Analyzing Toxicity Through Electrophilicity

Development of an effective QSAR-based hazard threshold prediction model for the ecological risk assessment of aromatic hydrocarbon compounds

The insufficient hazard thresholds of specific individual aromatic hydrocarbon compounds (AHCs) with diverse structures limit their ecological risk assessment. Thus, herein, quantitative structure-activity relationship (QSAR) models for estimating the hazard threshold of AHCs were developed based on the hazardous concentration for 5% of species (HC5) determined using the optimal species sensitivity distribution models and on the molecular descriptors calculated via the PADEL software and ORCA software. Results revealed that the optimal QSAR model, which involved eight descriptors, namely, Zagreb, GATS2m, VR3_Dzs, AATSC2s, GATS2c, ATSC2i, ω, and Vm, displayed excellent performance, as reflected by an optimal goodness of fit (R2adj = 0.918), robustness (Q2LOO = 0.869), and external prediction ability (Q2F1 = 0.760, Q2F2 = 0.782, and Q2F3 = 0.774). The hazard thresholds estimated using the optimal QSAR model were approximately close to the published water quality criteria developed by different countries and regions. The quantitative structure-toxicity relationship demonstrated that the molecular descriptors associated with electrophilicity and topological and electrotopological properties were important factors that affected the risks of AHCs. A new and reliable approach to estimate the hazard threshold of ecological risk assessment for various aromatic hydrocarbon pollutants was provided in this study, which can be widely popularised to similar contaminants with diverse structures.

Chronic aquatic toxicity assessment of diverse chemicals on Daphnia magna using QSAR and chemical read-across

We have modeled here chronic Daphnia toxicity taking pNOEC (negative logarithm of no observed effect concentration in mM) and pEC50 (negative logarithm of half-maximal effective concentration in mM) as endpoints using QSAR and chemical read-across approaches. The QSAR models were developed by strictly obeying the OECD guidelines and were found to be reliable, predictive, accurate, and robust. From the selected features in the developed models, we have found that an increase in lipophilicity and saturation, the presence of electrophilic or electronegative or heavy atoms, the presence of sulphur, amine, and their related functionality, an increase in mean atomic polarizability, and higher number of (thio-) carbamates (aromatic) groups are responsible for chronic toxicity. Therefore, this information might be useful for the development of environmentally friendly and safer chemicals and data-gap filling as well as reducing the use of identified toxic chemicals which have chronic toxic effects on aquatic ecosystems. Approved classes of drugs from DrugBank databases and diverse groups of chemicals from the Chemical and Product Categories (CPDat) database were also assessed through the developed models.

Density Functional Theory Study on the Interaction between Aflatoxin B1/M1 and Gold Substrate

Aflatoxin M1 (AFM1) and its precursor, Aflatoxin B1 (AFB1), are highly pathogenic and mutagenic substances, making the detection and sensing of AFB1/M1 a long-standing focus of researchers. Among various detection techniques, surface-enhanced Raman spectroscopy (SERS) is considered an ideal method for AFB1/M1 detection due to its ability not only to enhance characteristic frequencies but also to detect shifts in these frequencies with high repeatability. Therefore, we employed density functional theory in conjunction with surface-enhanced Raman spectroscopy to investigate the interaction between AFB1/M1 and a Au substrate in the context of the SERS effect for the first time. To predict the potential binding sites of AFB1/M1 and Au within the SERS effect, we performed calculations on the molecular electrostatic potential of AFB1/M1. Considering the crucial role of the binding energy in molecular docking studies, we computed the binding energy between two molecules interacting with Au at different binding sites. The molecular frontier orbitals and related chemical parameters of AFB1/M1 and "molecular-Au" complexes were computed to elucidate the alterations in AFB1/M1 molecules under the SERS effect. Subsequently, the theoretical Raman spectra of AFB1/M1 and the complexes were compared and analyzed, enabling determination of the adsorption conformation of AFB1/M1 on the gold surface based on SERS surface selection rules. These findings not only provide a deeper understanding of the interaction mechanism between molecules and substrates in the SERS effect but also offer theoretical support for developing novel aflatoxin SERS sensors.

Quantitative Structure-Toxicity Relationship in Bioactive Molecules from a Conceptual DFT Perspective

The preclinical drug discovery stage often requires a large amount of costly and time-consuming experiments using huge sets of chemical compounds. In the last few decades, this process has undergone significant improvements by the introduction of quantitative structure-activity relationship (QSAR) modelling that uses a certain percentage of experimental data to predict the biological activity/property of compounds with similar structural skeleton and/or containing a particular functional group(s). The use of machine learning tools along with it has made life even easier for pharmaceutical researchers. Here, we discuss the toxicity of certain sets of bioactive compounds towards Pimephales promelas and Tetrahymena pyriformis in terms of the global conceptual density functional theory (CDFT)-based descriptor, electrophilicity index (ω). We have compared the results with those obtained by using the commonly used hydrophobicity parameter, logP (where P is the n-octanol/water partition coefficient), considering the greater ease of computing the ω descriptor. The Human African trypanosomiasis (HAT) curing activity of 32 pyridyl benzamide derivatives is also studied against Tryphanosoma brucei. In this review article, we summarize these multiple linear regression (MLR)-based QSAR studies in terms of electrophilicity (ω, ω2) and hydrophobicity (logP, (logP)2) parameters.

Effect of monosodium glutamate on serum sex hormones and uterine histology in female rats along with its molecular docking and in-silico toxicity

Monosodium glutamate (MSG) is commonly used worldwide as a food flavour enhancer by the food industry. The current study investigated the in vivo toxic effects of MSG on the uterus in adult female Sprague Dawley rats and in vitro using MCF-7 and MDA-MB-231 cells, computational toxicity and molecular docking. The average levels of progesterone and oestrogen in the MSG-treated animals significantly altered. Besides, the average uterine lumen area (μm²) was smaller than the control group. MSG showed high-affinity binding to acetylcholine receptors and disrupted the normal nerve signal with a predicted LD50 of 4500 mg/kg. MSG also demonstrated good binding affinity to human oestrogen receptors beta and some other proteins that have an oxidative stress role in the female reproductive organs. Therefore, a precaution should be taken when utilising this compound, especially for females under the risk factor of hormonal abnormality.

From Density Functional Theory to Conceptual Density Functional Theory and Biosystems

The position of conceptual density functional theory (CDFT) in the history of density functional theory (DFT) is sketched followed by a chronological report on the introduction of the various DFT descriptors such as the electronegativity, hardness, softness, Fukui function, local version of softness and hardness, dual descriptor, linear response function, and softness kernel. Through a perturbational approach they can all be characterized as response functions, reflecting the intrinsic reactivity of an atom or molecule upon perturbation by a different system, including recent extensions by external fields. Derived descriptors such as the electrophilicity or generalized philicity, derived from the nature of the energy vs. N behavior, complete this picture. These descriptors can be used as such or in the context of principles such as Sanderson’s electronegativity equalization principle, Pearson’s hard and soft acids and bases principle, the maximum hardness, and more recently, the minimum electrophilicity principle. CDFT has known an ever-growing use in various subdisciplines of chemistry: from organic to inorganic chemistry, from polymer to materials chemistry, and from catalysis to nanotechnology. The increasing size of the systems under study has been coped with thanks to methodological evolutions but also through the impressive evolution in software and hardware. In this flow, biosystems entered the application portfolio in the past twenty years with studies varying (among others) from enzymatic catalysis to biological activity and/or the toxicity of organic molecules and to computational peptidology. On the basis of this evolution, one can expect that “the best is yet to come”.

Imidazole and nitroimidazole derivatives as NADH-fumarate reductase inhibitors: Density functional theory studies, homology modeling, and molecular docking

Chagas disease is caused by Trypanosoma cruzi. Benznidazole and nifurtimox are drugs used for its therapy; nevertheless, they have collateral effects. NADH-fumarate (FUM) reductase is a potential pharmacological target since it is essential for survival of parasite and is not found in humans. The objectives are to design and characterize the electronic structure of imidazole and nitroimidazole derivatives at DFT-M06-2X level in aqueous solution; also, to model the NADH-FUM reductase and analyze its intermolecular interactions by molecular docking. Quantum-chemical descriptors allowed to select the molecules with the best physicochemical properties and lowest toxicity. A high-quality three-dimensional structure of NADH-FUM reductase was obtained by homology modeling. Water molecules do not have influence in the interaction between FUM and NADH-FUM reductase. The main hydrogen-binding interactions for FUM were identified in NADH, Lys172, and Arg89; while hydrophobic interactions in Phe479, Thr174, Met63. The molecules S3-8, S2-8, and S1-8 could be inhibitors of NADH-FUM reductase.

Exploring flexibility, intermolecular interactions and ADMET profiles of anti-influenza agent isorhapontigenin: A quantum chemical and molecular docking study

Isorhapontigenin (IRPG) drug emerges as promising efficient inhibitor for H1N1 and H3N2 subtypes which belong to influenza A virus; reported with IC₅₀ value of 35.62 and 63.50 μM respectively. When experimental data are compared to the predicted geometrical parameters and vibrational assignments (FT-IR and FT-Raman), the findings indicated a strong correlation. The absorption bands of π→π∗ transitions are revealed through UV-Vis electronic properties; this confirms that the IRPG molecule shows strong bands. Through NBO and HOMO-LUMO analysis, the kinetic stability and chemical reactivity of the IRPG molecule were investigated. By using an MEP map, the IRPG's electrophilic and nucleophilic site selectivity was assessed. In a molecular docking investigation, the IRPG molecule shows a stronger inhibition constant and binding affinity for the H1N1 and H3N2 influenza virus. The IRPG molecule thus reveals good biological actions in nature and can be used as a potential therapeutic drug candidate for H1N1 and H3N2 virus A influenza.

Evaluation of apigenin-based biflavonoid derivatives as potential therapeutic agents against viral protease (3CLpro) of SARS-CoV-2 via molecular docking, molecular dynamics and quantum mechanics studies

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic COVID-19 disease that affects human respiratory function. Despite the scientific progression made in the development of the vaccine, there is an urgent need for the discovery of antiviral drugs for better performance at different stages of SARS-CoV-2 reproduction. The main protease (Mpro or 3CLpro) plays a pivotal role in the life cycle of the virus, making it an attractive target for the development of antiviral agents effective against the new strains of coronaviruses (CoVs). In this study, a series of apigenin-based natural biflavonoid derivatives as potential inhibitors of coronaviruses 3CLpro was investigated by in silico approaches. For this purpose, the molecular docking was performed to analyze the interaction of the natural biflavonoids with SARS-Cov-2 main protease and for further investigation, docking to the 3CLpro of SARS-CoV and MERS-CoV. Based on docking scores and comparison with the reference inhibitors (ritonavir and lopinavir), more than half of the biflavonoids had strong interactions with the residues of the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward the main protease than ritonavir and lopinavir. The top biflavonoids were further explored through molecular dynamics simulation, binding free energy calculation and residual energy contributions estimated by the MM-PBSA. Also, drug likeness property investigation by Swiss ADME tools and density functional theory (DFT) calculations were performed. The results confirmed that the 3CLpro-amentoflavone, 3CLpro-bilobetin, 3CLpro-ginkgetin, and 3CLpro-sotetsuflavone complexes possess a large amount of dynamic properties such as high stability, significant binding energy and fewer conformation fluctuations. Also, the pharmacokinetics and drug-likeness studies and HOMO-LUMO and DFT descriptor values indicated a promising result of the selected natural biflavonoids. Overall findings indicate that the apigenin-based biflavonoids may inhibit COVID-19 by significant interactions in the binding pocket and those results can pave the way in drug discovery although the effectiveness of these bioactive compounds should be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma.

Spectroscopic, electronic structure, molecular docking, and molecular dynamics simulation study of 7-Trifluoromethyl-1H-indole-2-carboxylic acid as an aromatase inhibitor

The present work encompasses a combined experimental and theoretical investigation of the molecular structure, vibrational wavenumbers, electronic structure at the ground and electronic excited states, molecular electrostatic potential surface of 7-(Trifluoromethyl)-1H-indole-2-carboxylic acid (TICA) and possibility of the title molecule as an aromatase inhibitor using molecular docking and molecular dynamic simulations. A stable conformer has been obtained using potential energy scans by varying appropriate dihedral angles. The obtained minimum energy conformer was further optimized at the 6-311++G (d, p) basis set by applying the most accepted B3LYP functional. A good agreement between experimental and calculated normal modes of vibration has been observed. The hydrogen-bonded interaction between two monomeric units of TICA has been investigated using NBO,QTAIM, and NCI (noncovalent interactions) analysis. Molecular docking of TICA with human placental aromatase (PDB ID: 3S79) reveals the formation of polar hydrogen bonds as well as hydrophobic interactions between the ligand and the protein, right in the binding cavity. TICA satisfies all pharmacokinetic filters (Lipinski rule of five, the Veber rule, Ghose rule, Egan rule, as well as the Muegge rule) and has a high bioavailability score of 0.85. Dynamic stability of the ligand within the binding pocket of the target protein has been confirmed by 100 ns molecular dynamics simulation results. The present study provides an excellent starting point for additional in vivo research, and TICA may eventually serve as a significant therapeutic candidate for the treatment of breast cancer.

Sequence Analysis, Structure Prediction of Receptor Proteins and In Silico Study of Potential Inhibitors for Management of Life Threatening COVID-19

Background:

Treatment of the Covid-19 pandemic caused by the highly contagious and pathogenic SARS-CoV-2 is a global menace. Day by day, this pandemic is getting worse. Doctors, scientists and researchers across the world are urgently scrambling for a cure for novel corona virus and continuously working at break neck speed to develop vaccines or drugs. But to date, there are no specific drugs or vaccines available in the market to cope up with the virus.

Objective:

The present study helps us to elucidate 3D structures of SARS-CoV-2 proteins and also to identify natural compounds as potential inhibitors against COVID-19.

Methods:

The 3D structures of the proteins were constructed using Modeller 9.16 modeling tool. Modelled proteins were validated with PROCHECK by Ramachandran plot analysis. In this study, a small library of natural compounds (fifty compounds) was docked to the hACE2 binding site of the modelled surface glycoprotein of SARS-CoV-2 using AutoDock Vina to repurpose these inhibitors against SARS-CoV-2. Conceptual density functional theory calculations of the best eight compounds had been performed by Gaussian-09. Geometry optimizations for these molecules were done at M06-2X/ def2-TZVP level of theory. ADME parameters, pharmacokinetic properties and drug likeness of the compounds were analyzed using swissADME website.

Results:

In this study, we analysed the sequences of surface glycoprotein, nucleocapsid phosphoprotein and envelope protein obtained from different parts of the globe. We modelled all the different sequences of surface glycoprotein and envelop protein in order to derive 3D structure of a molecular target, which is essential for the development of therapeutics. Different electronic properties of the inhibitors have been calculated using DFT through M06-2X functional with def2-TZVP basis set. Docking result at the hACE2 binding site of all modelled surface glycoproteins of SARSCoV- 2 showed that all the eight inhibitors (actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) studied here were many folds better compared to hydroxychloroquine which has been found to be effective to treat patients suffering from COVID-19. All the inhibitors meet most of the criteria of drug likeness assessment.

Conclusion:

We expect that eight compounds (actinomycin D, avellanin C, ichangin, kanglemycin A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) can be used as potential inhibitors against SARS-CoV-2.

In Silico Approaches In Carcinogenicity Hazard Assessment: Current Status and Future Needs

Historically, identifying carcinogens has relied primarily on tumor studies in rodents, which require enormous resources in both money and time. In silico models have been developed for predicting rodent carcinogens but have not yet found general regulatory acceptance, in part due to the lack of a generally accepted protocol for performing such an assessment as well as limitations in predictive performance and scope. There remains a need for additional, improved in silico carcinogenicity models, especially ones that are more human-relevant, for use in research and regulatory decision-making. As part of an international effort to develop in silico toxicological protocols, a consortium of toxicologists, computational scientists, and regulatory scientists across several industries and governmental agencies evaluated the extent to which in silico models exist for each of the recently defined 10 key characteristics (KCs) of carcinogens. This position paper summarizes the current status of in silico tools for the assessment of each KC and identifies the data gaps that need to be addressed before a comprehensive in silico carcinogenicity protocol can be developed for regulatory use.

Theoretical Studies on the Molecular Properties, Toxicity, and Biological Efficacy of 21 New Chemical Entities

New chemical entities (NCEs) such as small molecules and antibody-drug conjugates have strong binding affinity for biological targets, which provide deep insights into structure-specific interactions for the design of future drugs. As structures of drugs increase in complexity, the importance of computational predictions comes into sharp focus. Knowledge of various computational tools enables us to predict the molecular properties, toxicity, and biological efficacy of the drugs and help the medicinal chemists to discover new drugs more efficiently. Newly approved drugs have higher affinities for proteins and nucleic acids and are applied for the treatment of human diseases. We have carried out the computational studies of 21 such NCEs, specifically small molecules and antibody-drug conjugates, and studied the biological efficacy of these drugs. Their bioactivity score and molecular and pharmacokinetic properties were evaluated using online computer software programs, viz., Molinspiration and Osiris Property Explorer. The SwissTargetPrediction tool was used for the efficient prediction of protein targets for the NCEs. The results indicated higher stability for the drug complexes due to a larger HOMO-LUMO gap. A high electrophilicity index reflects good electrophilic behavior and high reactivity of the drugs. Lipinski's ''rule of five'' indicated that most of the drug complexes are likely to be orally active. These drugs also showed non-mutagenic, non-tumorigenic, non-irritant, and non-effective reproductive behavior. We hope that these studies will provide an insight into molecular recognition and definitely help the medicinal chemists to design new drugs in future.

Synthesis, characterization, cytotoxicity studies, theoretical approach of adsorptive removal and molecular calculations of four new phosphoramide derivatives and related graphene oxide

In this study, four novel phosphoramide ligands (L1-L4) are synthesized and characterized by ³¹PNMR, ¹HNMR, MASS, and FT-IR spectroscopies. In vitro cell growth inhibition is studied by the MTT assay to evaluate the cytotoxicity of ligands against MCF-7 cell line; the result of the assay demonstrates that all ligands significantly suppress the proliferation of breast cancer cells in a concentration-dependent manner. The calculated IC₅₀ values are in the range of 3.6-10.77 µg ml^-1, of which the lowest value is attributed to L1. Then a facile approach was developed to functionalize graphene oxide (GO) surface by L1. The data which are obtained by XRD, FT-IR, and EDX analysis confirmed the deposition of phosphoramide on the surface of GO. The cell viability of GO-L1 compound at different concentrations is investigated in 24 h experiment. Excellent synergistic antitumor effects of GO and L1 lead to a decrease in IC₅₀ value up to 2.13 μg ml^-1. The Quantum calculations of compounds are used to study energies and HOMO and LUMO values, dipole moments (µ), global hardness (η), global softness (σ), and electrophilicity index (ω) using DMol³ module in Material studio2017. The docking calculations are performed to describe the mode of the binding to DNA and DNA polymerase IIα. Adsorption calculations of ligands (L1-L4) on GO sheet in the presence of water showed that L1 and L2 were located on GO via π electrons of anisole ring. While, L3 and L4 were located on GO by π - π interactions of aniline ring.

Theoretical modeling of structure-toxicity relationship of cyanides

The global descriptors of chemical activity: ionization potential IP, electron affinity EA, chemical potential μ, absolute electronegativity χ, molecular hardness η and softness S, electrophilicity index ω for cyanides X(CN)_k with X=H, Na, K, Ag, Cu, Ca, Hg, Cd, Zn in the gas phase and water medium have been determined by taking advantage of the quantum-chemical computations. To this aim, the HOMO and LUMO energy levels were calculated using DFT B3LYP method and QZVP (Valence Quadruple-Zeta Polarization) basis set, which enables precise calculations for hydrogen cyanide and its salts containing both light (H, Na, Ca) and heavy (K, Ag, Cu, Cd, Hg, Zn) atoms. The results obtained indicate that while the EA-parameter roughly determines the LD₅₀ values for the cyanides considered, the ω-descriptor is related rather to the product of cyanide LD₅₀ and hydrolysis n-degree. Hence, the theoretical LD₅₀^CN(ω) function proposed is interconnected with the n⸳LD₅₀ collective variable, whereas LD₅₀(EA) directly approximates LD₅₀ values indicating that the toxicity of cyanides decreases with increasing EA, ω-values. The calculations carried out suggest that some of the LD₅₀(Exp) experimentally determined are incorrect (AgCN) or inaccurate (Cd(CN)₂) and require revision. Comparison of the theoretically estimated LD₅₀(ω) with NOAEL toxicity parameters indicates that they are well correlated ​​in contrast to LD₅₀(EA)​​ and LD₅₀(Exp),​​ exhibiting lower and marginal degrees of correlation, respectively.

Conceptual density functional theory based electronic structure principles

In this review article, we intend to highlight the basic electronic structure principles and various reactivity descriptors as defined within the premise of conceptual density functional theory (CDFT). Over the past several decades, CDFT has proven its worth in providing valuable insights into various static as well as time-dependent physicochemical problems. Herein, having briefly outlined the basics of CDFT, we describe various situations where CDFT based reactivity theory could be employed in order to gain insights into the underlying mechanism of several chemical processes.

Monophosphoramide derivatives: synthesis and crystal structure, theoretical and experimental studies of their biological effects

Synthesizing new chemical compounds and studying their biological applications have been important issues in scientific research. In this investigation, we synthesized and characterized ten new N-acetyl phosphoramidate compounds and explored the crystal structure of three others. Furthermore, not only were some kinetic inhibition parameters measured, like IC₅₀, K_i, k_p, K_D for 7 compounds on human acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), but also their hydrophobic parameter was determined by shake-flask technique. All compounds (number 1-10) were investigated for anti-bacterial activity against three Gram-positive and three Gram-negative bacteria, while chloramphenicol was used as a standard antibiotic. In order to find new insecticide, toxicities of 13 acephate (Ace)-derived compounds (number 20-32) were bioassayed on third larval instar of elm leaf beetle and Xanthogaleruca luteola. Additionally, screening in vivo tests revealed that two compounds had had the greatest insecticidal potential in comparison with others. It means these ones inhibited AChE (with mixed mechanisms) and general esterase more than the rest. According to ChE-QSAR models, the inhibitory potency for enzyme and bacteria is directly influenced by the electronic parameters versus structural descriptors. AChE-QSPR model of fluorescence assay indicated that the inhibitory power of AChE is primarily influenced by a set of electronic factors with the priority of: E_HB > PL > δ(³¹P) versus structural descriptor (SA and Mv). Synthesizing new chemical compounds and studying their biological applications have been important issues in scientific research. Toxicities of 13 acephate (Ace)-derived compounds (number 20-32) were bioassayed on third larval instar of elm leaf beetle and Xanthogaleruca luteola. Insect-QSAR equations of these compounds, based on MLR and PCA, showed that non-descriptor net charge nitrogen atom (which was affected by the polarization of N-H group) had the greatest effect on insecticidal potential.

Green Synthesis, SC-XRD, Non-Covalent Interactive Potential and Electronic Communication via DFT Exploration of Pyridine-Based Hydrazone

Ultrasound-based synthesis at room temperature produces valuable compounds greener and safer than most other methods. This study presents the sonochemical fabrication and characterization of a pyridine-based halogenated hydrazone, (E)-2-((6-chloropyridin-2-yl)oxy)-N′-(2-hydroxybenzylidene) acetohydrazide (HBPAH). The NMR spectroscopic technique was used to determine the structure, while SC-XRD confirmed its crystalline nature. Our structural studies revealed that strong, inter-molecular attractive forces stabilize this crystalline organic compound. Moreover, the compound was optimized at the B3LYP/6-311G(d,p) level using the Crystallographic Information File (CIF). Natural bonding orbital (NBO) and natural population analysis (NPA) were performed at the same level using optimized geometry. Time-dependent density functional theory (DFT) was performed at the B3LYP/6-311G (d,p) method to calculate the frontier molecular orbitals (FMOs) and molecular electrostatic potential (MEP). The global reactivity descriptors were determined using HOMO and LUMO energy gaps. Theoretical calculations based on the Quantum Theory of Atoms in Molecules (QT-AIM) and Hirshfeld analyses identified the non-covalent and covalent interactions of the HBPAH compound. Consequently, QT-AIM and Hirshfeld analyses agree with experimental results.

How the ascorbic acid and hesperidin do improve the biological activities of the cinnamon: theoretical investigation

DFT/B3LYP calculations have been performed on series of molecules of natural products containing cinnamon and citrus, namely, cinnamic aldehyd, ascorbic acid and hesperidin. This theoretical investigation predicts the biological activities of mixtures between cinnamon and ascorbic acid and between cinnamon and hesperidin based on already proven values for these molecules. The strength of the intermolecular interactions is evaluated in term of energy decomposition of the total interaction energy ΔE _int between molecules, which are mainly governed by electrostatic interactions. The HOMO-LUMO gaps explain that the possible charge transfer interactions that take place within the molecules are responsible for the molecular reactivity of the studied molecules. The chemical hardness, the chemical potential and the electrophilicity indexes are good indicators for biological activities showing their improvement to that of cinnamon itself. The mixture of hesperidin and cinnamon could be an excellent blood thinner with the regard to its polarity's enhancement.

Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4-dichlorodiuron

A set of experimental and computational techniques have been applied for the understanding of fundamental spectroscopic and reactive properties of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (diuron) compound. Experimental techniques employed in this study encompassed spectroscopic characterization via IR and Raman approaches, while optical properties were studied by measurements of UV/Vis spectra. The thermogravimetric analysis was also studied in order to analyze the stability of diuron. Aside from the determination of reactive properties, DFT calculations on isolated molecules were also used to thoroughly visualize and analyze spectroscopic properties such as IR and UV/Vis. MD simulations were used in order to understand interactions with water, while periodic DFT calculations were used in order to analyze band structure and density of states of the diuron crystal structure. Since the crystal structure of diuron is known, it was used in order to extract the relevant molecular pairs and investigate interactions between them by DFT and symmetry adapted perturbation theory approaches (SAPT).

An Electronic-structure Informatics Study on the Toxicity of Alkylphenols to Tetrahymena pyriformis

Alkylphenols (APs) dissolved in water are known to be toxic to animals including humans. In this study, regression models describing the toxicity of the 33 AP molecules were investigated for reproducing and thereby making it possible to predict a quantitative structure-activity relationship (QSAR). For this purpose, we tried to derive regression models for the experimental IGC₅₀ (growth inhibition concentration at 50 %) to Tetrahymena pyriformis by using various descriptor sets consisting of electronic and shape descriptors. By applying the multiple linear regression (MLR) analysis, it was successful to derive a quantitative regression model for the IGC₅₀ values. In this analysis, the size parameters of the molecules were found important, suggesting that bulky molecules should be less toxic. We could also obtain, when the size descriptors were excluded, an MLR model indicating that the electron affinity (EA) should be important, which is consistent with the previous QSAR studies. Through the correlation analysis among the descriptors, it was shown that, in the present set of molecules, EA and a size parameter are highly correlated. Since EA was calculated to be negative, indicating that the related process would be energetically unfavourable, it was concluded that the size of the molecules should be a dominant factor determining IGC₅₀ . This implies that a molecular recognition process would play a critical role in the mode of action for the toxicity.

A model of atomic compressibility and its application in QSAR domain for toxicological property prediction

A model for computing the atomic compressibility (β) based on two periodic descriptors, namely, absolute radius (r) and atomic electrophilicity index (ω), is proposed as[Formula: see text]The ansatz is invoked to compute compressibilities of atoms of 57 elements of the periodic table. The computed atomic data exhibits all sine qua non of periodic properties. Further, the concept group compressibility (Gβ) is also established invoking additivity property using some molecules with different functional groups and consequently utilized in correlating with molecular polarizability. Since toxicity prediction is an imperative need of the hour, chemical reactivity descriptors are of paramount importance in the study of toxicological behaviour along with a lot of other molecular reactivity studies within a Quantitative Structure-Activity Relationship (QSAR) context. Hence, this quantity is applied in the modelling of toxicological property through QSAR and a comprehensive study is performed in an effort to investigate and validate the application of compressibility in determining its toxicological power. Consequently, varied 209 organic molecules are selected for studying the toxic effect on Tetrahymena pyriformis. A QSAR model is constructed in terms of compressibility which offers a superior prediction of toxicity independently without adopting additional descriptors or properties as in some other QSAR studies. Graphical abstract.

Exploring the Binding Interaction Mechanism of Taxol in β-Tubulin and Bovine Serum Albumin: A Biophysical Approach

In this present study on understanding the taxol (PTX) binding interaction mechanism in both the β-tubulin and bovine serum albumin (BSA) molecule, various optical spectroscopy and computational techniques were used. The fluorescence steady-state emission spectroscopy result suggests that there is a static quenching mechanism of the PTX drug in both β-tubulin and BSA, and further time-resolved emission spectroscopy studies confirm that the quenching mechanism exists. The excitation-emission matrix (EEM), Fourier transform infrared, and resonance light scattering spectra (FT-IR) confirm that there are structural changes in both the BSA and β-tubulin molecule during the binding process of PTX. The molecular docking studies revealed the PTX binding information in BSA, β-tubulin, and modeled β-tubulin and the best binding pose to further subject the molecular dynamics simulation, and this study confirms the stability of PTX in the protein complex during the simulation. Density functional theory (DFT) calculations were performed between the free PTX drug and PTX drug (single point) in the protein molecule active site region to understand the internal stability.

Comparative Binding Analysis of N-Acetylneuraminic Acid in Bovine Serum Albumin and Human α-1 Acid Glycoprotein

The present study focuses on the determination of the biologically significant N-acetylneuraminic acid (NANA) drug binding interaction mechanism between bovine serum albumin (BSA) and human α-1 acid glycoprotein (HAG) using various optical spectroscopy and computational methods. The steady state fluorescence spectroscopy result suggests that the fluorescence intensity of BSA and HAG was quenched by NANA in a static mode of quenching. Further time-resolved emission spectroscopy measurements confirm that mode of quenching mechanism of NANA in the BSA and HAG system. The FT-IR, excitation-emission matrix and circular dichroism (CD) analysis confirms the presence of NANA in the HAG, BSA system, and fluorescence resonance energy transfer analysis shows that NANA transfers energy between the HAG and BSA system. The molecular docking result shows good binding affinity in both protein complexes, and further molecular dynamics simulations and charge distribution analysis were performed to gain more insight into the binding interaction mechanism of NANA in the HAG and BSA complex.

Toxicity of polyhalogenated dibenzo-p-furans in the light of nucleic acid bases interaction

Quantitative structure-activity relationship (QSAR) investigation utilizing quantum chemical descriptors under density functional theory is performed to predict the toxicity (pEC₅₀) of a series of polyhalogenated dibenzo-p-furans (PHDFs). PHDFs are very important concern to the researchers due to their presence and diverse effects in the environment. A successful two parameter QSAR model is developed with a combination of a global descriptor known as charge transfer (ΔN) between toxins and biosystem and a local descriptor as Fukui function (f_max⁺) for maximum nucleophilic attack at the toxin site. A systematic analysis is performed to identify the electron donation/acceptance nature of the considered PHDF compounds with the choice of a model biosystems comprising five different nucleic acid bases, namely Adenine, Thymine, Guanine, Cytosine and Uracil to identify proper ΔN descriptor. Accordingly, PHDFs are found to be electron acceptors with maximum charge transfer from Guanine and therefore, ΔN_G is utilized as the charge transfer parameter for all the toxins in the present work. The selected combination of global and local descriptors (ΔN_G andf_max⁺) are found to predict 93% of the observed toxicity (pEC₅₀) of the PHDFs. The developed QSAR model is tested for two different test sets: PHDFs and polyhalogenated biphenyls (PHBs) with about 90% of prediction of their toxicity values, which confirms the importance of the selected descriptors.

Bio-activity of aminosulfonyl ureas in the light of nucleic acid bases and DNA base pair interaction

The quantum chemical descriptors based on density functional theory (DFT) are applied to predict the biological activity (log IC₅₀) of one class of acyl-CoA: cholesterol O-acyltransferase (ACAT) inhibitors, viz. aminosulfonyl ureas. ACAT are very effective agents for reduction of triglyceride and cholesterol levels in human body. Successful two parameter quantitative structure-activity relationship (QSAR) models are developed with a combination of relevant global and local DFT based descriptors for prediction of biological activity of aminosulfonyl ureas. The global descriptors, electron affinity of the ACAT inhibitors (EA) and/or charge transfer (ΔN) between inhibitors and model biosystems (NA bases and DNA base pairs) along with the local group atomic charge on sulfonyl moiety (∑Q_Sul) of the inhibitors reveals more than 90% efficacy of the selected descriptors for predicting the experimental log (IC₅₀) values.

Effect of Constituent Units, Type of Interflavan Bond, and Conformation on the Antioxidant Properties of Procyanidin Dimers: A Computational Outlook

Procyanidin (PC) dimers are powerful antioxidants, abundant in plant tissues, and also bioavailable. However, the role of the molecular structure of PCs on their antioxidant properties is still a controversial and not fully understood issue that needs to be addressed in a more specific way. The objective of this study was to analyze the effect of the constituent units, type of interflavan bond, and conformation on the antioxidant properties of PC dimers including PB3, PB4, PB5, PB6, PB7, and PB8, using the density functional theory (DFT) computational method. The analysis was performed in function of parameters that allow determining the ability of the molecules to transfer or to capture electrons, among which the chemical potential, bond dissociation enthalpy (BDE), gap energy, Fukui indices, and charge distribution of HOMO-LUMO orbitals. The factors that showed the most notable effects on the antioxidant properties of the PC dimers were the type of interflavan bond and the conformation. The antioxidant ability of the dimers PB3 and PB4 containing the interflavan bond C4–C8, in their Compact conformation, was very similar to each other but greater than those of dimers PB5, PB6, PB7, and PB8 containing the C4–C6 interflavan bond. PB8 showed the lowest antioxidant ability.

Quantitative Structure-Activity/Property/Toxicity Relationships through Conceptual Density Functional Theory-Based Reactivity Descriptors

Developing effective structure-activity/property/toxicity relationships (QSAR/QSPR/QSTR) is very helpful in predicting biological activity, property, and toxicity of a given set of molecules. Regular change in these properties with the structural alteration is the main reason to obtain QSAR/QSPR/QSTR models. The advancement in making different QSAR/QSPR/QSTR models to describe activity, property, and toxicity of various groups of molecules is reviewed in this chapter. The successful implementation of Conceptual Density Functional Theory (CDFT)-based global as well as local reactivity descriptors in modeling effective QSAR/QSPR/QSTR is highlighted.