1
|
Himmelbauer MK, Bajrami B, Basile R, Capacci A, Chen T, Choi CK, Gilfillan R, Gonzalez-Lopez de Turiso F, Gu C, Hoemberger M, Johnson DS, Jones JH, Kadakia E, Kirkland M, Lin EY, Liu Y, Ma B, Magee T, Mantena S, Marx IE, Metrick CM, Mingueneau M, Murugan P, Muste CA, Nadella P, Nevalainen M, Parker Harp CR, Pattaropong V, Pietrasiewicz A, Prince RJ, Purgett TJ, Santoro JC, Schulz J, Sciabola S, Tang H, Vandeveer HG, Wang T, Yousaf Z, Helal CJ, Hopkins BT. Discovery and Preclinical Characterization of BIIB129, a Covalent, Selective, and Brain-Penetrant BTK Inhibitor for the Treatment of Multiple Sclerosis. J Med Chem 2024; 67:8122-8140. [PMID: 38712838 DOI: 10.1021/acs.jmedchem.4c00220] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Multiple sclerosis (MS) is a chronic disease with an underlying pathology characterized by inflammation-driven neuronal loss, axonal injury, and demyelination. Bruton's tyrosine kinase (BTK), a nonreceptor tyrosine kinase and member of the TEC family of kinases, is involved in the regulation, migration, and functional activation of B cells and myeloid cells in the periphery and the central nervous system (CNS), cell types which are deemed central to the pathology contributing to disease progression in MS patients. Herein, we describe the discovery of BIIB129 (25), a structurally distinct and brain-penetrant targeted covalent inhibitor (TCI) of BTK with an unprecedented binding mode responsible for its high kinome selectivity. BIIB129 (25) demonstrated efficacy in disease-relevant preclinical in vivo models of B cell proliferation in the CNS, exhibits a favorable safety profile suitable for clinical development as an immunomodulating therapy for MS, and has a low projected total human daily dose.
Collapse
Affiliation(s)
- Martin K Himmelbauer
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rebecca Basile
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Andrew Capacci
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - TeYu Chen
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Colin K Choi
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rab Gilfillan
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | | | - Chungang Gu
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marc Hoemberger
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Douglas S Johnson
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - J Howard Jones
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ekta Kadakia
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Melissa Kirkland
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Edward Y Lin
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ying Liu
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bin Ma
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Tom Magee
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Srinivasa Mantena
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Isaac E Marx
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Claire M Metrick
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Mingueneau
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Paramasivam Murugan
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Cathy A Muste
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Prasad Nadella
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marta Nevalainen
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Chelsea R Parker Harp
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Vatee Pattaropong
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Alicia Pietrasiewicz
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Robin J Prince
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Thomas J Purgett
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Joseph C Santoro
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jurgen Schulz
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Simone Sciabola
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Hao Tang
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - H George Vandeveer
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ti Wang
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Zain Yousaf
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Christopher J Helal
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Brian T Hopkins
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
2
|
Pitsawong W, Pádua RAP, Grant T, Hoemberger M, Otten R, Bradshaw N, Grigorieff N, Kern D. From primordial clocks to circadian oscillators. Nature 2023; 616:183-189. [PMID: 36949197 PMCID: PMC10076222 DOI: 10.1038/s41586-023-05836-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/13/2023] [Indexed: 03/24/2023]
Abstract
Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator1. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock2. Subsequent additions of KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood3-6, but little is known about more ancient systems that only possess KaiBC. However, there are reports that they might exhibit a basic, hourglass-like timekeeping mechanism7-9. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides, which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.
Collapse
Affiliation(s)
- Warintra Pitsawong
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
- Biomolecular Discovery, Relay Therapeutics, Cambridge, MA, USA
| | - Ricardo A P Pádua
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
| | - Timothy Grant
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc Hoemberger
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | - Renee Otten
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | - Niels Bradshaw
- Department of Biochemistry, Brandeis University, Waltham, MA, USA
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dorothee Kern
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA, USA.
| |
Collapse
|
3
|
Ma B, Metrick CM, Gu C, Hoemberger M, Bajrami B, Bame E, Huang J, Mingueneau M, Murugan P, Nevalainen M, Santoro JC, Tang H, Wang T, Hopkins BT. Corrigendum to "Optimization of a novel piperazinone series as potent selective peripheral covalent BTK inhibitors" [Bioorg. Med. Chem. Lett. 60 (2022) 128549]. Bioorg Med Chem Lett 2022; 72:128856. [PMID: 35728998 DOI: 10.1016/j.bmcl.2022.128856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Bin Ma
- Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
| | | | - Chungang Gu
- Drug Metabolism & Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Marc Hoemberger
- Bioassays & High-Throughput Screens, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Eris Bame
- Translational Science, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Jiansheng Huang
- Drug Metabolism & Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Michael Mingueneau
- Multiple Sclerosis and Neurorepair Research, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Paramasivam Murugan
- Bioassays & High-Throughput Screens, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Marta Nevalainen
- Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Joseph C Santoro
- Bioassays & High-Throughput Screens, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Hao Tang
- Multiple Sclerosis and Neurorepair Research, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Ti Wang
- Bioassays & High-Throughput Screens, Biogen, 225 Binney Street, Cambridge, MA 02142, USA
| | - Brian T Hopkins
- Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, MA 02142, USA.
| |
Collapse
|
4
|
Hopkins BT, Bame E, Bajrami B, Black C, Bohnert T, Boiselle C, Burdette D, Burns JC, Delva L, Donaldson D, Grater R, Gu C, Hoemberger M, Johnson J, Kapadnis S, King K, Lulla M, Ma B, Marx I, Magee T, Meissner R, Metrick CM, Mingueneau M, Murugan P, Otipoby KL, Polack E, Poreci U, Prince R, Roach AM, Rowbottom C, Santoro JC, Schroeder P, Tang H, Tien E, Zhang F, Lyssikatos J. Discovery and Preclinical Characterization of BIIB091, a Reversible, Selective BTK Inhibitor for the Treatment of Multiple Sclerosis. J Med Chem 2022; 65:1206-1224. [PMID: 34734694 DOI: 10.1021/acs.jmedchem.1c00926] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Multiple Sclerosis is a chronic autoimmune neurodegenerative disorder of the central nervous system (CNS) that is characterized by inflammation, demyelination, and axonal injury leading to permeant disability. In the early stage of MS, inflammation is the primary driver of the disease progression. There remains an unmet need to develop high efficacy therapies with superior safety profiles to prevent the inflammation processes leading to disability. Herein, we describe the discovery of BIIB091, a structurally distinct orthosteric ATP competitive, reversible inhibitor that binds the BTK protein in a DFG-in confirmation designed to sequester Tyr-551, an important phosphorylation site on BTK, into an inactive conformation with excellent affinity. Preclinical studies demonstrated BIB091 to be a high potency molecule with good drug-like properties and a safety/tolerability profile suitable for clinical development as a highly selective, reversible BTKi for treating autoimmune diseases such as MS.
Collapse
Affiliation(s)
- Brian T Hopkins
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Eris Bame
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Cheryl Black
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Tonika Bohnert
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Carrie Boiselle
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Doug Burdette
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Jeremy C Burns
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Luisette Delva
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Douglas Donaldson
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Richard Grater
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Chungang Gu
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Marc Hoemberger
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Josh Johnson
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Sudarshan Kapadnis
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kris King
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Mukesh Lulla
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Bin Ma
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Isaac Marx
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Tom Magee
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Robert Meissner
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Claire M Metrick
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Michael Mingueneau
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Paramasivam Murugan
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kevin L Otipoby
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Evelyne Polack
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Urjana Poreci
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Robin Prince
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Allie M Roach
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Chris Rowbottom
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Joseph C Santoro
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Patricia Schroeder
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Hao Tang
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Eric Tien
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Fengmei Zhang
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Joseph Lyssikatos
- Research & Development, Biogen, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
5
|
Abstract
Despite the outstanding success of the cancer drug imatinib, one obstacle in prolonged treatment is the emergence of resistance mutations within the kinase domain of its target, Abl. We noticed that many patient-resistance mutations occur in the dynamic hot spots recently identified to be responsible for imatinib's high selectivity toward Abl. In this study, we provide an experimental analysis of the mechanism underlying drug resistance for three major resistance mutations (G250E, Y253F, and F317L). Our data settle controversies, revealing unexpected resistance mechanisms. The mutations alter the energy landscape of Abl in complex ways: increased kinase activity, altered affinity, and cooperativity for the substrates, and, surprisingly, only a modestly decreased imatinib affinity. Only under cellular adenosine triphosphate (ATP) concentrations, these changes cumulate in an order of magnitude increase in imatinib's half-maximal inhibitory concentration (IC50). These results highlight the importance of characterizing energy landscapes of targets and its changes by drug binding and by resistance mutations developed by patients.
Collapse
Affiliation(s)
- Marc Hoemberger
- Department of Biochemistry, Brandeis University, Waltham, MA 02454
- HHMI, Brandeis University, Waltham, MA 02454
| | - Warintra Pitsawong
- Department of Biochemistry, Brandeis University, Waltham, MA 02454
- HHMI, Brandeis University, Waltham, MA 02454
| | - Dorothee Kern
- Department of Biochemistry, Brandeis University, Waltham, MA 02454;
- HHMI, Brandeis University, Waltham, MA 02454
| |
Collapse
|
6
|
Stiller JB, Kerns SJ, Hoemberger M, Cho YJ, Otten R, Hagan MF, Kern D. Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics. Nat Catal 2019; 2:726-734. [PMID: 32159076 DOI: 10.1038/s41929-019-0307-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein conformational changes are frequently essential for enzyme catalysis, and in several cases, shown to be the limiting factor for overall catalytic speed. However, a structural understanding of corresponding transition states, needed to rationalize the kinetics, remains obscure due to their fleeting nature. Here, we determine the transition-state ensemble of the rate-limiting conformational transition in the enzyme adenylate kinase, by a synergistic approach between experimental high-pressure NMR relaxation during catalysis and molecular dynamics simulations. By comparing homologous kinases evolved under ambient or high pressure in the deep-sea, we detail transition state ensembles that differ in solvation as directly measured by the pressure dependence of catalysis. Capturing transition-state ensembles begins to complete the catalytic energy landscape that is generally characterized by structures of all intermediates and frequencies of transitions among them.
Collapse
Affiliation(s)
- John B Stiller
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States
| | - S Jordan Kerns
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States.,Present addresses: S.J.K. 27 Drydock Ave, Boston MA 02110 , M.H. 225 Binney St, Cambridge, MA 02142, Y.J.C. 733 Concord Ave Cambridge, MA 02138
| | - Marc Hoemberger
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States.,Present addresses: S.J.K. 27 Drydock Ave, Boston MA 02110 , M.H. 225 Binney St, Cambridge, MA 02142, Y.J.C. 733 Concord Ave Cambridge, MA 02138
| | - Young-Jin Cho
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States.,Present addresses: S.J.K. 27 Drydock Ave, Boston MA 02110 , M.H. 225 Binney St, Cambridge, MA 02142, Y.J.C. 733 Concord Ave Cambridge, MA 02138
| | - Renee Otten
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts 02452, United States
| | - Dorothee Kern
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States
| |
Collapse
|
7
|
Nguyen V, Wilson C, Hoemberger M, Stiller JB, Agafonov RV, Kutter S, English J, Theobald DL, Kern D. Evolutionary drivers of thermoadaptation in enzyme catalysis. Science 2016; 355:289-294. [PMID: 28008087 DOI: 10.1126/science.aah3717] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/21/2016] [Indexed: 11/02/2022]
Abstract
With early life likely to have existed in a hot environment, enzymes had to cope with an inherent drop in catalytic speed caused by lowered temperature. Here we characterize the molecular mechanisms underlying thermoadaptation of enzyme catalysis in adenylate kinase using ancestral sequence reconstruction spanning 3 billion years of evolution. We show that evolution solved the enzyme's key kinetic obstacle-how to maintain catalytic speed on a cooler Earth-by exploiting transition-state heat capacity. Tracing the evolution of enzyme activity and stability from the hot-start toward modern hyperthermophilic, mesophilic, and psychrophilic organisms illustrates active pressure versus passive drift in evolution on a molecular level, refutes the debated activity/stability trade-off, and suggests that the catalytic speed of adenylate kinase is an evolutionary driver for organismal fitness.
Collapse
Affiliation(s)
- Vy Nguyen
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Christopher Wilson
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Marc Hoemberger
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - John B Stiller
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Roman V Agafonov
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Steffen Kutter
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - Justin English
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | | | - Dorothee Kern
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA.
| |
Collapse
|
8
|
Wilson C, Agafonov RV, Hoemberger M, Kutter S, Zorba A, Halpin J, Buosi V, Otten R, Waterman D, Theobald DL, Kern D. Kinase dynamics. Using ancient protein kinases to unravel a modern cancer drug's mechanism. Science 2015; 347:882-6. [PMID: 25700521 PMCID: PMC4405104 DOI: 10.1126/science.aaa1823] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [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] [Indexed: 01/02/2023]
Abstract
Macromolecular function is rooted in energy landscapes, where sequence determines not a single structure but an ensemble of conformations. Hence, evolution modifies a protein's function by altering its energy landscape. Here, we recreate the evolutionary pathway between two modern human oncogenes, Src and Abl, by reconstructing their common ancestors. Our evolutionary reconstruction combined with x-ray structures of the common ancestor and pre-steady-state kinetics reveals a detailed atomistic mechanism for selectivity of the successful cancer drug Gleevec. Gleevec affinity is gained during the evolutionary trajectory toward Abl and lost toward Src, primarily by shifting an induced-fit equilibrium that is also disrupted in the clinical T315I resistance mutation. This work reveals the mechanism of Gleevec specificity while offering insights into how energy landscapes evolve.
Collapse
Affiliation(s)
- C. Wilson
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - R. V. Agafonov
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - M. Hoemberger
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - S. Kutter
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - A. Zorba
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - J. Halpin
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - V. Buosi
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - R. Otten
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - D. Waterman
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - D. L. Theobald
- Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| | - D. Kern
- Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, Waltham, MA 02452, USA
| |
Collapse
|