Daniela Josa

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.

Substituted corannulenes and sumanenes as fullerene receptors. A dispersion-corrected density functional theory study.

Stacking interactions between substituted buckybowls (corannulene and sumanene) with fullerenes (C60 and C70) were studied at the B97-D2/TZVP level of theory. Corannulene and sumanene monomers were substituted with five and six Br, Cl, CH3, C2H, or CN units, respectively. A comprehensive study was conducted, analyzing the interaction of corannulenes and sumanenes with several faces of both fullerenes. According to our results, in all cases substitution gave rise to larger interaction energies if compared with those of unsubstituted buckybowls. The increase of dispersion seems to be the main source of the enhanced binding, so an excellent correlation between the increase of interaction energy and the increase of dispersion contribution takes place. One of the noteworthy phenomena that appears is the so-called CH···π interaction, which is responsible for the strong interaction of sumanene complexes (if compared with that of corannulene complexes). This interaction also causes the substitution with CH3 groups (in which one of the H atoms points directly to the π cloud of fullerene) to be the most favorable case. This fact can be easily visualized by noncovalent interaction plots.

Ring-annelated corannulenes as fullerene receptors. A DFT-D study

Stacking π⋯π interactions of ring-annelated corannulenes with fullerenes C60 and C70 were studied at the B97-D level. For this purpose three-, four-, and five-membered rings (saturated and unsaturated) were annelated to the five rim bonds of corannulene. Substitution effects with NH, O and S units on each one of the five saturated five-membered rings annelated to the rim of corannulene were also evaluated. In all cases, complexation energies were larger than that for the parent compound, corannulene C20H10; in the best case an increase of almost 90% is found. According to our results, the increase of complexation energy is directly related to the increase of the dispersion contribution, where CH⋯π interactions play a very important role. This kind of interaction has special relevance for compounds with saturated annelated rings, where the spatial disposition favours the interaction between hydrogen atoms of CH2 groups and the π cloud of fullerene. For compounds with unsaturated annelated rings the increase of dispersion is not so pronounced; however, this is fairly offset by the increase of the electrostatic interaction. Finally, stacking interactions between ring-annelated corannulenes and fullerene C70 show complexation energy values quite similar to those obtained with fullerene C60.

Molecular modeling of Mycobacterium tuberculosis dUTpase: docking and catalytic mechanism studies.

Abstract Mycobacterium tuberculosis is a leading cause of infectious disease in the world today. This outlook is aggravated by a growing number of M. tuberculosis infections in individuals who are immunocompromised as a result of HIV infections. Thus, new and more potent anti-TB agents are necessary. Therefore, dUTpase was selected as a target enzyme to combat M. tuberculosis. In this work, molecular modeling methods involving docking and QM/MM calculations were carried out to investigate the binding orientation and predict binding affinities of some potential dUTpase inhibitors. Our results suggest that the best potential inhibitor investigated, among the compounds studied in this work, is the compound dUPNPP. Regarding the reaction mechanism, we concluded that the decisive stage for the reaction is the stage 1. Furthermore, it was also observed that the compounds with a −1 electrostatic charge presented lower activation energy in relation to the compounds with a −2 charge.

Molecular modelling of Mycobacterium tuberculosis acetolactate synthase catalytic subunit and its molecular docking study with inhibitors

Mycobacterium tuberculosis is a leading cause of infectious disease in the world today. This outlook is aggravated by a growing number of M. tuberculosis infections in individuals who are immunocompromised as a result of HIV infections. Thus, new and more potent anti-TB agents are necessary. Therefore, acetolactate synthase (mtALS) was selected as a target enzyme to combat M. tuberculosis. In this work, the three-dimensional molecular model of the hypothetical structure for the ALS catalytic subunit of M. tuberculosis was elucidated by homology modelling. In addition, the orientations and binding affinities of sulfonylurea inhibitors with the new structure was investigated. Our findings could be helpful for the design of new, more potent mtAHAS inhibitors.

DFT and MP2 study of the interaction between corannulene and alkali cations

Corannulene is an unsaturated hydrocarbon composed of fused rings, with one central five-membered ring and five peripheral six-membered rings. Its structure can be considered as a portion of C60. Corannulene is a curved π surface, but unlike C60, it has two accessible different faces: one concave (inside) and one convex (outside). In this work, computational modeling of the binding between alkali metal cations (Li+, Na+, and K+) and corannulene has been performed at the DFT and MP2 levels. Different corannulene···M+ complexes have been studied and the transition states interconnecting local minima were located. The alkali cations can be bound to a five or six membered ring in both faces. At the DFT level, binding to the convex face (outside) is favored relative to the concave face for the three alkali cations studied, as it was previously published. This out preference was found to decrease as cation size increases. At the MP2 level, although a similar trend is found, some different conclusions related to the in/out preference were obtained. According to our results, migration of cations can take place on the convex or on the concave face. Also, there are two ways to transform a concave complex in a convex complex: migration across the edge of corannulene and bowl-to-bowl inversion.

Targeting inhibition of COX-2: a review of patents, 2002-2006.

The main COX inhibitors are the non-steroidal anti-inflammatory drugs (NSAIDs). NSAIDs exert anti-inflammatory and analgesic effects through the inhibition of prostaglandin synthesis by blocking COX activity. Currently two COX isoenzymes are known, COX-1 and COX-2. Prostaglandins influenced by COX-1 maintain the integrity of the gastric mucosa. On the other hand, prostaglandins influenced by COX-2 mediate the inflammatory process. The common anti-inflammatory drugs (like aspirin, ibuprofen, and naproxen) all act by blocking the action of both the COX-1 and COX-2 enzymes. The COX-2 inhibitors represent a new class of drugs that do not affect COX-1, but selectively block COX-2. This selective action provides the benefits of reducing inflammation without irritating the stomach. This review will focus on the most recent developments published in the field, paying particular attention to promising COX-2 inhibitors, their chemistry and biological evaluation, and to new chemical and pharmaceutical processes. Moreover, we will discuss recent patents of structural analogs of the COX-2 inhibitors celecoxib and valdecoxib, and novel potential pyridazine, triazole, indole, thione derivatives as a future target for the treatment of inflammation, pain and other diseases.

A MP2 and DFT study of the aromatic character of polyphosphaphospholes. Is the pyramidality the only factor to take into consideration

A comprehensive MP2/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) study of the aromatic character of phospholes, Pn(CH)4-nPH with n = 0-4 was conducted. For this purpose, the structures for these compounds were optimized at both theoretical levels and different magnetic properties (magnetic susceptibility anisotropy, χanis, and the nucleus-independent chemical shifts, NICS) were evaluated. For comparison, these magnetic properties were also calculated in the optimized structures with planarity constraints. We have also applied the ACID (anisotropy of the current-induced density) method in this analysis. The main conclusions are the aromatic character of these compounds, the relationship between aromaticity and planarity and the importance of other factors in this aromaticity.

Theoretical study of the decomposition of ethyl and ethyl 3-phenyl glycidate

AbstractThe mechanism of the decomposition of ethyl and ethyl 3-phenyl glycidate in gas phase was studied by density functional theory (DFT) and MP2 methods. A proposed mechanism for the reaction indicates that the ethyl side of the ester is eliminated as ethylene through a concerted six-membered cyclic transition state, and the unstable intermediate glycidic acid decarboxylates rapidly to give the corresponding aldehyde. Two possible pathways for glycidic acid decarboxylation were studied: one via a five-membered cyclic transition state, and the other via a four-membered cyclic transition state. The results of the calculations indicate that the decarboxylation reaction occurs via a mechanism with five-membered cyclic transition state. FigureTwo-step mechanism of decarboxylation of glycidic esters to give aldehydes and ketones