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Sabei FY, Y Safhi A, Almoshari Y, Salawi A, H Sultan M, Ali Bakkari M, Alsalhi A, A Madkhali O, M Jali A, Ahsan W. Structure-based virtual screening of natural compounds as inhibitors of HCV using molecular docking and molecular dynamics simulation studies. J Biomol Struct Dyn 2023:1-12. [PMID: 37776007 DOI: 10.1080/07391102.2023.2263588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/28/2023] [Indexed: 10/01/2023]
Abstract
The hepatitis C virus (HCV), which causes hepatitis C, is a viral infection that damages the liver and causes inflammation in the liver. New potentially effective antiviral drugs are required for its treatment owing to various issues associated with the existing medications, including moderate to severe adverse effects, higher costs, and the emergence of drug-resistant strains. The objective of the current study was to utilize computational techniques to assess the anti-HCV efficacy of certain phytochemicals against tetraspanin (CD81) and claudin 1 (CLDN1) entry proteins. A 200-nanosecond molecular dynamics (MD) simulation was employed to examine the stability of the lead-protein complexes. Free binding energy and molecular docking calculations were conducted utilizing MM/GBSA method, and the selectivity of hit compounds for CD81 and CLDN1 was determined. Five significant CD81 and CLDN1 inhibitors were identified: Petasiphenone, Silibinin, Tanshinone IIA, Taxifolin, and Topaquinone. The MM/GBSA analysis of the compounds revealed high free binding energies. All the identified compounds were stable within the CD81 and CLDN1 binding pockets. This study indicated the promising inhibitory potential of the identified compounds against CD81 and CLDN1 receptors and might develop into potential viral entry inhibitors. However, to validate the chemotherapeutic capabilities of the discovered leads extensive preclinical research is required.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fahad Y Sabei
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Awaji Y Safhi
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Yosif Almoshari
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Ahmad Salawi
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Muhammad H Sultan
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Mohammed Ali Bakkari
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Abdullah Alsalhi
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Osama A Madkhali
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Abdulmajeed M Jali
- Department of Pharmacology and Toxicology, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Waquar Ahsan
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
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2
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Dempsey SH, Kass SR. Liberating the Anion: Evaluating Weakly Coordinating Cations. J Org Chem 2022; 87:15466-15482. [DOI: 10.1021/acs.joc.2c02001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephen H. Dempsey
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Steven R. Kass
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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3
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Kamboj S, Rajput A, Rastogi A, Thakur A, Kumar M. Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches. Comput Struct Biotechnol J 2022; 20:3422-3438. [PMID: 35832613 PMCID: PMC9271984 DOI: 10.1016/j.csbj.2022.06.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Hepatitis C virus (HCV) infection causes viral hepatitis leading to hepatocellular carcinoma. Despite the clinical use of direct-acting antivirals (DAAs) still there is treatment failure in 5–10% cases. Therefore, it is crucial to develop new antivirals against HCV. In this endeavor, we developed the “Anti-HCV” platform using machine learning and quantitative structure–activity relationship (QSAR) approaches to predict repurposed drugs targeting HCV non-structural (NS) proteins. We retrieved experimentally validated small molecules from the ChEMBL database with bioactivity (IC50/EC50) against HCV NS3 (454), NS3/4A (495), NS5A (494) and NS5B (1671) proteins. These unique compounds were divided into training/testing and independent validation datasets. Relevant molecular descriptors and fingerprints were selected using a recursive feature elimination algorithm. Different machine learning techniques viz. support vector machine, k-nearest neighbour, artificial neural network, and random forest were used to develop the predictive models. We achieved Pearson’s correlation coefficients from 0.80 to 0.92 during 10-fold cross validation and similar performance on independent datasets using the best developed models. The robustness and reliability of developed predictive models were also supported by applicability domain, chemical diversity and decoy datasets analyses. The “Anti-HCV” predictive models were used to identify potential repurposing drugs. Representative candidates were further validated by molecular docking which displayed high binding affinities. Hence, this study identified promising repurposed drugs viz. naftifine, butalbital (NS3), vinorelbine, epicriptine (NS3/4A), pipecuronium, trimethaphan (NS5A), olodaterol and vemurafenib (NS5B) etc. targeting HCV NS proteins. These potential repurposed drugs may prove useful in antiviral drug development against HCV.
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Affiliation(s)
- Sakshi Kamboj
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Akanksha Rajput
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160036, India
| | - Amber Rastogi
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anamika Thakur
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Martínez-Aguirre MA, Ortega-Valdovinos LR, Villamil-Ramos R, Yatsimirsky AK. Anion Recognition by Benzoxaborole. J Org Chem 2022; 87:7734-7746. [PMID: 35612515 DOI: 10.1021/acs.joc.2c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding types (H-bonding or coordinate) and stability constants for complexes of 11 mono- and di-anions with benzoxaborole (1) were determined by 1H and 11B NMR titrations in DMSO or MeCN. Compared to phenylboronic acid (PBA), 1 is a stronger Lewis acid and a poorer H-bond donor with only one B-OH group, which is expected therefore to recognize anions mostly through the coordinate bonding. This is the case however only with F-, HPO42-, and PhPO32- anions, which are coordinately bonded to 1, and partially with SO42-, which forms only the H-bonded complex with PBA, but both H-bonded and coordinate complexes with 1. The majority of tested anions (AcO-, PhPO3H-, (PhO)2PO2-, Cl-, and Br-) form H-bonded complexes with both 1 and PBA, whereas H2PO4- changes the binding mode from coordinate for PBA to H-bonded for 1. The preferable binding type for each anion is confirmed by calculations of DFT-optimized structures of the anion complexes of 1. The preferable binding type can be rationalized considering the effects of the steric hindrance, more significant for the coordinate bonding, and of increased anion basicity, which is favorable for both binding types, but enhances the strength of coordinate bonding more significantly than the strength of H-bonding.
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Affiliation(s)
| | | | - Raúl Villamil-Ramos
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| | - Anatoly K Yatsimirsky
- Facultad de Química, Universidad Nacional Autónoma de México, 04510 México D.F., México
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Huang Y, Guo N, Xu C, Xie N, Liang F, Yang S, Lv S. Development and critical evaluation of a novel fluorescent nanosensor based on a molecularly imprinted polymer for the rapid detection of procymidone in ginseng. Analyst 2022; 147:2718-2730. [DOI: 10.1039/d1an02186a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Effective methods are required to quantify the organochlorine pesticide procymidone due to its potentially harmful effects toward human health and the environment.
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Affiliation(s)
- Yi Huang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, People's Republic of China
| | - Nan Guo
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, People's Republic of China
| | - Chaojian Xu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, People's Republic of China
| | - Ningkang Xie
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, People's Republic of China
| | - Feiyan Liang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, People's Republic of China
| | - Shuo Yang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, People's Republic of China
| | - Shaowu Lv
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun, People's Republic of China
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Quintard A. Copper Catalyzed Decarboxylative Functionalization of Ketoacids. CHEM REC 2021; 21:3382-3393. [PMID: 33750015 DOI: 10.1002/tcr.202100045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/30/2022]
Abstract
Selective copper catalyzed activation of ketoacids and notably bio-sourced 1,3-acetonedicarboxylic acid, represents an attractive strategy to solve key synthetic challenges. Condensation with aldehydes under exceedingly mild conditions can create more rapidly known natural products scaffolds such as 1,3 polyols. In this account, the recent progress in this field, notably through multicatalytic combination with organocatalysis is described. In addition to the rapid preparation of natural product fragments, cascade incorporation of fluorine also provided new type of synthetic analogues of improved properties in a broad range of applications.
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Affiliation(s)
- Adrien Quintard
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
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7
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Safaei S, Kassaee MZ, Khorshidvand N, Ahmadi A. Effects of H-bonding and structural constituents on the acidity and potential "anticancer activity" of D-mandelonitrile-β-D-glucuronic acid by density functional theory. RESEARCH ON CHEMICAL INTERMEDIATES 2020. [DOI: 10.1007/s11164-020-04204-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Sperandio C, Rodriguez J, Quintard A. Development of copper-catalyzed enantioselective decarboxylative aldolization for the preparation of perfluorinated 1,3,5-triols featuring supramolecular recognition properties. Chem Sci 2020; 11:1629-1635. [PMID: 32206281 PMCID: PMC7069514 DOI: 10.1039/c9sc05196a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/17/2019] [Indexed: 01/09/2023] Open
Abstract
Fluorine is able to confer unique properties to organic molecules but the scarcity of natural organofluorine sources renders the development of new synthetic methods highly desirable. Using a chiral BOX/Cu combination, enantioselective decarboxylative aldolization of perfluorinated aldehydes has been developed. Most notably, the reaction occurring under mild conditions and with high enantiocontrol can create ketodiols in one single synthetic operation, which are precursors of crucial perfluorinated 1,3,5-triols. In addition, the reaction performed with chloral, validates the proposed transition state model based on steric interactions and provides the first enantioselective synthesis of hexachlorinated ketodiol of great synthetic utility. The ability of perfluorinated 1,3,5-triols to form a central hydrogen-bonding framework allows strong coordination of anions and the chirality obtained through the catalyst-controlled synthetic sequence demonstrates the selective chiral anion recognition ability of polyols.
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Affiliation(s)
- Céline Sperandio
- Aix Marseille Univ , CNRS , Centrale Marseille , iSm2 , Marseille , France . ; http://ism2.univ-amu.fr/fr/annuaire/stereo/quintardadrien
| | - Jean Rodriguez
- Aix Marseille Univ , CNRS , Centrale Marseille , iSm2 , Marseille , France . ; http://ism2.univ-amu.fr/fr/annuaire/stereo/quintardadrien
| | - Adrien Quintard
- Aix Marseille Univ , CNRS , Centrale Marseille , iSm2 , Marseille , France . ; http://ism2.univ-amu.fr/fr/annuaire/stereo/quintardadrien
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Sperandio C, Quintard G, Naubron J, Giorgi M, Yemloul M, Parrain J, Rodriguez J, Quintard A. Strategic Stereoselective Halogen (F, Cl) Insertion: A Tool to Enhance Supramolecular Properties in Polyols. Chemistry 2019; 25:15098-15105. [PMID: 31453654 DOI: 10.1002/chem.201902983] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/26/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Céline Sperandio
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2 Marseille France
| | - Guilhem Quintard
- Université de Lyon, INSA LYON, Ingénierie des Matériaux Polymères, IMP-UMR CNRS 5223 69621 Villeurbanne France
| | - Jean‐Valere Naubron
- Aix Marseille Université, CNRS, Centrale Marseille, Spectropole Marseille France
| | - Michel Giorgi
- Aix Marseille Université, CNRS, Centrale Marseille, Spectropole Marseille France
| | - Mehdi Yemloul
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2 Marseille France
| | - Jean‐Luc Parrain
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2 Marseille France
| | - Jean Rodriguez
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2 Marseille France
| | - Adrien Quintard
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2 Marseille France
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Chiral Diol-Based Organocatalysts in Enantioselective Reactions. Molecules 2018; 23:molecules23092317. [PMID: 30208621 PMCID: PMC6225256 DOI: 10.3390/molecules23092317] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 12/22/2022] Open
Abstract
Organocatalysis has emerged as a powerful synthetic tool in organic chemistry in the last few decades. Among various classes of organocatalysis, chiral diol-based scaffolds, such as BINOLs, VANOLs, and tartaric acid derivatives, have been widely used to induce enantioselectivity due to the ability of the hydroxyls to coordinate with the Lewis acidic sites of reagents or substrates and create a chiral environment for the transformation. In this review, we will discuss the applications of these diol-based catalysts in different types of reactions, including the scopes of reactions and the modes of catalyst activation. In general, the axially chiral aryl diol BINOL and VANOL derivatives serve as the most competent catalyst for most examples, but examples of exclusive success using other scaffolds, herein, suggests that they should not be overlooked. Lastly, the examples, to date, are mainly from tartrate and biaryl diol catalysts, suggesting that innovation may be available from new diol scaffolds.
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12
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Wang XB. Cluster Model Studies of Anion and Molecular Specificities via Electrospray Ionization Photoelectron Spectroscopy. J Phys Chem A 2017; 121:1389-1401. [PMID: 28060511 DOI: 10.1021/acs.jpca.6b09784] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ion specificity, a widely observed macroscopic phenomenon in condensed phases and at interfaces, is a fundamental chemical physics issue. Herein we report our recent studies of such effects using cluster models in an "atom-by-atom" and "molecule-by-molecule" fashion not possible with the condensed-phase methods. We use electrospray ionization (ESI) to generate molecular and ionic clusters to simulate key molecular entities involved in local binding regions and characterize them by employing negative ion photoelectron spectroscopy (NIPES). Inter- and intramolecular interactions and binding configurations are directly obtained as functions of the cluster size and composition, providing molecular-level descriptions and characterization over the local active sites that play crucial roles in determining the solution chemistry and condensed-phase phenomena. The topics covered in this article are relevant to a wide range of research fields from ion specific effects in electrolyte solutions, ion selectivity/recognition in normal functioning of life, to molecular specificity in aerosol particle formation, as well as in rational material design and synthesis.
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Affiliation(s)
- Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory , P.O. Box 999, MS K8-88, Richland, Washington 99352, United States
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