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Kumar S, Manoharan A, J J, Abdelgawad MA, Mahdi WA, Alshehri S, Ghoneim MM, Pappachen LK, Zachariah SM, Aneesh TP, Mathew B. Exploiting butyrylcholinesterase inhibitors through a combined 3-D pharmacophore modeling, QSAR, molecular docking, and molecular dynamics investigation †. RSC Adv 2023; 13:9513-9529. [PMID: 36968055 PMCID: PMC10035067 DOI: 10.1039/d3ra00526g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/14/2023] [Indexed: 03/25/2023] Open
Abstract
Alzheimer's disease (AD), a neurodegenerative condition associated with ageing, can occur. AD gradually impairs memory and cognitive function, which leads to abnormal behavior, incapacity, and reliance. By 2050, there will likely be 100 million cases of AD in the world's population. Acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibition are significant components of AD treatment. This work developed models using the genetic method multiple linear regression, atom-based, field-based, and 3-D pharmacophore modelling. Due to internal and external validation, all of the models have solid statistical (R2 > 0.81 and Q2 > 0.77) underpinnings. From a pre-plated CNS library (6055), we discovered a hit compound using virtual screening on a QSAR model. Through molecular docking, additional hit compounds were investigated (XP mode). Finally, a molecular dynamics simulation revealed that the Molecule5093-4BDS complex was stable (100 ns). Finally, the expected ADME properties for the hit compounds (Molecule5093, Molecule1076, Molecule4412, Molecule1053, and Molecule3344) were found. According to the results of our investigation and the prospective hit compounds, BuChE inhibitors may be used as a treatment for AD. Alzheimer's disease (AD), a neurodegenerative condition associated with ageing, can occur.![]()
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Affiliation(s)
- Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences CampusKochi682 041India
| | - Amritha Manoharan
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences CampusKochi682 041India
| | - Jayalakshmi J
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences CampusKochi682 041India
| | - Mohamed A. Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf UniversitySakaka72341Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef UniversityBeni-SuefEgypt
| | - Wael A. Mahdi
- Department of Pharmaceutics, College of Pharmacy, King Saud UniversityRiyadh11451Saudi Arabia
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud UniversityRiyadh11451Saudi Arabia
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa UniversityAd Diriyah13713Saudi Arabia
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy, Al-Azhar UniversityCairo11884Egypt
| | - Leena K. Pappachen
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences CampusKochi682 041India
| | - Subin Mary Zachariah
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences CampusKochi682 041India
| | - T. P. Aneesh
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences CampusKochi682 041India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences CampusKochi682 041India
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Prasetyo WE, Kusumaningsih T, Wibowo FR. Gaining deeper insights into 2,5-disubstituted furan derivatives as potent α-glucosidase inhibitors and discovery of putative targets associated with diabetes diseases using an integrative computational approach. Struct Chem 2022. [DOI: 10.1007/s11224-022-01994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wang Y, Guo Y, Qiang S, Jin R, Li Z, Tang Y, Leung ELH, Guo H, Yao X. 3D-QSAR, Molecular Docking, and MD Simulations of Anthraquinone Derivatives as PGAM1 Inhibitors. Front Pharmacol 2021; 12:764351. [PMID: 34899321 PMCID: PMC8656170 DOI: 10.3389/fphar.2021.764351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/01/2021] [Indexed: 12/29/2022] Open
Abstract
PGAM1 is overexpressed in a wide range of cancers, thereby promoting cancer cell proliferation and tumor growth, so it is gradually becoming an attractive target. Recently, a series of inhibitors with various structures targeting PGAM1 have been reported, particularly anthraquinone derivatives. In present study, the structure–activity relationships and binding mode of a series of anthraquinone derivatives were probed using three-dimensional quantitative structure–activity relationships (3D-QSAR), molecular docking, and molecular dynamics (MD) simulations. Comparative molecular field analysis (CoMFA, r2 = 0.97, q2 = 0.81) and comparative molecular similarity indices analysis (CoMSIA, r2 = 0.96, q2 = 0.82) techniques were performed to produce 3D-QSAR models, which demonstrated satisfactory results, especially for the good predictive abilities. In addition, molecular dynamics (MD) simulations technology was employed to understand the key residues and the dominated interaction between PGAM1 and inhibitors. The decomposition of binding free energy indicated that the residues of F22, K100, V112, W115, and R116 play a vital role during the ligand binding process. The hydrogen bond analysis showed that R90, W115, and R116 form stable hydrogen bonds with PGAM1 inhibitors. Based on the above results, 7 anthraquinone compounds were designed and exhibited the expected predictive activity. The study explored the structure–activity relationships of anthraquinone compounds through 3D-QSAR and molecular dynamics simulations and provided theoretical guidance for the rational design of new anthraquinone derivatives as PGAM1 inhibitors.
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Affiliation(s)
- Yuwei Wang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yifan Guo
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Shaojia Qiang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Ruyi Jin
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Zhi Li
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Yuping Tang
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Elaine Lai Han Leung
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Hui Guo
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
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Faizan S, Prashantha Kumar BR, Lalitha Naishima N, Ashok T, Justin A, Vijay Kumar M, Bistuvalli Chandrashekarappa R, Manjunathaiah Raghavendra N, Kabadi P, Adhikary L. Design, parallel synthesis of Biginelli 1,4-dihydropyrimidines using PTSA as a catalyst, evaluation of anticancer activity and structure activity relationships via 3D QSAR studies. Bioorg Chem 2021; 117:105462. [PMID: 34753059 DOI: 10.1016/j.bioorg.2021.105462] [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: 03/22/2021] [Revised: 10/22/2021] [Accepted: 10/28/2021] [Indexed: 10/19/2022]
Abstract
Biginelli 1,4-dihydropyrimidines are extensively screened for their potential anticancer activity in the last decade. In this context, a series of Biginelli 1,4-dihydropyrimidines were designed and synthesised using PTSA as an efficient catalyst. The synthesised 1,4-dihydropyrimidines were screened for their anticancer activity against MCF-7 breast cancer cells by measuring cytotoxicity. The compounds exhibited activity ranging from weak to significant in terms of percentage cytotoxicity which is proportional to the anticancer activity. Amongst the screened compounds, compounds 4, 6 and 8 exhibited potential anticancer activity. Furthermore, CoMSIA studies were performed to derive the structure activity relationships in a 3D grid space by plotting experimental vs predicted cytotoxic activities. We have an opinion that, this developed model helps us in future to develop more potential 1,4-dihydropyrimidines for their cytotoxicity or anticancer activity.
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Affiliation(s)
- Syed Faizan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570 015, Constituent College of JSS Academy of Higher Education & Research, Mysuru 570 015. India
| | - B R Prashantha Kumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570 015, Constituent College of JSS Academy of Higher Education & Research, Mysuru 570 015. India
| | - Namburu Lalitha Naishima
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570 015, Constituent College of JSS Academy of Higher Education & Research, Mysuru 570 015. India
| | - T Ashok
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570 015, Constituent College of JSS Academy of Higher Education & Research, Mysuru 570 015. India
| | - Antony Justin
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty 643 001, Nilgiris, Tamil Nadu, India
| | - Merugumolu Vijay Kumar
- NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore 575018, Karnataka, India
| | | | | | - Pradeep Kabadi
- Bioanalytical Division, Biocon Pvt. Ltd, Bengaluru 560 100, India
| | - Laxmi Adhikary
- Bioanalytical Division, mAbxience Insud Pharma, Madrid 28050, Spain
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Itteboina R, Ballu S, Sivan SK, Manga V. Molecular docking, 3D-QSAR, molecular dynamics, synthesis and anticancer activity of tyrosine kinase 2 (TYK 2) inhibitors. J Recept Signal Transduct Res 2019; 38:462-474. [PMID: 31038024 DOI: 10.1080/10799893.2019.1585453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A therapeutic rationale is proposed by selectively targeting tyrosine kinase 2 (TYK 2) to obtain potent TYK 2 inhibitors by molecular modeling studies. In the present study, we have taken tyrosine kinase (TYK 2) inhibitors and carried out molecular docking, 3 D quantitative structure-activity relationship (3D-QSAR) analysis and molecular dynamics (MD). Based on the 3D-QSAR results thirteen new compounds (R-1 to R-13) were designed and synthesized in good yields. The synthesized molecules were evaluated for their in vitro anticancer activity against LnCap and A549 cell lines. The molecules R-1, R-3, R-5, R-7, and R-10 exhibited considerable anti cancer activity.
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Affiliation(s)
- Ramesh Itteboina
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad , Telangana State , India
| | - Srilata Ballu
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad , Telangana State , India
| | - Sree Kanth Sivan
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad , Telangana State , India
| | - Vijjulatha Manga
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad , Telangana State , India
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Ballu S, Itteboina R, Sivan SK, Manga V. Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations. J Recept Signal Transduct Res 2018; 38:61-70. [DOI: 10.1080/10799893.2018.1426607] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Srilata Ballu
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Ramesh Itteboina
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sree Kanth Sivan
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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Itteboina R, Ballu S, Sivan SK, Manga V. Molecular modeling-driven approach for identification of Janus kinase 1 inhibitors through 3D-QSAR, docking and molecular dynamics simulations. J Recept Signal Transduct Res 2017; 37:453-469. [DOI: 10.1080/10799893.2017.1328442] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ramesh Itteboina
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Srilata Ballu
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sree Kanth Sivan
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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Mohan CG, Gupta S. QSAR Models towards Cholinesterase Inhibitors for the Treatment of Alzheimer's Disease. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alzheimer's Disease (AD) is a multifactorial neurological syndrome with the combination of aging, genetic, and environmental factors triggering the pathological decline. Interestingly, the importance of the Acetylcholinesterase (AChE) enzyme has increased due to its involvement in the ß-amyloid peptide fibril formation during AD pathogenesis. In silico technique, QSAR has proven its usefulness in pharmaceutical research for the design/optimization of new chemical entities. Further, QSAR method advanced the scope of rational drug design and the search for the mechanism of drug action. It is a well-established fact that the chemical and pharmaceutical effects of a compound are closely related to its physico-chemical properties, which can be calculated by various methods from the compound structure. This chapter focuses on different Quantitative Structure-Activity Relationship (QSAR) studies carried out for a variety of cholinesterase inhibitors for the treatment of AD. These predictive models will be potentially used for further designing better and safer drugs against AD.
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Affiliation(s)
- C. Gopi Mohan
- Amrita Institute of Medical Sciences and Research Centre, India
| | - Shikhar Gupta
- National Institute of Pharmaceutical Education and Research, India
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Itteboina R, Ballu S, Sivan SK, Manga V. Molecular docking, 3D QSAR and dynamics simulation studies of imidazo-pyrrolopyridines as janus kinase 1 (JAK 1) inhibitors. Comput Biol Chem 2016; 64:33-46. [DOI: 10.1016/j.compbiolchem.2016.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 04/16/2016] [Accepted: 04/26/2016] [Indexed: 01/30/2023]
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Da C, Mooberry SL, Gupton JT, Kellogg GE. How to deal with low-resolution target structures: using SAR, ensemble docking, hydropathic analysis, and 3D-QSAR to definitively map the αβ-tubulin colchicine site. J Med Chem 2013; 56:7382-95. [PMID: 23961916 DOI: 10.1021/jm400954h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
αβ-Tubulin colchicine site inhibitors (CSIs) from four scaffolds that we previously tested for antiproliferative activity were modeled to better understand their effect on microtubules. Docking models, constructed by exploiting the SAR of a pyrrole subset and HINT scoring, guided ensemble docking of all 59 compounds. This conformation set and two variants having progressively less structure knowledge were subjected to CoMFA, CoMFA+HINT, and CoMSIA 3D-QSAR analyses. The CoMFA+HINT model (docked alignment) showed the best statistics: leave-one-out q(2) of 0.616, r(2) of 0.949, and r(2)pred (internal test set) of 0.755. An external (tested in other laboratories) collection of 24 CSIs from eight scaffolds were evaluated with the 3D-QSAR models, which correctly ranked their activity trends in 7/8 scaffolds for CoMFA+HINT (8/8 for CoMFA). The combination of SAR, ensemble docking, hydropathic analysis, and 3D-QSAR provides an atomic-scale colchicine site model more consistent with a target structure resolution much higher than the ~3.6 Å available for αβ-tubulin.
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Affiliation(s)
- Chenxiao Da
- Department of Medicinal Chemistry & Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
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Bitencourt M, Freitas MP, Rittner R. The MIA-QSAR Method for the Prediction of Bioactivities of Possible Acetylcholinesterase Inhibitors. Arch Pharm (Weinheim) 2012; 345:723-8. [DOI: 10.1002/ardp.201200079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 04/14/2012] [Accepted: 04/25/2012] [Indexed: 11/10/2022]
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Abstract
The use of Quantitative Structure-Activity Relationship models to address problems in drug discovery has a mixed history, generally resulting from the misapplication of QSAR models that were either poorly constructed or used outside of their domains of applicability. This situation has motivated the development of a variety of model performance metrics (r(2), PRESS r(2), F-tests, etc.) designed to increase user confidence in the validity of QSAR predictions. In a typical workflow scenario, QSAR models are created and validated on training sets of molecules using metrics such as Leave-One-Out or many-fold cross-validation methods that attempt to assess their internal consistency. However, few current validation methods are designed to directly address the stability of QSAR predictions in response to changes in the information content of the training set. Since the main purpose of QSAR is to quickly and accurately estimate a property of interest for an untested set of molecules, it makes sense to have a means at hand to correctly set user expectations of model performance. In fact, the numerical value of a molecular prediction is often less important to the end user than knowing the rank order of that set of molecules according to their predicted end point values. Consequently, a means for characterizing the stability of predicted rank order is an important component of predictive QSAR. Unfortunately, none of the many validation metrics currently available directly measure the stability of rank order prediction, making the development of an additional metric that can quantify model stability a high priority. To address this need, this work examines the stabilities of QSAR rank order models created from representative data sets, descriptor sets, and modeling methods that were then assessed using Kendall Tau as a rank order metric, upon which the Shannon entropy was evaluated as a means of quantifying rank-order stability. Random removal of data from the training set, also known as Data Truncation Analysis (DTA), was used as a means for systematically reducing the information content of each training set while examining both rank order performance and rank order stability in the face of training set data loss. The premise for DTA ROE model evaluation is that the response of a model to incremental loss of training information will be indicative of the quality and sufficiency of its training set, learning method, and descriptor types to cover a particular domain of applicability. This process is termed a "rank order entropy" evaluation or ROE. By analogy with information theory, an unstable rank order model displays a high level of implicit entropy, while a QSAR rank order model which remains nearly unchanged during training set reductions would show low entropy. In this work, the ROE metric was applied to 71 data sets of different sizes and was found to reveal more information about the behavior of the models than traditional metrics alone. Stable, or consistently performing models, did not necessarily predict rank order well. Models that performed well in rank order did not necessarily perform well in traditional metrics. In the end, it was shown that ROE metrics suggested that some QSAR models that are typically used should be discarded. ROE evaluation helps to discern which combinations of data set, descriptor set, and modeling methods lead to usable models in prioritization schemes and provides confidence in the use of a particular model within a specific domain of applicability.
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Tropsha A, Golbraikh A, Cho WJ. Development of kNN QSAR Models for 3-Arylisoquinoline Antitumor Agents. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.7.2397] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sivan SK, Manga V. Multiple receptor conformation docking and dock pose clustering as tool for CoMFA and CoMSIA analysis - a case study on HIV-1 protease inhibitors. J Mol Model 2011; 18:569-82. [PMID: 21547550 DOI: 10.1007/s00894-011-1048-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 03/18/2011] [Indexed: 11/25/2022]
Abstract
Multiple receptors conformation docking (MRCD) and clustering of dock poses allows seamless incorporation of receptor binding conformation of the molecules on wide range of ligands with varied structural scaffold. The accuracy of the approach was tested on a set of 120 cyclic urea molecules having HIV-1 protease inhibitory activity using 12 high resolution X-ray crystal structures and one NMR resolved conformation of HIV-1 protease extracted from protein data bank. A cross validation was performed on 25 non-cyclic urea HIV-1 protease inhibitor having varied structures. The comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were generated using 60 molecules in the training set by applying leave one out cross validation method, r (loo) (2) values of 0.598 and 0.674 for CoMFA and CoMSIA respectively and non-cross validated regression coefficient r(2) values of 0.983 and 0.985 were obtained for CoMFA and CoMSIA respectively. The predictive ability of these models was determined using a test set of 60 cyclic urea molecules that gave predictive correlation (r (pred) (2) ) of 0.684 and 0.64 respectively for CoMFA and CoMSIA indicating good internal predictive ability. Based on this information 25 non-cyclic urea molecules were taken as a test set to check the external predictive ability of these models. This gave remarkable out come with r (pred) (2) of 0.61 and 0.53 for CoMFA and CoMSIA respectively. The results invariably show that this method is useful for performing 3D QSAR analysis on molecules having different structural motifs.
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Affiliation(s)
- Sree Kanth Sivan
- Department of Chemistry, Nizam College, Osmania University, Hyderabad 500001, India
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Sakulsombat M, Zhang Y, Ramström O. Dynamic Systemic Resolution. CONSTITUTIONAL DYNAMIC CHEMISTRY 2011; 322:55-86. [DOI: 10.1007/128_2011_203] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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3D-QSAR and molecular docking studies on derivatives of MK-0457, GSK1070916 and SNS-314 as inhibitors against Aurora B kinase. Int J Mol Sci 2010; 11:4326-47. [PMID: 21151441 PMCID: PMC3000085 DOI: 10.3390/ijms11114326] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 09/21/2010] [Accepted: 09/29/2010] [Indexed: 12/30/2022] Open
Abstract
Development of anticancer drugs targeting Aurora B, an important member of the serine/threonine kinases family, has been extensively focused on in recent years. In this work, by applying an integrated computational method, including comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), homology modeling and molecular docking, we investigated the structural determinants of Aurora B inhibitors based on three different series of derivatives of 108 molecules. The resultant optimum 3D-QSAR models exhibited (q2 = 0.605, r2pred = 0.826), (q2 = 0.52, r2pred = 0.798) and (q2 = 0.582, r2pred = 0.971) for MK-0457, GSK1070916 and SNS-314 classes, respectively, and the 3D contour maps generated from these models were analyzed individually. The contour map analysis for the MK-0457 model revealed the relative importance of steric and electrostatic effects for Aurora B inhibition, whereas, the electronegative groups with hydrogen bond donating capacity showed a great impact on the inhibitory activity for the derivatives of GSK1070916. Additionally, the predictive model of the SNS-314 class revealed the great importance of hydrophobic favorable contour, since hydrophobic favorable substituents added to this region bind to a deep and narrow hydrophobic pocket composed of residues that are hydrophobic in nature and thus enhanced the inhibitory activity. Moreover, based on the docking study, a further comparison of the binding modes was accomplished to identify a set of critical residues that play a key role in stabilizing the drug-target interactions. Overall, the high level of consistency between the 3D contour maps and the topographical features of binding sites led to our identification of several key structural requirements for more potency inhibitors. Taken together, the results will serve as a basis for future drug development of inhibitors against Aurora B kinase for various tumors.
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Jiang Q, Liao H, Yang Q, Zan W, Zang Z. Pharmacophore-based 3D-QSAR as a predictive method for the QSAR analysis on a series of potent and selective inhibitors for three kinases of RTK family. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927021003752788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Singh R, Sobhia ME. Synergistic application of target structure-based alignment and 3D-QSAR study of protein tyrosine phosphatase 1B (PTP1B) inhibitors. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9365-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Dong X, Ebalunode JO, Cho SJ, Zheng W. A novel structure-based multimode QSAR method affords predictive models for phosphodiesterase inhibitors. J Chem Inf Model 2010; 50:240-50. [PMID: 20095527 DOI: 10.1021/ci900283j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantitative structure-activity relationship (QSAR) methods aim to build quantitatively predictive models for the discovery of new molecules. It has been widely used in medicinal chemistry for drug discovery. Many QSAR techniques have been developed since Hansch's seminal work, and more are still being developed. Motivated by Hopfinger's receptor-dependent QSAR (RD-QSAR) formalism and the Lukacova-Balaz scheme to treat multimode issues, we have initiated studies that focus on a structure-based multimode QSAR (SBMM QSAR) method, where the structure of the target protein is used in characterizing the ligand, and the multimode issue of ligand binding is systematically treated with a modified Lukacova-Balaz scheme. All ligand molecules are first docked to the target binding pocket to obtain a set of aligned ligand poses. A structure-based pharmacophore concept is adopted to characterize the binding pocket. Specifically, we represent the binding pocket as a geometric grid labeled by pharmacophoric features. Each pose of the ligand is also represented as a labeled grid, where each grid point is labeled according to the atom types of nearby ligand atoms. These labeled grids or three-dimensional (3D) maps (both the receptor map (R-map) and the ligand map (L-map)) are compared to each other to derive descriptors for each pose of the ligand, resulting in a multimode structure-activity relationship (SAR) table. Iterative partial least-squares (PLS) is employed to build the QSAR models. When we applied this method to analyze PDE-4 inhibitors, predictive models have been developed, obtaining models with excellent training correlation (r(2) = 0.65-0.66), as well as test correlation (R(2) = 0.64-0.65). A comparative analysis with 4 other QSAR techniques demonstrates that this new method affords better models, in terms of the prediction power for the test set.
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Affiliation(s)
- Xialan Dong
- Department of Pharmaceutical Sciences, BRITE Institute, North Carolina Central University, Durham, North Carolina 27707, USA
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Choi J, Ko Y, Lee HS, Park YS, Yang Y, Yoon S. Identification of (β-carboxyethyl)-rhodanine derivatives exhibiting peroxisome proliferator-activated receptor γ activity. Eur J Med Chem 2010; 45:193-202. [DOI: 10.1016/j.ejmech.2009.09.042] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 09/22/2009] [Accepted: 09/24/2009] [Indexed: 11/29/2022]
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Sippl W. 3D-QSAR – Applications, Recent Advances, and Limitations. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9783-6_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Chaudhaery SS, Roy KK, Saxena AK. Consensus Superiority of the Pharmacophore-Based Alignment, Over Maximum Common Substructure (MCS): 3D-QSAR Studies on Carbamates as Acetylcholinesterase Inhibitors. J Chem Inf Model 2009; 49:1590-601. [DOI: 10.1021/ci900049e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shailendra S. Chaudhaery
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow, India 226001
| | - Kuldeep K. Roy
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow, India 226001
| | - Anil K. Saxena
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow, India 226001
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Zaheer-ul H, Uddin R, Yuan H, Petukhov PA, Choudhary MI, Madura JD. Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm. J Chem Inf Model 2008; 48:1092-103. [PMID: 18444627 DOI: 10.1021/ci8000056] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of structurally related steroidal alkaloids as butyrylcholinesterase (BuChE) inhibitors. Docking studies were employed to position the inhibitors into the BuChE active site to determine the most probable binding mode. The strategy was to explore multiple inhibitor conformations in producing a more reliable 3D-QSAR model. These multiple conformations were derived using the FlexS program. The conformation selection step for CoMFA was done by genetic algorithm. The genetic algorithm based CoMFA approach was found to be the best. Both CoMFA and CoMSIA yielded significant cross-validated q(2) values of 0.701 and 0.627 and the r(2) values of 0.979 and 0.982, respectively. These statistically significant models were validated by a test set of five compounds. Comparison of CoMFA and CoMSIA contour maps helped to identify structural requirements for the inhibitors and serves as a basis for the design of the next generation of the inhibitor analogues. The results demonstrate that the combination of ligand-based and receptor-based modeling with use of a genetic algorithm is a powerful approach to build 3D-QSAR models. These data can be used for the lead optimization process with respect to inhibition enhancement which is important for the drug discovery and development for Alzheimer's disease.
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Affiliation(s)
- Haq Zaheer-ul
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical & Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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Braiuca P, Boscarol L, Ebert C, Linda P, Gardossi L. 3D-QSAR Applied to the Quantitative Prediction of Penicillin G Amidase Selectivity. Adv Synth Catal 2006. [DOI: 10.1002/adsc.200505346] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Larsson R, Ramström O. Dynamic Combinatorial Thiolester Libraries for EfficientCatalytic Self-Screening of Hydrolase Substrates. European J Org Chem 2006. [DOI: 10.1002/ejoc.200500699] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sung ND, Cho YK, Kwon BM, Hyun KH, Kim CK. 3D QSAR studies on cinnamaldehyde analogues as farnesyl protein transferase inhibitors. Arch Pharm Res 2005; 27:1001-8. [PMID: 15554254 DOI: 10.1007/bf02975421] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies on 59 cinnamaldehyde analogues as Farnesyl Protein Transferase (FPTase) inhibitors were investigated using comparative molecular field analysis (CoMFA) with the PLS region-focusing method. Forty-nine training set inhibitors were used for CoMFA with two different grid spacings, 2A and 1A. Ten compounds, which were not used in model generation, were used to validate the CoMFA models. After the PLS analysis, the best predictive CoMFA model showed that the cross-validated value (r2cv) and the non-cross validated conventional value (r2ncv) are 0.557 and 0.950, respectively. From the CoMFA contour maps, the steric and electrostatic properties of cinnamaldehyde analogues can be identified and verified.
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Affiliation(s)
- Nack-Do Sung
- Division of Applied Biology & Chemistry, College of Agricultural & Life Sciences, Chungnam National University, Daejeon 305-764, Korea
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Ligand-based QSAR Studies on the Indolinones Derivatives as Inhibitors of the Protein Tyrosine Kinase of Fibroblast Growth Factor Receptor by CoMFA and CoMSIA. B KOREAN CHEM SOC 2004. [DOI: 10.5012/bkcs.2004.25.12.1801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Wanchana S, Yamashita F, Hara H, Fujiwara SI, Akamatsu M, Hashida M. Two‐ and three‐dimensional QSAR of carrier‐mediated transport of β‐lactam antibiotics in Caco‐2 cells. J Pharm Sci 2004; 93:3057-65. [PMID: 15515011 DOI: 10.1002/jps.20220] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this study, we investigated whether such a topological descriptor-based approach is suitable for predicting the carrier-mediated transport of 20 beta-lactam antibiotics that are substrates of peptide transporters. To select the molecular descriptors that can effectively predict a targeted property in QSAR analysis, the genetic algorithm-combined partial least squares approach was used. The feasibility of the two-dimensional (2D)-QSAR approach was compared with that of comparative molecular field analysis (CoMFA). The logarithm of the uptake values of 20 beta-lactam antibiotics in Caco-2 cells obtained from the literature ranged from -1.15 to 1.09 (nmol/cm2/2 h). When preliminary leave-one-out cross-validated partial least squares analyses implemented in the SYBYL/CoMFA program were conducted, the r2pred was 0.759 and the standard error of prediction (s) was 0.373. However, the 2D-QSAR approach based on Molconn-Z descriptors gave a better predictability (r2pred = 0.923, s = 0.211), where 14 descriptors were selected and the optimal number of principal components was 4. Considering that the 2D-topological descriptors are less computationally intensive and practically completely automated, the simple 2D-QSAR model is also of great importance in drug discovery settings.
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Affiliation(s)
- Suchada Wanchana
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Hyun K, Lee D, Lee BS, Kim C. Receptor-based 3D QSAR Studies on PPAR? Agonists using CoMFA and CoMSIA Approaches. ACTA ACUST UNITED AC 2004. [DOI: 10.1002/qsar.200430878] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Wellenzohn B, Tonmunphean S, Khalid A, Choudhary MI, Rode BM. 3D-QSAR Studies on natural acetylcholinesterase inhibitors of Sarcococca saligna by comparative molecular field analysis (CoMFA). Bioorg Med Chem Lett 2003; 13:4375-80. [PMID: 14643329 DOI: 10.1016/j.bmcl.2003.09.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have derived a comprehensive structure-activity relationship (SAR) picture for a new series of natural acetylcholinesterase inhibitors isolated from Sarcococca saligna. A set of 32 previously isolated and tested pregnane-type steroidal alkaloids inhibitors were investigated with respect to their IC(50) values (pIC(50)) against the AChE enzyme in order to derive CoMFA models using atom-based alignment. A highly significant CoMFA model was obtained with r(2) value of 0.974. The q(2) (cross validation r(2)) value also confirms the statistical significance of our model.
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Sippl W. Binding affinity prediction of novel estrogen receptor ligands using receptor-based 3-D QSAR methods. Bioorg Med Chem 2002; 10:3741-55. [PMID: 12413831 DOI: 10.1016/s0968-0896(02)00375-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have recently reported the development of a 3-D QSAR model for estrogen receptor ligands showing a significant correlation between calculated molecular interaction fields and experimentally measured binding affinity. The ligand alignment obtained from docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection procedure, a significant and robust model was obtained (q(2)(LOO)=0.921, SDEP=0.345). To further analyze the robustness and the predictivity of the established model several recently developed estrogen receptor ligands were selected as external test set. An excellent agreement between predicted and experimental binding data was obtained indicated by an external SDEP of 0.531. Two other traditionally used prediction techniques were applied in order to check the performance of the receptor-based 3-D QSAR procedure. The interaction energies calculated on the basis of receptor-ligand complexes were correlated with experimentally observed affinities. Also ligand-based 3-D QSAR models were generated using program FlexS. The interaction energy-based model, as well as the ligand-based 3-D QSAR models yielded models with lower predictivity. The comparison with the interaction energy-based model and with the ligand-based 3-D QSAR models, respectively, indicates that the combination of receptor-based and 3-D QSAR methods is able to improve the quality of prediction.
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Affiliation(s)
- Wolfgang Sippl
- Institute for Pharmaceutical Chemistry, Heinrich-Heine-Universität Düsseldorf, Germany.
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Sippl W. Development of biologically active compounds by combining 3D QSAR and structure-based design methods. J Comput Aided Mol Des 2002; 16:825-30. [PMID: 12825795 DOI: 10.1023/a:1023888813526] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
One of the major challenges in computational approaches to drug design is the accurate prediction of the binding affinity of novel biomolecules. In the present study an automated procedure which combines docking and 3D-QSAR methods was applied to several drug targets. The developed receptor-based 3D-QSAR methodology was tested on several sets of ligands for which the three-dimensional structure of the target protein has been solved--namely estrogen receptor, acetylcholine esterase and protein-tyrosine-phosphatase 1B. The molecular alignments of the studied ligands were determined using the docking program AutoDock and were compared with the X-ray structures of the corresponding protein-ligand complexes. The automatically generated protein-based ligand alignment obtained was subsequently taken as basis for a comparative field analysis applying the GRID/GOLPE approach. Using GRID interaction fields and applying variable selection procedures, highly predictive models were obtained. It is expected that concepts from receptor-based 3D QSAR will be valuable tools for the analysis of high-throughput screening as well as virtual screening data.
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Affiliation(s)
- Wolfgang Sippl
- Institute for Pharmaceutical Chemistry, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany.
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Pilger C, Bartolucci C, Lamba D, Tropsha A, Fels G. Accurate prediction of the bound conformation of galanthamine in the active site of Torpedo californica acetylcholinesterase using molecular docking. J Mol Graph Model 2002; 19:288-96, 374-8. [PMID: 11449566 DOI: 10.1016/s1093-3263(00)00056-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The alkaloid (-)-galanthamine is known to produce significant improvement of cognitive performances in patients with the Alzheimer's disease. Its mechanism of action involves competitive and reversible inhibition of acetylcholinesterase (AChE). Herein, we correctly predict the orientation and conformation of the galanthamine molecule in the active site of AChE from Torpedo californica (TcAChE) using a combination of rigid docking and flexible geometry optimization with a molecular mechanics force field. The quality of the predicted model is remarkable, as indicated by the value of the RMS deviation of approximately 0.5A when compared with the crystal structure of the TcAChE-galanthamine complex. A molecular model of the complex between TcAChE and a galanthamine derivative, SPH1107, with a long chain substituent on the nitrogen has been generated as well. The side chain of this ligand is predicted to extend along the enzyme active site gorge from the anionic subsite, at the bottom, to the peripheral anionic site, at the top. The docking procedure described in this paper can be applied to produce models of ligand-receptor complexes for AChE and other macromolecular targets of drug design.
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Affiliation(s)
- C Pilger
- Universitaet-GH Paderborn, Chemie und Chemietechnik, Paderborn, Germany
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Sippl W, Contreras JM, Parrot I, Rival YM, Wermuth CG. Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors. J Comput Aided Mol Des 2001; 15:395-410. [PMID: 11394735 DOI: 10.1023/a:1011150215288] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The paper describes the construction, validation and application of a structure-based 3D QSAR model of novel acetylcholinesterase (AChE) inhibitors. Initial use was made of four X-ray structures of AChE complexed with small, non-specific inhibitors to create a model of the binding of recently developed aminopyridazine derivatives. Combined automated and manual docking methods were applied to dock the co-crystallized inhibitors into the binding pocket. Validation of the modelling process was achieved by comparing the predicted enzyme-bound conformation with the known conformation in the X-ray structure. The successful prediction of the binding conformation of the known inhibitors gave confidence that we could use our model to evaluate the binding conformation of the aminopyridazine compounds. The alignment of 42 aminopyridazine compounds derived by the docking procedure was taken as the basis for a 3D QSAR analysis applying the GRID/GOLPE method. A model of high quality was obtained using the GRID water probe, as confirmed by the cross-validation method (q2LOO = 0.937, q2L50%O = 0.910). The validated model, together with the information obtained from the calculated AChE-inhibitor complexes, were considered for the design of novel compounds. Seven designed inhibitors which were synthesized and tested were shown to be highly active. After performing our modelling study the X-ray structure of AChE complexed with donepezil, an inhibitor structurally related to the developed aminopyirdazines, has been made available. The good agreement found between the predicted binding conformation of the aminopyridazines and the one observed for donepezil in the crystal structure further supports our developed model.
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Affiliation(s)
- W Sippl
- Institut für Pharmazeutische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany.
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Sippl W. Receptor-based 3D QSAR analysis of estrogen receptor ligands--merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods. J Comput Aided Mol Des 2000; 14:559-72. [PMID: 10921772 DOI: 10.1023/a:1008115913787] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient (r2 = 0.617, q2Loo = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection, a significant and robust model was obtained (r2 = 0.991, q2LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment (r2 = 0.951, q2L00 = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model.
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Affiliation(s)
- W Sippl
- Institute for Pharmaceutical Chemistry, Heinrich-Heine-University Düsseldorf, Germany.
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36
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Sippl W, Höltje HD. Structure-based 3D-QSAR—merging the accuracy of structure-based alignments with the computational efficiency of ligand-based methods. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0166-1280(99)00361-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Hasegawa K, Funatsu K. Partial least squares modeling and genetic algorithm optimization in quantitative structure-activity relationships. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2000; 11:189-209. [PMID: 10969871 DOI: 10.1080/10629360008033231] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Quantitative structure-activity relationship (QSAR) studies based on chemometric techniques are reviewed. Partial least squares (PLS) is introduced as a novel robust method to replace classical methods such as multiple linear regression (MLR). Advantages of PLS compared to MLR are illustrated with typical applications. Genetic algorithm (GA) is a novel optimization technique which can be used as a search engine in variable selection. A novel hybrid approach comprising GA and PLS for variable selection developed in our group (GAPLS) is described. The more advanced method for comparative molecular field analysis (CoMFA) modeling called GA-based region selection (GARGS) is described as well. Applications of GAPLS and GARGS to QSAR and 3D-QSAR problems are shown with some representative examples. GA can be hybridized with nonlinear modeling methods such as artificial neural networks (ANN) for providing useful tools in chemometric and QSAR.
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Affiliation(s)
- K Hasegawa
- Nippon Roche Research Center, Nippon Roche K.K., Kanagawa, Japan
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Novel variable selection quantitative structure--property relationship approach based on the k-nearest-neighbor principle. JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES 2000; 40:185-94. [PMID: 10661566 DOI: 10.1021/ci980033m] [Citation(s) in RCA: 304] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel automated variable selection quantitative structure-activity relationship (QSAR) method, based on the kappa-nearest neighbor principle (kNN-QSAR) has been developed. The kNN-QSAR method explores formally the active analogue approach, which implies that similar compounds display similar profiles of pharmacological activities. The activity of each compound is predicted as the average activity of K most chemically similar compounds from the data set. The robustness of a QSAR model is characterized by the value of cross-validated R2 (q2) using the leave-one-out cross-validation method. The chemical structures are characterized by multiple topological descriptors such as molecular connectivity indices or atom pairs. The chemical similarity is evaluated by Euclidean distances between compounds in multidimensional descriptor space, and the optimal subset of descriptors is selected using simulated annealing as a stochastic optimization algorithm. The application of the kNN-QSAR method to 58 estrogen receptor ligands as well as to several other groups of pharmacologically active compounds yielded QSAR models with q2 values of 0.6 or higher. Due to its relative simplicity, high degree of automation, nonlinear nature, and computational efficiency, this method could be applied routinely to a large variety of experimental data sets.
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Bernard P, Kireev DB, Chrétien JR, Fortier PL, Coppet L. Automated docking of 82 N-benzylpiperidine derivatives to mouse acetylcholinesterase and comparative molecular field analysis with 'natural' alignment. J Comput Aided Mol Des 1999; 13:355-71. [PMID: 10425601 DOI: 10.1023/a:1008071118697] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Automated docking and three-dimensional Quantitative Structure-Activity Relationship studies (3D QSAR) were performed for a series of 82 reversible, competitive and selective acetylcholinesterase (AChE) inhibitors. The suggested automated docking technique, making use of constraints taken from experimental crystallographic data, allowed to dock all the 82 substituted N-benzylpiperidines to the crystal structure of mouse AChE, because of short computational times. A 3D QSAR model was then established using the CoMFA method. In contrast to conventional CoMFA studies, the compounds were not fitted to a reference molecule but taken in their 'natural' alignment obtained by the docking study. The established and validated CoMFA model was then applied to another series of 29 N-benzylpiperidine derivatives whose AChE inhibitory activity data were measured under different experimental conditions. A good correlation between predicted and experimental activity data shows that the model can be extended to AChE inhibitory activity data measured on another acetylcholinesterase and/or at different incubation times and pH level.
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Affiliation(s)
- P Bernard
- Laboratoire de Chimiométrie, Université d'Orléans, France
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Vaz RJ, McLean LR, Pelton JT. Evaluation of proposed modes of binding of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxy]phenyl]-3-(7-am idino- 2- naphthyl)propanoic acid hydrochloride and some analogs to factor Xa using a comparative molecular field analysis. J Comput Aided Mol Des 1998; 12:99-110. [PMID: 9690170 DOI: 10.1023/a:1007969517376] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The binding mode of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxy]phenyl]-3-(7-ami dino-2- naphthyl)propanoic acid hydrochloride (DX-9065a, 4) to Factor Xa is examined using inhibition data for a series of analogs that have a hydrophobic group as well as basic or dibasic functionality. Comparative molecular field analysis is utilized on a series of DX-9065a analogs in a series of proposed alternative binding modes. A quantitative measure is provided that distinguishes between the proposed binding modes that describes 'how well' the binding mode explains the structure-activity relationship or the best 3D QSAR agrees with the crystallographically determined binding mode. The best model is in agreement with recently available data [Brandstetter et al., J. Biol. Chem., 271 (1996) 29988]. The highest statistical correlation occurs with the second basic group accommodated in the vicinity of Glu97 and a hydrophobic group accommodated in the pocket defined by Phe174, Tyr99 and Trp215. Also, the best model arises when the conformation of the Glu97 side chain is modified such that an H-bond interaction is maintained with the inhibitor if possible. The model also shows a tightening of the S1 pocket as is shown in the recent data described above.
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Affiliation(s)
- R J Vaz
- Hoechst Marion Roussel Inc., Cincinnati, OH 45215, USA
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