1
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Colombo G. Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design. Curr Opin Struct Biol 2023; 83:102702. [PMID: 37716095 DOI: 10.1016/j.sbi.2023.102702] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The concept of allostery has become a central tenet in the study of biological systems. In parallel, the discovery of allosteric drugs is generating new opportunities to selectively modulate difficult targets involved in pathologic mechanisms. Molecular simulations can provide atomistically detailed insight into the processes involved in allosteric regulation and signaling, and at the same time, they have the potential to unveil regulatory hotspots or cryptic sites that are not immediately evident from the analysis of static structures. In this context, computational approaches should be able to connect the study of allosteric regulation at different scales to the possibility of leveraging this knowledge to expand the chemical space of new, active drugs. Here, we will discuss recent advances in the study of allosteric regulation via computational methods and connect the mechanistic knowledge generated to the possibility of designing new small molecules that can tweak the functions of their receptors.
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Affiliation(s)
- Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy.
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2
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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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3
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Alao JP, Obaseki I, Amankwah YS, Nguyen Q, Sugoor M, Unruh E, Popoola HO, Tehver R, Kravats AN. Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics. J Phys Chem B 2023; 127:5389-5409. [PMID: 37294929 PMCID: PMC10292203 DOI: 10.1021/acs.jpcb.3c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/17/2023] [Indexed: 06/11/2023]
Abstract
Grp94, an ER-localized molecular chaperone, is required for the folding and activation of many membrane and secretory proteins. Client activation by Grp94 is mediated by nucleotide and conformational changes. In this work, we aim to understand how microscopic changes from nucleotide hydrolysis can potentiate large-scale conformational changes of Grp94. We performed all-atom molecular dynamics simulations on the ATP-hydrolysis competent state of the Grp94 dimer in four different nucleotide bound states. We found that Grp94 was the most rigid when ATP was bound. ATP hydrolysis or nucleotide removal enhanced mobility of the N-terminal domain and ATP lid, resulting in suppression of interdomain communication. In an asymmetric conformation with one hydrolyzed nucleotide, we identified a more compact state, similar to experimental observations. We also identified a potential regulatory role of the flexible linker, as it formed electrostatic interactions with the Grp94 M-domain helix near the region where BiP is known to bind. These studies were complemented with normal-mode analysis of an elastic network model to investigate Grp94's large-scale conformational changes. SPM analysis identified residues that are important in signaling conformational change, many of which have known functional relevance in ATP coordination and catalysis, client binding, and BiP binding. Our findings suggest that ATP hydrolysis in Grp94 alters allosteric wiring and facilitates conformational changes.
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Affiliation(s)
- John Paul Alao
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Ikponwmosa Obaseki
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Yaa Sarfowah Amankwah
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Quinn Nguyen
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Meghana Sugoor
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Erin Unruh
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Cell,
Molecular, and Structural Biology Program, Department of Chemistry
& Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | | | - Riina Tehver
- Department
of Physics, Denison University, Granville, Ohio 43023, United States
| | - Andrea N. Kravats
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Cell,
Molecular, and Structural Biology Program, Department of Chemistry
& Biochemistry, Miami University, Oxford, Ohio 45056, United States
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4
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Meka PN, Amatya E, Kaur S, Banerjee M, Zuo A, Dobrowsky RT, Blagg BSJ. Synthesis and evaluation of 3'- and 4'-substituted cyclohexyl noviomimetics that modulate mitochondrial respiration. Bioorg Med Chem 2022; 70:116940. [PMID: 35905686 DOI: 10.1016/j.bmc.2022.116940] [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: 06/21/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/25/2022]
Abstract
KU-32 (2) and KU-596 (3), are first and second generation cytoprotective novologues that are derivatives of novobiocin (1), a heat shock protein 90 (Hsp90) C-terminal inhibitor. Although 2 and 3 improve mitochondrial bioenergetics and have demonstrated considerable cytoprotective activity, they contain a synthetically demanding noviose sugar. This issue was initially addressed by creating noviomimetics, such as KU-1202 (4), which replaced the noviose sugar with ether-linked cyclohexyl derivatives that retained some cytoprotective potential due to their ability to increase mitochondrial bioenergetics. Based on structure-activity relationship (SAR) studies of KU-1202 (4), the current study investigated 3'- and 4'-substituted cyclohexyl scaffolds as noviomimetics and determined their efficacy at increasing mitochondrial bioenergetic as a marker for cytoprotective potential.
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Affiliation(s)
- Penchala Narasimharao Meka
- Department of Chemistry and Biochemistry, 305 McCourtney Hall, The University of Notre Dame, Notre Dame, IN 46556, United States
| | - Eva Amatya
- Department of Chemistry and Biochemistry, 305 McCourtney Hall, The University of Notre Dame, Notre Dame, IN 46556, United States
| | - Sukhmanjit Kaur
- Department of Pharmacology and Toxicology Department, The University of Kansas, Lawrence, KS 66045, United States
| | - Monimoy Banerjee
- Department of Chemistry and Biochemistry, 305 McCourtney Hall, The University of Notre Dame, Notre Dame, IN 46556, United States
| | - Ang Zuo
- Department of Chemistry and Biochemistry, 305 McCourtney Hall, The University of Notre Dame, Notre Dame, IN 46556, United States
| | - Rick T Dobrowsky
- Department of Pharmacology and Toxicology Department, The University of Kansas, Lawrence, KS 66045, United States.
| | - Brian S J Blagg
- Department of Chemistry and Biochemistry, 305 McCourtney Hall, The University of Notre Dame, Notre Dame, IN 46556, United States.
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5
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In Silico Discovery and Optimisation of a Novel Structural Class of Hsp90 C-Terminal Domain Inhibitors. Biomolecules 2022; 12:biom12070884. [PMID: 35883440 PMCID: PMC9312846 DOI: 10.3390/biom12070884] [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: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022] Open
Abstract
Hsp90 is a promising target for the development of novel agents for cancer treatment. The N-terminal Hsp90 inhibitors have several therapeutic limitations, the most important of which is the induction of heat shock response, which can be circumvented by targeting the allosteric binding site on the C-terminal domain (CTD) of Hsp90. In the absence of an Hsp90—CTD inhibitor co-crystal structure, the use of structure-based design approaches for the Hsp90 CTD is difficult and the structural diversity of Hsp90 CTD inhibitors is limited. In this study, we describe the discovery of a novel structural class of Hsp90 CTD inhibitors. A structure-based virtual screening was performed by docking a library of diverse compounds to the Hsp90β CTD binding site. Three selected virtual hits were tested in the MCF-7 breast cancer cell line, with compound TVS-23 showing antiproliferative activity with an IC50 value of 26.4 ± 1.1 µM. We report here the optimisation, synthesis and biological evaluation of TVS-23 analogues. Several analogues showed significantly enhanced antiproliferative activities in MCF-7 breast cancer and SK-N-MC Ewing sarcoma cell lines, with 7l being the most potent (IC50 = 1.4 ± 0.4 µM MCF-7; IC50 = 2.8 ± 0.4 µM SK-N-MC). The results of this study highlight the use of virtual screening to expand the structural diversity of Hsp90 CTD inhibitors and provide new starting points for further development.
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6
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Djokovic N, Ruzic D, Rahnasto-Rilla M, Srdic-Rajic T, Lahtela-Kakkonen M, Nikolic K. Expanding the Accessible Chemical Space of SIRT2 Inhibitors through Exploration of Binding Pocket Dynamics. J Chem Inf Model 2022; 62:2571-2585. [PMID: 35467856 DOI: 10.1021/acs.jcim.2c00241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Considerations of binding pocket dynamics are one of the crucial aspects of the rational design of binders. Identification of alternative conformational states or cryptic subpockets could lead to the discovery of completely novel groups of the ligands. However, experimental characterization of pocket dynamics, besides being expensive, may not be able to elucidate all of the conformational states relevant for drug discovery projects. In this study, we propose the protocol for computational simulations of sirtuin 2 (SIRT2) binding pocket dynamics and its integration into the structure-based virtual screening (SBVS) pipeline. Initially, unbiased molecular dynamics simulations of SIRT2:inhibitor complexes were performed using optimized force field parameters of SIRT2 inhibitors. Time-lagged independent component analysis (tICA) was used to design pocket-related collective variables (CVs) for enhanced sampling of SIRT2 pocket dynamics. Metadynamics simulations in the tICA eigenvector space revealed alternative conformational states of the SIRT2 binding pocket and the existence of a cryptic subpocket. Newly identified SIRT2 conformational states outperformed experimentally resolved states in retrospective SBVS validation. After performing prospective SBVS, compounds from the under-represented portions of the SIRT2 inhibitor chemical space were selected for in vitro evaluation. Two compounds, NDJ18 and NDJ85, were identified as potent and selective SIRT2 inhibitors, which validated the in silico protocol and opened up the possibility for generalization and broadening of its application. The anticancer effects of the most potent compound NDJ18 were examined on the triple-negative breast cancer cell line. Results indicated that NDJ18 represents a promising structure suitable for further evaluation.
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Affiliation(s)
- Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Minna Rahnasto-Rilla
- School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70210 Kuopio, Finland
| | - Tatjana Srdic-Rajic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | | | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
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7
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Exploring Mechanisms of Allosteric Regulation and Communication Switching in the Multiprotein Regulatory Complexes of the Hsp90 Chaperone with Cochaperones and Client Proteins : Atomistic Insights from Integrative Biophysical Modeling and Network Analysis of Conformational Landscapes. J Mol Biol 2022; 434:167506. [DOI: 10.1016/j.jmb.2022.167506] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/16/2022]
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8
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Triveri A, Sanchez-Martin C, Torielli L, Serapian SA, Marchetti F, D'Acerno G, Pirota V, Castelli M, Moroni E, Ferraro M, Quadrelli P, Rasola A, Colombo G. Protein allostery and ligand design: Computational design meets experiments to discover novel chemical probes. J Mol Biol 2022; 434:167468. [DOI: 10.1016/j.jmb.2022.167468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
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9
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Kumari P, Som A. Comparative molecular dynamics simulation analysis of G20 and C92 mutations in c-di-GMP I riboswitch and the wild type with docked c-di-GMP ligand. Bioinformation 2021; 17:721-726. [PMID: 35540701 PMCID: PMC9049102 DOI: 10.6026/97320630017721] [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: 04/04/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/23/2022] Open
Abstract
Riboswitch, a bacterial regulatory RNA consists of an aptamer (specific ligand binding unit) and an expression platform (gene expression modulation unit), which act as a potential drug target as it regulates critical genes. Therefore, it is of interest to glean information on the binding of c-di-GMP ligand to mutated conserved G20 and C92 residues of cyclic diguanosine monophosphate I (c-di-GMP I) riboswitch using molecular dynamics simulation. The result shows that the binding energy of wild/native type riboswitch-ligand complex (3IRW) is lower than the mutant complexes suggesting that the binding affinity for c-di-GMP ligand decreases in case of mutant riboswitches. The hydrogen bonding interactions analysis also showed a high number of hydrogen bonds formation in the wild type riboswitch-ligand complex as compared to the mutant complexes illustrating stronger interaction of ligand to wild type riboswitch than the mutants. The simulation result shows that the mutations affected riboswitch-ligand interactions. The residues G14, G21, C46, A47, and U92 were identified as the key residues which contributed effectively to the binding of c-di-GMP I riboswitch with the natural ligand.
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Affiliation(s)
- Priyanka Kumari
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj – 211002, India
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj – 211002, India
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10
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Dernovšek J, Zajec Ž, Durcik M, Mašič LP, Gobec M, Zidar N, Tomašič T. Structure-Activity Relationships of Benzothiazole-Based Hsp90 C-Terminal-Domain Inhibitors. Pharmaceutics 2021; 13:pharmaceutics13081283. [PMID: 34452244 PMCID: PMC8400049 DOI: 10.3390/pharmaceutics13081283] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is a chaperone responsible for the maturation of many cancer-related proteins, and is therefore an important target for the design of new anticancer agents. Several Hsp90 N-terminal domain inhibitors have been evaluated in clinical trials, but none have been approved as cancer therapies. This is partly due to induction of the heat shock response, which can be avoided using Hsp90 C-terminal-domain (CTD) inhibition. Several structural features have been shown to be useful in the design of Hsp90 CTD inhibitors, including an aromatic ring, a cationic center and the benzothiazole moiety. This study established a previously unknown link between these structural motifs. Using ligand-based design methodologies and structure-based pharmacophore models, a library of 29 benzothiazole-based Hsp90 CTD inhibitors was prepared, and their antiproliferative activities were evaluated in MCF-7 breast cancer cells. Several showed low-micromolar IC50, with the most potent being compounds 5g and 9i (IC50, 2.8 ± 0.1, 3.9 ± 0.1 μM, respectively). Based on these results, a ligand-based structure-activity relationship model was built, and molecular dynamics simulation was performed to elaborate the binding mode of compound 9i. Moreover, compound 9i showed degradation of Hsp90 client proteins and no induction of the heat shock response.
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11
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Civera M, Moroni E, Sorrentino L, Vasile F, Sattin S. Chemical and Biophysical Approaches to Allosteric Modulation. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Monica Civera
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Elisabetta Moroni
- Istituto di Scienze e Tecnologie Chimiche Giulio Natta, SCITEC Via Mario Bianco 9 20131 Milan Italy
| | - Luca Sorrentino
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Francesca Vasile
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
| | - Sara Sattin
- Department of Chemistry Università degli Studi di Milano via C. Golgi, 19 20133 Milan Italy
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12
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Marchetti F, Moroni E, Pandini A, Colombo G. Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics. J Phys Chem Lett 2021; 12:3724-3732. [PMID: 33843228 PMCID: PMC8154828 DOI: 10.1021/acs.jpclett.1c00045] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/05/2021] [Indexed: 05/13/2023]
Abstract
Allosteric drugs have been attracting increasing interest over the past few years. In this context, it is common practice to use high-throughput screening for the discovery of non-natural allosteric drugs. While the discovery stage is supported by a growing amount of biological information and increasing computing power, major challenges still remain in selecting allosteric ligands and predicting their effect on the target protein's function. Indeed, allosteric compounds can act both as inhibitors and activators of biological responses. Computational approaches to the problem have focused on variations on the theme of molecular docking coupled to molecular dynamics with the aim of recovering information on the (long-range) modulation typical of allosteric proteins.
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Affiliation(s)
- Filippo Marchetti
- Department
of Chemistry, Università Degli Studi
di Pavia, Viale Taramelli 12, 27100 Pavia, Italy
- Università
Degli Studi di Milano, Via C. Golgi, 19, I-20133 Milan, Italy
| | - Elisabetta Moroni
- Istituto
di Scienze e Tecnologie Chimiche, Via Mario Bianco 9, 20131 Milano, Italy
| | | | - Giorgio Colombo
- Department
of Chemistry, Università Degli Studi
di Pavia, Viale Taramelli 12, 27100 Pavia, Italy
- Istituto
di Scienze e Tecnologie Chimiche, Via Mario Bianco 9, 20131 Milano, Italy
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13
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Mak OW, Sharma N, Reynisson J, Leung IKH. Discovery of novel Hsp90 C-terminal domain inhibitors that disrupt co-chaperone binding. Bioorg Med Chem Lett 2021; 38:127857. [PMID: 33609661 DOI: 10.1016/j.bmcl.2021.127857] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 12/20/2022]
Abstract
Heat shock protein 90 (Hsp90) is an essential molecular chaperone that performs vital stress-related and housekeeping functions in cells and is a current therapeutic target for diseases such as cancers. Particularly, the development of Hsp90 C-terminal domain (CTD) inhibitors is highly desirable as inhibitors that target the N-terminal nucleotide-binding domain may cause unwanted biological effects. Herein, we report on the discovery of two drug-like novel Hsp90 CTD inhibitors by using virtual screening and intrinsic protein fluorescence quenching binding assays, paving the way for future development of new therapies that employ molecular chaperone inhibitors.
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Affiliation(s)
- Oi Wei Mak
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Nabangshu Sharma
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; School of Pharmacy and Bioengineering, Hornbeam Building, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom.
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
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14
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Wang L, Zhang Q, You Q. Targeting the HSP90-CDC37-kinase chaperone cycle: A promising therapeutic strategy for cancer. Med Res Rev 2021; 42:156-182. [PMID: 33846988 DOI: 10.1002/med.21807] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022]
Abstract
Heat shock protein 90 (HSP90) is an indispensable molecular chaperone that facilitates the maturation of numerous oncoproteins in cancer cells, including protein kinases, ribonucleoproteins, steroid hormone receptors, and transcription factors. Although over 30 HSP90 inhibitors have steadily entered clinical trials, further clinical advancement has been restricted by their limited efficacy, inevitable heat shock response, and multiple side-effects, likely induced via an ATP inhibition mechanism. Since both ATP and various co-chaperones play essential roles in the HSP90 chaperone cycle to achieve integrated function, optimal therapeutics require an understanding of the dynamic interactions among HSP90, ATP, and cochaperones. To date, continuous research has promoted the exploration of the cochaperone cell division cycle 37 (CDC37) as a kinase-specific recognizer and has shown that the HSP90-CDC37-kinase complex is particularly relevant in cancers. Indeed, disrupting the HSP90-CDC37-kinase complex, rather than totally blocking the ATP function of HSP90, is emerging as an alternative way to avoid the limitations of current inhibitors. In this review, we first briefly introduce the HSP90-CDC37-kinase cycle and present the currently available approaches for inhibitor development targeting this cycle and provide insights into selective regulation of the kinase clients of HSP90 by more directional ways.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, China.,Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, China
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15
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Zhu D, Li S, Chen C, Wang S, Zhu J, Kong L, Luo J. Tubocapsenolide A targets C-terminal cysteine residues of HSP90 to exert the anti-tumor effect. Pharmacol Res 2021; 166:105523. [PMID: 33667688 DOI: 10.1016/j.phrs.2021.105523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/20/2021] [Accepted: 02/28/2021] [Indexed: 01/29/2023]
Abstract
Heat shock protein 90 (HSP90) is a chaperone protein that has been shown to regulate cancer progression. As a result, HSP90 has emerged as an attractive target for cancer therapy. Tubocapsenolide A (TA) is an anti-tumor component isolated from Tubocapsicum anomalum. Although the anti-tumor activity of TA was considered to be related to HSP90, the binding site and deep anti-tumor mechanisms still need to be elucidated. In this study, we found that TA is a covalent inhibitor of HSP90, which inhibits HSP90 ATPase activity without blocking ATP binding. Further studies indicated that TA targets the C-terminal Cys521 site, which led to HSP90 partial oligomerization and hindered its anti-aggregation and refolding activity. The damage of the chaperone activity disrupted the interaction between HSP90 and its cochaperone CDC37 as well as its client proteins, thereby inducing cell cycle arrest and apoptosis. Moreover, TA was found to have therapeutic effects on the xenograft tumor model by inducing the degradation of HSP90 client proteins. Together, our results identified HSP90 as the direct target of TA for mediating the anti-tumor activity. TA could serve as a lead compound for developing novel HSP90 C-terminal covalent inhibitors with binding site different from the ATP-binding domain.
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Affiliation(s)
- Dongrong Zhu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Shang Li
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Chen Chen
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Sibei Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Jiangmin Zhu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
| | - Jianguang Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
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16
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Astl L, Stetz G, Verkhivker GM. Dissecting Molecular Principles of the Hsp90 Chaperone Regulation by Allosteric Modulators Using a Hierarchical Simulation Approach and Network Modeling of Allosteric Interactions: Conformational Selection Dictates the Diversity of Protein Responses and Ligand-Specific Functional Mechanisms. J Chem Theory Comput 2020; 16:6656-6677. [PMID: 32941034 DOI: 10.1021/acs.jctc.0c00503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Conformational plasticity of the Hsp90 molecular chaperones underlies the diversity of functional mechanisms that these versatile molecular machines employ to coordinate their vast protein clientele in the cellular environment. Despite a steady progress in studies of the Hsp90 machinery, a great deal remains unknown about molecular principles and ligand-specific functional mechanisms of the Hsp90 regulation by allosteric modulators that attracted significant attention because of their therapeutic potential. Due to structural complexity and dynamic nature of the Hsp90 responses to allosteric modulators, the atomistic details about the mode of action of these small molecules continue to be fairly scarce and controversial. In this work, we employ an integrative strategy that encompassed atomistic simulations of the Hsp90 proteins and hierarchical modeling of Hsp90-ligand binding with network analysis to explore functional mechanisms of the Hsp90 regulation by a panel of allosteric modulators (novobiocin, KU-135, KU-174, and KU-32) with different models of action. The results show that functional mechanisms of allosteric modulation in the Hsp90 proteins may be driven by conformational selection principles in which ligands elicit pre-existing states of the unbound chaperone to drive ligand-specific protein responses and distinct scenarios of Hsp90 regulation. We found that novobiocin can selectively sequester an ensemble of open chaperone conformations and inhibit the progression of the functional cycle through a cascade of cumulative dynamic changes. In contrast, KU-32 displayed unique preferences toward partially closed dynamic states, inducing robust allosteric signaling and stimulation of the ATPase cycle. The proposed model of the Hsp90 regulation by allosteric modulators reconciled diverse experimental data and showed that allosteric modulators may operate via targeted exploitation of dynamic landscapes eliciting vastly different protein responses and diverse mechanisms of action.
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Affiliation(s)
- Lindy Astl
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gabrielle Stetz
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States.,Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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17
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Pote S, Kachhap S, Mank NJ, Daneshian L, Klapper V, Pye S, Arnette AK, Shimizu LS, Borowski T, Chruszcz M. Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus. Biochim Biophys Acta Gen Subj 2020; 1865:129750. [PMID: 32980502 DOI: 10.1016/j.bbagen.2020.129750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND The products of the lysine biosynthesis pathway, meso-diaminopimelate and lysine, are essential for bacterial survival. This paper focuses on the structural and mechanistic characterization of 4-hydroxy-tetrahydrodipicolinate reductase (DapB), which is one of the enzymes from the lysine biosynthesis pathway. DapB catalyzes the conversion of (2S, 4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate (HTPA) to 2,3,4,5-tetrahydrodipicolinate in an NADH/NADPH dependent reaction. Genes coding for DapBs were identified as essential for many pathogenic bacteria, and therefore DapB is an interesting new target for the development of antibiotics. METHODS We have combined experimental and computational approaches to provide novel insights into mechanism of the DapB catalyzed reaction. RESULTS Structures of DapBs originating from Mycobacterium tuberculosis and Vibrio vulnificus in complexes with NAD+, NADP+, as well as with inhibitors, were determined and described. The structures determined by us, as well as currently available structures of DapBs from other bacterial species, were compared and used to elucidate a mechanism of reaction catalyzed by this group of enzymes. Several different computational methods were used to provide a detailed description of a plausible reaction mechanism. CONCLUSIONS This is the first report presenting the detailed mechanism of reaction catalyzed by DapB. GENERAL SIGNIFICANCE Structural data in combination with information on the reaction mechanism provide a background for development of DapB inhibitors, including transition-state analogues.
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Affiliation(s)
- Swanandi Pote
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Sangita Kachhap
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Krakow, Poland
| | - Nicholas J Mank
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Leily Daneshian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Vincent Klapper
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Sarah Pye
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Amy K Arnette
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Linda S Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239 Krakow, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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18
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Tomašič T, Durcik M, Keegan BM, Skledar DG, Zajec Ž, Blagg BSJ, Bryant SD. Discovery of Novel Hsp90 C-Terminal Inhibitors Using 3D-Pharmacophores Derived from Molecular Dynamics Simulations. Int J Mol Sci 2020; 21:ijms21186898. [PMID: 32962253 PMCID: PMC7555175 DOI: 10.3390/ijms21186898] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022] Open
Abstract
Hsp90 C-terminal domain (CTD) inhibitors are promising novel agents for cancer treatment, as they do not induce the heat shock response associated with Hsp90 N-terminal inhibitors. One challenge associated with CTD inhibitors is the lack of a co-crystallized complex, requiring the use of predicted allosteric apo pocket, limiting structure-based (SB) design approaches. To address this, a unique approach that enables the derivation and analysis of interactions between ligands and proteins from molecular dynamics (MD) trajectories was used to derive pharmacophore models for virtual screening (VS) and identify suitable binding sites for SB design. Furthermore, ligand-based (LB) pharmacophores were developed using a set of CTD inhibitors to compare VS performance with the MD derived models. Virtual hits identified by VS with both SB and LB models were tested for antiproliferative activity. Compounds 9 and 11 displayed antiproliferative activities in MCF-7 and Hep G2 cancer cell lines. Compound 11 inhibited Hsp90-dependent refolding of denatured luciferase and induced the degradation of Hsp90 clients without the concomitant induction of Hsp70 levels. Furthermore, compound 11 offers a unique scaffold that is promising for the further synthetic optimization and development of molecules needed for the evaluation of the Hsp90 CTD as a target for the development of anticancer drugs.
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Affiliation(s)
- Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (M.D.); (D.G.S.); (Ž.Z.)
- Correspondence: ; Tel.: +386-1-4769-556
| | - Martina Durcik
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (M.D.); (D.G.S.); (Ž.Z.)
| | - Bradley M. Keegan
- Department of Chemistry and Biochemistry, The University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN 46556, USA; (B.M.K.); (B.S.J.B.)
| | - Darja Gramec Skledar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (M.D.); (D.G.S.); (Ž.Z.)
| | - Živa Zajec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia; (M.D.); (D.G.S.); (Ž.Z.)
| | - Brian S. J. Blagg
- Department of Chemistry and Biochemistry, The University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN 46556, USA; (B.M.K.); (B.S.J.B.)
| | - Sharon D. Bryant
- Inte:Ligand Softwareentwicklungs- und Consulting GmbH, Mariahilferstrasse 74B, 1070 Vienna, Austria;
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19
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De Vita S, Terracciano S, Bruno I, Chini MG. From Natural Compounds to Bioactive Molecules through NMR and
In Silico
Methodologies. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Simona De Vita
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Stefania Terracciano
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Ines Bruno
- Department of Pharmacy University of Salerno Via Giovanni Paolo II, n°132 84084 Fisciano (SA) Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory University of Molise C.da Fonte Lappone‐ 86090 Pesche (IS) Italy
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20
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Comparative structure, dynamics and evolution of acyl-carrier proteins from Borrelia burgdorferi, Brucella melitensis and Rickettsia prowazekii. Biochem J 2020; 477:491-508. [PMID: 31922183 DOI: 10.1042/bcj20190797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 12/11/2022]
Abstract
Acyl carrier proteins (ACPs) are small helical proteins found in all kingdoms of life, primarily involved in fatty acid and polyketide biosynthesis. In eukaryotes, ACPs are part of the fatty acid synthase (FAS) complex, where they act as flexible tethers for the growing lipid chain, enabling access to the distinct active sites in FAS. In the type II synthesis systems found in bacteria and plastids, these proteins exist as monomers and perform various processes, from being a donor for synthesis of various products such as endotoxins, to supplying acyl chains for lipid A and lipoic acid FAS (quorum sensing), but also as signaling molecules, in bioluminescence and activation of toxins. The essential and diverse nature of their functions makes ACP an attractive target for antimicrobial drug discovery. Here, we report the structure, dynamics and evolution of ACPs from three human pathogens: Borrelia burgdorferi, Brucella melitensis and Rickettsia prowazekii, which could facilitate the discovery of new inhibitors of ACP function in pathogenic bacteria.
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21
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Lobo MJ, Ray R, Shenoy GG. Gaining deeper insights into the surface binding of bedaquiline analogues with the ATP synthase subunit C of Mycobacterium tuberculosis using molecular docking, molecular dynamics simulation and 3D-QSAR techniques. NEW J CHEM 2020. [DOI: 10.1039/d0nj02062a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This computational study exclusively illustrates the key molecular features of bedaquiline and its analogues required for binding to mycobacterial ATP synthase.
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Affiliation(s)
- Manisha Joshel Lobo
- Department of Pharmaceutical Chemistry
- Manipal College of Pharmaceutical Sciences
- Manipal Academy of Higher Education
- Manipal
- India
| | - Rajdeep Ray
- Department of Pharmaceutical Chemistry
- Manipal College of Pharmaceutical Sciences
- Manipal Academy of Higher Education
- Manipal
- India
| | - G. Gautham Shenoy
- Department of Pharmaceutical Chemistry
- Manipal College of Pharmaceutical Sciences
- Manipal Academy of Higher Education
- Manipal
- India
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22
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D'Annessa I, Raniolo S, Limongelli V, Di Marino D, Colombo G. Ligand Binding, Unbinding, and Allosteric Effects: Deciphering Small-Molecule Modulation of HSP90. J Chem Theory Comput 2019; 15:6368-6381. [PMID: 31538783 DOI: 10.1021/acs.jctc.9b00319] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The molecular chaperone HSP90 oversees the functional activation of a large number of client proteins. Because of its role in multiple pathways linked to cancer and neurodegeneration, drug discovery targeting HSP90 has been actively pursued. Yet, a number of inhibitors failed to meet expectations due to induced toxicity problems. In this context, allosteric perturbation has emerged as an alternative strategy for the pharmacological modulation of HSP90 functions. Specifically, novel allosteric stimulators showed the interesting capability of accelerating HSP90 closure dynamics and ATPase activities while inducing tumor cell death. Here, we gain atomistic insight into the mechanisms of allosteric ligand recognition and their consequences on the functional dynamics of HSP90, starting from the fully unbound state. We integrate advanced computational sampling methods based on FunnelMetadynamics, with the analysis of internal dynamics of the structural ensembles visited during the simulations. We observe several binding/unbinding events, and from these, we derive an accurate estimation of the absolute binding free energy. Importantly, we show that different binding poses induce different dynamics states. Our work for the first time explicitly correlates HSP90 responses to binding/unbinding of an allosteric ligand to the modulation of functionally oriented protein motions.
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Affiliation(s)
| | - Stefano Raniolo
- Università della Svizzera Italiana (USI) , Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology , via G. Buffi 13 , CH-Lugano , Switzerland
| | - Vittorio Limongelli
- Università della Svizzera Italiana (USI) , Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology , via G. Buffi 13 , CH-Lugano , Switzerland.,Department of Pharmacy , University of Naples ″Federico II″ , via D. Montesano 49 , I-80131 Naples , Italy
| | - Daniele Di Marino
- Università della Svizzera Italiana (USI) , Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology , via G. Buffi 13 , CH-Lugano , Switzerland.,Department of Life and Environmental Sciences - New York-Marche Structural Biology Center (NY-MaSBiC) , Polytechnic University of Marche , Via Brecce Bianche , 60131 Ancona , Italy
| | - Giorgio Colombo
- ICRM-CNR , Via Mario Bianco 9 , 20131 Milano , Italy.,Department of Chemistry , University of Pavia , V.le Taramelli 12 , 27100 Pavia , Italy
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23
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Spinello A, Martini S, Berti F, Pennati M, Pavlin M, Sgrignani J, Grazioso G, Colombo G, Zaffaroni N, Magistrato A. Rational design of allosteric modulators of the aromatase enzyme: An unprecedented therapeutic strategy to fight breast cancer. Eur J Med Chem 2019; 168:253-262. [DOI: 10.1016/j.ejmech.2019.02.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/29/2022]
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24
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Modulation of Human Hsp90α Conformational Dynamics by Allosteric Ligand Interaction at the C-Terminal Domain. Sci Rep 2019; 9:1600. [PMID: 30733455 PMCID: PMC6367426 DOI: 10.1038/s41598-018-35835-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022] Open
Abstract
Recent years have seen heat shock protein 90 kDa (Hsp90) attract significant interest as a viable drug target, particularly for cancer. To date, designed inhibitors that target the ATPase domain demonstrate potent anti-proliferative effects, but have failed clinical trials due to high levels of associated toxicity. To circumvent this, the focus has shifted away from the ATPase domain. One option involves modulation of the protein through allosteric activation/inhibition. Here, we propose a novel approach: we use previously obtained information via residue perturbation scanning coupled with dynamic residue network analysis to identify allosteric drug targeting sites for inhibitor docking. We probe the open conformation of human Hsp90α for druggable sites that overlap with these allosteric control elements, and identify three putative natural compound allosteric modulators: Cephalostatin 17, 20(29)-Lupene-3β-isoferulate and 3'-Bromorubrolide F. We assess the allosteric potential of these ligands by examining their effect on the conformational dynamics of the protein. We find evidence for the selective allosteric activation and inhibition of Hsp90's conformational transition toward the closed state in response to ligand binding and shed valuable insight to further the understanding of allosteric drug design and Hsp90's complex allosteric mechanism of action.
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25
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Zhang Z, You Z, Dobrowsky RT, Blagg BSJ. Synthesis and evaluation of a ring-constrained Hsp90 C-terminal inhibitor that exhibits neuroprotective activity. Bioorg Med Chem Lett 2018; 28:2701-2704. [PMID: 29759728 PMCID: PMC6119633 DOI: 10.1016/j.bmcl.2018.03.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 11/26/2022]
Abstract
KU-596 is a second-generation C-terminal heat shock protein 90 KDa (Hsp90) modulator based on the natural product, novobiocin. KU-596 has been shown to induce Hsp70 levels and manifest neuroprotective activity through induction of the heat shock response. A ring-constrained analog of KU-596 was designed and synthesized to probe its binding orientation and ability to induce Hsp70 levels. Compound 2 was found to exhibit comparable or increased activity compared to KU-596, which is under clinical investigation for the treatment of neuropathy.
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Affiliation(s)
- Zheng Zhang
- Department of Chemistry and Biochemistry, The University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, United States
| | - Zhenyuan You
- Department of Pharmacology and Toxicology Department, The University of Kansas, Lawrence, KS 66045, United States
| | - Rick T Dobrowsky
- Department of Pharmacology and Toxicology Department, The University of Kansas, Lawrence, KS 66045, United States
| | - Brian S J Blagg
- Department of Chemistry and Biochemistry, The University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, United States.
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26
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Ferraro M, D’Annessa I, Moroni E, Morra G, Paladino A, Rinaldi S, Compostella F, Colombo G. Allosteric Modulators of HSP90 and HSP70: Dynamics Meets Function through Structure-Based Drug Design. J Med Chem 2018; 62:60-87. [DOI: 10.1021/acs.jmedchem.8b00825] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mariarosaria Ferraro
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Ilda D’Annessa
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | | | - Giulia Morra
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Antonella Paladino
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Silvia Rinaldi
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Federica Compostella
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Saldini, 50, 20133 Milano, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy
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27
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Roy SS, Kapoor M. In silico identification and analysis of the binding site for aminocoumarin type inhibitors in the C-terminal domain of Hsp90. J Mol Graph Model 2018; 84:215-235. [PMID: 30031951 DOI: 10.1016/j.jmgm.2018.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 11/15/2022]
Abstract
Hsp90 contains two Nucleotide Binding Sites (NBS): one each in its N-terminal domain (NTD) and C-terminal domain (CTD), respectively. Previously we used computational techniques to locate a nucleotide-binding site in the CTD. Nucleotide binding at this site stabilized the structurally labile region within this domain, thus providing a rationale for increased resistance to thermal denaturation and proteolysis. A scan for ligand-binding sites in CTD revealed four potential sites with the requisite volume to accommodate aminocoumarins and -derived inhibitors. Only one of these reproducibly formed docked complexes with inhibitors and showed excellent interactions with residues lining the site. Fortuitously, it was identical to the aforementioned nucleotide-binding site thus providing an explanation for the reported direct competition between inhibitors and nucleotides. Further studies with carefully chosen inhibitors and some inactive analogues provided an explanation for the known Structure-Activity Relationships (SAR) of aminocoumarin and -derived inhibitors. We also performed similar studies of the NTD to discern the reason(s) for its inability to bind aminocoumarins, given the family resemblance to prokaryotic Top-IV and Gyr-B. Our studies permitted the identification of the putative inhibitor binding site in the CTD, an explanation for increased resistance to thermal denaturation and proteolysis upon inhibitor binding as well as direct competition with ATP.
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Affiliation(s)
- Samir S Roy
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Manju Kapoor
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
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28
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Moroni E, Agard DA, Colombo G. The Structural Asymmetry of Mitochondrial Hsp90 (Trap1) Determines Fine Tuning of Functional Dynamics. J Chem Theory Comput 2018; 14:1033-1044. [DOI: 10.1021/acs.jctc.7b00766] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - David A. Agard
- Howard Hughes Medical Institute and Department of Biochemistry & Biophysics, University of California, 600 16th Street, San Francisco, California 94158, United States
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR Via Mario Bianco 9, 20131 Milano, Italy
- Dipartimento
di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy
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29
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Discovery of new molecular entities able to strongly interfere with Hsp90 C-terminal domain. Sci Rep 2018; 8:1709. [PMID: 29374167 PMCID: PMC5786060 DOI: 10.1038/s41598-017-14902-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/19/2017] [Indexed: 01/22/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is an ATP dependent molecular chaperone deeply involved in the complex network of cellular signaling governing some key functions, such as cell proliferation and survival, invasion and angiogenesis. Over the past years the N-terminal protein domain has been fully investigated as attractive strategy against cancer, but despite the many efforts lavished in the field, none of the N-terminal binders (termed "classical inhibitors"), currently in clinical trials, have yet successfully reached the market, because of the detrimental heat shock response (HSR) that showed to induce; thus, recently, the selective inhibition of Hsp90 C-terminal domain has powerfully emerged as a more promising alternative strategy for anti-cancer therapy, not eliciting this cell rescue cascade. However, the structural complexity of the target protein and, mostly, the lack of a co-crystal structure of C-terminal domain-ligand, essential to drive the identification of new hits, represent the largest hurdles in the development of new selective C-terminal inhibitors. Continuing our investigations on the identification of new anticancer drug candidates, by using an orthogonal screening approach, here we describe two new potent C-terminal inhibitors able to induce cancer cell death and a considerable down-regulation of Hsp90 client oncoproteins, without triggering the undesired heat shock response.
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30
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Paladino A, Marchetti F, Ponzoni L, Colombo G. The Interplay between Structural Stability and Plasticity Determines Mutation Profiles and Chaperone Dependence in Protein Kinases. J Chem Theory Comput 2018; 14:1059-1070. [DOI: 10.1021/acs.jctc.7b00997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonella Paladino
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Filippo Marchetti
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Luca Ponzoni
- Molecular
and Statistical Biophysics, International School for Advanced Studies (SISSA), I-34136 Trieste, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
- Dipartimento
di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy
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31
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Young ZT, Mok SA, Gestwicki JE. Therapeutic Strategies for Restoring Tau Homeostasis. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a024612. [PMID: 28159830 DOI: 10.1101/cshperspect.a024612] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Normal tau homeostasis is achieved when the synthesis, processing, and degradation of the protein is balanced. Together, the pathways that regulate tau homeostasis ensure that the protein is at the proper levels and that its posttranslational modifications and subcellular localization are appropriately controlled. These pathways include the enzymes responsible for posttranslational modifications, those systems that regulate mRNA splicing, and the molecular chaperones that control tau turnover and its binding to microtubules. In tauopathies, this delicate balance is disturbed. Tau becomes abnormally modified by posttranslational modification, it loses affinity for microtubules, and it accumulates in proteotoxic aggregates. How and why does this imbalance occur? In this review, we discuss how molecular chaperones and other components of the protein homeostasis (e.g., proteostasis) network normally govern tau quality control. We also discuss how aging might reduce the capacity of these systems and how tau mutations might further affect this balance. Finally, we discuss how small-molecule inhibitors are being used to probe and perturb the tau quality-control systems, playing a particularly prominent role in revealing the logic of tau homeostasis. As such, there is now interest in developing these chemical probes into therapeutics, with the goal of restoring normal tau homeostasis to treat disease.
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Affiliation(s)
- Zapporah T Young
- Institute for Neurodegenerative Disease, Department of Pharmaceutical Chemistry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158
| | - Sue Ann Mok
- Institute for Neurodegenerative Disease, Department of Pharmaceutical Chemistry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158
| | - Jason E Gestwicki
- Institute for Neurodegenerative Disease, Department of Pharmaceutical Chemistry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94158
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32
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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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33
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Byrd KM, Kent CN, Blagg BSJ. Synthesis and Biological Evaluation of Stilbene Analogues as Hsp90 C-Terminal Inhibitors. ChemMedChem 2017; 12:2022-2029. [PMID: 29058824 PMCID: PMC5892432 DOI: 10.1002/cmdc.201700630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Indexed: 12/22/2022]
Abstract
The design, synthesis, and biological evaluation of stilbene-based novobiocin analogues is reported. Replacement of the biaryl amide side chain with a triazole side chain produced compounds that exhibited good antiproliferative activities. Heat shock protein 90 (Hsp90) inhibition was observed when N-methylpiperidine was replaced with acyclic tertiary amines on the stilbene analogues that also contain a triazole-derived side chain. These studies revealed that ≈24 Å is the optimal length for compounds that exhibit good antiproliferative activity as a result of Hsp90 inhibition.
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Affiliation(s)
- Katherine M. Byrd
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Caitlin N. Kent
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Brian S. J. Blagg
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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34
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Jiang F, Guo AP, Xu JC, Wang HJ, Mo XF, You QD, Xu XL. Identification and optimization of novel 6-acylamino-2-aminoquinolines as potent Hsp90 C-terminal inhibitors. Eur J Med Chem 2017; 141:1-14. [DOI: 10.1016/j.ejmech.2017.07.080] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 01/04/2023]
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35
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Shao LD, Su J, Ye B, Liu JX, Zuo ZL, Li Y, Wang YY, Xia C, Zhao QS. Design, Synthesis, and Biological Activities of Vibsanin B Derivatives: A New Class of HSP90 C-Terminal Inhibitors. J Med Chem 2017; 60:9053-9066. [PMID: 29019670 DOI: 10.1021/acs.jmedchem.7b01395] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Previously, vibsanin B (ViB) was found to preferentially target HSP90β compared to HSP90α. In this study, multiple experiments, including pull-down assays of biotin-ViB with recombinant HSP90β-NTD, MD, CTD, and full-length HSP90β, molecular docking of ViB and its derivatives to the HSP90 CTD, and a inhibition assay of interaction of the HSP90β CTD with GST-tagged cyclophilin 40 (Cyp40) by ViB derivatives, suggest that ViB can directly bind to the HSP90 C-terminus. On the basis of the docking predictions and primary structure-activity relationships (SARs), a series of ViB analogues devised with focus on the C18 position, along with compounds derivatized at the C4, C7, and C8 positions, were designed and chemically synthesized. Compound 12f (IC50 = 1.12 μM against SK-BR-3) exhibits great potency with drug-like properties. Overall, our findings demonstrate that compounds with the vibsanin B scaffold are a new class of HSP90 C-terminal inhibitors with considerable potential as anticancer agents.
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Affiliation(s)
- Li-Dong Shao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Jia Su
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Baixin Ye
- State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025, China
| | - Jiang-Xin Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Zhi-Li Zuo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Yan Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Yue-Ying Wang
- State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai 200025, China
| | - Chengfeng Xia
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Qin-Shi Zhao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China.,University of Chinese Academy of Science , Beijing 100049, China
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36
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Goode KM, Petrov DP, Vickman RE, Crist SA, Pascuzzi PE, Ratliff TL, Davisson VJ, Hazbun TR. Targeting the Hsp90 C-terminal domain to induce allosteric inhibition and selective client downregulation. Biochim Biophys Acta Gen Subj 2017; 1861:1992-2006. [PMID: 28495207 DOI: 10.1016/j.bbagen.2017.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/20/2017] [Accepted: 05/05/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Inhibition of Hsp90 is desirable due to potential downregulation of oncogenic clients. Early generation inhibitors bind to the N-terminal domain (NTD) but C-terminal domain (CTD) inhibitors are a promising class because they do not induce a heat shock response. Here we present a new structural class of CTD binding molecules with a unique allosteric inhibition mechanism. METHODS A hit molecule, NSC145366, and structurally similar probes were assessed for inhibition of Hsp90 activities. A ligand-binding model was proposed indicating a novel Hsp90 CTD binding site. Client protein downregulation was also determined. RESULTS NSC145366 interacts with the Hsp90 CTD and has anti-proliferative activity in tumor cell lines (GI50=0.2-1.9μM). NSC145366 increases Hsp90 oligomerization resulting in allosteric inhibition of NTD ATPase activity (IC50=119μM) but does not compete with NTD or CTD-ATP binding. Treatment of LNCaP prostate tumor cells resulted in selective client protein downregulation including AR and BRCA1 but without a heat shock response. Analogs had similar potencies in ATPase and chaperone activity assays and variable effects on oligomerization. In silico modeling predicted a binding site at the CTD dimer interface distinct from the nucleotide-binding site. CONCLUSIONS A set of symmetrical scaffold molecules with bisphenol A cores induced allosteric inhibition of Hsp90. Experimental evidence and molecular modeling suggest that the binding site is independent of the CTD-ATP site and consistent with unique induction of allosteric effects. GENERAL SIGNIFICANCE Allosteric inhibition of Hsp90 via a mechanism used by the NSC145366-based probes is a promising avenue for selective oncogenic client downregulation.
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Affiliation(s)
- Kourtney M Goode
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
| | - Dino P Petrov
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
| | - Renee E Vickman
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | - Scott A Crist
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | - Pete E Pascuzzi
- Purdue University Libraries Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Tim L Ratliff
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - V Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Tony R Hazbun
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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37
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D'Annessa I, Sattin S, Tao J, Pennati M, Sànchez-Martìn C, Moroni E, Rasola A, Zaffaroni N, Agard DA, Bernardi A, Colombo G. Design of Allosteric Stimulators of the Hsp90 ATPase as New Anticancer Leads. Chemistry 2017; 23:5188-5192. [PMID: 28207175 PMCID: PMC5927549 DOI: 10.1002/chem.201700169] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Indexed: 01/23/2023]
Abstract
Allosteric compounds that stimulate Hsp90 adenosine triphosphatase (ATPase) activity were rationally designed, showing anticancer potencies in the low micromolar to nanomolar range. In parallel, the mode of action of these compounds was clarified and a quantitative model that links the dynamic ligand-protein cross-talk to observed cellular and in vitro activities was developed. The results support the potential of using dynamics-based approaches to develop original mechanism-based cancer therapeutics.
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Affiliation(s)
- Ilda D'Annessa
- Istituto di Chimica del Riconoscimento Molecolare, CNR, via Mario Bianco, 9, 20131, Milan, Italy
| | - Sara Sattin
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi, 19, 20133, Milan, Italy
| | - Jiahui Tao
- Howard Hughes Medical Institute and Dept. of Biochemistry & Biophysics, University of California, 600 16thStreet, San Francisco, CA, 94158, USA
| | - Marzia Pennati
- Dept. Experimental Oncology & Molecular Medicine, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, via Amadeo, 42, 20133, Milano, Italy
| | - Carlos Sànchez-Martìn
- Dipartimento di Scienze Biomediche-DSB, Università di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | | | - Andrea Rasola
- Dipartimento di Scienze Biomediche-DSB, Università di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Nadia Zaffaroni
- Dept. Experimental Oncology & Molecular Medicine, Molecular Pharmacology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, via Amadeo, 42, 20133, Milano, Italy
| | - David A Agard
- Howard Hughes Medical Institute and Dept. of Biochemistry & Biophysics, University of California, 600 16thStreet, San Francisco, CA, 94158, USA
| | - Anna Bernardi
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi, 19, 20133, Milan, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, via Mario Bianco, 9, 20131, Milan, Italy
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38
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Allosteric Regulation Points Control the Conformational Dynamics of the Molecular Chaperone Hsp90. J Mol Biol 2016; 428:4559-4571. [DOI: 10.1016/j.jmb.2016.09.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/15/2016] [Accepted: 09/15/2016] [Indexed: 01/02/2023]
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39
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Roy SS, Kapoor M. In silico identification and computational analysis of the nucleotide binding site in the C-terminal domain of Hsp90. J Mol Graph Model 2016; 70:253-274. [PMID: 27771574 DOI: 10.1016/j.jmgm.2016.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/02/2016] [Indexed: 12/28/2022]
Abstract
Hsp90 contains two distinct Nucleotide Binding Sites (NBS), in its N-terminal domain (NTD) and C-terminal domain (CTD), respectively. The NTD site belongs to the GHKL super-family of ATPases and has been the subject of extensive characterization. However, a structure of the nucleotide-bound form of CTD is still unavailable. In this study molecular modeling was employed to incorporate experimental data using partial constructs of the CTD, from work published by many research groups, onto existing structural models of its apo- form. Our attempts to locate potential nucleotide ligand-binding sites or cavities yielded one major candidate-a structurally unconventional site-exhibiting the requisite shape and volume for accommodation of tri-phosphate nucleotides. Its structure was refined by molecular dynamics (MD)-based techniques. We reproducibly docked the Mg2+ complexed form of ATP, GTP, CTP, TTP and UTP to this putative NBS. These docking simulations and calculated ligand-binding scores are in general agreement with published data about experimentally measured binding to the CTD. The overall pattern of interactions between residues lining the site and docked nucleotides is conserved and broadly similar to that of other nucleotide-binding sites. Our docking simulations suggest that nucleotide binding stabilizes the only structurally labile region, thereby providing a rationale for the increased resistance to thermal denaturation and proteolysis. The docked nucleotides do not intrude onto the surface of residues involved in dimerization or chaperoning. Our molecular modeling permitted recognition of larger structural changes in the nucleotide-bound CTD dimer, including stabilization of helix-2 in both chains and intra- and inter- chain interactions between three residues (I613, Q617, R620).
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Affiliation(s)
- Samir S Roy
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Manju Kapoor
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
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40
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Chini MG, Malafronte N, Vaccaro MC, Gualtieri MJ, Vassallo A, Vasaturo M, Castellano S, Milite C, Leone A, Bifulco G, De Tommasi N, Dal Piaz F. Identification of Limonol Derivatives as Heat Shock Protein 90 (Hsp90) Inhibitors through a Multidisciplinary Approach. Chemistry 2016; 22:13236-50. [DOI: 10.1002/chem.201602242] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Maria G. Chini
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Nicola Malafronte
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Maria C. Vaccaro
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Maria J. Gualtieri
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
- Department of Pharmacognosy and Organic Drug; University of Los Andes; Sector Campo de Oro, detrás del IAHULA 5101 Mérida Venezuela
| | - Antonio Vassallo
- Department of Science; University of Basilicata; Viale dell'Ateneo Lucano 10 85100 Potenza Italy
| | - Michele Vasaturo
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
- PhD Program in Drug Discovery and Development; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Sabrina Castellano
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
- Department of Medicine and Surgery; University of Salerno; Via Allende 84081 Baronissi Italy
| | - Ciro Milite
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Antonietta Leone
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Giuseppe Bifulco
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Nunziatina De Tommasi
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
| | - Fabrizio Dal Piaz
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano Italy
- Department of Medicine and Surgery; University of Salerno; Via Allende 84081 Baronissi Italy
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41
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Sattin S, Panza M, Vasile F, Berni F, Goti G, Tao J, Moroni E, Agard D, Colombo G, Bernardi A. Synthesis of Functionalized 2-(4-Hydroxyphenyl)-3-methylbenzofuran Allosteric Modulators of Hsp90 Activity. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600420] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sara Sattin
- Department of Chemistry; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Matteo Panza
- Department of Chemistry; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Francesca Vasile
- Department of Chemistry; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Francesca Berni
- Department of Chemistry; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Giulio Goti
- Department of Chemistry; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Jiahui Tao
- Howard Hughes Medical Institute and Dept. of Biochemistry & Biophysics; University of California; 94158 San Francisco California USA
| | - Elisabetta Moroni
- ICRM-CNR; Via Mario Bianco 9 20131 Milano Italy
- IRCCS MultiMedica; Via Fantoli 16/15 20138 Milano Italy
| | - David Agard
- Howard Hughes Medical Institute and Dept. of Biochemistry & Biophysics; University of California; 94158 San Francisco California USA
| | | | - Anna Bernardi
- Department of Chemistry; Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
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42
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Byrd KM, Subramanian C, Sanchez J, Motiwala HF, Liu W, Cohen MS, Holzbeierlein J, Blagg BSJ. Synthesis and Biological Evaluation of Novobiocin Core Analogues as Hsp90 Inhibitors. Chemistry 2016; 22:6921-31. [PMID: 27037933 DOI: 10.1002/chem.201504955] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/11/2016] [Indexed: 02/06/2023]
Abstract
Development of heat shock protein 90 (Hsp90) C-terminal inhibitors has emerged as an exciting strategy for the treatment of cancer. Previous efforts have focused on modifications to the natural products novobiocin and coumermycin. Moreover, variations in both the sugar and amide moieties have been extensively studied, whereas replacements for the coumarin core have received less attention. Herein, 24 cores were synthesized with varying distances and angles between the sugar and amide moieties. Compounds that exhibited good anti-proliferative activity against multiple cancer cell lines and Hsp90 inhibitory activity, were those that placed the sugar and amide moieties between 7.7 and 12.1 Å apart along with angles of 180°.
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Affiliation(s)
- Katherine M Byrd
- Department of Medicinal Chemistry, The University of Kansas, Wescoe Hall Drive, Malott 4070, Lawrence, KS, 66045-7563, USA
| | - Chitra Subramanian
- Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jacqueline Sanchez
- Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hashim F Motiwala
- Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Weiya Liu
- Department of Urology, The University of Kansas Medical Center, 3901 Rainbow Boulevard,Stop 3016, Kansas City, Kansas, 66160, USA
| | - Mark S Cohen
- Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Holzbeierlein
- Department of Urology, The University of Kansas Medical Center, 3901 Rainbow Boulevard,Stop 3016, Kansas City, Kansas, 66160, USA
| | - Brian S J Blagg
- Department of Medicinal Chemistry, The University of Kansas, Wescoe Hall Drive, Malott 4070, Lawrence, KS, 66045-7563, USA.
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43
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Terracciano S, Foglia A, Chini MG, Vaccaro MC, Russo A, Piaz FD, Saturnino C, Riccio R, Bifulco G, Bruno I. New dihydropyrimidin-2(1H)-one based Hsp90 C-terminal inhibitors. RSC Adv 2016. [DOI: 10.1039/c6ra17235k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The inhibition of the C-terminal domain of heat shock protein 90 (Hsp90) is emerging as a novel strategy for cancer therapy, therefore the identification of a new class of C-terminal inhibitors is strongly required.
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Affiliation(s)
- S. Terracciano
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
| | - A. Foglia
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
| | - M. G. Chini
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
| | - M. C. Vaccaro
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
| | - A. Russo
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
| | - F. Dal Piaz
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
- Department of Medicine and Surgery University of Salerno
| | - C. Saturnino
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
| | - R. Riccio
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
| | - G. Bifulco
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
| | - I. Bruno
- Department of Pharmacy
- University of Salerno
- Fisciano
- Italy
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44
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Lee SC, Min HY, Choi H, Bae SY, Park KH, Hyun SY, Lee HJ, Moon J, Park SH, Kim JY, An H, Park SJ, Seo JH, Lee S, Kim YM, Park HJ, Lee SK, Lee J, Lee J, Kim KW, Suh YG, Lee HY. Deguelin Analogue SH-1242 Inhibits Hsp90 Activity and Exerts Potent Anticancer Efficacy with Limited Neurotoxicity. Cancer Res 2015; 76:686-99. [DOI: 10.1158/0008-5472.can-15-1492] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/23/2015] [Indexed: 11/16/2022]
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45
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Strocchia M, Terracciano S, Chini MG, Vassallo A, Vaccaro MC, Dal Piaz F, Leone A, Riccio R, Bruno I, Bifulco G. Targeting the Hsp90 C-terminal domain by the chemically accessible dihydropyrimidinone scaffold. Chem Commun (Camb) 2015; 51:3850-3. [PMID: 25656927 DOI: 10.1039/c4cc10074c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Hsp90 C-terminal ligands are potential new anti-cancer drugs alternative to the more studied N-terminal inhibitors. Here we report the identification of a new dihydropyrimidinone binding the C-terminus, which is not structurally related to other well-known natural and nature-inspired inhibitors of this second druggable Hsp90 site.
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Affiliation(s)
- Maria Strocchia
- Department of Pharmacy, University of Salerno, via Giovanni Paolo II, 132, 84084, Fisciano, Italy.
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Guzzo G, Sciacovelli M, Bernardi P, Rasola A. Inhibition of succinate dehydrogenase by the mitochondrial chaperone TRAP1 has anti-oxidant and anti-apoptotic effects on tumor cells. Oncotarget 2015; 5:11897-908. [PMID: 25564869 PMCID: PMC4323003 DOI: 10.18632/oncotarget.2472] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 09/13/2014] [Indexed: 12/20/2022] Open
Abstract
TRAP1 is a mitochondrial chaperone highly expressed in many tumor types; it inhibits respiratory complex II, down-modulating its succinate dehydrogenase (SDH) enzymatic activity. SDH inhibition in turn leads to a pseudohypoxic state caused by succinate-dependent HIF1α stabilization and promotes neoplastic growth. Here we report that TRAP1 inhibition of SDH also shields cells from oxidative insults and from the ensuing lethal opening of the mitochondrial permeability transition pore. This anti-oxidant activity of TRAP1 protects tumor cells from death in conditions of nutrient paucity that mimic those encountered in the neoplasm during the process of malignant accrual, and it is required for in vitro tumorigenic growth. Our findings demonstrate that SDH inhibition by TRAP1 is oncogenic not only by inducing pseudohypoxia, but also by protecting tumor cells from oxidative stress.
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Affiliation(s)
- Giulia Guzzo
- CNR Neuroscience Institute and Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy
| | - Marco Sciacovelli
- CNR Neuroscience Institute and Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy. Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Paolo Bernardi
- CNR Neuroscience Institute and Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy
| | - Andrea Rasola
- CNR Neuroscience Institute and Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy
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Paladino A, Morra G, Colombo G. Structural Stability and Flexibility Direct the Selection of Activating Mutations in Epidermal Growth Factor Receptor Kinase. J Chem Inf Model 2015; 55:1377-87. [PMID: 26121158 DOI: 10.1021/acs.jcim.5b00270] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Herein we investigate the potential of novel methods of molecular dynamics analysis to provide information on the key factors that underlie the preferential localization and the effects of mutations modulating protein activities. Epidermal growth factor receptor (EGFR) kinases are selected as a test case. The combined analysis of protein energetics and internal dynamics indicates a clear polarization in the native protein, whereby a highly stable and ordered scaffold in one domain, namely the C-lobe, is combined to a flexible and loosely stabilized domain, the N-lobe. The subdivision in two portions with different properties directs the presence of point mutations mainly to the N-lobe. This allows modulating protein flexibility so that the protein can more efficiently sample the conformations necessary for substrate recognition, while leaving the stability of the protein unperturbed. In this context, comparative simulations of EGFR in the wild type sequence and in the presence of the activating oncogenic mutation G719S reveal flexibility changes in several key regions, involving in particular the part of the kinase devoted to the regulation of substrate recognition (regulatory core) and an increase in the number of stabilizing interactions in the N-lobe for the activated mutant. Our approaches represent a promising and simple strategy toward rationalizing the effects of mutations in modulating enzymatic activities.
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Affiliation(s)
- Antonella Paladino
- Istituto di Chimica del Riconoscimento Molecolare, CNR Via Mario Bianco 9, 20131, Milano, Italy
| | - Giulia Morra
- Istituto di Chimica del Riconoscimento Molecolare, CNR Via Mario Bianco 9, 20131, Milano, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR Via Mario Bianco 9, 20131, Milano, Italy
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Zhao H, Garg G, Zhao J, Moroni E, Girgis A, Franco LS, Singh S, Colombo G, Blagg BSJ. Design, synthesis and biological evaluation of biphenylamide derivatives as Hsp90 C-terminal inhibitors. Eur J Med Chem 2014; 89:442-66. [PMID: 25462258 DOI: 10.1016/j.ejmech.2014.10.034] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/13/2014] [Accepted: 10/12/2014] [Indexed: 11/18/2022]
Abstract
Modulation of Hsp90 C-terminal function represents a promising therapeutic approach for the treatment of cancer and neurodegenerative diseases. Current drug discovery efforts toward Hsp90 C-terminal inhibition focus on novobiocin, an antibiotic that was transformed into an Hsp90 inhibitor. Based on structural information obtained during the development of novobiocin derivatives and molecular docking studies, scaffolds containing a biphenyl moiety in lieu of the coumarin ring present in novobiocin were identified as new Hsp90 C-terminal inhibitors. Structure-activity relationship studies produced new derivatives that inhibit the proliferation of breast cancer cell lines at nanomolar concentrations, which corresponded directly with Hsp90 inhibition.
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Affiliation(s)
- Huiping Zhao
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, KS 66045-7563, USA
| | - Gaurav Garg
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, KS 66045-7563, USA
| | - Jinbo Zhao
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, KS 66045-7563, USA
| | - Elisabetta Moroni
- Istituto di chimica del riconoscimento molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Antwan Girgis
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, KS 66045-7563, USA
| | - Lucas S Franco
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, KS 66045-7563, USA
| | - Swapnil Singh
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, KS 66045-7563, USA
| | - Giorgio Colombo
- Istituto di chimica del riconoscimento molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Brian S J Blagg
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, KS 66045-7563, USA.
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Meli M, Pagano K, Ragona L, Colombo G. Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors. PLoS One 2014; 9:e97153. [PMID: 24865844 PMCID: PMC4035249 DOI: 10.1371/journal.pone.0097153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 04/14/2014] [Indexed: 12/04/2022] Open
Abstract
In this paper, we investigate the dynamic aspects of the molecular recognition between a small molecule ligand and a flat, exposed protein surface, representing a typical target in the development of protein-protein interaction inhibitors. Specifically, we analyze the complex between the protein Fibroblast Growth Factor 2 (FGF2) and a recently discovered small molecule inhibitor, labeled sm27 for which the binding site and the residues mainly involved in small molecule recognition have been previously characterized. We have approached this problem using microsecond MD simulations and NMR-based characterizations of the dynamics of the apo and holo states of the system. Using direct combination and cross-validation of the results of the two techniques, we select the set of conformational states that best recapitulate the principal dynamic and structural properties of the complex. We then use this information to generate a multi-structure representation of the sm27-FGF2 interaction. We propose this kind of representation and approach as a useful tool in particular for the characterization of systems where the mutual dynamic influence between the interacting partners is expected to play an important role. The results presented can also be used to generate new rules for the rational expansion of the chemical diversity space of FGF2 inhibitors.
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Affiliation(s)
- Massimiliano Meli
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
| | | | - Laura Ragona
- Istituto per lo Studio delle Macromolecole, CNR, Milano, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
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