Thio Analogues of Pyrimidine Bases: Syntheses and Spectral Study of New Potentially Biologically Active 2,4-Di-Ortho-(Meta- and Para-)Bromo- (Chloro and Nitro)-Benzylthio-5-Bromouracils (and 6-Methyluracils)

Eighteen new 2,4-di-ortho- (meta- and para-) bromo-(chloro- and nitro-)benzylthio-5-bromouracils (and 6-methyluracils) have been prepared. The structures of these compounds were confirmed by spectral (IR, UV/vis, ¹H NMR) and elemental analyses. Estimation of pharmacotherapeutic potential has been made for synthesized compounds on the basis of prediction of activity spectra for substances (PASS).     

Ruellia prostrata Poir. activity evaluated by phytoconstituents,antioxidant, anti-inflammatory,antibacterial activity,and in silico molecular functions

Ruellia prostrata Poir. has been used historically as an anti-cancer, wound healing agent and to treat gonorrhea. We aimed to determine the phytochemicals present in ethyl acetate extract of R. prostrata Poir. (EAERP). We sought to determine the antioxidant, anti-inflammatory, and antibacterial activities in vitro, and toxicity properties in vivo. We also analyzed the Prediction of Activity Spectra for Substances (PASS), physicochemical, ADMET, and drug-likeness properties of phytochemicals in EAERP. To determine phytoconstituents, preliminary phytochemical screening and GC–MS were performed, while FT-IR was used to identify functional groups. The antioxidant activity was evaluated using a DPPH scavenging assay, whereas BSA denaturation and RBC hemolysis inhibition were used to assess anti-inflammatory activity. An agar-well-diffusion assay was performed to estimate the antibacterial activity. Brine shrimp lethality bioassay and oral delivery of EAERP of single-dose were performed to determine cytotoxicity and acute toxicity, respectively. The phytochemical screening revealed the presence of phenols, triterpenoids, saponins, steroids, amino acids, and fat and fixed oils. FT-IR analysis of EAERP showed the presence of many functional groups: alcohols/phenols, carboxylic acids, aldehydes, alkanes, esters, amines, amides, aromatic hydrocarbons, sulfoxides, and alkyl halides. GC–MS revealed the presence of 39 phytoconstituents including steroids, consistent with compounds and functional groups found in preliminary screening and FT-IR. EAERP showed dose-dependent antioxidant activity with an IC₅₀ value of 21.402 µg/mL and anti-inflammatory activity with an IC₅₀ value of 20.564 µg/mL in RBC hemolysis inhibition and 21.115 µg/mL in BSA denaturation assays. EAERP also exhibited dose-related antibacterial activity. EAERP exerted cytotoxicity with an LC₅₀ value of 17.619 μg/mL and acute toxicity with an LD₅₀ value of 4095.328 mg/kg without any adverse effects. The PASS server also predicted that the phytoconstituents of EAERP have antioxidant, anti-inflammatory, and antibacterial activities with probable activity (Pa) ranging from 0.310 to 0.717. Analysis of physicochemical, ADMET, and drug-likeness properties revealed the drug-able efficacy and safety of most compounds. The findings of this study indicated that R. prostrata Poir. contains phytoconstituents with potent antioxidant, anti-inflammatory, and antibacterial activities. Taken together, our measurements suggest that R. prostrata Poir. is a prime candidate for further exploration as a potential therapeutic agent.     

How to acquire new biological activities in old compounds by computer prediction

Due to the directed way of testing chemical compounds' in drug research and development many projects fail because serious adverse effects and toxicity are discovered too late, and many existing prospective activities remain unstudied. Evaluation of the general biological potential of molecules is possible using a computer program PASS that predicts more than 780 pharmacological effects, mechanisms of action, mutagenicity, carcinogenicity, etc. on the basis of structural formulae of compounds, with average accuracy 85%. PASS applications to both databases of available samples included hundreds of thousands compounds, and small collections of compounds synthesized by separate medicinal chemists are described. It is shown that 880 compounds from Prestwick chemical library represent a very diverse pharmacological space. New activities can be found in existing compounds by prediction. Therefore, on this basis, the selection of compounds with required and without unwanted properties is possible. Even when PASS cannot predict very new activities, it may recognize some unwanted actions at the early stage of R&D, providing the medicinal chemist with the means to increase the efficiency of projects.     

Application of cogwheel phase cycling to sideband manipulation experiments in solid-state NMR

Cogwheel phase-cycling schemes are applied to sideband suppression and sideband separation experiments in solid-state NMR. It is shown that cogwheel phase cycles lead to the elimination of most pulse imperfection effects, while using far fewer experimental signal acquisitions than conventional phase-cycling methods.     

PASS-based prediction of metabolites detection in biological systems

ABSTRACT

Metabolite identification is an essential part of the drug discovery and development process. Experimental methods allow identifying metabolites and estimating their relative amount, but they require cost-intensive and time-consuming techniques. Computational methods for metabolite prediction are devoid of these shortcomings and may be applied at the early stage of drug discovery. In this study, we investigated the possibility of creating SAR models for the prediction of the qualitative metabolite yield (‘major’, ‘minor’, ”trace” and ”negligible”) depending on species and biological experimental systems. In addition, we have created models for prediction of xenobiotic excretion depending on its administration route for different species. The prediction is based on an algorithm of naïve Bayes classifier implemented in PASS software. The average accuracy of prediction was 0.91 for qualitative metabolite yield prediction and 0.89 for prediction of xenobiotic excretion. The created models were included as a component of MetaTox web application, which allows predicting the xenobiotic metabolism pathways (http://www.way2drug.com/mg).     

Synthesis,Antimicrobial, Anticancer,PASS, Molecular Docking,Molecular Dynamic Simulations & Pharmacokinetic Predictions of Some Methyl β-D-Galactopyranoside Analogs

A series of methyl β-D-galactopyranoside (MGP, 1) analogs were selectively acylated with cinnamoyl chloride in anhydrous N,N-dimethylformamide/triethylamine to yield 6-O-substitution products, which was subsequently converted into 2,3,4-tri-O-acyl analogs with different acyl halides. Analysis of the physicochemical, elemental, and spectroscopic data of these analogs revealed their chemical structures. In vitro antimicrobial testing against five bacteria and two fungi and the prediction of activity spectra for substances (PASS) showed promising antifungal functionality comparing to their antibacterial activities. Minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) tests were conducted for four compounds (4, 5, 6, and 9) based on their activity. MTT assay showed low antiproliferative activity of compound 9 against Ehrlich’s ascites carcinoma (EAC) cells with an IC₅₀ value of 2961.06 µg/mL. Density functional theory (DFT) was used to calculate the thermodynamic and physicochemical properties whereas molecular docking identified potential inhibitors of the SARS-CoV-2 main protease (6Y84). A 150-ns molecular dynamics simulation study revealed the stable conformation and binding patterns in a stimulating environment. In-silico ADMET study suggested all the designed molecules to be non-carcinogenic, with low aquatic and non-aquatic toxicity. In summary, all these antimicrobial, anticancer and in silico studies revealed that newly synthesized MGP analogs possess promising antiviral activity, to serve as a therapeutic target for COVID-19.     

Computer-aided prediction and cytotoxicity evaluation of dithiocarbamates of 9,10-anthracenedione as new anticancer agents

Anticancer activity as an associated action for a series of dithiocarbamates of 9,10-anthracenedione was predicted using the PASS computer program and analysed with PharmaExpert software. The predicted cytotoxic activity of the dithiocarbamate derivatives of 9,10-anthracenedione was evaluated in vitro on cancer cells of the human lung (A549), prostate (PC3), colon (HT29) and human breast (MCF7) using the sulforhodamine B (SRB) cell viability assay. Among these compounds, 9,10-dioxo-9,10-dihydroanthracen-1-yl pyrrolidin-1-carbodithioate and 9,10-dioxo-9,10-dihydroanthracen-2-yl pyrrolidin-1-carbodithioate were identified as the most potent anticancer agents with cytotoxic activity against the MCF-7 human breast cell line with GI₅₀ values of 1.40 μM and 1.52 μM, whereas the GI₅₀ value for the reference anticancer drug mitoxantrone was 3.93 μM. Thus, anticancer activity predicted by PASS with a probability Pa > 30% was confirmed by the experiment. Relatively small Pa values estimated by PASS indicated the novelty of the considered derivatives comparing to the compounds from the PASS training set.     

Solid-state NMR studies and DFT calculations of flavonoids: baicalein, baicalin and wogonoside

Three flavonoids of pharmaceutical importance-baicalein, baicalin, and wogonoside-were isolated from a Chinese medicinal plant Scutellaria baicalensis Georgi and studied by 13C NMR in solution and solid state. Two-dimensional (2D) NMR spectroscopy in the liquid phase and dipolar dephasing (DD) experiments in magic-angle spinning (MAS) spectra enabled the assignment of 13C resonances. The cross-polarization (CP) time constants T(CH) and relaxation times T(H) (1rho) were obtained from the variable-contact time experiments. The principal elements of the 13C chemical shift tensor were determined in the spectra recorded under slow sample spinning (2 kHz) using phase-adjusted spinning sideband (PASS)-2D NMR technique, and were verified by density functional theory gauge-independent atomic orbital (DFT GIAO) calculations of shielding constants. Analysis of the 13C delta(ii) and comparison with shielding parameters calculated for different conformers of compounds 1-3 enabled the selection of the most reliable geometry in the solid phase. In all three compounds, an intramolecular hydrogen bond C5--OH...=C4 is formed; the existence of baicalein and baicalin with 'anticlockwise' orientation of OH groups is more probable.