Identification of a novel dual-target scaffold for 3CLpro and RdRp proteins of SARS-CoV-2 using 3D-similarity search, molecular docking, molecular dynamics and ADMET evaluation.

The new SARS-CoV-2 coronavirus is the causative agent of the COVID-19 pandemic outbreak that affected whole the world with more than 6 million confirmed cases and over 370,000 deaths. At present, there are no effective treatments or vaccine for this disease, which constitutes a serious global health crisis. As the pandemic still spreading around the globe, it is of interest to use computational methods to identify potential inhibitors for the virus. The crystallographic structures of 3CLpro (PDB: 6LU7) and RdRp (PDB 6ML7) were used in virtual screening of 50000 chemical compounds obtained from the CAS Antiviral COVID19 database using 3D-similarity search and standard molecular docking followed by ranking and selection of compounds based on their binding affinity, computational techniques for the sake of details on the binding interactions, absorption, distribution, metabolism, excretion, and toxicity prediction; we report three 4-(morpholin-4-yl)-1,3,5-triazin-2-amine derivatives; two compounds (2001083-68-5 and 2001083-69-6) with optimal binding features to the active site of the main protease and one compound (833463-19-7) with optimal binding features to the active site of the polymerase for further consideration to fight COVID-19. The structural stability and dynamics of lead compounds at the active site of 3CLpro and RdRp were examined using molecular dynamics (MD) simulation. Essential dynamics demonstrated that the three complexes remain stable during simulation of 20 ns, which may be suitable candidates for further experimental analysis. As the identified leads share the same scaffold, they may serve as promising leads in the development of dual 3CLpro and RdRp inhibitors against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

3D QSAR studies, molecular docking and ADMET evaluation, using thiazolidine derivatives as template to obtain new inhibitors of PIM1 kinase.

Proviral Integration site for Moloney murine leukemia virus-1 (PIM1) belongs to the serine/threonine kinase family of Ca2+-calmodulin-dependent protein kinase (CAMK) group, which is involved in cell survival and proliferation as well as a number of other signal transduction pathways. Thus, PIM1 is regarded as a promising target for treatment of cancers. In the present paper, a three-dimensional quantitative structure activity relationship (3D-QSAR) and molecular docking were performed to investigate the binding between PIM1 and thiazolidine inhibitors in order to design potent inhibitors. The comparative molecular similarity indices analysis (CoMSIA) was developed using twenty-six molecules having pIC50 ranging from 8.854 to 6.011 (IC50 in nM). The best CoMSIA model gave significant statistical quality. The determination coefficient (R2) and Leave-One-Out cross-validation coefficient (Q2) are 0.85 and 0.58, respectively. Furthermore, the predictive ability of this model was evaluated by external validation((n = 11, R2test = 0.72, and MAE = 0.170 log units). The graphical contour maps could provide structural features to improve inhibitory activity. Furthermore, a good consistency between contour maps and molecular docking strongly demonstrates that the molecular modeling is reliable. Based on these satisfactory results, we designed several new potent PIM1 inhibitors and their inhibitory activities were predicted by the molecular models. Additionally, those newly designed inhibitors, showed promising results in the preliminary in silico ADMET evaluations, compared to the best inhibitor from the studied dataset. The results expand our understanding of thiazolidines as inhibitors of PIM1 and could be of great help in lead optimization for early drug discovery of highly potent inhibitors.

QSAR study and rustic ligand-based virtual screening in a search for aminooxadiazole derivatives as PIM1 inhibitors.

BACKGROUND: Quantitative structure-activity relationship (QSAR) was carried out to study a series of aminooxadiazoles as PIM1 inhibitors having pki ranging from 5.59 to 9.62 (k i in nM). The present study was performed using Genetic Algorithm method of variable selection (GFA), multiple linear regression analysis (MLR) and non-linear multiple regression analysis (MNLR) to build unambiguous QSAR models of 34 substituted aminooxadiazoles toward PIM1 inhibitory activity based on topological descriptors. RESULTS: Results showed that the MLR and MNLR predict activity in a satisfactory manner. We concluded that both models provide a high agreement between the predicted and observed values of PIM1 inhibitory activity. Also, they exhibit good stability towards data variations for the validation methods. Furthermore, based on the similarity principle we performed a database screening to identify putative PIM1 candidates inhibitors, and predict their inhibitory activities using the proposed MLR model. CONCLUSIONS: This approach can be easily handled by chemists, to distinguish, which ones among the future designed aminooxadiazoles structures could be lead-like and those that couldn't be, thus, they can be eliminated in the early stages of drug discovery process.

Computer aided drug design based on 3D-QSAR and molecular docking studies of 5-(1H-indol-5-yl)-1,3,4-thiadiazol-2-amine derivatives as PIM2 inhibitors: a proposal to chemists.

PIM2 kinase plays a crucial role in the cell cycle events including survival, proliferation, and differentiation in normal and neoplastic neuronal cells. Thus, it is regarded as an essential target for cancer pharmaceutical. Design of novel 5-(1H-indol-5-yl)-1,3,4-thiadiazol-2-amine derivatives with enhanced PIM2 inhibitory activity. A series of twenty-five PIM2 inhibitors reported in the literature containing 5-(1H-indol-5-yl)-1,3,4-thiadiazol-2-amines scaffold was studied by using two computational techniques, namely, three-dimensional quantitative structure activity relationship (3D-QSAR) and molecular docking. The comparative molecular field analysis (CoMFA) and comparative molecular similarity indexes analysis (CoMSIA) studies were developed using nineteen molecules having pIC50 ranging from 8.222 to 4.157. The best generated CoMFA and CoMSIA models exhibit conventional determination coefficients R2 of 0.91 and 0.90 as well as the Leave One Out cross-validation determination coefficients Q2 of 0.68 and 0.62, respectively. Moreover, the predictive ability of those models was evaluated by the external validation using a test set of six compounds with predicted determination coefficients Rtest 2 of 0.96 and 0.96, respectively. Besides, y-randomization test was also performed to validate our 3D-QSAR models. The most and the least active compounds were docked into the active site of the protein (PDB ID: 4 × 7q) to confirm those obtained results from 3D-QSAR models and elucidate the binding mode between this kind of compounds and the PIM2 enzyme. These satisfactory results are not offered help only to understand the binding mode of 5-(1H-indol-5-yl)-1,3,4-thiadiazol series compounds into this kind of targets, but provide information to design new potent PIM2 inhibitors.

QSAR studies on PIM1 and PIM2 inhibitors using statistical methods: a rustic strategy to screen for 5-(1H-indol-5-yl)-1,3,4-thiadiazol analogues and predict their PIM inhibitory activity.

BACKGROUND: Quantitative structure activity relationship was carried out to study a series of PIM1 and PIM2 inhibitors. The present study was performed on twenty-five substituted 5-(1H-indol-5-yl)-1,3,4-thiadiazols as PIM1 and PIM2 inhibitors having pIC50 ranging from 5.55 to 9 µM and from 4.66 to 8.22 µM, respectively, using genetic function algorithm for variable selection and multiple linear regression analysis (MLR) to establish unambiguous and simple QSAR models based on topological molecular descriptors. RESULTS: Results showed that the MLR predict activity in a satisfactory manner for both activities. Consequently, the aim of the current study is twofold, first, a simple linear QSAR model was developed, which could be easily handled by chemist to screen chemical databases, or design for new potent PIM1 and PIM2 inhibitors. Second, the outcomes extracted from the current study were exploited to predict the PIM inhibitory activity of some studied compound analogues. CONCLUSIONS: The goal of this study is to develop easy and convenient QSAR model could be handled by everyone to screen chemical databases or to design newly PIM1 and PIM2 inhibitors derived from 5-(1H-indol-5-yl)-1,3,4-thiadiazol. Graphical abstract Flow chart of the methodology used in this work.

Total Fluorescence Fingerprinting of Pesticides: A Reliable Approach for Continuous Monitoring of Soils and Waters.

The present work relates to the creation/extension of a database of Total Excitation-Emission and Total Synchronous Fluorescence Matrices (TEEMs and TSFMs) along with optimal Synchronous Fluorescence Spectra (SFS) to fingerprint pesticides widely used in Morocco. This spectrometric multi-component fingerprinting may permit the direct detection of pesticides persisting in soil or water. The objective of the current investigation is to detect four pesticide remains in agricultural soils by applying the spectrometric fingerprinting results. They are the commercial: i) insecticide Axlera 5G (carbamate), ii) fungicide Orsalis 5% SC (triazole), iii) insecticide Force 0,5 G (pyrethrinoid) and iv) insecticide Proclaim 05 SG (non-assigned). The agricultural plantations monitored are located in the great agricultural Doukkala region at the western Atlantic side of Morocco, where these chemicals are in large sale and use.

Catalog of total excitation-emission and total synchronous fluorescence maps with synchronous fluorescence spectra of homologated fluorescent pesticides in large use in Morocco: development of a spectrometric low cost and direct analysis as an alert method in case of massive contamination of soils and waters by fluorescent pesticides.

The purpose of this research is to develop a direct spectrometric approach to monitor soils and waters, at a lower cost than the widely used chromatographic techniques; a spectrometric approach that is effective, reliable, fast, easy to implement, and without any use of organic solvents whose utilization is subject to law limitation. It could be suitable at least as an alert method in case of massive contamination. Here, we present for the first time a catalog of excitation-emission and total synchronous fluorescence maps that may be considered as fingerprints of a series of homologated pesticides, in large use in Morocco, aiming at a direct detection of their remains in agricultural soils and neighboring waters. After a large survey among farmers, agricultural workers and product distributors in two important agricultural regions of Morocco (Doukkala-Abda and Sebou basin), 48 commercial pesticides, which are fluorescent, were chosen. A multi-component spectral database of these targeted commercial pesticides was elaborated. For each pesticide, dissolved in water at the lowest concentration giving a no-noise fluorescence spectrum, the total excitation-emission matrix (TEEM), the total synchronous fluorescence matrix (TSFM) in addition to synchronous fluorescence spectra (SFS) at those offsets giving the highest fluorescence intensity were recorded. To test this preliminary multi-component database, two real soil samples, collected at a wheat field and at a vine field in the region of Doukkala, were analyzed. Remains of the commercial Pirimor (Carbamate) and Atlantis (Sulfonylurea) were identified by comparison of the recorded TEEM, TSFM, and SFS to those of the preliminary catalog at one hand, and on the basis of the results of a field pre-survey. The developed approach seems satisfactory, and the fluorimetric fingerprint database is under extension to a higher number of fluorescent pesticides in common use among the Moroccan agricultural regions.

Photophysics of Genistein isoflavone: Solvent and concentration effects studied by UV-visible spectroscopy and theoretical simulation.

Genistein isoflavone is shown to exist in two different conformations which are the 90 degrees completely twisted geometry and the 50 degrees less twisted one. Specific interactions with the solvent cage as well as self-association processes seem shifting the isoflavone from the perpendicular conformation towards the less twisted one. The theoretical simulation, using analytical atom-atom pair potential, predicts a self-dimer in a slipped non-sandwich, face to river, perpendicular structure. From the UV-visible photophysics investigations it is revealed that monomeric species cannot exist alone even at very low solute concentration (approximately 10(-6) M), the self-association process occurs already in this concentration range.