Segmental analysis of molecular surface electrostatic potentials: application to enzyme inhibition

DFT investigation of SiO2 nanotube for adsorption of methyl- and propyl-paraben

A huge number of parabens, esters of p-hydroxybenzoic acid, are used in cosmetic and personal care products as preservative substances. Due to their detrimental effects on ecosystem and human health, taking precautionary measures to remove these compounds is an important task regarding the environmental issues. In this study, a silica (SiO2) nanotube has been selected as a novel sensor to adsorb the most common parabens which are methyl paraben and propyl paraben molecules. To this aim, density functional theory (DFT) calculations were used to evaluate the properties for investigated compounds. The calculated adsorption energies of the most stable configurations for methyl parban@SiO2 and propyl paraben@SiO2 complexes were found to be –0.238 and –0.242 eV, respectively. The electronic properties of nanotubes experienced dramatic changes in case of interactions with parabens, which led to declining the HOMO/LUMO energy gap of the nanotube to its original value. Such adsorption could also enhance the electrical conductivity of the nanotubes meaning that the utilized SiO2 nanotube could detect the existence of methyl and propyl parabens molecules in the environment. As a concluding remark, the investigated SiO2 nanotube could work as a possible sensor for hazardous paraben with the importance of environmental issues.

Machine learning meets mechanistic modelling for accurate prediction of experimental activation energies

Accurate prediction of chemical reactions in solution is challenging for current state-of-the-art approaches based on transition state modelling with density functional theory. Models based on machine learning have emerged as a promising alternative to address these problems, but these models currently lack the precision to give crucial information on the magnitude of barrier heights, influence of solvents and catalysts and extent of regio- and chemoselectivity. Here, we construct hybrid models which combine the traditional transition state modelling and machine learning to accurately predict reaction barriers. We train a Gaussian Process Regression model to reproduce high-quality experimental kinetic data for the nucleophilic aromatic substitution reaction and use it to predict barriers with a mean absolute error of 0.77 kcal mol-1 for an external test set. The model was further validated on regio- and chemoselectivity prediction on patent reaction data and achieved a competitive top-1 accuracy of 86%, despite not being trained explicitly for this task. Importantly, the model gives error bars for its predictions that can be used for risk assessment by the end user. Hybrid models emerge as the preferred alternative for accurate reaction prediction in the very common low-data situation where only 100-150 rate constants are available for a reaction class. With recent advances in deep learning for quickly predicting barriers and transition state geometries from density functional theory, we envision that hybrid models will soon become a standard alternative to complement current machine learning approaches based on ground-state physical organic descriptors or structural information such as molecular graphs or fingerprints.

Study of molecular structure and hydrogen bond interactions in dipfluzine-benzoic acid (DIP-BEN) cocrystal using spectroscopic and quantum chemical method

The purpose of this article is to predict the molecular structure of the cocrystal of dipfluzine-benzoic acid (DIP-BEN) through computational approach (DFT calculations) and validate it using vibrational spectroscopic studies. The molecular structure of the DIP-BEN cocrystal has been predicted by forming models on the basis of the active sites available to form H-bonds between dipfluzine (DIP) and benzoic acid (BEN). Conformational study has been performed and potential energy surface scans are plotted around the flexible bonds of the cocrystal molecule and three stable conformers have been obtained. Quantum theory of atoms in molecules (QTAIM) explains that all the interactions are medium and partially covalent in nature. Natural bond orbital analysis of the second order perturbation theory of the Fock matrix suggests that interactions LP (2) O2 → σ*(O74H75) and LP (2) F1 → σ* (O89H90) are responsible for the stabilization of the molecule. The HOMO and LUMO energies and electronic charge transfer (ECT) confirms that charge flows from BEN to DIP. Global reactivity descriptor parameters suggest that DIP-BEN cocrystal is softer, thus more reactive in comparison to DIP. Local reactivity descriptor parameter is used to predict reactive sites of the cocrystal. The experimental and theoretical results support the formation of cocrystal through strong hydrogen bond (O89H90⋯F1 and O74H75⋯O2) interactions present in cocrystal.

Vibrational, UV spectra, NBO, first order hyperpolarizability and HOMO-LUMO analysis of carvedilol

In this work, we have investigated experimentally and theoretically on the molecular structure, vibrational spectra, UV spectral analysis and NBO studies of cardio-protective drug carvedilol. The FT-Raman and FT-IR spectra for carvedilol in the solid phase have been recorded in the region 4000-100 cm(-1) and 4000-400 cm(-1) respectively. Theoretical calculations were performed by using density functional theory (DFT) method at B3LYP/6-31G(d,p) and B3LYP/6-31++G(d,p) basis set levels. The harmonic vibrational frequencies, the optimized geometric parameters have been interpreted and compared with the reported experimental values. The complete vibrational assignments were performed on the basis of potential energy distribution (PED) of the vibrational modes. The thermodynamic properties and molecular electrostatic potential surfaces of the molecule were constructed. The electronic absorption spectrum was recorded in the region 400-200 nm and electronic properties such as HOMO and LUMO energies were calculated. The stability of the molecule arising from hyper conjugative interactions and charge delocalization have been analyzed from natural bond orbital (NBO) analysis. The first order hyperpolarizability of the title molecule was also calculated. The photo stability of carvedilol under different storage conditions were analyzed using UV-Vis spectral technique.

Transcription Factor STAT3 as a Novel Molecular Target for Cancer Prevention

Signal Transducers and Activators of Transcription (STATs) are a family of transcription factors that regulate cell proliferation, differentiation, apoptosis, immune and inflammatory responses, and angiogenesis. Cumulative evidence has established that STAT3 has a critical role in the development of multiple cancer types. Because it is constitutively activated during disease progression and metastasis in a variety of cancers, STAT3 has promise as a drug target for cancer therapeutics. Recently, STAT3 was found to have an important role in maintaining cancer stem cells in vitro and in mouse tumor models, suggesting STAT3 is integrally involved in tumor initiation, progression and maintenance. STAT3 has been traditionally considered as nontargetable or undruggable, and the lag in developing effective STAT3 inhibitors contributes to the current lack of FDA-approved STAT3 inhibitors. Recent advances in cancer biology and drug discovery efforts have shed light on targeting STAT3 globally and/or specifically for cancer therapy. In this review, we summarize current literature and discuss the potential importance of STAT3 as a novel target for cancer prevention and of STAT3 inhibitors as effective chemopreventive agents.

Comprehensive quantum chemical and spectroscopic (FTIR, FT-Raman, 1H, 13C NMR) investigations of O-desmethyltramadol hydrochloride an active metabolite in tramadol--an analgesic drug

O-desmethyltramadol is one of the main metabolites of tramadol widely used clinically and has analgesic activity. The FTIR and FT-Raman spectra of O-desmethyl tramadol hydrochloride are recorded in the solid phase in the regions 4000-400 cm(-1) and 4000-100 cm(-1), respectively. The observed fundamentals are assigned to different normal modes of vibration. Theoretical studies have been performed as its hydrochloride salt. The structure of the compound has been optimised with B3LYP method using 6-31G(**) and cc-pVDZ basis sets. The optimised bond length and bond angles are correlated with the X-ray data. The experimental wavenumbers were compared with the scaled vibrational frequencies determined by DFT methods. The IR and Raman intensities are determined with B3LYP method using cc-pVDZ and 6-31G(d,p) basic sets. The total electron density and molecular electrostatic potential surfaces of the molecule are constructed by using B3LYP/cc-pVDZ method to display electrostatic potential (electron+nuclei) distribution. The electronic properties HOMO and LUMO energies were measured. Natural bond orbital analysis of O-desmethyltramadol hydrochloride has been performed to indicate the presence of intramolecular charge transfer. The (1)H and (13)C NMR chemical shifts of the molecule have been anlysed.

STAT3 Activation in Glioblastoma: Biochemical and Therapeutic Implications

Signal transducer and activator of transcription 3 (STAT3) is a potent regulator of gliomagenesis through its induction of angiogenesis, host immunosuppression, and tumor invasion. Gain of function mutations result in constitutive activation of STAT3 in glioma cells, making STAT3 an attractive target for inhibition in cancer therapy. Nevertheless, some studies show that STAT3 also participates in terminal differentiation and apoptosis of various cell lines and in glioma with phosphatase and tensin homolog (PTEN)-deficient genetic backgrounds. In light of these findings, the utility of STAT3 as a prognostic indicator and as a target of drug therapies will be contingent on a more nuanced understanding of its pro- and anti-tumorigenic effects.

PTEN regulation of ERK1/2 signaling in cancer

Since its discovery, the tumor suppressor phosphatase and tensin homolog (PTEN) has become a molecule with a wide spectrum of functions, which is typically meditated through its lipid phosphatase activity; however, PTEN also functions in a phosphatase-independent manner. It is well established that PTEN regulates several signaling pathways, such as phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT), janus kinase (JAK)/signal transducers and activators of transcription (STAT), focal adhesion kinase (FAK), and more recent, extracellular signal-regulated kinase (ERK)1/2, where activation of these pathways typically leads to cancer development and progression. In regard to most of these pathways, the underlining molecular mechanism of PTEN-mediated regulation is well established, but not so much for the ERK1/2 pathway. Indeed, accumulating evidence has shown an inverse correlation between PTEN expression and ERK1/2 in several malignancies. However, the detailed mechanism by which PTEN regulates ERK1/2 is poorly understood. In this review, we discuss the role of PTEN in regulating ERK1/2 by directly targeting shc/Raf/MEK and PI3K/AKT cascades, and a putative cross-talk between the two.

Decabromobiphenyl (PBB-209) activates the aryl hydrocarbon receptor while decachlorobiphenyl (PCB-209) is inactive: experimental evidence and computational rationalization of the different behavior of some halogenated biphenyls

In rat H4IIE cells permanently transfected with a luciferase gene under the control of AhR, incubation with PBB-209 led to a statistically significant increase of luminescence. In this system, PCB-209 only caused a small induction of luciferase activity. In a fish cell line, only PBB-209 was able to provoke an induction of ethoxyresorufin- O-deethylase activity. Ligand binding to the AhR was studied by means of a cell-free in vitro system in which the activation of AhR is very unlikely to occur without ligand binding. None of the biphenyls studied provoked any activation of AhR in this system. To rationalize the results and to get insight into the molecular mechanism of activation of AhR by PBB-209 as compared with PCB-209, a comprehensive computational study was carried out on these congeners as well as on PCB-126 and PCB-169, two potent AhR activators through ligand binding. The calculations include (i) conformational analysis and dipole moments of each conformer, (ii) aromaticity indices, (iii) molecular electrostatic potentials, (iv) quadrupole moments, (v) electronic and reactivity descriptors, and (vi) dissociation energies of C-Cl and C-Br bonds in model aromatic compounds. It was found that some molecular features of PBB-209, such as the electrostatic potential (EP) and EP-derived descriptors (Politzer's parameters), indicate that PBB-209 is more similar to PCB-126 and PCB-169 than to PCB-209, which share quite similar geometries based on the substitution pattern. The similarity between PBB-209, PCB-126, and PCB-169 seems to hint that these three compounds can share, at least partially, similar mechanisms of activation of AhR. It is unquestionable that PCB-126 and PCB-169 directly bind AhR and PBB-209 does not. We hypothesize that there are several simultaneous mechanisms for activation of AhR, and the most active compounds act for more than one mechanism.

Analysis of two intramolecular proton transfer processes in terms of the reaction force

The negative derivative of the potential energy along an intrinsic reaction coordinate defines a force that has qualitatively a universal form for any process having an energy barrier: it passes through a negative minimum before the transition state, at which it is zero, followed by a positive maximum. We have analyzed two intramolecular proton transfer reactions in terms of several computed properties: internal charge separation, the electrostatic potentials of the atoms involved, their Fukui functions, and the local ionization energies. The variation of each of these properties along the intrinsic reaction coordinate shows a marked correlation with the characteristic features of the reaction force. We present a description of the proton transfer processes in terms of this force.