QSAR Modelling of Biological Activity in Cannabinoids with Quantum Similarity Combinations of Charge Fitting Schemes and 3D-QSAR.

Quantitative structure-activity relationship(QSAR) modeled the biological activities of 30 cannabinoids with quantum similarity descriptors(QSD) and Comparative Molecular Field Analysis (CoMFA). The PubChem[https://pubchem.ncbi.nlm.nih.gov/] database provided the geometries, binding affinities(Ki ) to the cannabinoid receptors type 1(CB1) and 2(CB2), and the median lethal dose(LD50 ) to breast cancer cells. An innovative quantum similarity approach combining (self)-similarity indexes calculated with different charge-fitting schemes under the Topo-Geometrical Superposition Algorithm(TGSA) were used to obtain QSARs. The determination coefficient(R2 ) and leave-one-out cross-validation[Q2 (LOO)] quantified the quality of multiple linear regression and support vector machine models. This approach was efficient in predicting the activities, giving predictive and robust models for each endpoint [pLD50 : R2 =0.9666 and Q2 (LOO)=0.9312; pKi (CB1): R2 =1.0000 and Q2 (LOO)=0.9727, and pKi (CB2): R2 =0.9996 and Q2 (LOO)=0.9460], where p is the negative logarithm. The descriptors based on the electrostatic potential encrypted better electronic information involved in the interaction. Moreover, the similarity-based descriptors generated unbiased models independent of an alignment procedure. The obtained models showed better performance than those reported in the literature. An additional 3D-QSAR CoMFA analysis was applied to 15 cannabinoids, taking THC as a template in a ligand-based approach. From this analysis, the region surrounding the amino group of the SR141716 ligand is the more favorable for the antitumor activity.

Enhanced Tetracycline Removal from Highly Concentrated Aqueous Media by Lipid-Free Chlorella sp. Biomass.

Microalgae are used as a lipid source for different applications, such as cosmetics and biofuel. The nonliving biomass and the byproduct from the lipid extraction procedure can efficiently remove antibiotics. This work has explored the potential use of Chlorella sp. biomasses for tetracycline (Tc) removal from highly concentrated aqueous media. Non-living biomass (NLB) is the biomass before the lipid extraction procedure, while lipid-extracted biomass (LEB) is the byproduct mentioned before. LEB removed 76.9% of Tc at 40 mg/L initial concentration and 40 mg of biomass, representing an adsorption capacity of 19.2 mg/g. Subsequently, NLB removed 68.0% of Tc at 50 mg/L and 60 mg of biomass, equivalent to 14.2 mg/g of adsorptive capacity. These results revealed an enhanced removal capacity by LEB compared with NLB and other microalgae-based materials. On the other hand, the adsorption kinetics followed the pseudo-second-order and Elovich models, suggesting chemisorption with interactions between adsorbates. The adsorption isotherms indicate a multilayer mechanism on a heterogeneous surface. Additionally, the interactions between the surface and the first layer of tetracycline are weak, and the formation of the subsequent layers is favored. The Chlorella sp. biomass after the lipid extraction process is a promising material for removing tetracycline; moreover, the use of this residue contributes to the zero-waste strategy.

LEGO-based generalized set of two linear algebraic 3D bio-macro-molecular descriptors: Theory and validation by QSARs.

Novel 3D protein descriptors based on bilinear, quadratic and linear algebraic maps in Rn are proposed. The latter employs the kth 2-tuple (dis) similarity matrix to codify information related to covalent and non-covalent interactions in these biopolymers. The calculation of the inter-amino acid distances is generalized by using several dis-similarity coefficients, where normalization procedures based on the simple stochastic and mutual probability schemes are applied. A new local-fragment approach based on amino acid-types and amino acid-groups is proposed to characterize regions of interest in proteins. Topological and geometric macromolecular cutoffs are defined using local and total indices to highlight non-covalent interactions existing between the side-chains of each amino acid. Moreover, local and total indices calculations are generalized considering a LEGO approach, by using several aggregation operators. Collinearity and variability analyses are performed to evaluate every generalizing component applied to the definition of these novel indices. These experiments are oriented to reduce the number of MDs obtained for performing prediction models. The predictive power of the proposed indices was evaluated using two benchmark datasets, folding rate and secondary structural classification of proteins. The proposed MDs are modeled using the following strategies: Multiple Linear Regression (MLR) and Support Vector Machine (SVM), respectively. The best regression model developed for the folding rate of proteins yields a cross-validation coefficient of 0.875 (Test Set) and the best model developed for secondary structural classification obtained 98% of instances correctly classified (Test Set). These statistical parameters are superior to the ones obtained with existing MDs reported in the literature. Overall, the new theoretical generalization enhanced the information extraction into the MDs, allowing a better correlation between these two evaluated benchmark datasets and the proposed indices. The optimal theoretical configurations defined for the calculation of these MDs consider low collinearity and less information redundancy among them. These theoretical configurations and the software are available at http://tomocomd.com/mulims-mcompas.

Synthesis of (E)-Ethyl-4-(2-(furan-2-ylmethylene)hydrazinyl)benzoate, crystal structure, and studies of its interactions with human serum albumin by spectroscopic fluorescence and molecular docking methods.

A novel hydrazone, (E)-Ethyl-4-(2-(furan-2-ylmethylene)hydrazinyl)benzoate (EFHB), has been synthesized and characterized by FT-IR, NMR and Mass spectroscopy, and X-ray diffraction; compound crystallized as translucent light yellow thin plates. EFHB was studied for their binding to human serum albumin (HSA) using the fluorescence quench titration method. Molecular docking was also performed to get a more detailed insight into their interaction with HSA at the binding site. Addition of this hydrazone to HSA produced significant fluorescence quenching and splitting of emission spectra of HSA through static quenching mechanism with binding constants of about 104 M-1 at 292.15, 298.15, 304.15 and 310.15 K. According to the synchronous fluorescence, tryptophan and tyrosine residues of the protein are most perturbed by the binding process. Thermodynamic parameters ΔG, ΔH, and ΔS were got and the main sort of acting force between EFHB and HSA was studied. Results of molecular docking have shown that EFHB binds to subdomain IIA of HSA mainly by hydrophobic interaction, energy binding are in good agreement with those obtained by fluorescence study (ΔGthe = -7.32 ±â€¯0.09 kcal mol-1 and ΔGexp = -6.76 ±â€¯0.03 kcal mol-1).

Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes.

In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝ(n) space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝ(n) space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragments of interest in proteins. On the other hand, with the objective of taking into account specific interactions among amino acids in global or local indices, geometric and topological cut-offs are defined. To assess the utility of global and local indices a classification model for the prediction of the major four protein structural classes, was built with the Linear Discriminant Analysis (LDA) technique. The developed LDA-model correctly classifies the 92.6% and 92.7% of the proteins on the training and test sets, respectively. The obtained model showed high values of the generalized square correlation coefficient (GC(2)) on both the training and test series. The statistical parameters derived from the internal and external validation procedures demonstrate the robustness, stability and the high predictive power of the proposed model. The performance of the LDA-model demonstrates the capability of the proposed indices not only to codify relevant biochemical information related to the structural classes of proteins, but also to yield suitable interpretability. It is anticipated that the current method will benefit the prediction of other protein attributes or functions.

Preferential solvation of thiophene and furan-2-carboxaldehyde phenylhydrazone derivatives in DMSO-water and DMSO-n-octanol mixtures.

The preferential solvation of thiophene- and furan-2-carboxaldehyde phenylhydrazone derivatives in DMSO-water and DMSO-n-octanol mixtures has been studied using visible absorption spectroscopy with a previous characterization of the electronic transitions by Time-Dependent Density Functional Theory (TDDFT) and solvatochromic study in several solvents with different hydrogen-bond donor capacity. The results indicate that the phenylhydrazones are preferentially solvated by clusters of DMSO-water existing in the solvent mixture and the dielectric enrichment as preferential solvation mechanism was discarded. A relation between local DMSO concentration with nitro groups and the electronegativity of the heteroatom of the five-membered ring was found. For DMSO-1-octanol mixtures, the results showed no preferential solvation.

Characterization of Xenorhabdus and Photorhabdus bacteria by Fourier transform mid-infrared spectroscopy with attenuated total reflection (FT-IR/ATR).

The use of Fourier transform mid-infrared spectroscopy with attenuated total reflection for characterizing entomopathogenic bacteria from genera Xenorhabdus and Photorhabdus is evaluated for the first time. The resulting spectra of Xenorhabdus poinarii and Photorhabdus luminiscens were compared with the spectrum of Escherichia coli samples. The absorption spectra generated by the bacteria samples, were very different at the region below 1400cm(-1) which represents the stretching vibrations of phosphate and carbohydrates. Star diagrams of the fingerprint section of nematodes spectra (between 1,350 and 1,650 cm(-1)) for separation between spectra was used and showed to be a useful tool for classification purposes.

Nucleotide's bilinear indices: novel bio-macromolecular descriptors for bioinformatics studies of nucleic acids. I. Prediction of paromomycin's affinity constant with HIV-1 Psi-RNA packaging region.

A new set of nucleotide-based bio-macromolecular descriptors are presented. This novel approach to bio-macromolecular design from a linear algebra point of view is relevant to nucleic acids quantitative structure-activity relationship (QSAR) studies. These bio-macromolecular indices are based on the calculus of bilinear maps on Re(n)[b(mk)(x (m),y (m)):Re(n) x Re(n)-->Re] in canonical basis. Nucleic acid's bilinear indices are calculated from kth power of non-stochastic and stochastic nucleotide's graph-theoretic electronic-contact matrices, M(m)(k) and (s)M(m)(k), respectively. That is to say, the kth non-stochastic and stochastic nucleic acid's bilinear indices are calculated using M(m)(k) and (s)M(m)(k) as matrix operators of bilinear transformations. Moreover, biochemical information is codified by using different pair combinations of nucleotide-base properties as weightings (experimental molar absorption coefficient epsilon(260) at 260 nm and pH=7.0, first (Delta E(1)) and second (Delta E(2)) single excitation energies in eV, and first (f(1)) and second (f(2)) oscillator strength values (of the first singlet excitation energies) of the nucleotide DNA-RNA bases. As example of this approach, an interaction study of the antibiotic paromomycin with the packaging region of the HIV-1 Psi-RNA have been performed and it have been obtained several linear models in order to predict the interaction strength. The best linear model obtained by using non-stochastic bilinear indices explains about 91% of the variance of the experimental Log K (R=0.95 and s=0.08 x 10(-4)M(-1)) as long as the best stochastic bilinear indices-based equation account for 93% of the Log K variance (R=0.97 and s=0.07 x 10(-4)M(-1)). The leave-one-out (LOO) press statistics, evidenced high predictive ability of both models (q(2)=0.86 and s(cv)=0.09 x 10(-4)M(-1) for non-stochastic and q(2)=0.91 and s(cv)=0.08 x 10(-4)M(-1) for stochastic bilinear indices). The nucleic acid's bilinear indices-based models compared favorably with other nucleic acid's indices-based approaches reported nowadays. These models also permit the interpretation of the driving forces of the interaction process. In this sense, developed equations involve short-reaching (k

Influence of the dielectric medium on the carbonyl infrared absorption peak of acetylferrocene.

The solvent effect on the position of the carbonyl vibrational stretching of acetylferrocene in aprotic media was studied in this work. The solvent-induced shifts in this organometallic compound were interpreted in terms of the alternative reaction field model(SCRF-MO) proposed by Kolling. In contrast to the established trends for carbonyl groups in organic systems, the results suggest that the continuum models for the reaction field are not adequate and that the influence of dipolarity-polarizability described by an inhomogeneous coupling function theta(epsilon )L(n(2)) that assumes optical dielectric saturation is responsible for the carbonyl band shift and, there is empirical evidence that the effect of field-induced intermolecular interaction on band shift, interpreted in terms of the van der Waals forces from the solvent, have a important contribution to this phenomena.