DFT Chemical Reactivity Driven by Biological Activity: Applications for the Toxicological Fate of Chlorinated PAHs

Improved molecular softness of tadalafil hapten enhancing antibody performance in immunoassay: Evidence from computational chemistry

The tadalafil-like compounds have appeared recently as adulterants in drinks and healthcare dietary supplements sourced from medicinal and edible food, which may cause illness and even death. In this work, the rationality of haptens was explored by computational chemistry and molecular simulation theories such as frontier molecular orbital (FMO)-based softness (S), three-dimensional (3D) structure, surface electrostatic potential (ESP), and lipophilic potential (LP). An antiserum from hapten H5 with the highest softness and maintaining the appropriate three-dimensional (3D) structure showed the optimal immunoassay performance, indicating an increasing softness was a critical factor for effective hapten. Based on the antibody induced by hapten H5, an indirect competitive enzyme-linked immunosorbent assay (icELISA) method for detecting multiple tadalafil-like adulterants was established. The icELISA showed a limit of detection (LOD), 50% inhibition concentration (IC₅₀ ), and a working range of 0.004-0.396, 0.89-4.27, and 0.094-16.71 ng/ml for tadalafil, amino tadalafil, acetamino tadalafil, nortadalafil, and N-desmethyl ent-tadalafil, respectively. The spiked recoveries of tadalafil-like adulterants in samples ranged from 84.9% to 116.2%. The results of the icELISA and HPLC-MS/MS methods had a good correlation for real samples with the R² of 0.9955. Specially, this work not only provided a convenient immunoassay method for measuring tadalafil-like adulterants in spirit drinks and dietary supplements in group-screening manner, but also suggested that softness was likely to be a general theory for rational hapten design. PRACTICAL APPLICATION: Rapid monitoring of tadalafil-like adulterants in food samples is very necessary and important for consumers, regulatory agencies, and the food industry.

Chemical Bonding by the Chemical Orthogonal Space of Reactivity

The fashionable Parr-Pearson (PP) atoms-in-molecule/bonding (AIM/AIB) approach for determining the exchanged charge necessary for acquiring an equalized electronegativity within a chemical bond is refined and generalized here by introducing the concepts of chemical power within the chemical orthogonal space (COS) in terms of electronegativity and chemical hardness. Electronegativity and chemical hardness are conceptually orthogonal, since there are opposite tendencies in bonding, i.e., reactivity vs. stability or the HOMO-LUMO middy level vs. the HOMO-LUMO interval (gap). Thus, atoms-in-molecule/bond electronegativity and chemical hardness are provided for in orthogonal space (COS), along with a generalized analytical expression of the exchanged electrons in bonding. Moreover, the present formalism surpasses the earlier Parr-Pearson limitation to the context of hetero-bonding molecules so as to also include the important case of covalent homo-bonding. The connections of the present COS analysis with PP formalism is analytically revealed, while a numerical illustration regarding the patterning and fragmentation of chemical benchmarking bondings is also presented and fundamental open questions are critically discussed.

Sugars and Sweeteners: Structure, Properties and In Silico Modeling

Several studies report the effects of excessive use of sugars and sweeteners in the diet. These include obesity, cardiac diseases, diabetes, and even lymphomas, leukemias, cancers of the bladder and brain, chronic fatigue syndrome, Parkinson's disease, Alzheimer's disease, multiple sclerosis, autism, and systemic lupus. On the other hand, each sugar and sweetener has a distinct metabolic assimilation process, and its chemical structure plays an important role in this process. Several scientific papers present the biological effects of the sugars and sweeteners in relation to their chemical structure. One important issue dealing with the sugars is the degree of similarity in their structures, focusing mostly on optical isomerism. Finding and developing new sugars and sweeteners with desired properties is an emerging research area, in which in silico approaches play an important role.

Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions

Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions.

Determining chemical reactivity driving biological activity from SMILES transformations: the bonding mechanism of anti-HIV pyrimidines

Assessing the molecular mechanism of a chemical-biological interaction and bonding stands as the ultimate goal of any modern quantitative structure-activity relationship (QSAR) study. To this end the present work employs the main chemical reactivity structural descriptors (electronegativity, chemical hardness, chemical power, electrophilicity) to unfold the variational QSAR though their min-max correspondence principles as applied to the Simplified Molecular Input Line Entry System (SMILES) transformation of selected uracil derivatives with anti-HIV potential with the aim of establishing the main stages whereby the given compounds may inhibit HIV infection. The bonding can be completely described by explicitly considering by means of basic indices and chemical reactivity principles two forms of SMILES structures of the pyrimidines, the Longest SMILES Molecular Chain (LoSMoC) and the Branching SMILES (BraS), respectively, as the effective forms involved in the anti-HIV activity mechanism and according to the present work, also necessary intermediates in molecular pathways targeting/docking biological sites of interest.