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Xie X, Zhang N, Li X, Huang H, Peng C, Huang W, Foster LJ, He G, Han B. Small-molecule dual inhibitors targeting heat shock protein 90 for cancer targeted therapy. Bioorg Chem 2023; 139:106721. [PMID: 37467620 DOI: 10.1016/j.bioorg.2023.106721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/21/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023]
Abstract
Heat shock protein 90, also known as Hsp90, is an extensively preserved molecular chaperone that performs a critical function in organizing various biological pathways and cellular operations. As a potential drug target, Hsp90 is closely linked to cancer. Hsp90 inhibitors are a class of drugs that have been extensively studied in preclinical models and have shown promise in a variety of diseases, especially cancer. However, Hsp90 inhibitors have encountered several challenges in clinical development, such as low efficacy, toxicity, or drug resistance, few Hsp90 small molecule inhibitors have been approved worldwide. Nonetheless, combining Hsp90 inhibitors with other tumor inhibitors, such as HDAC inhibitors, tubulin inhibitors, and Topo II inhibitors, has been shown to have synergistic antitumor effects. Consequently, the development of Hsp90 dual-target inhibitors is an effective strategy in cancer treatment, as it enhances potency while reducing drug resistance. This article provides an overview of Hsp90's domain structure and biological functions, as well as a discussion of the design, discovery, and structure-activity relationships of Hsp90 dual inhibitors, aiming to provide insights into clinical drug research from a medicinal chemistry perspective and discover novel Hsp90 dual inhibitors.
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Affiliation(s)
- Xin Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Nan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Dermatology & Venereology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - He Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada.
| | - Gu He
- Department of Dermatology & Venereology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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Heterocyclic Compounds as Hsp90 Inhibitors: A Perspective on Anticancer Applications. Pharmaceutics 2022; 14:pharmaceutics14102220. [PMID: 36297655 PMCID: PMC9610671 DOI: 10.3390/pharmaceutics14102220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 11/22/2022] Open
Abstract
Heat shock proteins (Hsps) have garnered special attention in cancer therapy as molecular chaperones with regulatory/mediatory effects on folding, maintenance/stability, maturation, and conformation of proteins as well as their effects on prevention of protein aggregation. Hsp90 ensures the stability of various client proteins needed for the growth of cells or the survival of tumor cells; therefore, they are overexpressed in tumor cells and play key roles in carcinogenesis. Accordingly, Hsp90 inhibitors are recognized as attractive therapeutic agents for investigations pertaining to tumor suppression. Natural Hsp90 inhibitors comprising geldanamycin (GM), reclaimed analogs of GM including 17-AAG and DMAG, and radicicol, a natural macrocyclic antifungal, are among the first potent Hsp90 inhibitors. Herein, recently synthesized heterocyclic compounds recognized as potent Hsp90 inhibitors are reviewed along with the anticancer effects of heterocyclic compounds, comprising purine, pyrazole, triazine, quinolines, coumarin, and isoxazoles molecules.
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Fiedler W, Freisleben F, Wellbrock J, Kirschner KN. Mebendazole's Conformational Space and Its Predicted Binding to Human Heat-Shock Protein 90. J Chem Inf Model 2022; 62:3604-3617. [PMID: 35867562 DOI: 10.1021/acs.jcim.2c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent experimental evidence suggests that mebendazole, a popular antiparasitic drug, binds to heat shock protein 90 (Hsp90) and inhibits acute myeloid leukemia cell growth. In this study we use quantum mechanics (QM), molecular similarity, and molecular dynamics (MD) calculations to predict possible binding poses of mebendazole to the adenosine triphosphate (ATP) binding site of Hsp90. Extensive conformational searches and minimization of the five mebendazole tautomers using the MP2/aug-cc-pVTZ theory level resulted in 152 minima. Mebendazole-Hsp90 complex models were subsequently created using the QM optimized conformations and protein coordinates obtained from experimental crystal structures that were chosen through similarity calculations. Nine different poses were identified from a total of 600 ns of explicit solvent, all-atom MD simulations using two different force fields. All simulations support the hypothesis that mebendazole is able to bind to the ATP binding site of Hsp90.
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Affiliation(s)
- Walter Fiedler
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Fabian Freisleben
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Jasmin Wellbrock
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald University Cancer Center, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Karl N Kirschner
- Department of Computer Science, University of Applied Sciences Bonn-Rhein-Sieg, 53757 Sankt Augustin, Germany
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Pan- and isoform-specific inhibition of Hsp90: Design strategy and recent advances. Eur J Med Chem 2022; 238:114516. [DOI: 10.1016/j.ejmech.2022.114516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/11/2022]
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Heat Shock Protein 90 (HSP90) Inhibitors as Anticancer Medicines: A Review on the Computer-Aided Drug Discovery Approaches over the Past Five Years. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2147763. [PMID: 35685897 PMCID: PMC9173959 DOI: 10.1155/2022/2147763] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/08/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022]
Abstract
Cancer is a disease caused by the uncontrolled, abnormal growth of cells in different anatomic sites. In 2018, it was predicted that the worldwide cancer burden would rise to 18.1 million new cases and 9.6 million deaths. Anticancer compounds, often known as chemotherapeutic medicines, have gained much interest in recent cancer research. These medicines work through various biological processes in targeting cells at various stages of the cell's life cycle. One of the most significant roadblocks to developing anticancer drugs is that traditional chemotherapy affects normal cells and cancer cells, resulting in substantial side effects. Recently, advancements in new drug development methodologies and the prediction of the targeted interatomic and intermolecular ligand interaction sites have been beneficial. This has prompted further research into developing and discovering novel chemical species as preferred therapeutic compounds against specific cancer types. Identifying new drug molecules with high selectivity and specificity for cancer is a prerequisite in the treatment and management of the disease. The overexpression of HSP90 occurs in patients with cancer, and the HSP90 triggers unstable harmful kinase functions, which enhance carcinogenesis. Therefore, the development of potent HSP90 inhibitors with high selectivity and specificity becomes very imperative. The activities of HSP90 as chaperones and cochaperones are complex due to the conformational dynamism, and this could be one of the reasons why no HSP90 drugs have made it beyond the clinical trials. Nevertheless, HSP90 modulations appear to be preferred due to the competitive inhibition of the targeted N-terminal adenosine triphosphate pocket. This study, therefore, presents an overview of the various computational models implored in the development of HSP90 inhibitors as anticancer medicines. We hereby suggest an extensive investigation of advanced computational modelling of the three different domains of HSP90 for potent, effective inhibitor design with minimal off-target effects.
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Tavili N, Mokhtari S, Salehabadi H, Esfahanizadeh M, Mohebbi S. Novel N-substituted indole hydrazones as potential antiplatelet agents: synthesis, biological evaluations, and molecular docking studies. Res Pharm Sci 2021; 17:53-65. [PMID: 34909044 PMCID: PMC8621843 DOI: 10.4103/1735-5362.329926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/19/2021] [Accepted: 10/28/2021] [Indexed: 11/05/2022] Open
Abstract
Background and purpose: Antiplatelet agents can diminish the chance of coronary heart diseases due to the prevention of unusual clotting in the arteries by inhibiting platelet aggregation and avoiding the formation of a blood clot. This mechanism can help to prevent ischemic stroke likewise. To improve the activity of these drugs and reduce their side effects, further studies are required. Experimental approach: Based on the previous studies representing the promising antiplatelet activity of indole hydrazones, a series of their homologs containing twenty-one compounds were prepared in two steps. First, alkylation reaction on the nitrogen of the indole ring, and second, chiff base formation by condensation of a primary amine and N-substituted indole-3 carbaldehyde. Consequently, their platelet anti-aggregation activity was evaluated based on the Born turbidimetric method. Findings/Results: Most of the compounds exhibited noticeable activity against platelet aggregation induced by arachidonic acid. Amongst them, two compounds 2e and 2f showed higher activity with IC50 values that made comparable to indomethacin and acetylsalicylic acid as standard drugs and had no toxicity on platelets. Conclusion and implications: The synthesized compounds exhibited promising activity against arachidonic acid-induced aggregation; however, none of them showed noticeable antiplatelet activity induced by adenosine di-phosphate. Chemical structure comparison of the prepared derivatives indicated the existence of a lipophilic medium-sized group on the phenyl ring increased their activity. In addition, the docking studies confirmed this hydrophobic interaction in the lipophilic pocket of cyclooxygenase-1 enzyme suggesting that hydrophobicity of this region plays a pivotal role in the anti-platelet activity of these compounds. To prove this finding, the enzymatic evaluation with the target enzyme is required.
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Affiliation(s)
- Navid Tavili
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, I.R. Iran
| | - Shaya Mokhtari
- Central Research Laboratories, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran.,Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Hafezeh Salehabadi
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, I.R. Iran
| | - Marjan Esfahanizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Shohreh Mohebbi
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, I.R. Iran
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Understanding the Molecular Basis of 5-HT 4 Receptor Partial Agonists through 3D-QSAR Studies. Int J Mol Sci 2021; 22:ijms22073602. [PMID: 33808456 PMCID: PMC8036435 DOI: 10.3390/ijms22073602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/15/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder whose prevalence has an incidence in senior citizens. Unfortunately, current pharmacotherapy only offers symptom relief for patients with side effects such as bradycardia, nausea, and vomiting. Therefore, there is a present need to provide other therapeutic alternatives for treatments for these disorders. The 5-HT4 receptor is an attractive therapeutic target since it has a potential role in central and peripheral nervous system disorders such as AD, irritable bowel syndrome, and gastroparesis. Quantitative structure-activity relationship analysis of a series of 62 active compounds in the 5-HT4 receptor was carried out in the present work. The structure-activity relationship was estimated using three-dimensional quantitative structure-activity relationship (3D-QSAR) techniques based on these structures' field molecular (force and Gaussian field). The best force-field QSAR models achieve a value for the coefficient of determination of the training set of R2training = 0.821, and for the test set R2test = 0.667, while for Gaussian-field QSAR the training and the test were R2training = 0.898 and R2test = 0.695, respectively. The obtained results were validated using a coefficient of correlation of the leave-one-out cross-validation of Q2LOO = 0.804 and Q2LOO = 0.886 for force- and Gaussian-field QSAR, respectively. Based on these results, novel 5-HT4 partial agonists with potential biological activity (pEC50 8.209-9.417 for force-field QSAR and 9.111-9.856 for Gaussian-field QSAR) were designed. In addition, for the new analogues, their absorption, distribution, metabolism, excretion, and toxicity properties were also analyzed. The results show that these new derivatives also have reasonable pharmacokinetics and drug-like properties. Our findings suggest novel routes for the design and development of new 5-HT4 partial agonists.
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Bahrami H, Salehabadi H, Nazari Z, Amanlou M. Combined Virtual Screening, DFT Calculations and Molecular Dynamics Simulations to Discovery of Potent MMP-9 Inhibitors. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666181008095950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background:
Matrix metalloproteinase-9 (MMP-9) plays a crucial role in the development
and progression of cancer. Therefore, identifying its inhibitors has enjoyed numerous
attentions. In this report, a hybrid approach, including pharmacophore-based virtual screening,
docking studies, and density functional theory (DFT) binding energy calculations followed by
molecular dynamics simulations, was used to identify potential MMP-9 inhibitors.
Methods:
Pharmacophore modeling based on ARP101, as a known MMP-9 inhibitor, was performed
and followed by virtual screening of ZINC database and docking studies to introduce a set
of new ligands as candidates for potent inhibitors of MMP-9. The binding energies of MMP-9
and the selected ligands as well as ARP101, were estimated via the DFT energy calculations.
Subsequently, molecular dynamics simulations were applied to evaluate and compare the behavior
of ARP101 and the selected ligand in a dynamic environment.
Results:
(S,Z)-6-(((2,3-dihydro-1H-benzo[d]imidazol-2-yl)thio)methylene)-2-((4,6,7- trimethylquinazolin-
2-yl)amino)-1,4,5,6-tetrahydropyrimidin-4-ol, ZINC63611396, with the largest
DFT binding energy, was selected as a proper potent MMP-9 inhibitor. Molecular dynamics simulations
indicated that the new ligand was stable in the active site.
Conclusion:
The results of this study revealed that compared to the binding energies achieved
from the docking studies, the binding energies obtained from the DFT calculations were more
consistent with the intermolecular interactions. Also, the interaction between the Zinc ion and
ligand, in particular the Zn2+-ligand distance, played a profound role in the quantity of DFT
binding energies.
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Affiliation(s)
- Hamed Bahrami
- Department of Chemistry, University of Zanjan, P.O. Box 45371-38791 Zanjan, Iran
| | - Hafezeh Salehabadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 14176-53955, Iran
| | - Zahra Nazari
- Department of Chemistry, University of Zanjan, P.O. Box 45371-38791 Zanjan, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 14176-53955, Iran
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Allen B, Mehta S, Ember SWJ, Zhu JY, Schönbrunn E, Ayad NG, Schürer SC. Identification of a Novel Class of BRD4 Inhibitors by Computational Screening and Binding Simulations. ACS OMEGA 2017; 2:4760-4771. [PMID: 28884163 PMCID: PMC5579542 DOI: 10.1021/acsomega.7b00553] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/27/2017] [Indexed: 06/07/2023]
Abstract
Computational screening is a method to prioritize small-molecule compounds based on the structural and biochemical attributes built from ligand and target information. Previously, we have developed a scalable virtual screening workflow to identify novel multitarget kinase/bromodomain inhibitors. In the current study, we identified several novel N-[3-(2-oxo-pyrrolidinyl)phenyl]-benzenesulfonamide derivatives that scored highly in our ensemble docking protocol. We quantified the binding affinity of these compounds for BRD4(BD1) biochemically and generated cocrystal structures, which were deposited in the Protein Data Bank. As the docking poses obtained in the virtual screening pipeline did not align with the experimental cocrystal structures, we evaluated the predictions of their precise binding modes by performing molecular dynamics (MD) simulations. The MD simulations closely reproduced the experimentally observed protein-ligand cocrystal binding conformations and interactions for all compounds. These results suggest a computational workflow to generate experimental-quality protein-ligand binding models, overcoming limitations of docking results due to receptor flexibility and incomplete sampling, as a useful starting point for the structure-based lead optimization of novel BRD4(BD1) inhibitors.
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Affiliation(s)
- Bryce
K. Allen
- Department
of Molecular and Cellular Pharmacology, Miller School
of Medicine, Center for Computational Science, Center for Therapeutic Innovation Miller School
of Medicine, Miami Project to Cure Paralysis, Department of Psychiatry and Behavioral
Sciences, Miller School of Medicine, and Sylvester Comprehensive Cancer Center,
Miller School of Medicine, University of
Miami, Miami, Florida 33136, United States
| | - Saurabh Mehta
- Department
of Molecular and Cellular Pharmacology, Miller School
of Medicine, Center for Computational Science, Center for Therapeutic Innovation Miller School
of Medicine, Miami Project to Cure Paralysis, Department of Psychiatry and Behavioral
Sciences, Miller School of Medicine, and Sylvester Comprehensive Cancer Center,
Miller School of Medicine, University of
Miami, Miami, Florida 33136, United States
- Department
of Applied Chemistry, Delhi
Technological University, Delhi 110042, India
| | - Stuart W. J. Ember
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center and Research Institute, Tampa, Florida 33612-9416, United States
| | - Jin-Yi Zhu
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center and Research Institute, Tampa, Florida 33612-9416, United States
| | - Ernst Schönbrunn
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center and Research Institute, Tampa, Florida 33612-9416, United States
| | - Nagi G. Ayad
- Department
of Molecular and Cellular Pharmacology, Miller School
of Medicine, Center for Computational Science, Center for Therapeutic Innovation Miller School
of Medicine, Miami Project to Cure Paralysis, Department of Psychiatry and Behavioral
Sciences, Miller School of Medicine, and Sylvester Comprehensive Cancer Center,
Miller School of Medicine, University of
Miami, Miami, Florida 33136, United States
| | - Stephan C. Schürer
- Department
of Molecular and Cellular Pharmacology, Miller School
of Medicine, Center for Computational Science, Center for Therapeutic Innovation Miller School
of Medicine, Miami Project to Cure Paralysis, Department of Psychiatry and Behavioral
Sciences, Miller School of Medicine, and Sylvester Comprehensive Cancer Center,
Miller School of Medicine, University of
Miami, Miami, Florida 33136, United States
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Abbasi M, Sadeghi-Aliabadi H, Amanlou M. Prediction of new Hsp90 inhibitors based on 3,4-isoxazolediamide scaffold using QSAR study, molecular docking and molecular dynamic simulation. ACTA ACUST UNITED AC 2017; 25:17. [PMID: 28666484 PMCID: PMC5493083 DOI: 10.1186/s40199-017-0182-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/07/2017] [Indexed: 12/15/2022]
Abstract
Background Heat shock protein90 (Hsp90) are overexpressed in tumor cells, so the inhibition of the Hsp90 ATPase activity would be a significantly effective strategy in cancer therapy. Methods In the current study, 3,4-isoxazolediamide derivatives were suggested as an Hsp90 inhibitor for anti-cancer therapy. Multiple linear regression (MLR) and genetic algorithm of partial least square (GA-PLS) methods were performed to build models to predict the inhibitory activity of Hsp90. The leave-one out (LOO) cross-validation and Y-randomization tests were performed to models’ validation. The new ligands were monitored by applicability domain. Molecular docking studies were also conducted to evaluate the mode of interaction of these compounds with Hsp90. Identification of the likely pathways into the active site pocket and the involved residues were performed by CAVAER 3.0.1 software. According to QSAR models and docking analysis, three new compounds were predicted. 50 ns molecular dynamic simulation was performed for the strongest synthesized compound and the best predicted compound in terms of binding energy and interactions between ligand and protein. Results The made models showed the significance of size, shape, symmetry, and branching of molecules in inhibitory activities of Hsp90. Docking studies indicated that two hydroxyl groups in the resorcinol ring were important in interacting with Asp93 and the orientation of these groups was related to substitution of different R1 groups. Comparing of molecular dynamic simulation (MDs) results shows that new compound perched in active site with lower binding energy than the best synthesized compound. Conclusion The QSAR and docking analyses shown to be beneficial tools in the proposal of anti-cancer activities and a leader to the synthesis of new Hsp90 inhibitors based 3,4-isoxazolediamide. The MDs confirmed that predicted ligand is steady in the Hsp90 active sites. Graphical Abstract ![]()
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Affiliation(s)
- Maryam Abbasi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
| | - Hojjat Sadeghi-Aliabadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran.
| | - Massoud Amanlou
- Computational Chemistry Group, Pharmaceutical Sciences Research Center and Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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Abbasi M, Sadeghi-Aliabadi H, Amanlou M. 3D-QSAR, molecular docking, and molecular dynamic simulations for prediction of new Hsp90 inhibitors based on isoxazole scaffold. J Biomol Struct Dyn 2017; 36:1463-1478. [PMID: 28482755 DOI: 10.1080/07391102.2017.1326319] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Heat shock protein 90(Hsp90), as a molecular chaperone, play a crucial role in folding and proper function of many proteins. Hsp90 inhibitors containing isoxazole scaffold are currently being used in the treatment of cancer as tumor suppressers. Here in the present studies, new compounds based on isoxazole scaffold were predicted using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamic (MD) simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were also done. The steric and electrostatic contour map of CoMFA and CoMSIA were created. Hydrophobic, hydrogen bond donor and acceptor of CoMSIA model also were generated, and new compounds were predicted by CoMFA and CoMSIA contour maps. To investigate the binding modes of the predicted compounds in the active site of Hsp90, a molecular docking simulation was carried out. MD simulations were also conducted to evaluate the obtained results on the best predicted compound and the best reported Hsp90 inhibitors in the 3D-QSAR model. Findings indicate that the predicted ligands were stable in the active site of Hsp90.
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Affiliation(s)
- Maryam Abbasi
- a Faculty of Pharmacy, Department of Medicinal Chemistry , Isfahan University of Medical Sciences , 81746-73461 Isfahan , Iran
| | - Hojjat Sadeghi-Aliabadi
- a Faculty of Pharmacy, Department of Medicinal Chemistry , Isfahan University of Medical Sciences , 81746-73461 Isfahan , Iran
| | - Massoud Amanlou
- b Faculty of Pharmacy, Department of Medicinal Chemistry , Drug Design and Development Research Center, Tehran University of Medical Sciences , Tehran , Iran
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12
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Chen YJ, Yang CN. Molecular modeling of structural and functional variance in the SAGA deubiquitinating module caused by Sgf73 Y57A mutation. RSC Adv 2016. [DOI: 10.1039/c6ra12647b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Summary of the structural and dynamic impact caused by Sgf73 Y57A mutation.
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Affiliation(s)
- Ya-Jyun Chen
- Department of Life Sciences
- National University of Kaohsiung
- Kaohsiung
- Taiwan
| | - Chia-Ning Yang
- Department of Life Sciences
- National University of Kaohsiung
- Kaohsiung
- Taiwan
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