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Mealka M, Sierra NA, Avellaneda Matteo D, Albekioni E, Khoury R, Mai T, Conley BM, Coleman NJ, Sabo KA, Komives EA, Bobkov AA, Cooksy AL, Silletti S, Schiffer JM, Huxford T, Sohl CD. Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms. Nat Commun 2024; 15:3785. [PMID: 38710674 PMCID: PMC11074275 DOI: 10.1038/s41467-024-48277-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/26/2024] [Indexed: 05/08/2024] Open
Abstract
Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant unusually preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employ static and dynamic structural methods and observe that, compared to R132H, the R132Q active site adopts a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling reveals a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.
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Affiliation(s)
- Matthew Mealka
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nicole A Sierra
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | | | - Elene Albekioni
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Rachel Khoury
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Timothy Mai
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Brittany M Conley
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nalani J Coleman
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Kaitlyn A Sabo
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Elizabeth A Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Andrew L Cooksy
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Steve Silletti
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | | | - Tom Huxford
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Christal D Sohl
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA.
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Mealka M, Sierra NA, Matteo DA, Albekioni E, Khoury R, Mai T, Conley BM, Coleman NJ, Sabo KA, Komives EA, Bobkov AA, Cooksy AL, Silletti S, Schiffer JM, Huxford T, Sohl CD. Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms. RESEARCH SQUARE 2024:rs.3.rs-3889456. [PMID: 38464189 PMCID: PMC10925425 DOI: 10.21203/rs.3.rs-3889456/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant uniquely preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employed static and dynamic structural methods and found that, compared to R132H, the R132Q active site adopted a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling revealed a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.
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Affiliation(s)
- Matthew Mealka
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nicole A. Sierra
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | | | - Elene Albekioni
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Rachel Khoury
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Timothy Mai
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Brittany M. Conley
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nalani J. Coleman
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Kaitlyn A. Sabo
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Elizabeth A. Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Andrey A. Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA
| | - Andrew L. Cooksy
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Steve Silletti
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | | | - Tom Huxford
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Christal D. Sohl
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
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Mealka M, Sierra NA, Matteo DA, Albekioni E, Khoury R, Mai T, Conley BM, Coleman NJ, Sabo KA, Komives EA, Bobkov AA, Cooksy AL, Silletti S, Schiffer JM, Huxford T, Sohl CD. Active site remodeling in tumor-relevant IDH1 mutants drives distinct kinetic features and potential resistance mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574970. [PMID: 38260668 PMCID: PMC10802581 DOI: 10.1101/2024.01.10.574970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Mutations in human isocitrate dehydrogenase 1 (IDH1) drive tumor formation in a variety of cancers by replacing its conventional activity with a neomorphic activity that generates an oncometabolite. Little is understood of the mechanistic differences among tumor-driving IDH1 mutants. We previously reported that the R132Q mutant uniquely preserves conventional activity while catalyzing robust oncometabolite production, allowing an opportunity to compare these reaction mechanisms within a single active site. Here, we employed static and dynamic structural methods and found that, compared to R132H, the R132Q active site adopted a conformation primed for catalysis with optimized substrate binding and hydride transfer to drive improved conventional and neomorphic activity over R132H. This active site remodeling revealed a possible mechanism of resistance to selective mutant IDH1 therapeutic inhibitors. This work enhances our understanding of fundamental IDH1 mechanisms while pinpointing regions for improving inhibitor selectivity.
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Affiliation(s)
- Matthew Mealka
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nicole A. Sierra
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | | | - Elene Albekioni
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Rachel Khoury
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Timothy Mai
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Brittany M. Conley
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Nalani J. Coleman
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Kaitlyn A. Sabo
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Elizabeth A. Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Andrey A. Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA USA
| | - Andrew L. Cooksy
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Steve Silletti
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | | | - Tom Huxford
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
| | - Christal D. Sohl
- Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA, USA
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Herold RA, Schofield CJ, Armstrong FA. Electrochemical Nanoreactor Provides a Comprehensive View of Isocitrate Dehydrogenase Cancer-drug Kinetics. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202309149. [PMID: 38529044 PMCID: PMC10962547 DOI: 10.1002/ange.202309149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 03/27/2024]
Abstract
The ability to control enzyme cascades entrapped in a nanoporous electrode material (the "Electrochemical Leaf", e-Leaf) has been exploited to gain detailed kinetic insight into the mechanism of an anti-cancer drug. Ivosidenib, used to treat acute myeloid leukemia, acts on a common cancer-linked variant of isocitrate dehydrogenase 1 (IDH1 R132H) inhibiting its "gain-of-function" activity-the undesired reduction of 2-oxoglutarate (2OG) to the oncometabolite 2-hydroxyglutarate (2HG). The e-Leaf quantifies the kinetics of IDH1 R132H inhibition across a wide and continuous range of conditions, efficiently revealing factors underlying the inhibitor residence time. Selective inhibition of IDH1 R132H by Ivosidenib and another inhibitor, Novartis 224, is readily resolved as a two-stage process whereby initial rapid non-inhibitory binding is followed by a slower step to give the inhibitory complex. These kinetic features are likely present in other allosteric inhibitors of IDH1/2. Such details, essential for understanding inhibition mechanisms, are not readily resolved in conventional steady-state kinetics or by techniques that rely only on measuring binding. Extending the new method and analytical framework presented here to other enzyme systems will be straightforward and should rapidly reveal insight that is difficult or often impossible to obtain using other methods.
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Affiliation(s)
- Ryan A. Herold
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Christopher J. Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordMansfield RoadOxfordOX1 3QYUK
| | - Fraser A. Armstrong
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
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Herold RA, Schofield CJ, Armstrong FA. Electrochemical Nanoreactor Provides a Comprehensive View of Isocitrate Dehydrogenase Cancer-drug Kinetics. Angew Chem Int Ed Engl 2023; 62:e202309149. [PMID: 37607127 PMCID: PMC10962598 DOI: 10.1002/anie.202309149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
The ability to control enzyme cascades entrapped in a nanoporous electrode material (the "Electrochemical Leaf", e-Leaf) has been exploited to gain detailed kinetic insight into the mechanism of an anti-cancer drug. Ivosidenib, used to treat acute myeloid leukemia, acts on a common cancer-linked variant of isocitrate dehydrogenase 1 (IDH1 R132H) inhibiting its "gain-of-function" activity-the undesired reduction of 2-oxoglutarate (2OG) to the oncometabolite 2-hydroxyglutarate (2HG). The e-Leaf quantifies the kinetics of IDH1 R132H inhibition across a wide and continuous range of conditions, efficiently revealing factors underlying the inhibitor residence time. Selective inhibition of IDH1 R132H by Ivosidenib and another inhibitor, Novartis 224, is readily resolved as a two-stage process whereby initial rapid non-inhibitory binding is followed by a slower step to give the inhibitory complex. These kinetic features are likely present in other allosteric inhibitors of IDH1/2. Such details, essential for understanding inhibition mechanisms, are not readily resolved in conventional steady-state kinetics or by techniques that rely only on measuring binding. Extending the new method and analytical framework presented here to other enzyme systems will be straightforward and should rapidly reveal insight that is difficult or often impossible to obtain using other methods.
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Affiliation(s)
- Ryan A. Herold
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
| | - Christopher J. Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordMansfield RoadOxfordOX1 3QYUK
| | - Fraser A. Armstrong
- Inorganic Chemistry LaboratoryDepartment of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QRUK
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