus for the synthesis of anti-tubercular treatment. Inspired from the offering biological actions of phytoconstituents from Allium sativum, the current research concentrates on looking at novel lead compounds from the plant. Molecular docking studies were carried out employing specific phytoconstituents from A.sativum with the protein InhA target. Ajoene shows much more encouragingresults with a Mol Dock rating of 80.6047Kcal/mol, as opposed to the typical initial line drug isoniazid (Moldock score: -58.7028 Kcal/mol). Molecular docking prediction indicate that Ajoene could be formulated into a possible treatment drug for Mycobacterium tuberculosis.