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Fernandes PO, Dias ALT, Dos Santos Júnior VS, Sá Magalhães Serafim M, Sousa YV, Monteiro GC, Coutinho ID, Valli M, Verzola MMSA, Ottoni FM, Pádua RMD, Oda FB, Dos Santos AG, Andricopulo AD, da Silva Bolzani V, Mota BEF, Alves RJ, de Oliveira RB, Kronenberger T, Maltarollo VG. Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus. J Chem Inf Model 2024; 64:1932-1944. [PMID: 38437501 DOI: 10.1021/acs.jcim.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
The application of computer-aided drug discovery (CADD) approaches has enabled the discovery of new antimicrobial therapeutic agents in the past. The high prevalence of methicillin-resistantStaphylococcus aureus(MRSA) strains promoted this pathogen to a high-priority pathogen for drug development. In this sense, modern CADD techniques can be valuable tools for the search for new antimicrobial agents. We employed a combination of a series of machine learning (ML) techniques to select and evaluate potential compounds with antibacterial activity against methicillin-susceptible S. aureus (MSSA) and MRSA strains. In the present study, we describe the antibacterial activity of six compounds against MSSA and MRSA reference (American Type Culture Collection (ATCC)) strains as well as two clinical strains of MRSA. These compounds showed minimal inhibitory concentrations (MIC) in the range from 12.5 to 200 μM against the different bacterial strains evaluated. Our results constitute relevant proven ML-workflow models to distinctively screen for novel MRSA antibiotics.
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Affiliation(s)
- Philipe Oliveira Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Anna Letícia Teotonio Dias
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Valtair Severino Dos Santos Júnior
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Yamara Viana Sousa
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Gustavo Claro Monteiro
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Isabel Duarte Coutinho
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Marilia Valli
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física, Universidade de São Paulo (USP), São Carlos, São Paulo 13.563-120, Brazil
| | - Marina Mol Sena Andrade Verzola
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Flaviano Melo Ottoni
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Rodrigo Maia de Pádua
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Fernando Bombarda Oda
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara 14.800-903, Brazil
| | - André Gonzaga Dos Santos
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara 14.800-903, Brazil
| | - Adriano Defini Andricopulo
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física, Universidade de São Paulo (USP), São Carlos, São Paulo 13.563-120, Brazil
| | - Vanderlan da Silva Bolzani
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Ricardo José Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
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Singh S, Karthikeyan C, Moorthy NSHN. Classification analysis of fatty acid synthase inhibitors using multialgorithms on topological descriptors and structural fingerprints. Chem Biol Drug Des 2023; 101:395-407. [PMID: 36065591 DOI: 10.1111/cbdd.14138] [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: 04/17/2022] [Revised: 08/21/2022] [Accepted: 08/28/2022] [Indexed: 01/14/2023]
Abstract
Fatty acid synthase (FASN) is one of the enzymes required for fatty acid biosynthesis and is expressed as low or absent in most normal cells/tissues. However, this enzyme is upregulated in various cancer cells; hence, it can act as an important target to design and develop novel FASN inhibitors for cancer therapy. In the present investigation, a series of structurally diverse compounds that possessed FASN inhibitory activities were subjected to classification analysis using different algorithms such as support vector machine, decision tree, Naïve Bayes and random forest. The physicochemical descriptors and MACCS fingerprints were calculated using PaDEL software, and the WEKA software was utilized for the classification model building. The statistical parameters/confusion matrix calculated from the analysis revealed that the selected models have significant predictive performances. The results showed that the topological properties of the molecules are the main determinant for the activity classification. The key descriptors comprised of hydrogen bonding groups, especially acceptor (nHBAcc, minHBint9, minHBint5 and nwHBa), charge on the topological surface of the molecules (JGI10 & GGI2), ionization potential (GATS5i and GATS1i) and branching and distance between the groups (ETA_Eta_B_RC) are significantly contributed in the classification models. Further, the presence of heteroatoms (MACCSFP82, MACCSFP93 and MACCSFP131), especially nitrogen atom(s) and hydrogen bond acceptor groups (N-N group, NC(=O)N, N-C(=O)), actively contributed to the inhibitory activities. The results concluded that the topological polar properties concentrated in a specific region have significant FASN inhibitory activity. Hence, these results shall be used to develop novel molecules with increased FASN inhibitory activity.
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Affiliation(s)
- Shailendra Singh
- Cancept Therapeutics Laboratory, Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak, India
| | - Chandrabose Karthikeyan
- Cancept Therapeutics Laboratory, Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak, India
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3
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Cheng H, Fu L, Yang X, Yang Y, Zhang Z, Tao Y, Wan J, Tu Z, Chen J, Li Y. Screening and identification of 3-aryl-quinolin-2-one derivatives as antiviral agents against influenza A. J Med Virol 2023; 95:e28327. [PMID: 36415105 DOI: 10.1002/jmv.28327] [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: 06/04/2022] [Revised: 11/03/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022]
Abstract
Quinolin-2-one represents an important and valuable chemical motif that possesses a wide variety of biological activities; however, the anti-influenza activities of quinolin-2-one-containing compounds were rarely reported. Herein, we describe the screening and identification of 3-aryl-quinolin-2-one derivatives as a novel class of antiviral agents. The 3-aryl-quinolinone derivatives were synthesized via an efficient copper-catalyzed reaction cascade that we previously developed. Using this synthetic method, preliminary structure-activity relationships of this scaffold against the influenza A virus infection were systematically explored. The most potent compound 34 displayed IC50 values of 2.14 and 4.88 μM against the replication of H3N2 (A/HK/8/68) and H1N1 (A/WSN/33) strains, respectively, without apparent cytotoxicity on MDCK cells. We further demonstrated that 27 and 34 potently inhibited the plaque formation of the IAV, rendering this scaffold attractive for pursuing novel anti-influenza agents.
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Affiliation(s)
- Huimin Cheng
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd), Shenzhen, China
| | - Liangbing Fu
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
| | - Xia Yang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yujian Yang
- Academy for Advanced Interdisciplinary Studies and Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
| | - Zhening Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yuan Tao
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
| | - Junting Wan
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhengchao Tu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, Guangzhou, China
| | - Jianxin Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yingjun Li
- Academy for Advanced Interdisciplinary Studies and Department of Chemistry, Southern University of Science and Technology, Shenzhen, China.,State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen, China
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4
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Yuan WC, Zuo J, Yuan SP, Zhao JQ, Wang ZH, You Y. Ring expansion and ring opening of 3-halooxindoles with N-alkoxycarbonyl- O-tosylhydroxylamines for divergent access to 4-aminoquinolin-2-ones and N-Cbz- N’-arylureas. Org Chem Front 2021. [DOI: 10.1039/d0qo01335h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The reaction of N-alkoxycarbonyl-O-tosylhydroxylamines with indol-2-ones in situ generated from 3-halooxindoles has been developed for divergently accessing 4-aminoquinolin-2-ones and N-Cbz-N’-arylureas in good to excellent yields.
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Affiliation(s)
- Wei-Cheng Yuan
- Institute for Advanced Study
- Chengdu University
- Chengdu 610106
- China
| | - Jian Zuo
- National Engineering Research Center of Chiral Drugs
- Chengdu Institute of Organic Chemistry
- Chinese Academy of Sciences
- Chengdu
- China
| | - Shu-Pei Yuan
- National Engineering Research Center of Chiral Drugs
- Chengdu Institute of Organic Chemistry
- Chinese Academy of Sciences
- Chengdu
- China
| | - Jian-Qiang Zhao
- Institute for Advanced Study
- Chengdu University
- Chengdu 610106
- China
| | - Zhen-Hua Wang
- Institute for Advanced Study
- Chengdu University
- Chengdu 610106
- China
| | - Yong You
- Institute for Advanced Study
- Chengdu University
- Chengdu 610106
- China
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5
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Zhu T, Chen W, Cheng H, Wang Y, Singh RP. Prediction of polydimethylsiloxane-water partition coefficients based on the pp-LFER and QSAR models. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 182:109374. [PMID: 31254853 DOI: 10.1016/j.ecoenv.2019.109374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 06/09/2023]
Abstract
Obtaining accurate measurements of the partition coefficients between sorbent materials and water is of major importance for the analysis of the adsorption behavior and dissolved concentrations of organic compounds in the environment. In the passive-sampling approach, polydimethylsiloxane (PDMS) has a wide range of applications. Therefore, we established a poly-parameter linear-free energy relationship (pp-LFER) and a quantitative structure-activity relationship (QSAR) model to predict the log KPDMS-w values for a large dataset of 290 organic chemicals from 11 diverse classes. For the pp-LFER model, E (excess molar refractivity), A (molecular H-bond donor ability), V (McGowan volume), and B (the H-bond acceptor properties) were introduced as the main correlated variables. However, the obtained model is much limited in terms of acquiring available descriptors. For this reason, we developed a QSAR model, and CrippenLogP (Crippen octanol-water partition coefficient), RNCG (Relative negative charge-most negative charge/total negative charge), ATSC4e (Centered Broto-Moreau autocorrelation-lag4/weighted by Sanderson electronegativities) and GATS6p (Geary autocorrelation-lag6/weighted by polarizabilities) were selected as the significant parameters. The predictive power and functional reliability of the presented models were confirmed with validation methods as described in previous studies. The adjusted determination coefficients (R2adj) of 0.851 and 0.922 and leave-one-out cross-validated (Q2LOO) of 0.841 and 0.907 revealed that the models have good predictive power and generalizability. Thus, the proposed models are simple yet accurate tools for predicting the log KPDMS-w values and providing new insights to further understand the adsorption mechanism of organic compounds.
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Affiliation(s)
- Tengyi Zhu
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China.
| | - Wenxuan Chen
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Haomiao Cheng
- School of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, Jiangsu, China
| | - Yajun Wang
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
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6
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Gholivand K, Pooyan M, Mohammadpanah F, Pirastefar F, Junk PC, Wang J, Ebrahimi Valmoozi AA, Mani-Varnosfaderani A. Synthesis, crystal structure and biological evaluation of new phosphoramide derivatives as urease inhibitors using docking, QSAR and kinetic studies. Bioorg Chem 2019; 86:482-493. [DOI: 10.1016/j.bioorg.2019.01.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/20/2019] [Accepted: 01/27/2019] [Indexed: 12/24/2022]
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7
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Jiang H, Gan T, Zhang J, Ma Q, Liang Y, Zhao Y. The Structures and Bioactivities of Fatty Acid Synthase Inhibitors. Curr Med Chem 2019; 26:7081-7101. [DOI: 10.2174/0929867326666190507105022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 02/12/2018] [Accepted: 05/18/2018] [Indexed: 11/22/2022]
Abstract
Background:
Fatty Acid Synthase (FAS or FASN) is a vital enzyme which catalyzes
the de novo synthesis of long chain fatty acids. A number of studies have recently been reported
that FAS was combined targets for the discovery of anti-obesity and anti-cancer drugs. Great interest
has been developed in finding novel FAS inhibitors, and result in more than 200 inhibitors being
reported.
Methods:
The reported research literature about the FAS inhibitors was collected and analyzedsised
through major databases including Web of Science, and PubMed. Then the chemical stractures,
FAS inhibitory activities, and Structure-Activity Relationships (SAR) were summarized
focused on all these reported FAS inhibitors.
Results:
The 248 FAS inhibitors, which were reported during the past 20 years, could be divided
into thiolactone, butyrolactone and butyrolactam, polyphenols, alkaloids, terpenoids, and other
structures, in view of their structure characteristics. And the SAR of high inhibitory structures of
each type was proposed in this paper.
Conclusion:
A series of synthetic quinolinone derivatives show strongest inhibitory activity in the
reported FAS inhibitors. Natural polyphenols, existing in food and herbs, show more adaptive in
medicine exploration because of their safety and efficiency. Moreover, screening the FAS inhibitors
from microorganism and marine natural products could be the hot research directions in the
future.
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Affiliation(s)
- Hezhong Jiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Tian Gan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Jiasui Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Qingyun Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yan Liang
- School of Kinesiology and Health, Capital University of Physical Education and Sports, Beijing 100191, China
| | - Youxing Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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8
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Gholivand K, Ebrahimi Valmoozi AA, Salahi M, Taghipour F, Torabi E, Ghadimi S, Sharifi M, Ghadamyari M. Bisphosphoramidate derivatives: synthesis, crystal structure, anti-cholinesterase activity, insecticide potency and QSAR analysis. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2016. [DOI: 10.1007/s13738-016-0991-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Angeles TS, Hudkins RL. Recent advances in targeting the fatty acid biosynthetic pathway using fatty acid synthase inhibitors. Expert Opin Drug Discov 2016; 11:1187-1199. [PMID: 27701891 DOI: 10.1080/17460441.2016.1245286] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Elevated lipogenesis has been associated with a variety of diseases including obesity, cancer and nonalcoholic fatty liver disease (NAFLD). Fatty acid synthase (FASN) plays a pivotal role in de novo lipogenesis, making this multi-catalytic protein an attractive target for therapeutic intervention. Recently, the first FASN inhibitor successfully advanced through the drug development process and entered clinical evaluation in oncology. Areas covered: This review discusses the biological roles of FASN in three prominent disease areas: cancer, obesity-related disorders and NAFLD. Recent advances in drug discovery strategies and design of newer FASN inhibitors are also highlighted. Expert opinion: Despite the abundance of evidence linking the lipogenic pathway to cancer, progression of FASN-targeted molecules has been rather slow and challenging and no compounds have moved past the preclinical phase. The landscape has recently changed with the recent advancement of the first FASN inhibitor into clinical evaluation for solid tumors. Needless to say, the successful translation into the clinical setting will open opportunities for expanding the therapeutic utility of FASN inhibitors not just in oncology but in other diseases associated with elevated lipogenesis such as obesity, type 2 diabetes, and NAFLD.
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Affiliation(s)
- Thelma S Angeles
- a Discovery and Product Development , Teva Branded Pharmaceutical Products R&D, Inc ., West Chester , PA , USA
| | - Robert L Hudkins
- a Discovery and Product Development , Teva Branded Pharmaceutical Products R&D, Inc ., West Chester , PA , USA
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10
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Zhang YM, Chang MJ, Yang XS, Han X. In silico investigation of agonist activity of a structurally diverse set of drugs to hPXR using HM-BSM and HM-PNN. JOURNAL OF HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY. MEDICAL SCIENCES = HUA ZHONG KE JI DA XUE XUE BAO. YI XUE YING DE WEN BAN = HUAZHONG KEJI DAXUE XUEBAO. YIXUE YINGDEWEN BAN 2016; 36:463-468. [PMID: 27376821 DOI: 10.1007/s11596-016-1609-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 04/28/2016] [Indexed: 10/21/2022]
Abstract
The human pregnane X receptor (hPXR) plays a critical role in the metabolism, transport and clearance of xenobiotics in the liver and intestine. The hPXR can be activated by a structurally diverse of drugs to initiate clinically relevant drug-drug interactions. In this article, in silico investigation was performed on a structurally diverse set of drugs to identify critical structural features greatly related to their agonist activity towards hPXR. Heuristic method (HM)-Best Subset Modeling (BSM) and HM-Polynomial Neural Networks (PNN) were utilized to develop the linear and non-linear quantitative structure-activity relationship models. The applicability domain (AD) of the models was assessed by Williams plot. Statistically reliable models with good predictive power and explain were achieved (for HM-BSM, r (2)=0.881, q LOO (2) =0.797, q EXT (2) =0.674; for HM-PNN, r (2)=0.882, q LOO (2) =0.856, q EXT (2) =0.655). The developed models indicated that molecular aromatic and electric property, molecular weight and complexity may govern agonist activity of a structurally diverse set of drugs to hPXR.
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Affiliation(s)
- Yi-Ming Zhang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 210029, China
| | - Mei-Jia Chang
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Xu-Shu Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Xiao Han
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 210029, China.
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11
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Gholivand K, EbrahimiValmoozi AA, Gholami A, Dusek M, Eigner V, Abolghasemi S. Synthesis, characterization, crystal structures, QSAR study and antibacterial activities of organotin bisphosphoramidates. J Organomet Chem 2016. [DOI: 10.1016/j.jorganchem.2015.09.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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12
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Gholivand K, Asadi L, Ebrahimi Valmoozi AA, Hodaii M, Sharifi M, Kashani HM, Mahzouni HR, Ghadamyari M, Kalate AA, Davari E, Salehi S, Bonsaii M. Phosphorhydrazide inhibitors: toxicological profile and antimicrobial evaluation assay, molecular modeling and QSAR study. RSC Adv 2016. [DOI: 10.1039/c5ra24209f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A series of 23 novel phosphorhydrazide derivatives were synthesized and characterized by spectral techniques, and their anti-ChE, antibacterial and insecticide activities were investigated.
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Affiliation(s)
| | - Lida Asadi
- Department of Chemistry
- Islamic Azad University
- Tehran
- Iran
| | | | - Meraat Hodaii
- Department of Chemistry
- Islamic Azad University
- Tehran
- Iran
| | | | | | | | | | | | - Ehsan Davari
- Department of Chemistry
- Tarbiat Modares University
- Tehran
- Iran
| | - Sami Salehi
- Department of Chemistry
- Tarbiat Modares University
- Tehran
- Iran
| | - Mahyar Bonsaii
- Department of Chemistry
- Islamic Azad University
- Tehran
- Iran
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13
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March S, Pelletier SMC, Plant A. Expedient synthesis of substituted 4-hydroxy-quinolin-2(1H)-ones. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.08.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Ibrahim MA, Hassanin HM, Alnamer YA. Synthesis, Characterization, and Antimicrobial Evaluation of Some Novel 4-Hydroxyquinolin-2(1H)-ones. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2014.949775] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Gholivand K, Ebrahimi Valmoozi AA, Bonsaii M. Synthesis and crystal structure of new temephos analogues as cholinesterase inhibitor: molecular docking, QSAR study, and hydrogen bonding analysis of solid state. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:5761-5771. [PMID: 24893121 DOI: 10.1021/jf5011726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A series of temephos (Tem) derivatives were synthesized and characterized by 31P, 13C, and 1H NMR and FT-IR spectral techniques. Also, the crystal structure of compound 9 was investigated. The hydrogen bonding energies (E2) were calculated by NBO analysis of the crystal cluster. The activities and the mixed-type mechanism of Tem derivatives were evaluated using the modified Ellman's and Lineweaver-Burk's methods on cholinesterase (ChE) enzymes. The inhibitory activities of Tem derivatives with a P═S moiety were higher than those with a P═O moiety. Docking analysis disclosed that the hydrogen bonds occurred between the OR (R=CH3 and C2H5) oxygen and N-H nitrogen atoms of the selected compounds and the receptor site (GLN and GLU) of ChEs. PCA-QSAR indicated that the correlation coefficients of the electronic variables were dominant compared to the structural descriptors. MLR-QSAR models clarified that the net charges of nitrogen and phosphorus atoms contribute important electronic function in the inhibition of ChEs. The validity of the QSAR model was confirmed by a LOO cross-validation method with q2=0.965 between the training and testing sets.
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Affiliation(s)
- Khodayar Gholivand
- Department of Chemistry, Tarbiat Modares University , P.O. Box 14115-175, Tehran, Iran
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Gholivand K, Valmoozi AAE, Mahzouni HR, Ghadimi S, Rahimi R. Molecular docking and QSAR studies: noncovalent interaction between acephate analogous and the receptor site of human acetylcholinesterase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:6776-6785. [PMID: 23796225 DOI: 10.1021/jf401092h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Twelve new compounds of acephate (Ace) analogues were synthesized and characterized by (31)P, (13)C, and (1)H NMR and IR spectroscopy. The probable insecticide potential of these compounds as well as 23 previously prepared molecules with a general skeleton of RC(O)-NH-P(O)X1X2 was predicted by PASS software. Docking analysis showed that hydrophobic interaction and hydrogen bonding were created between the functional groups of Ace derivatives and the receptor sites of acetylcholinesterase. PCA-QSAR indicated that the electronic descriptors are dominated in comparison with the structural descriptors. The experimental-QSAR (R(2) = 0.903 and VIF < 2.997) and DFT-QSAR (R(2) = 0.990 and VIF ≤ 10) models clarified that the net charge of functional groups contributes an important function in an inhibition mechanism. Validity and integrity of this model were confirmed by the LOO cross-validation method with q(2) = 0.940 and low residuals between the training and testing sets. The correlation matrix of DFT-QSAR model confirmed the molecular docking results.
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Worachartcheewan A, Nantasenamat C, Isarankura-Na-Ayudhya C, Prachayasittikul V. Predicting antimicrobial activities of benzimidazole derivatives. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0539-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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de Melo EB, Ferreira MMC. Four-dimensional structure-activity relationship model to predict HIV-1 integrase strand transfer inhibition using LQTA-QSAR methodology. J Chem Inf Model 2012; 52:1722-32. [PMID: 22657398 DOI: 10.1021/ci300039a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite highly active antiretroviral therapy (HAART) implementation, there is a continuous need to search for new anti-HIV agents. HIV-1 integrase (HIV-1 IN) is a recently validated biological target for AIDS therapy. In this work, a four-dimensional quantitative structure-activity relationship (4D-QSAR) study using the new methodology named LQTA-QSAR approach with a training set of 85 HIV-1 IN strand transfer inhibitors (INSTI), containing the β-diketo acid (DKA) substructure, was carried out. The GROMACS molecular dynamic package was used to obtain a conformational ensemble profile (CEP) and LQTA-QSAR was employed to calculate Coulomb and Lennard-Jones potentials and to generate the field descriptors. The partial least-squares (PLS) regression model using 14 field descriptors and 8 latent variables (LV) yielded satisfactory statistics (R2= 0.897, SEC = 0.270, and F = 72.827), good performance in internal (QLOO2 = 0.842 and SEV = 0.314) and external prediction (Rpred2 = 0.839, SEP = 0.384, AREpred = 4.942%, k = 0.981, k′ = 1.016, and |R02 – R0′2 = 0.0257). The QSAR model was shown to be robust (leave-N-out cross validation; average QLNO2 = 0.834) and was not built by chance (y-randomization test; R2 intercept = 0.109; Q2 intercept = -0.398). Fair chemical interpretation of the model could be traced, including descriptors related to interaction with the metallic cofactors and the hydrophobic loop. The model obtained has a good potential for aid in the design of new INSTI, and it is a successful example of application of LQTA-QSAR as an useful tool to be used in computer-aided drug design (CADD).
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Affiliation(s)
- Eduardo B de Melo
- Theoretical Medicinal and Environmental Chemistry Laboratory (LQMAT), Department of Pharmacy, Western Parana State University-Unioeste, 2069 Universitaria St, Cascavel, PR 85819-110, Brazil
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de Melo EB. A QSAR Study of Matrix Metalloproteinases Type 2 (MMP-2) Inhibitors with Cinnamoyl Pyrrolidine Derivatives. Sci Pharm 2012; 80:265-81. [PMID: 22896815 PMCID: PMC3383210 DOI: 10.3797/scipharm.1112-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 01/31/2012] [Indexed: 11/22/2022] Open
Abstract
A multivariate PLS-QSAR study with a data set of 31 cinnamoyl pyrrolidine derivatives described as type 2 matrix metalloproteinases (MMP-2) inhibitors is presented in this paper. The variable selection was performed with the Ordered Predictors Selection (OPS) algorithm. The PLS model presented six descriptors and three Latent Variables (LV) that cumulated 71.845% of variance. Leave-N-out (LNO) cross validation and y-randomization tests showed that the model presented robustness and no chance correlation, respectively. The descriptors indicated that MMP-2 inhibition depends mainly on the electronic properties of the compounds. The model obtained can be useful as a support tool in the design of new MMP-2 inhibitors.
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Affiliation(s)
- Eduardo Borges de Melo
- Theoretical Medicinal and Environmental Chemistry Laboratory (LQMAT), Department of Pharmacy, Western Paraná State University (Unioeste), 2069 Universitária St, 8519110, CascaveI, PR, Brazil
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de Melo EB. A new quantitative structure-property relationship model to predict bioconcentration factors of polychlorinated biphenyls (PCBs) in fishes using E-state index and topological descriptors. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2012; 75:213-222. [PMID: 21959189 DOI: 10.1016/j.ecoenv.2011.08.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 08/31/2011] [Accepted: 08/31/2011] [Indexed: 05/31/2023]
Abstract
A quantitative structure-property relationship (QSPR) study for predicting the logarithm of bioconcentration factors (LogBCF) of polychlorinated biphenyls (PCBs) is presented in this work. For this, the descriptors were obtained using only the Simplified Molecular Input Line Entry System (SMILES) strings in the free web server Parameter Client. The model was built using the Partial Least Squares (PLS) regression method. The best model presented five descriptors (one E-state index and four topological descriptors) and a high quality for fit, internal, and external predictions. The leave-N-out (LNO) cross validation and the y-randomization test showed the model is robust and has no shown chance correlation. With a second test set, the model was compared to other models and presented a root mean square error (RMSE) very close to the best model. The mechanistic interpretation was corroborated by other works in the literature and by the descriptors' theory. Thus, the results meet the five Organization for Economic Co-operation and Development (OECD) principles for validation of QSA(P)R models, and it is expected the model can effectively predict the BCF values in fishes of the PCB congeners without highly reliable experimental BCF.
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Reviewing ligand-based rational drug design: the search for an ATP synthase inhibitor. Int J Mol Sci 2011; 12:5304-18. [PMID: 21954360 PMCID: PMC3179167 DOI: 10.3390/ijms12085304] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 08/04/2011] [Accepted: 08/11/2011] [Indexed: 12/14/2022] Open
Abstract
Following major advances in the field of medicinal chemistry, novel drugs can now be designed systematically, instead of relying on old trial and error approaches. Current drug design strategies can be classified as being either ligand- or structure-based depending on the design process. In this paper, by describing the search for an ATP synthase inhibitor, we review two frequently used approaches in ligand-based drug design: The pharmacophore model and the quantitative structure-activity relationship (QSAR) method. Moreover, since ATP synthase ligands are potentially useful drugs in cancer therapy, pharmacophore models were constructed to pave the way for novel inhibitor designs.
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Farran D, Archirel P, Toupet L, Martinez J, Dewynter G. Enantiodivergent Transannular Rearrangement of 3-Isopropyl-1,4-benzodiazepine-2,5-dione by Memory of Chirality. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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