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Hantz ER, Tikunova SB, Belevych N, Davis JP, Reiser PJ, Lindert S. Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship. J Chem Inf Model 2023; 63:3462-3473. [PMID: 37204863 PMCID: PMC10496875 DOI: 10.1021/acs.jcim.3c00196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Despite large investments from academia and industry, heart failure, which results from a disruption of the contractile apparatus, remains a leading cause of death. Cardiac muscle contraction is a calcium-dependent mechanism, which is regulated by the troponin protein complex (cTn) and specifically by the N-terminal domain of its calcium-binding subunit (cNTnC). There is an increasing need for the development of small molecules that increase calcium sensitivity without altering the systolic calcium concentration, thereby strengthening the cardiac function. Here, we examined the effect of our previously identified calcium-sensitizing small molecule, ChemBridge compound 7930079, in the context of several homologous muscle systems. The effect of this molecule on force generation in isolated cardiac trabeculae and slow skeletal muscle fibers was measured. Furthermore, we explored the use of Gaussian accelerated molecular dynamics in sampling highly predictive receptor conformations based on NMR-derived starting structures. Additionally, we took a rational computational approach for lead optimization based on lipophilic diphenyl moieties. This integrated structural-biochemical-physiological approach led to the identification of three novel low-affinity binders, which had similar binding affinities to the known positive inotrope trifluoperazine. The most potent identified calcium sensitizer was compound 16 with an apparent affinity of 117 ± 17 μM.
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Affiliation(s)
- Eric R. Hantz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
| | - Svetlana B. Tikunova
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210
| | - Natalya Belevych
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH 43210
| | - Jonathan P. Davis
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210
| | - Peter J. Reiser
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH 43210
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
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Hantz ER, Tikunova SB, Belevych N, Davis JP, Reiser PJ, Lindert S. Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscle and Structure Activity Relationship. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527323. [PMID: 36798160 PMCID: PMC9934531 DOI: 10.1101/2023.02.06.527323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Despite large investments from academia and industry, heart failure, which results from a disruption of the contractile apparatus, remains a leading cause of death. Cardiac muscle contraction is a calcium-dependent mechanism, which is regulated by the troponin protein complex (cTn) and specifically by the N-terminal domain of its calcium binding subunit (cNTnC). There is an increasing need for the development of small molecules that increase calcium sensitivity without altering systolic calcium concentration, thereby strengthening cardiac function. Here, we examined the effect of our previously identified calcium sensitizing small molecule, ChemBridge compound 7930079, in the context of several homologous muscle systems. The effect of this molecule on force generation in isolated cardiac trabeculae and slow skeletal muscle fibers was measured. Furthermore, we explored the use of Gaussian accelerated molecular dynamics in sampling highly predictive receptor conformations based on NMR derived starting structures. Additionally, we took a rational computational approach for lead optimization based on lipophilic diphenyl moieties. This led to the identification of three novel low affinity binders, which had similar binding affinities to known positive inotrope trifluoperazine. The most potent identified calcium sensitizer was compound 16 with an apparent affinity of 117 ± 17 μM .
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Affiliation(s)
- Eric R. Hantz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210
| | - Svetlana B. Tikunova
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210
| | - Natalya Belevych
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH 43210
| | - Jonathan P. Davis
- Davis Heart and Lung Research Institute and Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, 43210
| | - Peter J. Reiser
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH 43210
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210,Correspondence to: Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 W. 18th Avenue, Columbus, OH 43210, 614-292-8284 (office), 614-292-1685 (fax),
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Yan C, Sack JS. X-ray structure of a human cardiac muscle troponin C/troponin I chimera in two crystal forms. Acta Crystallogr F Struct Biol Commun 2022; 78:17-24. [PMID: 34981771 PMCID: PMC8725003 DOI: 10.1107/s2053230x21012395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/22/2021] [Indexed: 01/03/2023] Open
Abstract
The X-ray crystal structure of a human cardiac muscle troponin C/troponin I chimera has been determined in two different crystal forms and shows a conformation of the complex that differs from that previously observed by NMR. The chimera consists of the N-terminal domain of troponin C (cTnC; residues 1-80) fused to the switch region of troponin I (cTnI; residues 138-162). In both crystal forms, the cTnI residues form a six-turn α-helix that lays across the hydrophobic groove of an adjacent cTnC molecule in the crystal structure. In contrast to previous models, the cTnI helix runs in a parallel direction relative to the cTnC groove and completely blocks the calcium desensitizer binding site of the cTnC-cTnI interface.
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Affiliation(s)
- Chunhong Yan
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - John S. Sack
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA,Correspondence e-mail:
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Li MX, Mercier P, Hartman JJ, Sykes BD. Structural Basis of Tirasemtiv Activation of Fast Skeletal Muscle. J Med Chem 2021; 64:3026-3034. [PMID: 33703886 DOI: 10.1021/acs.jmedchem.0c01412] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Troponin regulates the calcium-mediated activation of skeletal muscle. Muscle weakness in diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy occurs from diminished neuromuscular output. The first direct fast skeletal troponin activator, tirasemtiv, amplifies the response of muscle to neuromuscular input. Tirasemtiv binds selectively and strongly to fast skeletal troponin, slowing the rate of calcium release and sensitizing muscle to calcium. We report the solution NMR structure of tirasemtiv bound to a fast skeletal troponin C-troponin I chimera. The structure reveals that tirasemtiv binds in a hydrophobic pocket between the regulatory domain of troponin C and the switch region of troponin I, which overlaps with that of Anapoe in the X-ray structure of skeletal troponin. Multiple interactions stabilize the troponin C-troponin I interface, increase the affinity of troponin C for the switch region of fast skeletal troponin I, and drive the equilibrium toward the active state.
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Affiliation(s)
- Monica X Li
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Pascal Mercier
- National High Field NMR Centre, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - James J Hartman
- Cytokinetics, Inc., South San Francisco, California 94080, United States
| | - Brian D Sykes
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Li MX, Hwang PM. Structure and function of cardiac troponin C (TNNC1): Implications for heart failure, cardiomyopathies, and troponin modulating drugs. Gene 2015; 571:153-66. [PMID: 26232335 DOI: 10.1016/j.gene.2015.07.074] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/24/2015] [Accepted: 07/21/2015] [Indexed: 10/23/2022]
Abstract
In striated muscle, the protein troponin complex turns contraction on and off in a calcium-dependent manner. The calcium-sensing component of the complex is troponin C, which is expressed from the TNNC1 gene in both cardiac muscle and slow-twitch skeletal muscle (identical transcript in both tissues) and the TNNC2 gene in fast-twitch skeletal muscle. Cardiac troponin C (cTnC) is made up of two globular EF-hand domains connected by a flexible linker. The structural C-domain (cCTnC) contains two high affinity calcium-binding sites that are always occupied by Ca(2+) or Mg(2+) under physiologic conditions, stabilizing an open conformation that remains anchored to the rest of the troponin complex. In contrast, the regulatory N-domain (cNTnC) contains a single low affinity site that is largely unoccupied at resting calcium concentrations. During muscle activation, calcium binding to cNTnC favors an open conformation that binds to the switch region of troponin I, removing adjacent inhibitory regions of troponin I from actin and allowing muscle contraction to proceed. Regulation of the calcium binding affinity of cNTnC is physiologically important, because it directly impacts the calcium sensitivity of muscle contraction. Calcium sensitivity can be modified by drugs that stabilize the open form of cNTnC, post-translational modifications like phosphorylation of troponin I, or downstream thin filament protein interactions that impact the availability of the troponin I switch region. Recently, mutations in cTnC have been associated with hypertrophic or dilated cardiomyopathy. A detailed understanding of how calcium sensitivity is regulated through the troponin complex is necessary for explaining how mutations perturb its function to promote cardiomyopathy and how post-translational modifications in the thin filament affect heart function and heart failure. Troponin modulating drugs are being developed for the treatment of cardiomyopathies and heart failure.
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Affiliation(s)
- Monica X Li
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada; Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Peter M Hwang
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada; Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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Pineda-Sanabria SE, Robertson IM, Sykes BD. Structure and Dynamics of the Acidosis-Resistant A162H Mutant of the Switch Region of Troponin I Bound to the Regulatory Domain of Troponin C. Biochemistry 2015; 54:3583-93. [DOI: 10.1021/acs.biochem.5b00178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sandra E. Pineda-Sanabria
- Department of Biochemistry, ‡Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ian M. Robertson
- Department of Biochemistry, ‡Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Brian D. Sykes
- Department of Biochemistry, ‡Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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Denessiouk K, Permyakov S, Denesyuk A, Permyakov E, Johnson MS. Two structural motifs within canonical EF-hand calcium-binding domains identify five different classes of calcium buffers and sensors. PLoS One 2014; 9:e109287. [PMID: 25313560 PMCID: PMC4196763 DOI: 10.1371/journal.pone.0109287] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/29/2014] [Indexed: 11/18/2022] Open
Abstract
Proteins with EF-hand calcium-binding motifs are essential for many cellular processes, but are also associated with cancer, autism, cardiac arrhythmias, and Alzheimer's, skeletal muscle and neuronal diseases. Functionally, all EF-hand proteins are divided into two groups: (1) calcium sensors, which function to translate the signal to various responses; and (2) calcium buffers, which control the level of free Ca2+ ions in the cytoplasm. The borderline between the two groups is not clear, and many proteins cannot be described as definitive buffers or sensors. Here, we describe two highly-conserved structural motifs found in all known different families of the EF-hand proteins. The two motifs provide a supporting scaffold for the DxDxDG calcium binding loop and contribute to the hydrophobic core of the EF hand domain. The motifs allow more precise identification of calcium buffers and calcium sensors. Based on the characteristics of the two motifs, we could classify individual EF-hand domains into five groups: (1) Open static; (2) Closed static; (3) Local dynamic; (4) Dynamic; and (5) Local static EF-hand domains.
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Affiliation(s)
- Konstantin Denessiouk
- Biochemistry, Department of Biosciences, Åbo Akademi University, Turku, Finland
- * E-mail:
| | - Sergei Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
| | - Alexander Denesyuk
- Biochemistry, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Eugene Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
| | - Mark S. Johnson
- Biochemistry, Department of Biosciences, Åbo Akademi University, Turku, Finland
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