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Metwally E, Mak V, Soriano A, Zebisch M, Silvestre HL, McEwan PA, Ermakov G, Beaumont M, Tawa P, Barker JJ, Yen R, Patel A, Lim YH, Healy D, Hanisak J, Cheng AC, Greshock T, Fischmann TO. Structural insights into selective small molecule activation of PKG1α. Commun Biol 2023; 6:798. [PMID: 37524852 PMCID: PMC10390508 DOI: 10.1038/s42003-023-05095-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/04/2023] [Indexed: 08/02/2023] Open
Abstract
cGMP-dependent protein kinase I-α (PKG1α) is a target for pulmonary arterial hypertension due to its role in the regulation of smooth muscle function. While most work has focused on regulation of cGMP turnover, we recently described several small molecule tool compounds which were capable of activating PKG1α via a cGMP independent pathway. Selected molecules were crystallized in the presence of PKG1α and were found to bind to an allosteric site proximal to the low-affinity nucleotide binding domain. These molecules act to displace the switch helix and cause activation of PKG1α representing a new mechanism for the activation and control of this critical therapeutic path. The described structures are vital to understanding the function and control of this key regulatory pathway.
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Affiliation(s)
- Essam Metwally
- Modeling and Informatics, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA.
| | - Victor Mak
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Aileen Soriano
- Quantitative Biosciences, MRL, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Matthias Zebisch
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - H Leonardo Silvestre
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Paul A McEwan
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Grigori Ermakov
- Discovery Bioanalytics, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Maribel Beaumont
- Discovery Bioanalytics, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Paul Tawa
- Quantitative Biosciences, MRL, Merck & Co., Inc., Kenilworth, NJ, USA
| | - John J Barker
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Rose Yen
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Akash Patel
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Yeon-Hee Lim
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - David Healy
- Discovery Biology, MRL, Merck & Co., Inc., Boston, MA, USA
| | - Jennifer Hanisak
- Discovery Chemistry, MRL, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Alan C Cheng
- Modeling and Informatics, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Tom Greshock
- Discovery Chemistry, MRL, Merck & Co., Inc., 213 E. Grand Avenue, South San Francisco, CA, USA
| | - Thierry O Fischmann
- Protein and Structural Chemistry, MRL, Merck & Co., Inc., Kenilworth, NJ, USA.
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Mak VW, Patel AM, Yen R, Hanisak J, Lim YH, Bao J, Zheng R, Seganish WM, Yu Y, Healy DR, Ogawa A, Ren Z, Soriano A, Ermakov GP, Beaumont M, Metwally E, Cheng AC, Verras A, Fischmann T, Zebisch M, Silvestre HL, McEwan PA, Barker J, Rearden P, Greshock TJ. Optimization and Mechanistic Investigations of Novel Allosteric Activators of PKG1α. J Med Chem 2022; 65:10318-10340. [PMID: 35878399 DOI: 10.1021/acs.jmedchem.1c02109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Activation of PKG1α is a compelling strategy for the treatment of cardiovascular diseases. As the main effector of cyclic guanosine monophosphate (cGMP), activation of PKG1α induces smooth muscle relaxation in blood vessels, lowers pulmonary blood pressure, prevents platelet aggregation, and protects against cardiac stress. The development of activators has been mostly limited to cGMP mimetics and synthetic peptides. Described herein is the optimization of a piperidine series of small molecules to yield activators that demonstrate in vitro phosphorylation of vasodilator-stimulated phosphoprotein as well as antiproliferative effects in human pulmonary arterial smooth muscle cells. Hydrogen/deuterium exchange mass spectrometry experiments with the small molecule activators revealed a mechanism of action consistent with cGMP-induced activation, and an X-ray co-crystal structure with a construct encompassing the regulatory domains illustrated a binding mode in an allosteric pocket proximal to the low-affinity cyclic nucleotide-binding domain.
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Affiliation(s)
- Victor W Mak
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Akash M Patel
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Rose Yen
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Jennifer Hanisak
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yeon-Hee Lim
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Jianming Bao
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States.,Ionova Life Science, Shenzhen 518122, Guangdong, China
| | - Rong Zheng
- IDSU, Wuxi AppTec Co., Ltd, Shanghai 200131, China
| | - W Michael Seganish
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Yang Yu
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - David R Healy
- Discovery Biology, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Aimie Ogawa
- Quantitative Biosciences, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Zhao Ren
- Quantitative Biosciences, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Aileen Soriano
- Mass Spectrometry and Biophysics, Computation and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Grigori P Ermakov
- PPDM Discovery Bioanalytics, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Maribel Beaumont
- PPDM Discovery Bioanalytics, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Essam Metwally
- Computational and Structural Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Alan C Cheng
- Computational and Structural Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Andreas Verras
- Schrodinger Inc., 120 West 45th Street, 17th Floor, New York, New York 10036-4041, United States.,Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Thierry Fischmann
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Matthias Zebisch
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - H Leonardo Silvestre
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Paul A McEwan
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - John Barker
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Paul Rearden
- DMPK, Recursion Pharmaceuticals, Salt Lake City, Utah 84101, United States.,PPDM, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Thomas J Greshock
- Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
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Tawa P, Zhang L, Metwally E, Hou Y, McCoy MA, Seganish WM, Zhang R, Frank E, Sheth P, Hanisak J, Sondey C, Bauman D, Soriano A. Mechanistic insights on novel small molecule allosteric activators of cGMP-dependent protein kinase PKG1α. J Biol Chem 2022; 298:102284. [PMID: 35868561 PMCID: PMC9425037 DOI: 10.1016/j.jbc.2022.102284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 11/30/2022] Open
Abstract
cGMP-dependent protein kinase (PKG) represents a compelling drug target for treatment of cardiovascular diseases. PKG1 is the major effector of beneficial cGMP signaling which is involved in smooth muscle relaxation and vascular tone, inhibition of platelet aggregation and signaling that leads to cardioprotection. In this study, a novel piperidine series of activators previously identified from an ultrahigh-throughput screen were validated to directly bind partially activated PKG1α and subsequently enhance its kinase activity in a concentration-dependent manner. Compounds from initial optimization efforts showed an ability to activate PKG1α independent of the endogenous activator, cGMP. We demonstrate these small molecule activators mimic the effect of cGMP on the kinetic parameters of PKG1α by positively modulating the KM of the peptide substrate and negatively modulating the apparent KM for ATP with increase in catalytic efficiency, kcat. In addition, these compounds also allosterically modulate the binding affinity of cGMP for PKG1α by increasing the affinity of cGMP for the high-affinity binding site (CNB-A) and decreasing the affinity of cGMP for the low-affinity binding site (CNB-B). We show the mode of action of these activators involves binding to an allosteric site within the regulatory domain, near the CNB-B binding site. To the best of our knowledge, these are the first reported non-cGMP mimetic small molecules shown to directly activate PKG1α. Insights into the mechanism of action of these compounds will enable future development of cardioprotective compounds that function through novel modes of action for the treatment of cardiovascular diseases.
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Affiliation(s)
- Paul Tawa
- Mass Spectrometry & Biophysics, Computational & Structural Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Lei Zhang
- Biologics AR&D Immunoassay Group, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Essam Metwally
- Computational & Structural Chemistry, Merck & Co., Inc., South San Francisco, CA, USA
| | - Yan Hou
- Mass Spectrometry & Biophysics, Computational & Structural Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Mark A McCoy
- Mass Spectrometry & Biophysics, Computational & Structural Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | | | - Rumin Zhang
- Mass Spectrometry & Biophysics, Computational & Structural Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Emily Frank
- Quantitative Biosciences, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Payal Sheth
- Mass Spectrometry & Biophysics, Computational & Structural Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
| | | | | | - David Bauman
- Discovery Biology, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Aileen Soriano
- Mass Spectrometry & Biophysics, Computational & Structural Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA.
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