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In Silico Docking of Rhodanine Derivatives and 3D-QSAR Study to Identify Potent Prostate Cancer Inhibitors

Computational Chemistry 2022年第2期10卷 19-52页

作者： Koffi Alexis Respect Kouassi Adenidji Ganiyou Diomande Gbe Gondo Didier Anoubilé Benié Ziao Nahossé Laboratoire de Thermodynamique et de Physico-Chimie du Milieu UFR SFA Université Nangui Abrogoua Abidjan C&#244 te d’Ivoire Laboratoire de Constitution et de Réaction de la matière UFR-SSMT Université Félix Houphou&#235 t-Boigny Abidjan C&#244 te d’Ivoire Laboratoire de Chimie Bio-Organique et de Substances Naturelles UFR-SFA Université Nangui Abrogoua Abidjan C&#244 te d’Ivoire

The 3VHE protein is considered as a potential target for the treatment of prostate cancer. In order to find new 3VHE inhibitors, pharmacophore models based on the molecular structure of rhodanine derivatives and a three-dimensional quantitative structure-activity relationship model (3D-QSAR) have been developed and validated by different methods. The 3D-QSAR model was evaluated for its predictive performance on a diverse test set containing 18 prostate cancer inhibitors. It presents very interesting internal and external statistical validation parameters (SD = 0.081;R2 = 0.903;Q2 = 0.869;;F = 247.2). This result suggests that the 3D-QSAR combinatorial model can be used to search for new 3VHE inhibitors and predict their potential activity. Based on the combinatorial pharmacophore model, a virtual screening of the Enamine database was performed. Compounds selected after virtual screening were subjected to molecular docking protocols (HTVS, SP, XP and IFD). Twenty new active compounds have been identified and their absorption, distribution, metabolism and excretion (ADME) property calculated using Schr?dinger’s Qikprop module. These results suggest that these new compounds could constitute new chemical starting points for further structural optimization of 3VHE inhibitors.

关键词： Rhodanine pharmacophores 3D-QSAR Molecular Docking

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Trisubstituted Aryl Cyclohexanecarboxylates (TACC): A Simple, New Molecular Scaffold for Antibiotics Design

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International Journal of Organic Chemistry 2019年第3期9卷 142-162页

作者： Olusegun B. Olubanwo Arianna Kazez Daniel W. Carney Jason K. Sello Department of Chemistry Brown University Providence RI USA Department of Chemistry and Biochemistry University of Massachusetts North Dartmouth MA USA

A new class of potential antibacterial agents has been synthesized on a new molecular scaffold of cyclohexane carboxylate. We have tagged this new class of compounds TACCs (Trisubstituted Aryl Cyclohexanecarboxylate). These new molecules are structural analogues of an Activators of Self-Compartmentalizing Proteases 4 and 5 (ACP 4 and 5), and were synthesized to circumvent the drug-like property (drug-ability) challenges and liability noted in ACP 4 and 5. A pseudo-Robinson annulation protocol was used to furnish this new class of potential antibiotics. Structure-activity relationship (SAR) study was done to identify the pharmacophore(s) in this molecular scaffold. A selection of these compounds was used in our preliminary antibacterial inhibitory activities’ studies on Bacillus mycoides and Bacillus subtilis. These preliminary studies show that the TACCs exhibited equal, and in some cases better, antibacterial activity than ACP 4 and 5.

关键词： Cyclohexanecarboxylate Oxocyclohexanecarboxylate ClpP Activator Bacillus Subtilis Antibacterial Antibiotics Pseudo-Robinson Protocol pharmacophores Clp Protease

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Screening for cyclooxygenase 2 inhibitors from natural compounds of Radix Glycyrrhizae using computer simulation

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Traditional Medicine Research 2018年第3期3卷 115-130页

作者： Ming Yang Yi Jin Li-Ping Yang Department of Pharmacy of Beijing Hospital National Center of Gerontology Assessment of Clinical Drugs Risk and Individual Application Key Laboratory National Clinical Research Center of Respiratory Diseases Beijing China School of Life Sciences and Biopharmaceuticals Shenyang Pharmaceutical University Shenyang China

Objective： To explore the molecular basis of the effects of Gancao （Radix Glycyrrhizae, GC） on inflammation throughthe inhibition of cyclooxygenase 2 （COX-2）. Methods： The Discovery Studio 4.5 System was used to predict thephysicochemical properties of GC molecular compounds. The Ligand Profiler was used to screen for natural GCcomponents that could combine with the COX-2 pharmacophores. The AutoDock Vina 1.1.2 software was used for themolecular docking of the natural GC components with the COX-2 protein. Results： The aromatics were the closest to thenon-steroidal anti-inflammatory drugs in terms of the three properties, namely molecular weight, molecular surface area,and molecular solubility, followed by the flavonoids; whereas the terpenoids/saponins differed most from thenon-steroidal anti-inflammatory drugs in terms of the three properties; and the aliphatics were inconsistent. One hundredand eighteen small molecules were obtained through the pharmacophore screening using GC. The molecular bindingenergy （MBE） results demonstrated that the MBE value of the flavonoids/aromatics, obtained from their binding with theCOX-2 protein, was lower than that obtained from their binding with the substrate, metabolism of arachidonic acid,whereas the MBE value of the aliphatics/terpenoids, obtained from their binding with the COX-2 protein, was higherthan that obtained from their binding with the substrate, arachidonic acid. Finally, further filtration, based on thephysicochemical properties and the molecular binding energies of the small molecules, was carried out. Forty-twonatural GC components, including 35 flavonoid and 7 aromatic constituents, with low binding energies and potentialinhibitory effects on COX-2, were screened. Conclusion： Using the three-step program, pharmacophore screening,molecular docking, and physicochemical properties analysis, we screened out 35 flavonoid molecules and 7 aromaticmolecules, which may be potential COX-2 inhibitors, from GC. Two of the

关键词： Radix Glycyrrhizae COX-2 pharmacophores Molecular docking Physicochemical properties

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