0000000000117172
AUTHOR
Cláudio Nahum Alves
Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues.
Abstract Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. S-1360 is a potent and selective inhibitor of HIV-1 IN. In this work, we have carried out molecular dynamics (MD) simulations using a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach, to determine the protein–ligand interaction energy for S-1360 and two analogues. Analysis of the MD trajectories reveals that the strongest protein–inhibitor interactions, observed in the three studied complexes, are established with Lys-159 residue and Mg 2+ cation. Calculations of binding energy using BLYP/MM level of theory reveal that there is a direct rela…
The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key enzyme involved in glycolysis processes for energy production in the Trypanosoma cruzi parasite. This enzyme catalyses the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) in the presence of inorganic phosphate (Pi) and nicotinamide adenosine dinucleotide (NAD+). The catalytic mechanism used by GAPDH has been intensively investigated. However, the individual roles of Pi and the C3 phosphate of G3P (Ps) sites, as well as some residues such as His194 in the catalytic mechanism, remain unclear. In this study, we have employed Molecular Dynamics (MD) simulations within hybrid quantum mechanical/molecular …
A QM/MM study of the reaction mechanism for the 3′-processing step catalyzed by HIV-1 integrase
Integrase (IN) is one of the three human immunodeficiency virus type 1 enzymes (HIV-1) essential for effective viral replication. This viral enzyme is involved in the integration of HIV DNA into host chromosomal DNA. In this work we have carried out molecular dynamics simulations using a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach to study the reaction mechanism for the 3′-processing step of DNA integration using a model substrate. The results obtained by QM(AM1)/MM and QM(PM3)/MM simulations have been improved by single-point corrections using an ab initio method to describe the quantum subsystem. The results obtained within this computational model can be used to obtain …
A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase.
Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-c…
A DFT Study of the Molecular Mechanisms of the Diels−Alder Reaction between Cyclopentadiene and 3-Phenyl-1-(2-pyridyl)-2-propen-1-one − Role of the Zn2+ Lewis Acid Catalyst and Water Solvent
The molecular mechanism of the Diels−Alder reaction between cyclopentadiene (1) and 3-phenyl-1-(2-pyridyl)-2-propen-1-one (2) in the absence and in the presence of a Zn2+ Lewis acid catalyst has been studied by quantum mechanical calculations at the B3LYP/6-31G* level of theory. A continuum model was selected to represent the effects of the water as solvent. For the uncatalyzed process, two channels, endo and exo, were characterized, and the mechanism corresponded to an asynchronous concerted reaction associated with a [4+2] process. The presence of a Lewis acid catalyst changed the mechanism drastically, the reaction taking place by a polar stepwise mechanism. In the first step, a C−C sigm…
A density functional study of flavonoid compounds with anti-HIV activity.
Abstract Quantum chemical calculations at the DFT/B3LYP theory level, with the 6-31G* basis set, was employed to calculate a set of molecular properties of 26 flavonoid compounds with anti-HIV activity. The correlation between biological activity and structural properties was obtained by using the multiple linear regression method. The model obtained showed not only statistical significance but also predictive ability. We demonstrate in this paper that the anti-HIV activity of compounds can be related with the molecular hydrophobicity (ClogP), the electronegativity ( χ ) and the charges on some key atoms, while that the toxicity can be related with the electronic affinities (EA), ClogP and …
Azo-hydrazo conversion via [1,5]-hydrogen shifts. A combined experimental and theoretical study
Abstract Azoalkenes 6e , 6g , 6h , and 8c underwent an easy azo-hydrazo conversion via a [1,5]-hydrogen shift yielding α,β-unsaturated hydrazones. The isomerization products were characterized through spectroscopic and spectrometric techniques. In order to understand the nature of the mechanism of these [1,5]-hydrogen shifts, the transition state structures of the reactions were theoretically studied at the B3LYP/6-31G(d,p) level. Substitution effects in the propenylazo system on the kinetic and thermodynamic parameters were analyzed. An electron localization function (ELF) analysis of the electronic structure of the transition state structure associated with the azo-hydrazo conversion of t…
A DFT study of the Diels–Alder reaction between methyl acrolein derivatives and cyclopentadiene. Understanding the effects of Lewis acids catalysts based on sulfur containing boron heterocycles
Abstract The effects of Lewis acid catalysts based on sulfur containing boron heterocycles on the Diels–Alder reactions of two methyl acroleins with cyclopentadiene have been studied using DFT methods. These reactions take place along highly asynchronous concerted processes. While the reaction with crotonaldehyde leads to the expected endo adduct, the reaction with methacrolein leads to exo one in agreement with the experiments. The catalytic effect can be explained through the analysis of the electrophilicity index (ω) of the reagents, and the molecular structure of the corresponding transition structures.
A Quantum Mechanic/Molecular Mechanic Study of the Wild-Type and N155S Mutant HIV-1 Integrase Complexed with Diketo Acid
Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. Recently, mutation studies have been reported that have shown that a certain degree of viral resistance to diketo acids (DKAs) appears when some amino acid residues of the IN active site are mutated. Mutations represent a fascinating experimental challenge, and we invite theoretical simulations for the disclosure of still unexplored features of enzyme reactions. The aim of this work is to understand the molecular mechanisms of HIV-1 IN drug resistance, which will be useful for designing anti-HIV inhibitors with unique resistance profiles. In this study, we use mo…
Enzyme molecular mechanism as a starting point to design new inhibitors: a theoretical study of O-GlcNAcase.
O-Glycoprotein 2-acetamino-2-deoxy-β-d-glucopyranosidase (O-GlcNAcase) hydrolyzes O-linked 2-acetamido-2-deoxy-β-d-glucopyranoside (O-GlcNAc) residues from post-translationally modified serine/threonine residues of nucleocytoplasmic protein. The chemical process involves substrate-assisted catalysis, where two aspartate residues have been identified as the two key catalytic residues of O-GlcNAcase. In this report, the first step of the catalytic mechanism used by O-GlcNAcase involving substrate-assisted catalysis has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) Molecular Dynamics (MD) calculations. The free energy profile shows that the formation of the oxazol…