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Camara A, Chugh H, George A, Dolidze L, Ryu K, Holly KJ, Flaherty DP, Mattoo S. Discovery and validation of a novel inhibitor of HYPE-mediated AMPylation. Cell Stress Chaperones 2024; 29:404-424. [PMID: 38599565 PMCID: PMC11053294 DOI: 10.1016/j.cstres.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
Adenosyl monophosphate (AMP)ylation (the covalent transfer of an AMP from Adenosine Triphosphate (ATP) onto a target protein) is catalyzed by the human enzyme Huntingtin Yeast Interacting Partner E (HYPE)/FicD to regulate its substrate, the heat shock chaperone binding immunoglobulin protein (BiP). HYPE-mediated AMPylation of BiP is critical for maintaining proteostasis in the endoplasmic reticulum and mounting a unfolded protein response in times of proteostatic imbalance. Thus, manipulating HYPE's enzymatic activity is a key therapeutic strategy toward the treatment of various protein misfolding diseases, including neuropathy and early-onset diabetes associated with two recently identified clinical mutations of HYPE. Herein, we present an optimized, fluorescence polarization-based, high-throughput screening (HTS) assay to discover activators and inhibitors of HYPE-mediated AMPylation. After challenging our HTS assay with over 30,000 compounds, we discovered a novel AMPylase inhibitor, I2.10. We also determined a low micromolar IC50 for I2.10 and employed biorthogonal counter-screens to validate its efficacy against HYPE's AMPylation of BiP. Further, we report low cytotoxicity of I2.10 on human cell lines. We thus established an optimized, high-quality HTS assay amenable to tracking HYPE's enzymatic activity at scale, and provided the first novel small-molecule inhibitor capable of perturbing HYPE-directed AMPylation of BiP in vitro. Our HTS assay and I2.10 compound serve as a platform for further development of HYPE-specific small-molecule therapeutics.
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Affiliation(s)
- Ali Camara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Heerak Chugh
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Drug Discovery and Development Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Alyssa George
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Lukas Dolidze
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Kevin Ryu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Katrina J Holly
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Seema Mattoo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA; Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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Buchner J, Alasady MJ, Backe SJ, Blagg BSJ, Carpenter RL, Colombo G, Gelis I, Gewirth DT, Gierasch LM, Houry WA, Johnson JL, Kang BH, Kao AW, LaPointe P, Mattoo S, McClellan AJ, Neckers LM, Prodromou C, Rasola A, Sager RA, Theodoraki MA, Truman AW, Truttman MC, Zachara NE, Bourboulia D, Mollapour M, Woodford MR. Second international symposium on the chaperone code, 2023. Cell Stress Chaperones 2024; 29:88-96. [PMID: 38316354 PMCID: PMC10939070 DOI: 10.1016/j.cstres.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Affiliation(s)
- Johannes Buchner
- Department of Bioscience, Technical University of Munich, D85748, Garching, Germany.
| | - Milad J Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Brian S J Blagg
- Department of Chemistry and Biochemistry, Warren Family Research Center for Drug Discovery and Development, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Richard L Carpenter
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Bloomington, IN, 47405, USA; Medical Sciences, Indiana University School of Medicine, Bloomington, IN, 47405, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 47405, USA
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Ioannis Gelis
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Daniel T Gewirth
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Lila M Gierasch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA; Hauptman-Woodward Medical Research Institute, Buffalo, NY, 14203, USA
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
| | - Jill L Johnson
- Department of Biological Sciences and the Center for Reproductive Biology, University of Idaho, Moscow, ID, 83844, USA
| | - Byoung Heon Kang
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Aimee W Kao
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Paul LaPointe
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Seema Mattoo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Amie J McClellan
- Division of Science and Mathematics, Bennington College, Bennington, VT, 05201, USA
| | - Leonard M Neckers
- Center for Cancer Research, National Cancer Institute, Rockville, MD, 20892, USA
| | | | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | | | - Andrew W Truman
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Matthias C Truttman
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA; Geriatrics Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Natasha E Zachara
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
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Castelli M, Marchetti F, Osuna S, F. Oliveira AS, Mulholland AJ, Serapian SA, Colombo G. Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. J Am Chem Soc 2024; 146:901-919. [PMID: 38116743 PMCID: PMC10785808 DOI: 10.1021/jacs.3c11396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
Protein functions are dynamically regulated by allostery, which enables conformational communication even between faraway residues, and expresses itself in many forms, akin to different "languages": allosteric control pathways predominating in an unperturbed protein are often unintuitively reshaped whenever biochemical perturbations arise (e.g., mutations). To accurately model allostery, unbiased molecular dynamics (MD) simulations require integration with a reliable method able to, e.g., detect incipient allosteric changes or likely perturbation pathways; this is because allostery can operate at longer time scales than those accessible by plain MD. Such methods are typically applied singularly, but we here argue their joint application─as a "multilingual" approach─could work significantly better. We successfully prove this through unbiased MD simulations (∼100 μs) of the widely studied, allosterically active oncotarget K-Ras4B, solvated and embedded in a phospholipid membrane, from which we decrypt allostery using four showcase "languages": Distance Fluctuation analysis and the Shortest Path Map capture allosteric hotspots at equilibrium; Anisotropic Thermal Diffusion and Dynamical Non-Equilibrium MD simulations assess perturbations upon, respectively, either superheating or hydrolyzing the GTP that oncogenically activates K-Ras4B. Chosen "languages" work synergistically, providing an articulate, mutually coherent, experimentally consistent picture of K-Ras4B allostery, whereby distinct traits emerge at equilibrium and upon GTP cleavage. At equilibrium, combined evidence confirms prominent allosteric communication from the membrane-embedded hypervariable region, through a hub comprising helix α5 and sheet β5, and up to the active site, encompassing allosteric "switches" I and II (marginally), and two proposed pockets. Upon GTP cleavage, allosteric perturbations mostly accumulate on the switches and documented interfaces.
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Affiliation(s)
- Matteo Castelli
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
- INSTM, via G. Giusti 9, 50121 Florence, Italy
- E4
Computer Engineering, via Martiri delle libertà 66, 42019 Scandiano (RE), Italy
| | - Sílvia Osuna
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Girona, Catalonia E-17071, Spain
- ICREA, Barcelona, Catalonia E-08010, Spain
| | - A. Sofia F. Oliveira
- Centre for
Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Adrian J. Mulholland
- Centre for
Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Stefano A. Serapian
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
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Castelli M, Magni A, Bonollo G, Pavoni S, Frigerio F, Oliveira ASF, Cinquini F, Serapian SA, Colombo G. Molecular mechanisms of chaperone-directed protein folding: Insights from atomistic simulations. Protein Sci 2023; 33:e4880. [PMID: 38145386 PMCID: PMC10895457 DOI: 10.1002/pro.4880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Molecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task-specific co-chaperones, process ATP and become part of a complex network that undergoes extensive compositional and conformational variations. Despite impressive advances in structural knowledge, the mechanisms that regulate the dynamics of functional assemblies, their response to nucleotides, and their relevance for client remodeling are still elusive. Here, we focus on the glucocorticoid receptor (GR):Hsp90:Hsp70:co-chaperone Hop client-loading and the GR:Hsp90:co-chaperone p23 client-maturation complexes, key assemblies in the folding cycle of glucocorticoid receptor (GR), a client strictly dependent upon Hsp90/Hsp70 for activity. Using a combination of molecular dynamics simulation approaches, we unveil with unprecedented detail the mechanisms that underpin function in these chaperone machineries. Specifically, we dissect the processes by which the nucleotide-encoded message is relayed to the client and how the distinct partners of the assemblies cooperate to (pre)organize partially folded GR during Loading and Maturation. We show how different ligand states determine distinct dynamic profiles for the functional interfaces defining the interactions in the complexes and modulate their overall flexibility to facilitate progress along the chaperone cycle. Finally, we also show that the GR regions engaged by the chaperone machinery display peculiar energetic signatures in the folded state, which enhance the probability of partial unfolding fluctuations. From these results, we propose a model where a dynamic cross-talk emerges between the chaperone dynamics states and remodeling of client-interacting regions. This factor, coupled to the highly dynamic nature of the assemblies and the conformational heterogeneity of their interactions, provides the basis for regulating the functions of distinct assemblies during the chaperoning cycle.
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Affiliation(s)
| | - Andrea Magni
- Dipartimento di Chimica, Università di Pavia, Pavia, Italy
| | | | - Silvia Pavoni
- Department of Physical Chemistry, R&D Eni SpA, San Donato Milanese, Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D Eni SpA, San Donato Milanese, Italy
| | - A Sofia F Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Fabrizio Cinquini
- Upstream & Technical Services - TECS/STES - Eni Spa, San Donato Milanese, Italy
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