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Kanan D, Kanan T, Dogan B, Orhan MD, Avsar T, Durdagi S. An Integrated in silico Approach and in vitro Study for the Discovery of Small-Molecule USP7 Inhibitors as Potential Cancer Therapies. ChemMedChem 2020; 16:555-567. [PMID: 33063944 DOI: 10.1002/cmdc.202000675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/06/2020] [Indexed: 02/06/2023]
Abstract
The ubiquitin-specific protease 7 (USP7) is a highly promising well-validated target for a variety of malignancies. USP7 is critical in regulating the tumor suppressor p53 along with numerous epigenetic modifiers and transcription factors. Previous studies showed that USP7 inhibitors led to increased levels of p53 and anti-proliferative effects in hematological and solid tumor cell lines. Thus, this study aimed to identify potent and safe USP7 hit inhibitors as potential anti-cancer therapeutics via an integrated computational approach that combines pharmacophore modeling, molecular docking, molecular dynamics (MD) simulations and post-MD free energy calculations. In this study, the crystal structure of USP7 has been extensively investigated using a combination of three different chemical pharmacophore modeling approaches. We then screened ∼220.000 drug-like small molecule library and the hit ligands predicted to be nontoxic were evaluated further. The identified hits from each pharmacophore modeling study were further examined by 1-ns short MD simulations and MM/GBSA free energy analysis. In total, we ran 1 ns MD simulations for 1137 selected on small compounds. Based on their average MM/GBSA scores, 18 ligands were selected for 50 ns MD simulations along with one highly potent USP7 inhibitor used as a positive control. The in vitro enzymatic inhibition assay testing of our lead 18 molecules confirmed that 7 of these molecules were successful in USP7 inhibition. Screening results showed that within the used screening approaches, the most successful one was structure-based pharmacophore modeling with the success rate of 75 %. The identification of potent and safe USP7 small molecules as potential inhibitors is a step closer to finding appropriate effective therapies for cancer. Our lead ligands can be used as a scaffold for further structural optimization and development, enabling further research in this promising field.
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Affiliation(s)
- Duaa Kanan
- Bahcesehir University School of Medicine, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey.,Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, Bahcesehir University School of Medicine, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey
| | - Tarek Kanan
- Bahcesehir University School of Medicine, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey.,Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, Bahcesehir University School of Medicine, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey
| | - Berna Dogan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, Bahcesehir University School of Medicine, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey
| | - Muge Didem Orhan
- Neuroscience Program, Institute of Health Sciences, Bahcesehir University, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey
| | - Timucin Avsar
- Neuroscience Program, Institute of Health Sciences, Bahcesehir University, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey.,Department of Medical Biology, Bahcesehir University School of Medicine, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, Bahcesehir University School of Medicine, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey.,Neuroscience Program, Institute of Health Sciences, Bahcesehir University, Batman Sk. No: 66, Kadıköy, İstanbul, 34734, Turkey
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Selvakumar R, Anantha Krishnan D, Ramakrishnan C, Velmurugan D, Gunasekaran K. Identification of novel NAD(P)H dehydrogenase [quinone] 1 antagonist using computational approaches. J Biomol Struct Dyn 2019; 38:682-696. [DOI: 10.1080/07391102.2019.1585291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Rajendran Selvakumar
- CAS in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | | | - Chandrasekaran Ramakrishnan
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
| | - Devadasan Velmurugan
- CAS in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | - Krishnasamy Gunasekaran
- CAS in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
- Bioinformatics Infrastructure Facility, University of Madras, Chennai, Tamil Nadu, India
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Kovačević SZ, Karadžić MŽ, Vukić DV, Vukić VR, Podunavac-Kuzmanović SO, Jevrić LR, Ajduković JJ. Toward steroidal anticancer drugs: Non-parametric and 3D-QSAR modeling of 17-picolyl and 17-picolinylidene androstanes with antiproliferative activity on breast adenocarcinoma cells. J Mol Graph Model 2018; 87:240-249. [PMID: 30594032 DOI: 10.1016/j.jmgm.2018.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 02/08/2023]
Abstract
The present study is aimed to analyze lipophilicity and ADMET profiles, and to develop field based 3D-QSAR and ligand-based pharmacophore hypothesis for a series of 17α-picolyl and 17(E)-picolinylidene androstane derivatives in order to give detailed structural insights and to highlight important binding features of novel androstane derivatives, as compounds with antiproliferative activity toward breast adenocarcinoma cells. This study can provide guidelines for the rational design of novel potent compounds. Sum of ranking differences (SRD), as a non-parametric method, was applied for compounds ranking. 3D-QSAR methods, including comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), were applied to predict the antiproliferative effect on breast adenocarcinoma cells and provide the regions in space where interactive fields may influence the activity. The compounds are ranked so the compounds with the most favorable ADME and lipophilicity features together with significant anticancer activity can be distinguished. The established 3D-QSAR model could be used for design of new compounds with antiproliferative activity on the human ER- breast adenocarcinoma cells. The pharmacophore model is able to accurately predict antiproliferative activity. Generally, the present study provides significant guidelines for further selection, synthesis and rational design of new highly potential androstane derivatives as anticancer drugs.
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Affiliation(s)
- Strahinja Z Kovačević
- University of Novi Sad, Faculty of Technology Novi Sad, Bulevar cara Lazara 1, 21000, Novi Sad, Serbia.
| | - Milica Ž Karadžić
- University of Novi Sad, Faculty of Technology Novi Sad, Bulevar cara Lazara 1, 21000, Novi Sad, Serbia
| | - Dajana V Vukić
- University of Novi Sad, Faculty of Technology Novi Sad, Bulevar cara Lazara 1, 21000, Novi Sad, Serbia
| | - Vladimir R Vukić
- University of Novi Sad, Faculty of Technology Novi Sad, Bulevar cara Lazara 1, 21000, Novi Sad, Serbia
| | | | - Lidija R Jevrić
- University of Novi Sad, Faculty of Technology Novi Sad, Bulevar cara Lazara 1, 21000, Novi Sad, Serbia
| | - Jovana J Ajduković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg Dositeja Obradovića 3, 21000, Novi Sad, Serbia
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Venkatesan A, Rambabu M, Jayanthi S, Febin Prabhu Dass J. Pharmacophore feature prediction and molecular docking approach to identify novel anti-HCV protease inhibitors. J Cell Biochem 2017; 119:960-966. [PMID: 28691304 DOI: 10.1002/jcb.26262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/05/2017] [Indexed: 02/06/2023]
Abstract
Discovering a potential drug for HCV treatment is a challenging task in the field of drug research. This study initiates with computational screening and modeling of promising ligand molecules. The foremost modeling method involves the identification of novel compound and its molecular interaction based on pharmacophore features. A total of 197 HCV compounds for NS3/4A protein target were screened for our study. The pharmacophore models were generated using PHASE module implemented in Schrodinger suite. The pharmacophore features include one hydrogen bond acceptor, one hydrogen bond donor, and three hydrophobic sites. As a result, based on mentioned hypothesis the model ADHHH.159 corresponds to the CID 59533233. Furthermore, docking was performed using maestro for all the 197 compounds. Among these, the CID 59533313 and 59533233 possess the best binding energy of -11.75 and -10.40 kcal/mol, respectively. The interactions studies indicated that the CID complexed with the NS3/4A protein possess better binding affinity with the other compounds. Further the compounds were subjected to calculate the ADME properties. Therefore, it can be concluded that these two compounds could be a potential alternative drug for the development of HCV.
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Affiliation(s)
- Arthi Venkatesan
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
| | - Majji Rambabu
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
| | - Sivaraman Jayanthi
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
| | - J Febin Prabhu Dass
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, India
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Ugale VG, Patel HM, Surana SJ. Molecular modeling studies of quinoline derivatives as VEGFR-2 tyrosine kinase inhibitors using pharmacophore based 3D QSAR and docking approach. ARAB J CHEM 2017. [DOI: 10.1016/j.arabjc.2013.07.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Patel HM, Bari P, Karpoormath R, Noolvi M, Thapliyal N, Surana S, Jain P. Design and synthesis of VEGFR-2 tyrosine kinase inhibitors as potential anticancer agents by virtual based screening. RSC Adv 2015. [DOI: 10.1039/c5ra05277g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Design and synthesis of VEGFR-2 tyrosine kinase inhibitors as potential anticancer agents has been done by a virtual based screening approach.
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Affiliation(s)
- Harun M. Patel
- Dept. of Pharmaceutical Chemistry
- University of KwaZulu-Natal (Westville Campus)
- Durban-4000
- South Africa
- Department of Pharmaceutical Chemistry
| | - Pankaj Bari
- Department of Pharmaceutical Chemistry
- R.C. Patel College of Pharmacy
- Dhule 425405
- India
| | - Rajshekhar Karpoormath
- Dept. of Pharmaceutical Chemistry
- University of KwaZulu-Natal (Westville Campus)
- Durban-4000
- South Africa
| | - Malleshappa Noolvi
- Department of Pharmaceutical Chemistry
- Shree Dhanvantary Pharmacy College
- Surat-3941110
- India
| | - Neeta Thapliyal
- Dept. of Pharmaceutical Chemistry
- University of KwaZulu-Natal (Westville Campus)
- Durban-4000
- South Africa
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry
- R.C. Patel College of Pharmacy
- Dhule 425405
- India
| | - Pritam Jain
- Department of Pharmaceutical Chemistry
- R.C. Patel College of Pharmacy
- Dhule 425405
- India
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Marella A, Tanwar O, Saha R, Alam MM, Zaman MS, Akhter M. 3D quantitative structure–activity relationship for quinoline, benzimidazole and benzofuran-based analogs as phosphodiesterases IV (PDE-IV) inhibitors. Med Chem Res 2013. [DOI: 10.1007/s00044-012-0457-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Urniaż RD, Jóźwiak K. X-ray crystallographic structures as a source of ligand alignment in 3D-QSAR. J Chem Inf Model 2013; 53:1406-14. [PMID: 23705769 DOI: 10.1021/ci400004e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-dimensional quantitative structure-activity relationships (3D-QSAR) analyses are methods correlating a pharmacological property with a mathematical representation of a molecular property distribution around three-dimensional molecular models for a set of congeners. 3D-QSAR methods are known to be highly sensitive to ligand conformation and alignment method. The current study collects 32 unique positions of congeneric ligands co-crystallized with the binding domain of AMPA receptors and aligns them using protein coordinates. Thus, it allows for a unique opportunity to consider a ligands' orientation aligned by their mode of binding in a native molecular target. Comparative molecular field analysis (CoMFA) models were generated for this alignment and compared with the results of analogous modeling using standard structure-based alignment or obtained in docking simulations of the ligands' molecules. In comparison with classically derived models, the model based on X-ray crystallographic studies showed much better performance and statistical significance. Although the 3D-QSAR methods are mainly employed when crystallographic information is limited, the current study underscores the importance that the selection of inappropriate molecular conformations and alignment methods can lead to generation of erroneous models and false conclusions.
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Affiliation(s)
- Rafał D Urniaż
- Medical University of Lublin, Laboratory of Medicinal Chemistry and Neuroengineering, Chodźki 4a Street, 20-093 Lublin, Poland
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Tanwar O, Marella A, Shrivastava S, Mumtaz Alam M, Akhtar M. Pharmacophore model generation and 3D-QSAR analysis of N-acyl and N-aroylpyrazolines for enzymatic and cellular B-Raf kinase inhibition. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0210-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Monga J, Khokra SL, Husain A. Pharmacophore modeling studies on N-hydroxyphenyl acrylamides and N-hydroxypyridin-2-yl-acrylamides as inhibitor of human cancer leukemia K562 cells. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0182-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Mustyala KK, Chitturi AR, Naikal James PS, Vuruputuri U. Pharmacophore mapping and in silico screening to identify new potent leads for A2Aadenosine receptor as antagonists. J Recept Signal Transduct Res 2012; 32:102-13. [DOI: 10.3109/10799893.2012.660532] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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12
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Arooj M, Thangapandian S, John S, Hwang S, Park JK, Lee KW. 3D QSAR pharmacophore modeling, in silico screening, and density functional theory (DFT) approaches for identification of human chymase inhibitors. Int J Mol Sci 2011; 12:9236-64. [PMID: 22272131 PMCID: PMC3257128 DOI: 10.3390/ijms12129236] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/18/2011] [Accepted: 11/23/2011] [Indexed: 11/18/2022] Open
Abstract
Human chymase is a very important target for the treatment of cardiovascular diseases. Using a series of theoretical methods like pharmacophore modeling, database screening, molecular docking and Density Functional Theory (DFT) calculations, an investigation for identification of novel chymase inhibitors, and to specify the key factors crucial for the binding and interaction between chymase and inhibitors is performed. A highly correlating (r = 0.942) pharmacophore model (Hypo1) with two hydrogen bond acceptors, and three hydrophobic aromatic features is generated. After successfully validating "Hypo1", it is further applied in database screening. Hit compounds are subjected to various drug-like filtrations and molecular docking studies. Finally, three structurally diverse compounds with high GOLD fitness scores and interactions with key active site amino acids are identified as potent chymase hits. Moreover, DFT study is performed which confirms very clear trends between electronic properties and inhibitory activity (IC(50)) data thus successfully validating "Hypo1" by DFT method. Therefore, this research exertion can be helpful in the development of new potent hits for chymase. In addition, the combinational use of docking, orbital energies and molecular electrostatic potential analysis is also demonstrated as a good endeavor to gain an insight into the interaction between chymase and inhibitors.
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Affiliation(s)
- Mahreen Arooj
- Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Gazwa-dong, Jinju 660-701, Korea; E-Mails: (M.A.); (S.T.); (S.J.); (S.H.)
| | - Sundarapandian Thangapandian
- Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Gazwa-dong, Jinju 660-701, Korea; E-Mails: (M.A.); (S.T.); (S.J.); (S.H.)
| | - Shalini John
- Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Gazwa-dong, Jinju 660-701, Korea; E-Mails: (M.A.); (S.T.); (S.J.); (S.H.)
| | - Swan Hwang
- Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Gazwa-dong, Jinju 660-701, Korea; E-Mails: (M.A.); (S.T.); (S.J.); (S.H.)
| | - Jong Keun Park
- Department of Chemistry Education, Research Institute of Natural Science (RINS), Educational Research Institute, Gyeongsang National University, Jinju 660-701, Korea; E-Mail:
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science(RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Gazwa-dong, Jinju 660-701, Korea; E-Mails: (M.A.); (S.T.); (S.J.); (S.H.)
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López-Vallejo F, Peppard TL, Medina-Franco JL, Martínez-Mayorga K. Computational methods for the discovery of mood disorder therapies. Expert Opin Drug Discov 2011; 6:1227-45. [PMID: 22647063 DOI: 10.1517/17460441.2011.637106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Despite the significant progress, research is still needed to reveal details of the complex and dynamic chemical processes operating in the central nervous system (CNS) and their relationship to psychological effects such as mood disorders. The incidence of behavioral depression is widely spread worldwide, with an estimated 14.8 million adults diagnosed yearly in the United States alone. The efficacy of current antidepressants on 50 - 60% of patients, their slow onset of action and the prevalence of adverse side effects highlight the need for developing a new generation of improved antidepressants. Computational methods have the potential to aid in the discovery of mood modulators. AREAS COVERED This review contains three main sections: historical evolution of marketed antidepressants, physicochemical and structural properties of antidepressant compounds reported in the ChEMBL database and recent efforts in the design and discovery of antidepressants using computational methods. The authors provide details of the computational methods employed, from chemoinformatic analyses to molecular modeling. EXPERT OPINION While there have been numerous and important findings in depression research, the high cost and time spent on research into new therapies for brain disorders is a risky undertaking. Computational methodologies can be employed to speed up the discovery of new antidepressants and to detect new sources of chemical compounds with potential antidepressant activity. Compound collections containing compounds already approved in the pharmaceutical and food industries that cover the property space and complement the structural space of CNS drugs represent a promising starting point for the discovery of new antidepressant agents.
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WITHDRAWN: Predicting substituted 2-butylbenzimidazoles derivatives as angiotensin II receptor antagonists: 3D-QSAR and pharmacophore modeling. JOURNAL OF SAUDI CHEMICAL SOCIETY 2011. [DOI: 10.1016/j.jscs.2011.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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3D-QSAR and docking-based combined in silico study on C-5 methyl substituted 4-arylthio and 4-aryloxy-3-iodopyridin-2-(1H)-one as HIV-1 RT inhibitors. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9720-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Reddy KK, Singh SK, Dessalew N, Tripathi SK, Selvaraj C. Pharmacophore modelling and atom-based 3D-QSAR studies on N-methyl pyrimidones as HIV-1 integrase inhibitors. J Enzyme Inhib Med Chem 2011; 27:339-47. [PMID: 21699459 DOI: 10.3109/14756366.2011.590803] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pharmacophore modelling and atom-based 3D-QSAR studies were carried out for a series of compounds belonging to N-methyl pyrimidones as HIV-1 integrase inhibitors. Based on the ligand-based pharmacophore model, we got 5-point pharmacophore model AADDR, with two hydrogen bond acceptors (A), two hydrogen bond donors (D) and one aromatic ring (R). The generated pharmacophore-based alignment was used to derive a predictive atom-based 3D-QSAR model for the training set (r(2) = 0.92, SD = 0.16, F = 84.8, N = 40) and for test set (Q(2) = 0.71, RMSE = 0.06, Pearson R = 0.90, N = 10). From these results, AADDR pharmacophore feature was selected as best common pharmacophore hypothesis, and atom-based 3D-QSAR results also support the outcome by means of favourable and unfavourable regions of hydrophobic and electron-withdrawing groups for the most potent compound 30. These results can be useful for further design of new and potent HIV-1 IN inhibitors.
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Affiliation(s)
- Karnati Konda Reddy
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Noscapinoids with anti-cancer activity against human acute lymphoblastic leukemia cells (CEM): a three dimensional chemical space pharmacophore modeling and electronic feature analysis. J Mol Model 2011; 18:307-18. [DOI: 10.1007/s00894-011-1057-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Accepted: 03/22/2011] [Indexed: 10/18/2022]
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Xiao D, Palani A, Sofolarides M, Huang Y, Aslanian R, Vaccaro H, Hong L, McKittrick B, West RE, Williams SM, Wu RL, Hwa J, Sondey C, Lachowicz J. Discovery of a series of potent arylthiadiazole H3 antagonists. Bioorg Med Chem Lett 2011; 21:861-4. [DOI: 10.1016/j.bmcl.2010.11.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 11/07/2010] [Accepted: 11/16/2010] [Indexed: 10/18/2022]
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Tawari NR, Degani MS. Pharmacophore mapping and electronic feature analysis for a series of nitroaromatic compounds with antitubercular activity. J Comput Chem 2010; 31:739-51. [PMID: 19569203 DOI: 10.1002/jcc.21371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A five point pharmacophore was generated using PHASE for a series of nitroaromatic compounds and their congeners as antitubercular agents. The generated pharmacophore yielded significant 3D-QSAR model with r(2) of 0.890 for a training set of 92 molecules. The model also showed excellent predictive power with correlation coefficient Q(2) of 0.857 for a test set of 31 compounds. The pharmacophore indicated that presence of a nitro group, a piperazine moiety, one aromatic ring feature and two acceptor features are necessary for potent antitubercular activity. The pharmacophore was supported by electronic property analysis using density functional theory (DFT) at B3LYP/3-21*G level. Molecular electrostatic profile of the compounds was consistent with the generated pharmacophore model, particularly appearance of localized negative potential regions near both the oxygen atoms of nitro group extending laterally to the isoxazole ring system/amide bond in the most active compounds. Calculated data further revealed that all active compounds have smaller LUMO energies located over the nitro group, furan ring, and isoxazole ring/amide bond attached to it. Higher negative values of LUMO energies concentrated over the nitro group are indicative of the electron acceptor capacity of the compounds, suggesting that these compounds are prodrugs and must be activated by TB-nitroreductase. The results obtained from this study should aid in efficient design and development of nitroaromatic compounds as antitubercular agents.
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Affiliation(s)
- Nilesh R Tawari
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, University of Mumbai, Matunga (E), Mumbai 400019, India
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Straßer A, Wittmann HJ. 3D-QSAR CoMFA Study to Predict Orientation of Suprahistaprodifens and Phenoprodifens in the Binding-Pocket of Four Histamine H1-Receptor Species. Mol Inform 2010; 29:333-41. [DOI: 10.1002/minf.200900036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 02/22/2010] [Indexed: 11/08/2022]
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Pharmacophore modeling and 3D-QSAR analysis of phosphoinositide 3-kinase p110α inhibitors. J Mol Model 2010; 16:1449-60. [DOI: 10.1007/s00894-010-0659-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 01/06/2010] [Indexed: 11/26/2022]
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Telvekar VN, Patel DJ, Jadhav NC, Mishra SJ. Three-dimensional QSAR and pharmacophore mapping of biphenyl benzoic acid derivatives as selective human β3-adrenergic receptor agonists. Med Chem Res 2009. [DOI: 10.1007/s00044-009-9261-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Tuccinardi T, Ortore G, Santos MA, Marques SM, Nuti E, Rossello A, Martinelli A. Multitemplate Alignment Method for the Development of a Reliable 3D-QSAR Model for the Analysis of MMP3 Inhibitors. J Chem Inf Model 2009; 49:1715-24. [DOI: 10.1021/ci900118v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Tiziano Tuccinardi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, and Centro de Química Estrutural, Instituto Superior Técnico, Rua Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Gabriella Ortore
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, and Centro de Química Estrutural, Instituto Superior Técnico, Rua Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - M. Amélia Santos
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, and Centro de Química Estrutural, Instituto Superior Técnico, Rua Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Sérgio M. Marques
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, and Centro de Química Estrutural, Instituto Superior Técnico, Rua Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Elisa Nuti
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, and Centro de Química Estrutural, Instituto Superior Técnico, Rua Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Armando Rossello
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, and Centro de Química Estrutural, Instituto Superior Técnico, Rua Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Adriano Martinelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, and Centro de Química Estrutural, Instituto Superior Técnico, Rua Rovisco Pais 1, 1049-001 Lisboa, Portugal
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Bag S, Tawari N, Degani M. Insight into Inhibitory Activity ofMycobacterialDihydrofolate Reductase Inhibitors byIn-silicoMolecular Modeling Approaches. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200860067] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Fan F, Zhu J, Ni S, Cheng J, Tang Y, Kang C, Li J, Jiang H. Refinement and 3D-QSAR Studies of Inhibitors of Cyclophilin A Containing Amide Linker. QSAR & COMBINATORIAL SCIENCE 2009; 28:183-193. [PMID: 32327951 PMCID: PMC7168557 DOI: 10.1002/qsar.200860076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 09/27/2008] [Accepted: 10/02/2008] [Indexed: 11/07/2022]
Abstract
Cyclophilin A (CypA) is a ubiquitous cellular enzyme playing essential role in many biological processes, and the discovery of CypA inhibitor is now of special interest in the treatment of immunological disorders. In this work, molecular modeling studies were performed to develop a predictive Common Pharmacophore Hypothesis (CPH) and use it for alignment in 3D-QSAR studies using CoMFA and CoMSIA. A total of 30 compounds containing an amide fragment as the key linker, consisting of 17 of our previously discovered CypA inhibitors and 13 other inhibitors reported in the literature, were selected for pharmacophore refinement and 3D-QSAR studies. The best pharmacophore hypothesis AADR, which had two hydrogen bond acceptors, a hydrogen bond donor, and an aromatic ring, was obtained and used for the alignment of molecules in CoMFA and CoMSIA model development. The models showed a good r 2 value of 0.992 and 0.949 for CoMFA and CoMSIA, respectively. The contour maps of the models were analyzed to give structural insight for activity improvement of future novel CypA inhibitors. The CPH can also provide a powerful template for virtual screening and design of new CypA inhibitors.
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Affiliation(s)
- Feng Fan
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
- Shanghai Key Laboratory of Chemical Biology, East China University of Science and Technology, PO Box 544, 130 Meilong Road, Shanghai 200237, China
| | - Jin Zhu
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
| | - Shuaishuai Ni
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
| | - Jiagao Cheng
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
- Shanghai Key Laboratory of Chemical Biology, East China University of Science and Technology, PO Box 544, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
| | - Congmin Kang
- College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 260042, China
| | - Jian Li
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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Yang Q, Du L, Tsai KC, Wang X, Li M, You Q. Pharmacophore Mapping for Kv1.5 Potassium Channel Blockers. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200810050] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Telvekar V, Kundaikar H, Patel K, Chaudhari H. 3-D QSAR and Molecular Docking Studies on Aryl Benzofuran-2-yl Ketoxime Derivatives asCandida albicansN-myristoyl transferase Inhibitors. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200810017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Tawari NR, Bag S, Degani MS. Pharmacophore mapping of a series of pyrrolopyrimidines, indolopyrimidines and their congeners as multidrug-resistance-associated protein (MRP1) modulators. J Mol Model 2008; 14:911-21. [DOI: 10.1007/s00894-008-0330-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2008] [Accepted: 06/03/2008] [Indexed: 11/28/2022]
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