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Tamang JSD, Banerjee S, Baidya SK, Ghosh B, Adhikari N, Jha T. Employing comparative QSAR techniques for the recognition of dibenzofuran and dibenzothiophene derivatives toward MMP-12 inhibition. J Biomol Struct Dyn 2023:1-17. [PMID: 37498149 DOI: 10.1080/07391102.2023.2239923] [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: 04/26/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
Among various matrix metalloproteinases (MMPs), MMP-12 is one of the potential targets for cancer and other diseases. However, none of the MMP-12 inhibitors has passed the clinical trials to date. Therefore, designing potential MMP-12 inhibitors as new drug molecules can provide effective therapeutic strategies for several diseases. In this study, a series of dibenzofuran and dibenzothiophene derivatives were subjected to different 2D and 3D-QSAR techniques to point out the crucial structural contributions highly influential toward the MMP-12 inhibitory activity. These techniques identified some structural attributes of these compounds that are responsible for influencing their MMP-12 inhibition. The carboxylic group may enhance proper binding with catalytic Zn2+ ion at the MMP-12 active site. Again, the i-propyl sulfonamido carboxylic acid function contributed positively toward MMP-12 inhibition. Moreover, the dibenzofuran moiety conferred stable binding at the S1' pocket for higher MMP-12 inhibition. The steric and hydrophobic groups were found favourable near the furan ring substituted at the dibenzofuran moiety. Besides these ligand-based approaches, molecular docking and molecular dynamic (MD) simulation studies not only elucidated the importance of several aspects of these MMP-12 inhibitors while disclosing the significance of the finding of these QSAR studies and their influences toward MMP-12 inhibition. The MD simulation study also revealed stable and compact binding between such compounds at the MMP-12 active site. Therefore, the findings of these validated ligand-based and structure-based molecular modeling studies can aid the development of selective and potent lead molecules that can be used for the treatment of MMP-12-associated diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jigme Sangay Dorjay Tamang
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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2
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Yadav V, Banerjee S, Baidya SK, Adhikari N, Jha T. Applying comparative molecular modelling techniques on diverse hydroxamate-based HDAC2 inhibitors: an attempt to identify promising structural features for potent HDAC2 inhibition. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:1-22. [PMID: 34979835 DOI: 10.1080/1062936x.2021.2013317] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Histone deacetylase 2 (HDAC2) has been implicated in a variety of cardiovascular and neurodegenerative disorders as well as in cancers. Thus, HDAC2 has become an exclusive target for anticancer drug development. Therefore, the development of newer HDAC2 inhibitors in disease conditions is a prime goal to restrain such a scenario. Although a handful of HDAC inhibitors was accepted for the treatment of HDAC-related disease conditions, the non-selective nature of these entities is one of the major setbacks in the treatment of specific HDAC isoform-related pathophysiology. In this framework, the analyses of pre-existing molecules are essential to identify the important structural features that can fulfil the requirements for the cap and linker moieties to obtain potent and effective HDAC2 inhibition. Thus, in this study, the implementation of a combined comparative 2D and 3D molecular modelling techniques was done on a group of 92 diverse hydroxamate derivatives having a wide range of HDAC2 inhibitory potency. Besides other crucial features, this study upheld the importance of groups like triazole and benzyl moieties along with the molecular fields that are crucial for regulating HDAC2 inhibition. The outcomes of this study may be employed for the designing of HDAC2 inhibitors in future.
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Affiliation(s)
- V Yadav
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S K Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Sharma V, Das R, Mehta DK, Sharma D, Sahu RK. Exploring quinolone scaffold: Unravelling the chemistry of anticancer drug design. Mini Rev Med Chem 2021; 22:69-88. [PMID: 33438536 DOI: 10.2174/1389557521666210112142136] [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: 01/24/2020] [Revised: 10/24/2020] [Accepted: 11/30/2020] [Indexed: 11/22/2022]
Abstract
Globally, cancer is considered as the major leading cause in decreasing the patient health care system of human beings. The growing threat from drug-resistant cancers makes heterocyclic moieties as an urgent need to develop more successful candidates for anti-cancer therapy. In view of outstanding pharmacological activities Quinolone and its derivatives have attracted more attention towards drug designing and biological evaluation in the search of new drug molecules. The inspired researchers attempted efforts in order to discover quinolone based analogs due to its wide range of biological activities. Due to immense pharmacological importance, distinct synthetic methods have been executed to attain new drug entities from quinolones and all the reported molecules have shown constructive anticancer activity. Some of the synthetic protocol like, one pot synthesis, post-Ugi-transformation, catalysed based synthesis, enzyme-based synthesis and nano-catalyst based synthetic procedures are also discussed as recent advancement in production of quinolone derivatives. In this review, recent synthetic approaches in the medicinal chemistry of quinolones and potent quinolone derivatives on the basis of structural activity relationship are outlined. Moreover, their major methods and modifications are discussed.
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Affiliation(s)
- Vishal Sharma
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Hr. India
| | - Rina Das
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Hr. India
| | - Dinesh Kumar Mehta
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Hr. India
| | - Diksha Sharma
- Faculty of Pharmaceutical Sciences, Kurukshetra University, Kurukshetra-Hr. India
| | - Ram Kumar Sahu
- Dept of Pharmaceutical Science, Assam University (A Central University), Silchar, Assam-788011. India
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4
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Pinto AMV, Leite JPG, Marinho RS, Forezi LDS, Batalha PN, Boechat FDC, Cunha AC, Silva DO, Gama IL, Faro LV, de Souza MC, Paixão ICP. Antiviral activity of 4-oxoquinoline-3-carboxamide derivatives against bovine herpesvirus type 5. Antivir Ther 2019; 25:13-20. [PMID: 31538962 DOI: 10.3851/imp3329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Bovine herpesvirus type 5 is an important agent of meningoencephalitis in cattle and has been identified in outbreaks of bovine neurological disease in several Brazilian states. In recent years, oxoquinoline derivatives have become an important focus in antiviral drug research. METHODS The cytotoxicity and anti BoHV-5RJ42/01 activity of a set of synthetic 4-oxoquinoline derivatives 4a-k were assayed on Madin-Darby Bovine Kidney cell and antiviral activity by plaque reduction assay. RESULTS The most promising substance (4h) exhibited CC50 and EC50 values of 1,239 µM ±5.5 and 6.0 µM ±1.5, respectively, with an SI =206. Two other compounds 4j (CC50 = 35 µM ±2 and EC50 = 24 µM ±7.0) and 4k (CC50= 55 µM ±2 and EC50 = 24 µM ±5.1) presented similar inhibitory profile and selectivity indexes of 1.4 and 2.9, respectively. The results of the time-of-addition studies revealed expressive reduction of virus production (≥80%) in different stages of virus replication cycle except for compound 4h that slightly inhibited virus yield in the first 2 h post infection, but it showed expressive virus inhibition after this time. CONCLUSIONS All three compounds slightly interact with the virus on the virucidal assay and they are not able to block virus attachment and penetration. Antiviral effect of oxoquinoline 4h was more prominent than acyclovir which leads us to suggest compound 4h as a promising molecule for further anti-BoHV-5 drug design.
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Affiliation(s)
- Ana Maria V Pinto
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, Niterói, Brazil.,Laboratório de Virologia Comparada e Ambiental, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil.,Instituto de Biologia, Universidade Federal Fluminense, Pós-graduação em Ciências e Biotecnologia e de Neurologia/Neurociências, Campus do Valonguinho, Niterói, Brazil
| | - José Paulo G Leite
- Laboratório de Virologia Comparada e Ambiental, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Robson Ss Marinho
- Instituto Biomédico, Universidade Federal Fluminense, Rua Professor Hernani Melo, Niterói, Brazil
| | - Luana da Sm Forezi
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Pedro N Batalha
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Fernanda da Cs Boechat
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Anna C Cunha
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - David O Silva
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Ivson L Gama
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Letícia V Faro
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Maria Cbv de Souza
- Instituto de Química, Universidade Federal Fluminense, Pós-graduação em Química, Campus do Valonguinho - Centro - Niterói, Brazil
| | - Izabel Christina P Paixão
- Instituto de Biologia, Universidade Federal Fluminense, Pós-graduação em Ciências e Biotecnologia e de Neurologia/Neurociências, Campus do Valonguinho, Niterói, Brazil
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5
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Wang R, Xu K, Shi W. Quinolone derivatives: Potential anti‐HIV agent—development and application. Arch Pharm (Weinheim) 2019; 352:e1900045. [DOI: 10.1002/ardp.201900045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Ruo Wang
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
| | - Kai Xu
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
| | - Weixiong Shi
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
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6
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Amin SA, Adhikari N, Gayen S, Jha T. Reliable structural information for rational design of benzoxazole type potential cholesteryl ester transfer protein (CETP) inhibitors through multiple validated modeling techniques. J Biomol Struct Dyn 2019; 37:4528-4541. [DOI: 10.1080/07391102.2018.1552895] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, Madhya Pradesh, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, West Bengal, India
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7
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Adhikari N, Amin SA, Jha T, Gayen S. Integrating regression and classification-based QSARs with molecular docking analyses to explore the structure-antiaromatase activity relationships of letrozole-based analogs. CAN J CHEM 2017. [DOI: 10.1139/cjc-2017-0419] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aromatase is a multienzyme complex responsible for the biosynthesis of estrogen and its level has been found higher in breast cancer. Although the designing strategy of aromatase inhibitors (AIs) has continued for more than four decades, it may still be in demand to design highly effective and less toxic AIs. In this study, several chemometric approaches have been used to explore the important structural features of a series of letrozole-based analogs for their promising aromatase inhibitory activity. All techniques are statistically validated individually and in turn, validated with each other along with the structure–activity relationship (SAR) observations. The imidazole ring has been found to interact with the heme iron, whereas the triazole ring system has not shown any interaction. Moreover, imidazole function is better than 1,2,3-triazole, whereas 1,2,3-triazole is better than the 1,2,5-triazole ring system. Additionally, a bulky aryl substitution in the azole ring along with the orientation of the azole nitrogens and the cyanophenyl function has an essential role in the inhibition of aromatase. Furthermore, a cyano group substituted at the phenyl moiety interacts with Arg115, Met374, and Ser478 at the enzyme active site to form hydrogen bonding interactions. These observations are useful for designing potential AIs in the future.
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Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020, Jadavpur University, Kolkata 700032, (WB), India
| | - Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020, Jadavpur University, Kolkata 700032, (WB), India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020, Jadavpur University, Kolkata 700032, (WB), India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar 470003, (MP), India
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8
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Wang Y, Yan F, Jia Q, Dai Y, Wang Q. Quantitative structure-activity relationship of anti-HIV integrase and reverse transcriptase inhibitors using norm indexes. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:1025-1044. [PMID: 29157005 DOI: 10.1080/1062936x.2017.1397055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/23/2017] [Indexed: 06/07/2023]
Abstract
The development of new and safe anti-human immunodeficiency virus (anti-HIV) drugs has been an urgent task for medical research recently. Herein, based on the norm-index descriptors proposed in this work and previous works, a couple of models were developed for investigating the quantitative structure-activity/toxicity relationship (QSAR/QSTR) of dual-target anti-HIV integrase (IN) and reverse transcriptase (RT) inhibitors. The validation results proved that the developed models were stable and reliable, both in statistical quality and predictive capacity. Moreover, potential dual-target inhibitors with high activity and low toxicity were deduced from the developed models; molecular docking results indicated that these inhibitors could interact with some important residues of HIV IN and RT through H-bonding. Accordingly, the norm indexes descriptors proposed by this work might be helpful for the research and development of dual-target anti-HIV drugs.
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Affiliation(s)
- Y Wang
- a School of Chemical Engineering and Material Science , Tianjin University of Science and Technology , Tianjin , PR China
| | - F Yan
- a School of Chemical Engineering and Material Science , Tianjin University of Science and Technology , Tianjin , PR China
| | - Q Jia
- b School of Marine and Environmental Science , Tianjin University of Science and Technology , Tianjin , PR China
| | - Y Dai
- c School of Bioengineering , Tianjin University of Science and Technology , Tianjin , PR China
| | - Q Wang
- a School of Chemical Engineering and Material Science , Tianjin University of Science and Technology , Tianjin , PR China
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9
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An integrated QSAR modeling approach to explore the structure-property and selectivity relationships of N-benzoyl-L-biphenylalanines as integrin antagonists. Mol Divers 2017; 22:129-158. [PMID: 29147824 DOI: 10.1007/s11030-017-9789-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022]
Abstract
Integrins [Formula: see text] and [Formula: see text] are important targets to treat different inflammatory diseases, such as multiple sclerosis, inflammatory bowel diseases, rheumatoid arthritis, atherosclerosis, and asthma. Despite being valuable targets, only a few work has been reported to date regarding molecular modeling studies on these integrins. Not only that, none of these reports addressed the selectivity issue between integrins [Formula: see text] and [Formula: see text]. Therefore, a major challenge regarding the design and discovery of selective integrin antagonists remains. In this study, a series of 142 N-benzoyl-L-biphenylalanines having both integrin [Formula: see text] and [Formula: see text] inhibitory activities were considered for a variety of QSAR approaches including regression and classification-based 2D-QSARs, Hologram QSARs, 3D-QSAR CoMFA and CoMSIA studies to identify the structural requirements of these integrin antagonists. All these QSAR models were statistically validated and subsequently correlated with each other to get a detailed understanding of the activity and selectivity profiles of these molecules.
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10
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Melo BCL, Bernardino AMR, Polillo G, Pereira HS, Paixão ICP, Ribeiro MS, Borges JC. Novel 4-arylaminoquinoline-3-carbonitriles as Inhibitors of HIV-1 Reverse Transcriptase. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.2914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Beatriz C. L. Melo
- Instituto de Química, Programa de Pós-Graduação em Química, Departamento de Química Orgânica, Campus do Valonguinho; Universidade Federal Fluminense; CEP 24020-141 Niterói RJ Brazil
| | - Alice M. R. Bernardino
- Instituto de Química, Programa de Pós-Graduação em Química, Departamento de Química Orgânica, Campus do Valonguinho; Universidade Federal Fluminense; CEP 24020-141 Niterói RJ Brazil
| | - Gustavo Polillo
- Instituto de Química, Programa de Pós-Graduação em Química, Departamento de Química Orgânica, Campus do Valonguinho; Universidade Federal Fluminense; CEP 24020-141 Niterói RJ Brazil
| | - Helena S. Pereira
- Instituto de Biologia, Programa de Pós-Graduação em Ciências e Biotecnologia, Departamento de Biologia Celular e Molecular, Campus do Valonguinho; Universidade Federal Fluminense; CEP 24210-150 Niterói RJ Brazil
| | - Izabel C. P. Paixão
- Instituto de Biologia, Programa de Pós-Graduação em Ciências e Biotecnologia, Departamento de Biologia Celular e Molecular, Campus do Valonguinho; Universidade Federal Fluminense; CEP 24210-150 Niterói RJ Brazil
| | - Michele S. Ribeiro
- Instituto de Biologia, Programa de Pós-Graduação em Ciências e Biotecnologia, Departamento de Biologia Celular e Molecular, Campus do Valonguinho; Universidade Federal Fluminense; CEP 24210-150 Niterói RJ Brazil
| | - Julio C. Borges
- Instituto de Química, Programa de Pós-Graduação em Química, Departamento de Química Orgânica, Campus do Valonguinho; Universidade Federal Fluminense; CEP 24020-141 Niterói RJ Brazil
- Instituto Federal de Educação Ciência e Tecnologia do Rio de Janeiro, Campus Nilópolis; CEP 26530-060 Nilópolis RJ Brazil
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Possible anticancer agents: synthesis, pharmacological activity, and molecular modeling studies on some 5-N
-Substituted-2-N-(substituted benzenesulphonyl)-L(+)Glutamines. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1858-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Pan S, Gupta AK, Subramanian V, Chattaraj PK. Quantitative Structure-Activity/Property/Toxicity Relationships through Conceptual Density Functional Theory-Based Reactivity Descriptors. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Developing effective structure-activity/property/toxicity relationships (QSAR/QSPR/QSTR) is very helpful in predicting biological activity, property, and toxicity of a given set of molecules. Regular change in these properties with the structural alteration is the main reason to obtain QSAR/QSPR/QSTR models. The advancement in making different QSAR/QSPR/QSTR models to describe activity, property, and toxicity of various groups of molecules is reviewed in this chapter. The successful implementation of Conceptual Density Functional Theory (CDFT)-based global as well as local reactivity descriptors in modeling effective QSAR/QSPR/QSTR is highlighted.
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Affiliation(s)
- Sudip Pan
- Indian Institute of Technology Kharagpur, India
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13
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Wu Y, Doering JA, Ma Z, Tang S, Liu H, Zhang X, Wang X, Yu H. Identification of androgen receptor antagonists: In vitro investigation and classification methodology for flavonoid. CHEMOSPHERE 2016; 158:72-79. [PMID: 27258897 DOI: 10.1016/j.chemosphere.2016.05.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/20/2016] [Indexed: 06/05/2023]
Abstract
A tremendous gap exists between the number of potential endocrine disrupting chemicals (EDCs) possibly in the environment and the limitation of traditional regulatory testing. In this study, the anti-androgenic potencies of 21 flavonoids were analyzed in vitro, and another 32 flavonoids from the literature were selected as additional chemicals. Molecular dynamic simulations were employed to obtain four different separation approaches based on the different behaviors of ligands and receptors during the process of interaction. Specifically, ligand-receptor complex which highlighted the discriminating features of ligand escape or retention via "mousetrap" mechanism, hydrogen bonds formed during simulation times, ligand stability and the stability of the helix-12 of the receptor were investigated. Together, a methodology was generated that 87.5% of flavonoids could be discriminated as active versus inactive antagonists, and over 90% inactive antagonists could be filtered out before QSAR study. This methodology could be used as a "proof of concept" to identify inactive anti-androgenic flavonoids, as well could be beneficial for rapid risk assessment and regulation of multiple new chemicals for androgenicity.
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Affiliation(s)
- Yang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jon A Doering
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Zhiyuan Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Song Tang
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Hongling Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaoxiang Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
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14
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Amin SA, Adhikari N, Jha T, Gayen S. Exploring structural requirements of unconventional Knoevenagel-type indole derivatives as anticancer agents through comparative QSAR modeling approaches. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0050] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
An indole ring system is considered as a versatile scaffold in the pharmaceutical field. In this article, comparative QSAR modeling (2D-QSAR, 3D-QSAR; kNN-MFA and CoMSIA) was performed on some Knoevenagel-type cytotoxic indole derivatives to understand the structural requirements for the cytotoxic property of these compounds. The 2D-QSAR model was statistically significant and imparted high predictive ability (nTrain = 30; R = 0.917; [Formula: see text] = 0.801; [Formula: see text] = 0.757; Q2 = 0.722; nTest = 9; [Formula: see text] = 0.799). A statistically significant 3D-QSAR kNN-MFA model (both with stepwise forward and simulated annealing model selection method) as well as a 3D-QSAR CoMSIA model was developed to identify the key chemical features associated with enhancing the cytotoxic activities of these indoles. The results suggest that the presence of bulky group in R position can cause better cytotoxic activities. Consequently, substitution with cyano group at X portion and cyano/ester/keto/sulphonyl features at Y position is favourable for the cytotoxicity. However, hydrophobic features in R′ region are unfavourable for the biological activity. The chemical and structural features identified from the study may provide important avenues to modulate the structure of these indoles to a desirable biological end point.
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Affiliation(s)
- Sk. Abdul Amin
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar 470003, (MP), India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020, Jadavpur University, Kolkata 700032, (WB), India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020, Jadavpur University, Kolkata 700032, (WB), India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar 470003, (MP), India
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Adhikari N, Halder AK, Saha A, Das Saha K, Jha T. Structural findings of phenylindoles as cytotoxic antimitotic agents in human breast cancer cell lines through multiple validated QSAR studies. Toxicol In Vitro 2015; 29:1392-404. [DOI: 10.1016/j.tiv.2015.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
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