Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains
The design of compounds that can discriminate between closely related target proteins remains a central challenge in drug discovery. Specific therapeutics targeting the highly conserved myosin motor family are urgently needed as mutations in at least six of its members cause numerous diseases. Allos...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2023-01-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/83602 |
| _version_ | 1811158060465389568 |
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| author | Artur Meller Jeffrey M Lotthammer Louis G Smith Borna Novak Lindsey A Lee Catherine C Kuhn Lina Greenberg Leslie A Leinwand Michael J Greenberg Gregory R Bowman |
| author_facet | Artur Meller Jeffrey M Lotthammer Louis G Smith Borna Novak Lindsey A Lee Catherine C Kuhn Lina Greenberg Leslie A Leinwand Michael J Greenberg Gregory R Bowman |
| author_sort | Artur Meller |
| collection | DOAJ |
| description | The design of compounds that can discriminate between closely related target proteins remains a central challenge in drug discovery. Specific therapeutics targeting the highly conserved myosin motor family are urgently needed as mutations in at least six of its members cause numerous diseases. Allosteric modulators, like the myosin-II inhibitor blebbistatin, are a promising means to achieve specificity. However, it remains unclear why blebbistatin inhibits myosin-II motors with different potencies given that it binds at a highly conserved pocket that is always closed in blebbistatin-free experimental structures. We hypothesized that the probability of pocket opening is an important determinant of the potency of compounds like blebbistatin. To test this hypothesis, we used Markov state models (MSMs) built from over 2 ms of aggregate molecular dynamics simulations with explicit solvent. We find that blebbistatin’s binding pocket readily opens in simulations of blebbistatin-sensitive myosin isoforms. Comparing these conformational ensembles reveals that the probability of pocket opening correctly identifies which isoforms are most sensitive to blebbistatin inhibition and that docking against MSMs quantitatively predicts blebbistatin binding affinities (R2=0.82). In a blind prediction for an isoform (Myh7b) whose blebbistatin sensitivity was unknown, we find good agreement between predicted and measured IC50s (0.67 μM vs. 0.36 μM). Therefore, we expect this framework to be useful for the development of novel specific drugs across numerous protein targets. |
| first_indexed | 2024-04-10T05:16:48Z |
| format | Article |
| id | doaj.art-376094e3254c440f9fdb0628df390ca2 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-10T05:16:48Z |
| publishDate | 2023-01-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-376094e3254c440f9fdb0628df390ca22023-03-08T16:20:47ZengeLife Sciences Publications LtdeLife2050-084X2023-01-011210.7554/eLife.83602Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domainsArtur Meller0https://orcid.org/0000-0002-5504-2684Jeffrey M Lotthammer1https://orcid.org/0000-0002-5022-7006Louis G Smith2Borna Novak3Lindsey A Lee4Catherine C Kuhn5Lina Greenberg6Leslie A Leinwand7https://orcid.org/0000-0003-1470-4810Michael J Greenberg8https://orcid.org/0000-0003-1320-3547Gregory R Bowman9https://orcid.org/0000-0002-2083-4892Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United States; Medical Scientist Training Program, Washington University in St. Louis, Philadelphia, United StatesDepartment of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United StatesDepartment of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United States; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United StatesDepartment of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United States; Medical Scientist Training Program, Washington University in St. Louis, Philadelphia, United StatesMolecular, Cellular, and Developmental Biology Department, University of Colorado Boulder, Boulder, United States; BioFrontiers Institute, Boulder, United StatesDepartment of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United StatesDepartment of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United StatesMolecular, Cellular, and Developmental Biology Department, University of Colorado Boulder, Boulder, United States; BioFrontiers Institute, Boulder, United StatesDepartment of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United StatesDepartment of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United States; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, United StatesThe design of compounds that can discriminate between closely related target proteins remains a central challenge in drug discovery. Specific therapeutics targeting the highly conserved myosin motor family are urgently needed as mutations in at least six of its members cause numerous diseases. Allosteric modulators, like the myosin-II inhibitor blebbistatin, are a promising means to achieve specificity. However, it remains unclear why blebbistatin inhibits myosin-II motors with different potencies given that it binds at a highly conserved pocket that is always closed in blebbistatin-free experimental structures. We hypothesized that the probability of pocket opening is an important determinant of the potency of compounds like blebbistatin. To test this hypothesis, we used Markov state models (MSMs) built from over 2 ms of aggregate molecular dynamics simulations with explicit solvent. We find that blebbistatin’s binding pocket readily opens in simulations of blebbistatin-sensitive myosin isoforms. Comparing these conformational ensembles reveals that the probability of pocket opening correctly identifies which isoforms are most sensitive to blebbistatin inhibition and that docking against MSMs quantitatively predicts blebbistatin binding affinities (R2=0.82). In a blind prediction for an isoform (Myh7b) whose blebbistatin sensitivity was unknown, we find good agreement between predicted and measured IC50s (0.67 μM vs. 0.36 μM). Therefore, we expect this framework to be useful for the development of novel specific drugs across numerous protein targets.https://elifesciences.org/articles/83602myosinspecificitymolecular dynamicscryptic pocketsprotein dynamics |
| spellingShingle | Artur Meller Jeffrey M Lotthammer Louis G Smith Borna Novak Lindsey A Lee Catherine C Kuhn Lina Greenberg Leslie A Leinwand Michael J Greenberg Gregory R Bowman Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains eLife myosin specificity molecular dynamics cryptic pockets protein dynamics |
| title | Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains |
| title_full | Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains |
| title_fullStr | Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains |
| title_full_unstemmed | Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains |
| title_short | Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains |
| title_sort | drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains |
| topic | myosin specificity molecular dynamics cryptic pockets protein dynamics |
| url | https://elifesciences.org/articles/83602 |
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