Elaine F. F. da Cunha

Molecular modeling of Mycobacterium tuberculosis DNA gyrase and its molecular docking study with gatifloxacin inhibitors.

Abstract Mycobacterium tuberculosis (Mt) is a leading cause of infectious disease in the world today. This outlook is aggravated by a growing number of Mt infections in individuals who are immunocompromised as a result of HIV infections. Thus, new and more potent anti-tuberculosis agents are necessary. Therefore, DNA gyrase was selected as a target enzyme to combat Mt. In this work, the first three-dimensional molecular model of the hypothetical structures for the Mycobacterium tuberculosis DNA gyrase (mtDNAg) was elucidated by a homology modeling method. In addition, the orientations and binding affinities of some gatifloxacin analogs with those new structures were investigated. Our findings could be helpful for the design of new more potent gatifloxacin analogs.

Construction and Assessment of Reaction Models of Class I EPSP Synthase: Molecular Docking and Density Functional Theoretical Calculations

Abstract The high frequency of contamination by herbicides suggests the need for more active and selective herbicides. Glyphosate is the active component of one of the top-selling herbicides, which is also a potent EPSP synthase inhibitor. That is a key enzyme in the shikimic acid pathway, which is found only in plants and some microorganisms. Thus, EPSP synthase is regarded as a prime target for herbicides. In this line, molecular modeling studies using molecular dynamics simulations and DFT techniques were performed to understand the interaction of glyphosate and its analogs with the wild type enzyme and Gly96Ala mutant EPSP synthase. In addition, we investigated the reaction mechanism of the natural substrate. Our findings indicate some key points to the design of new selective glyphosate derivates.

Homology modeling of wild-type, D516V, and H526L Mycobacterium tuberculosis RNA polymerase and their molecular docking study with inhibitors.

Abstract Rifamicyns (Rifs) are antibiotic widely used for the treatment of tuberculosis (TB); nevertheless, their efficacy has been limited by a high percentage of mutations, principally in the rpoB gene. In this work, the first three-dimensional molecular model of the hypothetical structures for the wild-type and D516V and H526L mutants of Mycobacterium tuberculosis (mtRNAP) were elucidated by a homology modeling method. In addition, the orientations and binding affinities of some Rifs with those new structures were investigated. Our findings could be helpful for the design of new more potent rifamycin analogs.

Binding Mode Analysis of 2,4-diamino-5-methyl-5-deaza-6-substituted Pteridines with Mycobacterium tuberculosis and Human Dihydrofolate Reductases

Abstract There are major differences between the structures of human dihydrofolate reductase (hD-HFR) and Mycobacterium tuberculosis dihydrofolate reductase (mtDHFR). These differences may allow the design of more selective mtDHFR inhibitors. In this paper, we have used docking approaches to study the binding orientations and predict binding affinities of 2,4-diamino-5-methyl-5-deazapteridines derivatives in both hDHFR and mtDHFR. Our results of molecular docking combined with experimental data for inhibition of the human and mycobacterial dihydrofolate reductases suggest the presence of empty spaces around the 2,4-diaminodeazapteridine and N10-phenyl rings in the mtDHFR active site that are not found in the hDHFR-bound structures. Preparation of new analogs with substituents attached to C7 of the pteridine nucleus and positions 3 and 4 of the N10-phenyl group should increase the affinity and selectivity for mtDHFR.

Solvent effects on 13C and 15N shielding tensors of nitroimidazoles in the condensed phase: a sequential molecular dynamics/quantum mechanics study

Na nd 13 CN MR chemical shifts for three nitroimidazoles have been calculated and compared with experimental data. The solvent effects on NMR spectra were simulated with the polarizable continuum model (PCM) and an alternative sequential molecular dynamics/quantum mechanics methodology (S-MD/QM). The sampling of the structures for the quantum mechanical calculations is made by using the interval of statistical correlation obtained from the autocorrelation function of the energy. Magnetic shielding tensors were evaluated .

Understanding the Molecular Behavior of Organotin Compounds to Design their Effective Use as Agrochemicals: Exploration via Quantum Chemistry and Experiments

Abstract The high frequency of contamination by herbicides suggests the need for more active and selective agrochemicals. Organotin compounds are the active component of some herbicides, such as Du-Ter and Brestan, which is also a potent inhibitor of the F1Fo ATP Synthase. That is a key enzyme, because the ATP production is one of the major chemical reactions in living organisms. Thus ATP Synthase is regarded as a prime target for organotin compounds. In this line, molecular modeling studies and DFT calculations were performed in order to understand the molecular behavior of those compounds in solution. In addition, we investigated the reaction mechanism by ESI-MS analyses of the diphenyltin dichloride. Our findings indicate that an unstable key-intermediate generated in situ might take place in the reaction with ATP Synthase.

Design of New Chemotherapeutics Against the Deadly Anthrax Disease. Docking and Molecular Dynamics studies of Inhibitors Containing Pyrrolidine and Riboamidrazone Rings on Nucleoside Hydrolase from Bacillus anthracis

Abstract Anthrax is a disease caused by Bacillus anthracis, a dangerous biological warfare agent already used for both military and terrorist purposes. An important selective target for chemotherapy against this disease is nucleoside hydrolase (NH), an enzyme still not found in mammals. Having this in mind we have performed molecular docking studies, aiming to analyze the three-dimensional positioning of six known inhibitors of Trypanosoma vivax NH (TvNH) in the active site of B. anthracis NH (BaNH). We also analyzed the main interactions of these compounds with the active site residues of BaNH and the relevant factors to biological activity. These results, together with further molecular dynamics (MD) simulations, pointed out to the most promising compounds as lead for the design of potential inhibitors of BaNH. Most of the docking and MD results obtained corroborated to each other. Additionally, the docking results also suggested a good correlation with experimental data.

Development of new acetylcholinesterase reactivators: molecular modeling versus in vitro data.

In this work a theoretical methodology for evaluation of the association and kinetic reactivation constants of oximes using the Molegro and Spartan softwares was proposed and validated facing in vitro data previously reported in the literature. Results showed a very good agreement between the theoretical binding free energies of the reactivators and experimental data, suggesting that the proposed methodology could work well in the prediction of kinetic and thermodynamics parameters for oximes that might be helpful for the design and selection of new and more effective oximes.

The search for new DHFR inhibitors: a review of patents, January 2001 – February 2005

During the past 5 years, intense research activity has come from both private companies and academic institutions, aimed at the discovery of new, effective dihydrofolate reductase (DHFR) inhibitors. This important enzyme was discovered in the late 1950s, and, after nearly five decades, it still continues to draw the attention of researchers worldwide. Its low molecular weight makes it ideal as one of the main tools in molecular biology research: that is, in X-ray crystallography, NMR spectroscopy, kinetic measurements, and site-directed mutagenesis. This review will focus on the most recent developments published in the field, paying particular attention to promising DHFR inhibitors, their chemistry and biological evaluation, and to new chemical and pharmaceutical processes.

QSAR and docking studies of novel antileishmanial diaryl sulfides and sulfonamides

Leishmaniasis is a neglected disease transmitted in many tropical and sub-tropical countries, with few studies devoted to its treatment. In this work, the activities of two antileishmanial compound classes were modeled using Dragon descriptors, and multiple linear (MLR) and support vector machines (SVM) as linear and nonlinear regression methods, respectively. Both models were highly predictive, with calibration, leave-one-out validation and external validation R(2) of 0.79, 0.72 and 0.78, respectively, for the MLR-based model, improving significantly to 0.98, 0.93 and 0.90 when using SVM modeling. Therefore, novel compounds were proposed using the QSAR models built by combining the substructures of the main active compounds of both classes. The most promising structures were docked into the active site of Leishmania donovani α,β tubulin (Ld-Tub), demonstrating the high affinity of some new structures when compared to existing antileishmanial compounds.