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Novel series of 1,2,3-triazolyl-acetamide scaffolds: Synthesis, biological activity and computational molecular modeling. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Verma H, Narendra G, Raju B, Kumar M, Jain SK, Tung GK, Singh PK, Silakari O. 3D-QSAR and scaffold hopping based designing of benzo[d]ox-azol-2(3H)-one and 2-oxazolo[4,5-b]pyridin-2(3H)-one derivatives as selective aldehyde dehydrogenase 1A1 inhibitors: Synthesis and biological evaluation. Arch Pharm (Weinheim) 2022; 355:e2200108. [PMID: 35618489 DOI: 10.1002/ardp.202200108] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 01/16/2023]
Abstract
Aldehyde dehydrogenase 1 (ALDH1A1), an oxidoreductase class of enzymes, is overexpressed in various types of cancer cell lines and is the major cause of resistance to the Food and Drug Administration (FDA)-approved drug, cyclophosphamide (CP). In cancer conditions, CP undergoes a sequence of biotransformations to form an active metabolite, aldophosphamide, which further biotransforms to its putative cytotoxic metabolite, phosphoramide mustard. However, in resistant cancer conditions, aldophosphamide is converted into its inactive metabolite, carboxyphosphamide, via oxidation with ALDH1A1. Herein, to address the issue of ALDH1A1 mediated CP resistance, we report a series of benzo[d]oxazol-2(3H)-one and 2-oxazolo[4,5-b]pyridin-2(3H)-one derivatives as selective ALDH1A1 inhibitors. These inhibitors were designed using a validated 3D-quantitative structure activity relationship (3D-QSAR) model coupled with scaffold hopping. The 3D-QSAR model was developed using reported indole-2,3-diones based ALDH1A1 inhibitors, which provided field points in terms of electrostatic, van der Waals and hydrophobic potentials required for selectively inhibiting ALDH1A1. The most selective indole-2,3-diones-based compound, that is, cmp 3, was further considered for scaffold hopping. Two top-ranked bioisosteres, that is, benzo[d]oxazol-2(3H)-one and 2-oxazolo[4,5-b]pyridin-2(3H)-one, were selected for designing new inhibitors by considering the field pattern of 3D-QSAR. All designed molecules were mapped perfectly on the 3D-QSAR model and found to be predictive with good inhibitory potency (pIC50 range: 7.5-6.8). Molecular docking was carried out for each designed molecule to identify key interactions that are required for ALDH1A1 inhibition and to authenticate the 3D-QSAR result. The top five inhibitor-ALDH1A1 complexes were also submitted for molecular dynamics simulations to access their stability. In vitro enzyme assays of 21 compounds suggested that these compounds are selective toward ALDH1A1 over the other two isoforms, that is, ALDH2 and ALDH3A1. All the compounds were found to be at least three and two times more selective toward ALDH1A1 over ALDH2 and ALDH3A1, respectively. All the compounds showed an IC50 value in the range of 0.02-0.80 μM, which indicates the potential for these to be developed as adjuvant therapy for CP resistance.
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Affiliation(s)
- Himanshu Verma
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - Gera Narendra
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - Baddipadige Raju
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - Manoj Kumar
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
| | - Subheet K Jain
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, India
| | - Gurleen K Tung
- Centre for Basic and Translational Research in Health Sciences, Guru Nanak Dev University, Amritsar, India
| | - Pankaj K Singh
- Faculty of Medicine, Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Om Silakari
- Molecular Modelling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, India
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Li W, Liu X, Muhammad S, Shi J, Meng Y, Wang J. Computational investigation of TGF-β receptor inhibitors for treatment of idiopathic pulmonary fibrosis: Field-based QSAR model and molecular dynamics simulation. Comput Biol Chem 2018; 76:139-150. [PMID: 30015175 DOI: 10.1016/j.compbiolchem.2018.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 10/28/2022]
Abstract
The discovery of drugs relevant to transforming growth factor β (TGF-β) receptor inhibitors have been considered as a considerable challenge during therapy idiopathic pulmonary fibrosis diseases. For the first time, herein we illustrate a field-based quantitative structure-activity relationship (QSAR) model and molecular dynamics (MD) simulations for novel 7-substituted-pyrazolo [4, 3-b] pyridine derivatives with biological activity for the TGF-β receptor, with an attempt of elucidating the 3D structural features that are essential for the activity. Results demonstrate that the field-based model (Q2 = 0.548, R2training = 0.840, R2test = 0.750) are acceptable with good predictive capabilities. In addition, MD studies were also carried out on the training set with the aim of exploring their binding modes in the active pocket of TGF-β receptor, resulting in some of the crucial structural fragments which are responsible for inhibitory activity. Therefore, we summarized the following features required for TGF-β receptor inhibition: electronegative in region1, bulky groups in region2 and smaller groups in region3. Based on the model and related information, we hope the above information provides an important insight for understanding the interactions of the inhibitors and TGF-β receptor, which may be useful in discovering novel potent inhibitors.
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Affiliation(s)
- Wei Li
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Xue Liu
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology, Shenyang, China
| | - Suleiman Muhammad
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - JiYue Shi
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - YanQiu Meng
- Department of Pharmaceutical Engineering, Shenyang University of Chemical Technology, Shenyang, China.
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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Abdou NS, Serya RAT, Esmat A, Tolba MF, Ismail NSM, Abouzid KAM. Synthesis and in vitro antiproliferative activity of novel pyrazolo[3,4-d]pyrimidine derivatives. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00127g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel series of pyrazolo[3,4-d]pyrimidine derivatives were designed, synthesized and evaluated for their antiproliferative activity.
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Affiliation(s)
- Nermin S. Abdou
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Cairo 11566
- Egypt
| | - Rabah A. T. Serya
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Cairo 11566
- Egypt
| | - Ahmed Esmat
- Department of Pharmacology & Toxicology
- Faculty of Pharmacy
- Ain Shams University
- Cairo 11566
- Egypt
| | - Mai F. Tolba
- Department of Pharmacology & Toxicology
- Faculty of Pharmacy
- Ain Shams University
- Cairo 11566
- Egypt
| | - Nasser S. M. Ismail
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Cairo 11566
- Egypt
| | - Khaled A. M. Abouzid
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Cairo 11566
- Egypt
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Slomczynska U, South MS, Bunkers GJ, Edgecomb D, Wyse-Pester D, Selness S, Ding Y, Christiansen J, Ediger K, Miller W, Charumilind P, Hartmann G, Williams J, Dimmic M, Shortt B, Haakenson W, Wideman A, Crawford M, Hresko M, McCarter J. Tioxazafen: A New Broad-Spectrum Seed Treatment Nematicide. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1204.ch010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Urszula Slomczynska
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Michael S. South
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Greg J. Bunkers
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Donald Edgecomb
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Dawn Wyse-Pester
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Shaun Selness
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Yiwei Ding
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Jessica Christiansen
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Kent Ediger
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - William Miller
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Pana Charumilind
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Gregory Hartmann
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Jeremy Williams
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Matthew Dimmic
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Barry Shortt
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - William Haakenson
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Al Wideman
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Michael Crawford
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - Michelle Hresko
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
| | - James McCarter
- Monsanto Corporation, 700 Chesterfield Parkway W., Mail Code BB2A, Chesterfield, Missouri 63017
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Kumar V, Krishna S, Siddiqi MI. Virtual screening strategies: recent advances in the identification and design of anti-cancer agents. Methods 2014; 71:64-70. [PMID: 25171960 DOI: 10.1016/j.ymeth.2014.08.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/31/2014] [Accepted: 08/19/2014] [Indexed: 01/29/2023] Open
Abstract
Virtual screening (VS) is a well-established technique, which is now routinely employed in computer aided drug designing process. VS can be broadly classified into two categories, i.e., ligand-based and structure-based approach. In recent years, VS has emerged as a time saving and cost effective technique, capable of screening millions of compounds in a user friendly manner. In the area of cancer drug design, VS methods have been widely used and helped in identifying novel molecules as potential anti-cancer agents. Both ligand-based VS (LBVS) structure-based VS (SBVS) methods have been highly useful in the identification of a number of potential anti-cancer agents exhibiting activities in nanomolar range. In tune with the rapid progress in the enhancement of computational power, VS has witnessed significant change in terms of speed and hit rate and in future it is expected that VS will be a preferential alternative to high throughput screening (HTS). This review, discusses recent trends and contribution of VS in the area of anti-cancer drug discovery.
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Affiliation(s)
- Vikash Kumar
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shagun Krishna
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India; Academy of Scientific and Innovative Research, New Delhi, India.
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Chaudhuri A, Sarkar I, Chakraborty S. Comparative analysis of binding sites of human meprins with hydroxamic acid derivative by molecular dynamics simulation study. J Biomol Struct Dyn 2013; 32:1969-78. [DOI: 10.1080/07391102.2013.848173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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