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Khan MI, Park T, Imran MA, Gowda Saralamma VV, Lee DC, Choi J, Baig MH, Dong JJ. Development of machine learning models for the screening of potential HSP90 inhibitors. Front Mol Biosci 2022; 9:967510. [PMID: 36339714 PMCID: PMC9626531 DOI: 10.3389/fmolb.2022.967510] [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: 06/13/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone playing a significant role in the folding of client proteins. This cellular protein is linked to the progression of several cancer types, including breast cancer, lung cancer, and gastrointestinal stromal tumors. Several oncogenic kinases are Hsp90 clients and their activity depends on this molecular chaperone. This makes HSP90 a prominent therapeutic target for cancer treatment. Studies have confirmed the inhibition of HSP90 as a striking therapeutic treatment for cancer management. In this study, we have utilized machine learning and different in silico approaches to screen the KCB database to identify the potential HSP90 inhibitors. Further evaluation of these inhibitors on various cancer cell lines showed favorable inhibitory activity. These inhibitors could serve as a basis for future development of effective HSP90 inhibitors.
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Affiliation(s)
- Mohd Imran Khan
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Taehwan Park
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Mohammad Azhar Imran
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | | | - Duk Chul Lee
- Department of Family Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Jaehyuk Choi
- BNJBiopharma, Yonsei University International Campus, Incheon, South Korea
| | - Mohammad Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- *Correspondence: Jae-June Dong, ; Mohammad Hassan Baig,
| | - Jae-June Dong
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- *Correspondence: Jae-June Dong, ; Mohammad Hassan Baig,
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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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Piven YA, Yastrebova MA, Khamidullina AI, Scherbakov AM, Tatarskiy VV, Rusanova JA, Baranovsky AV, Zinovich VG, Khlebnicova TS, Lakhvich FA. Novel O-acylated (E)-3-aryl-6,7-dihydrobenzisoxazol-4(5H)-one oximes targeting HSP90-HER2 axis in breast cancer cells. Bioorg Med Chem 2022; 53:116521. [PMID: 34844036 DOI: 10.1016/j.bmc.2021.116521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/04/2023]
Abstract
Novel O-acylated (E)-3-aryl-6,7-dihydrobenzisoxazol-4(5H)-one oximes were designed as potential HSP90 inhibitors. A series of the compounds was synthesized by oximation of (E)-3-aryl-6,7-dihydrobenzisoxazol-4(5H)-ones followed by O-acylation with acylamidobenzoic acids. The obtained compounds showed an antiproliferative effect on three breast cancer cell lines (MCF7, MDA-MB-231 and HCC1954). Compound 16s exhibited high antiproliferative potency against HCC1954 breast cancer cells with the IC50 value of 6 µM was selected for in-depth evaluation. Compound 16s did not inhibit the growth of normal epithelial cells. We have demonstrated that the compound 16s can induce apoptosis in cancer cells via inhibition of HSP90 "client" proteins including a key oncogenic receptor, HER2/neu. Described here compounds can be considered for further basic and preclinical investigation as a part of HSP90/HER2-targeted therapies.
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Affiliation(s)
- Yuri A Piven
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha st. 5/2, Minsk 220141, Belarus
| | - Margarita A Yastrebova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Vavilova st. 34/5, Moscow 119334, Russian Federation
| | - Alvina I Khamidullina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Vavilova st. 34/5, Moscow 119334, Russian Federation
| | - Alexander M Scherbakov
- Department of Experimental Tumor Biology, Blokhin N.N. National Medical Research Center of Oncology, Kashirskoye sh. 24, Moscow 115522, Russian Federation
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Vavilova st. 34/5, Moscow 119334, Russian Federation
| | - Julia A Rusanova
- Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska str., Kyiv 01601, Ukraine
| | - Alexander V Baranovsky
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha st. 5/2, Minsk 220141, Belarus
| | - Veronica G Zinovich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha st. 5/2, Minsk 220141, Belarus
| | - Tatyana S Khlebnicova
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha st. 5/2, Minsk 220141, Belarus
| | - Fedor A Lakhvich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha st. 5/2, Minsk 220141, Belarus
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Magwenyane AM, Mhlongo NN, Lawal MM, Amoako DG, Somboro AM, Sosibo SC, Shunmugam L, Khan RB, Kumalo HM. Understanding the Hsp90 N-terminal Dynamics: Structural and Molecular Insights into the Therapeutic Activities of Anticancer Inhibitors Radicicol (RD) and Radicicol Derivative (NVP-YUA922). Molecules 2020; 25:E1785. [PMID: 32295059 PMCID: PMC7221724 DOI: 10.3390/molecules25081785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 11/23/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is a crucial component in carcinogenesis and serves as a molecular chaperone that facilitates protein maturation whilst protecting cells against temperature-induced stress. The function of Hsp90 is highly dependent on adenosine triphosphate (ATP) binding to the N-terminal domain of the protein. Thus, inhibition through displacement of ATP by means of competitive binding with a suitable organic molecule is considered an attractive topic in cancer research. Radicicol (RD) and its derivative, resorcinylic isoxazole amine NVP-AUY922 (NVP), have shown promising pharmacodynamics against Hsp90 activity. To date, the underlying binding mechanism of RD and NVP has not yet been investigated. In this study, we provide a comprehensive understanding of the binding mechanism of RD and NVP, from an atomistic perspective. Density functional theory (DFT) calculations enabled the analyses of the compounds' electronic properties and results obtained proved to be significant in which NVP was predicted to be more favorable with solvation free energy value of -23.3 kcal/mol and highest stability energy of 75.5 kcal/mol for a major atomic delocalization. Molecular dynamic (MD) analysis revealed NVP bound to Hsp90 (NT-NVP) is more stable in comparison to RD (NT-RD). The Hsp90 protein exhibited a greater binding affinity for NT-NVP (-49.4 ± 3.9 kcal/mol) relative to NT-RD (-28.9 ± 4.5 kcal/mol). The key residues influential in this interaction are Gly 97, Asp 93 and Thr 184. These findings provide valuable insights into the Hsp90 dynamics and will serve as a guide for the design of potent novel inhibitors for cancer treatment.
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Affiliation(s)
- Ayanda M. Magwenyane
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Ndumiso N. Mhlongo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Monsurat M. Lawal
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Daniel G. Amoako
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Anou M. Somboro
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
- Biomedical Resource Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Sphelele C. Sosibo
- School of Physical and Chemical Sciences, Department of Chemistry, North West University, Mafikeng Campus, Mmabatho 2790, South Africa;
| | - Letitia Shunmugam
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Rene B. Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.M.M.); (N.N.M.); (M.M.L.); (D.G.A.); (A.M.S.); (L.S.); (R.B.K.)
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Stress-induced phosphoprotein 1 mediates hepatocellular carcinoma metastasis after insufficient radiofrequency ablation. Oncogene 2018; 37:3514-3527. [DOI: 10.1038/s41388-018-0169-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/20/2018] [Accepted: 01/21/2018] [Indexed: 12/25/2022]
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Kim HH, Hyun JS, Choi J, Choi KE, Jee JG, Park SJ. Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain. Sci Rep 2018; 8:368. [PMID: 29321504 PMCID: PMC5762686 DOI: 10.1038/s41598-017-18332-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/08/2017] [Indexed: 12/17/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is one of the most abundant cellular proteins and plays a substantial role in the folding of client proteins. The inhibition of Hsp90 has been regarded as an attractive therapeutic strategy for treating cancer because many oncogenic kinases are Hsp90 client proteins. In this study, we report new inhibitors that directly bind to N-terminal ATP-binding pocket of Hsp90. Optimized structure-based virtual screening predicted candidate molecules, which was followed by confirmation using biophysical and cell-based assays. Among the reported crystal structures, we chose the two structures that show the most favourable early enrichments of true-positives in the receiver operating characteristic curve. Four molecules showed significant changes in the signals of 2D [1H, 15N] correlation NMR spectroscopy. Differential scanning calorimetry analysis supported the results indicating direct binding. Quantified dissociation constant values of the molecules, determined by a series of 2D NMR experiments, lie in the range of 0.1–33 μM. Growth inhibition assay with breast and lung cancer cells confirmed the cellular activities of the molecules. Cheminformatics revealed that the molecules share limited chemical similarities with known inhibitors. Molecular dynamics simulations detailed the putative binding modes of the inhibitors.
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Affiliation(s)
- Hyun-Hwi Kim
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon, 21936, Republic of Korea
| | - Ja-Shil Hyun
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon, 21936, Republic of Korea
| | - Joonhyeok Choi
- Research Institute of Pharmaceutical Researches, College of Pharmacy, Kyungpook, National University, Daegu, 41566, Republic of Korea
| | - Kwang-Eun Choi
- Research Institute of Pharmaceutical Researches, College of Pharmacy, Kyungpook, National University, Daegu, 41566, Republic of Korea
| | - Jun-Goo Jee
- Research Institute of Pharmaceutical Researches, College of Pharmacy, Kyungpook, National University, Daegu, 41566, Republic of Korea.
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon, 21936, Republic of Korea.
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Verkhivker GM. Computational Modeling of the Hsp90 Interactions with Cochaperones and Small-Molecule Inhibitors. Methods Mol Biol 2018; 1709:253-273. [PMID: 29177665 DOI: 10.1007/978-1-4939-7477-1_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Allosteric interactions of the molecular chaperone Hsp90 with a diverse array of cochaperones and client proteins, such as protein kinases and transcription factors, allow for efficient molecular communication in signal transduction networks. Deregulation of pathways involving these proteins is commonly associated with cancer pathologies and allosteric inhibition of oncogenic clients by targeting Hsp90 provides a powerful therapeutic strategy in cancer research. We review several validated computational approaches and tools used in the studies of the Hsp90 interactions with proteins and small molecules. These methods include experimentally guided docking to predict Hs90-protein interactions, molecular and binding free energy simulations to analyze Hsp90 binding with small molecules, and structure-based network modeling to evaluate allosteric interactions and communications in the Hsp90 regulatory complexes. Through the lens of allosteric-centric view on Hsp90 function and regulation, we discuss newly emerging computational tools that link protein structure modeling with biophysical simulations and network-based systems biology approaches.
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Affiliation(s)
- Gennady M Verkhivker
- Schmid College of Science and Technology, Chapman University, University Drive, Orange, CA, 92866, USA.
- Chapman University School of Pharmacy, Irvine, CA, USA.
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Balmith M, Soliman MES. Potential Ebola drug targets — filling the gap: a critical step forward towards the design and discovery of potential drugs. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Lettini G, Maddalena F, Sisinni L, Condelli V, Matassa DS, Costi MP, Simoni D, Esposito F, Landriscina M. TRAP1: a viable therapeutic target for future cancer treatments? Expert Opin Ther Targets 2017; 21:805-815. [PMID: 28664757 DOI: 10.1080/14728222.2017.1349755] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION HSP90 molecular chaperones (i.e., HSP90α, HSP90β, GRP94 and TRAP1) are potential therapeutic targets to design novel anticancer agents. However, despite numerous designed HSP90 inhibitors, most of them have failed due to unfavorable toxicity profiles and lack of specificity toward different HSP90 paralogs. Indeed, a major limitation in this field is the high structural homology between different HSP90 chaperones, which significantly limits our capacity to design paralog-specific inhibitors. Area covered: This review examines the relevance of TRAP1 in tumor development and progression, with an emphasis on its oncogenic/oncosuppressive role in specific human malignancies and its multifaceted and context-dependent functions in cancer cells. Herein, we discuss the rationale for considering TRAP1 as a potential molecular target and the strategies used to date, to achieve its compartmentalized inhibition directly in mitochondria. Expert opinion: TRAP1 targeting may represent a promising strategy for cancer therapy, based on the increasing and compelling evidence supporting TRAP1 involvement in human carcinogenesis. However, considering the complexity of TRAP1 biology, future strategies of drug discovery need to improve selectivity and specificity toward TRAP1 respect to other HSP90 paralogs. The characterization of specific human malignancies suitable for TRAP1 targeting is also mandatory.
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Affiliation(s)
- Giacomo Lettini
- a Laboratory of Pre-Clinical and Translational Research , IRCCS, Referral Cancer Center of Basilicata , Rionero in Vulture , Italy
| | - Francesca Maddalena
- a Laboratory of Pre-Clinical and Translational Research , IRCCS, Referral Cancer Center of Basilicata , Rionero in Vulture , Italy
| | - Lorenza Sisinni
- a Laboratory of Pre-Clinical and Translational Research , IRCCS, Referral Cancer Center of Basilicata , Rionero in Vulture , Italy
| | - Valentina Condelli
- a Laboratory of Pre-Clinical and Translational Research , IRCCS, Referral Cancer Center of Basilicata , Rionero in Vulture , Italy
| | - Danilo Swann Matassa
- b Department of Molecular Medicine and Medical Biotechnology , University of Naples Federico II , Napoli , Italy
| | - Maria Paola Costi
- c Department of Life Sciences , University of Modena and Reggio Emilia , Modena , Italy
| | - Daniele Simoni
- d Department of Chemical and Pharmaceutical Sciences , University of Ferrara , Ferrara , Italy
| | - Franca Esposito
- b Department of Molecular Medicine and Medical Biotechnology , University of Naples Federico II , Napoli , Italy
| | - Matteo Landriscina
- a Laboratory of Pre-Clinical and Translational Research , IRCCS, Referral Cancer Center of Basilicata , Rionero in Vulture , Italy.,e Medical Oncology Unit, Department of Medical and Surgical Sciences , University of Foggia , Foggia , Italy
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Design, synthesis and biological evaluation of 7-(aryl)-2,3-dihydro-[1,4]dioxino[2,3- g ]quinoline derivatives as potential Hsp90 inhibitors and anticancer agents. Bioorg Med Chem 2017; 25:1294-1302. [DOI: 10.1016/j.bmc.2016.12.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/18/2016] [Accepted: 12/29/2016] [Indexed: 01/16/2023]
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11
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Selwa E, Martiny VY, Iorga BI. Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets. J Comput Aided Mol Des 2016; 30:829-839. [DOI: 10.1007/s10822-016-9983-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/28/2016] [Indexed: 12/15/2022]
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12
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Cele FN, Kumalo H, Soliman MES. Mechanism of Inhibition of Hsp90 Dimerization by Gyrase B Inhibitor Coumermycin A1 (C-A1) Revealed by Molecular Dynamics Simulations and Thermodynamic Calculations. Cell Biochem Biophys 2016; 74:353-63. [PMID: 27376828 PMCID: PMC7090554 DOI: 10.1007/s12013-016-0743-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 06/09/2016] [Indexed: 12/14/2022]
Abstract
Heat shock protein (Hsp) 90 an emerging and attracting target in the anti-HIV drug discovery process due to the key role it plays in the pathogenicity of HIV-1 virus. In this research study, long-range all-atom molecular dynamics simulations were engaged for the bound and the unbound proteins to enhance the understanding of the molecular mechanisms of the Hsp90 dimerization and inhibition. Results evidently showed that coumermycin A1 (C-A1), a recently discovered Hsp90 inhibitor, binds at the dimer's active site of the Hsp90 protein and leads to a substantial parting between dimeric opposed residues, which include Arg591.B, Lys594.A, Ser663.A, Thr653.B, Ala665.A, Thr649.B, Leu646.B and Asn669.A. Significant differences in magnitudes were observed in radius of gyration, root-mean-square deviation and root-mean-square fluctuation, which confirms a reasonably more flexible state in the apo conformation associated with it dimerization. In contrast, the bound conformer of Hsp90 showed less flexibility. This visibly highpoints the inhibition process resulting from the binding of the ligand. These findings were further validated by principal component analysis. We believe that the detailed dynamic analyses of Hsp90 presented in this study, would give an imperative insight and better understanding to the function and mechanisms of inhibition. Furthermore, information obtained from the binding mode of the inhibitor would be of great assistance in the design of more potent inhibitors against the HIV target Hsp90.
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Affiliation(s)
- Favourite N Cele
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Hezekiel Kumalo
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.
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