The Development of Computational Chemistry in Canada. In: Lipkowitz KB, Boyd DB, editors. Reviews in Computational Chemistry. Hoboken: John Wiley & Sons, Inc.; 2000. pp. 213-99. [DOI: 10.1002/9780470125922.ch4]

Binding mechanism of naringenin with monoamine oxidase - B enzyme: QM/MM and molecular dynamics perspective

The reduced level of dopamine at midbrain (substantia nigra) leads to Parkinson disease by the influence of monoamine oxidation process of monoamine oxidase B (MAO-B) enzyme. This disease mostly affects the aged people. Reports outline that the naringenin molecule acts as an inhibitor of MAO-B enzyme and it potentially prevents the development of PD. To elucidate the binding mechanism of naringenin with MAO-B, we performed the molecular docking, QM/MM and molecular dynamics (MD) simulations. The molecular docking results confirm that the naringenin strongly binds with the substrate binding site of MAO-B enzyme (-12.0 kcal/mol). The low values of RMSD, RMSF and Rg indicate that the naringenin - MAO-B complex is stable over the entire period of MD simulation. Naringenin forms strong interaction with the orient keeper residue Tyr326 and other binding site residues Leu171, Glu206 and these interactions were maintained throughout the MD simulation. It is also important to block the function of MAO-B enzyme. The QM/MM study coupled with the charge density analysis reveals the charge density distribution and the strength of intermolecular interactions of naringenin-MAO-B complex. The above results suggest that this molecule is a potential inhibitor of MAO-B enzyme.

Identification of novel flavonoid inhibitor of Catechol-O-Methyltransferase enzyme by molecular screening, quantum mechanics/molecular mechanics and molecular dynamics simulations

The low level of dopamine at substantia nigra (mid-brain) has been considered to be one of the reasons for Parkinson's disease (PD). This dopamine deficit is due to the influence of Catechol-O-Methyltransferase (COMT). A recent report outline that the flavonoid family of molecules are able to inhibit the COMT enzyme. To identify a potential molecule from the flavonoid family, we performed molecular screening over a group of flavonoid molecules using glide method. Among the screened molecules, morin molecule shows, relatively larger binding affinity (-7.90 kcal/mol) towards COMT enzyme. Further, an Induced Fit Docking (IFD) has been carried out for morin with COMT enzyme; the corresponding docking score value is -8.17 kcal/mol. To understand the conformational flexibility of morin in the active site of COMT, its conformation has been compared with the corresponding gas phase conformation. Further, molecular dynamics (MD) simulation has been performed to understand the dynamical behavior and the stability of morin molecule in the active site of COMT enzyme. The morin strongly binds with the catalytic triad and gatekeeper residues and these interactions have been maintained during the 50 ns MD simulation. Notably, the O(1) atom of morin forms interaction with Glu198, Mg ion and catalytic residue Asn169; in which, Glu198 is more stable during the simulation. The O(11) atom blocks the ionization process through the interaction with Lys143. Both of these interactions are essential to inhibit the enzymatic function of COMT enzyme. The binding free energy study shows morin molecule exhibit good binding towards COMT enzyme.Communicated by Ramaswamy H. Sarma.