1
|
Cottrell KM, Briggs KJ, Whittington DA, Jahic H, Ali JA, Davis CB, Gong S, Gotur D, Gu L, McCarren P, Tonini MR, Tsai A, Wilker EW, Yuan H, Zhang M, Zhang W, Huang A, Maxwell JP. Discovery of TNG908: A Selective, Brain Penetrant, MTA-Cooperative PRMT5 Inhibitor That Is Synthetically Lethal with MTAP-Deleted Cancers. J Med Chem 2024; 67:6064-6080. [PMID: 38595098 PMCID: PMC11056935 DOI: 10.1021/acs.jmedchem.4c00133] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024]
Abstract
It has been shown that PRMT5 inhibition by small molecules can selectively kill cancer cells with homozygous deletion of the MTAP gene if the inhibitors can leverage the consequence of MTAP deletion, namely, accumulation of the MTAP substrate MTA. Herein, we describe the discovery of TNG908, a potent inhibitor that binds the PRMT5·MTA complex, leading to 15-fold-selective killing of MTAP-deleted (MTAP-null) cells compared to MTAPintact (MTAP WT) cells. TNG908 shows selective antitumor activity when dosed orally in mouse xenograft models, and its physicochemical properties are amenable for crossing the blood-brain barrier (BBB), supporting clinical study for the treatment of both CNS and non-CNS tumors with MTAP loss.
Collapse
Affiliation(s)
| | | | | | - Haris Jahic
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | - Janid A. Ali
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | | | - Shanzhong Gong
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | - Deepali Gotur
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | - Lina Gu
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | | | | | - Alice Tsai
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | - Erik W. Wilker
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | - Hongling Yuan
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | - Minjie Zhang
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | - Wenhai Zhang
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | - Alan Huang
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| | - John P. Maxwell
- Tango Therapeutics, Boston, Massachusetts 02215, United States
| |
Collapse
|
2
|
Ahronian LG, Fenoglio S, Das N, Aird D, Guerin D, Whittington D, Jahic H, Brophy E, McCarren P, McMillan B, Tepper J, Mentzer M, Li F, Zhang H, Pan X, Maxwell J, Andersen J, Huang A, Sjin RTT. Abstract P146: Loss of HS2ST1 cooperates with MAPK inhibition to impair growth of mesenchymal KRAS mutant NSCLC. Mol Cancer Ther 2021. [DOI: 10.1158/1535-7163.targ-21-p146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Activating mutations in the KRAS oncogene occur in approximately 30% of non-small cell lung cancers (NSCLC). Hence, multiple therapeutic strategies have been explored to block RAS including inhibition of downstream effector molecules in the MAPK pathway and direct pharmacological inhibition of the KRAS G12C mutant protein. However, inhibition of the RAS-RAF-MEK-ERK cascade with MEK inhibitor monotherapy has been insufficient to induce robust clinical responses. To identify novel drug targets that are synthetic lethal with MEK inhibition, CRISPR screens were conducted in multiple KRAS mutant NSCLC cell lines with or without trametinib treatment. Consistent with previous reports, several known MAPK-pathway genes, including KRAS, MEK, ERK, and FGFR1, were identified as top sensitizers validating our functional genomics approach. Interestingly, several novel targets were ranked among these top hits, including several members of the heparan sulfate biosynthesis pathway, such as the heparan sulfate 2-O-sulfotransferase (HS2ST1). In cells, HS2ST1 is responsible for transferring a sulfate from PAPS (3-phosphoadenosine-5’-phosphosulfate) to the 2-O position of a growing heparan sulfate chain. These chains partner with receptor tyrosine kinases at the cell surface to facilitate their interactions with growth factors. In this case, the interaction of FGF2 and FGFR1 has been shown to require HS2ST1-mediated 2-O sulfation, making HS2ST1 a novel druggable target in a well-validated FGFR-MAPK adaptive signaling axis. Here, we report that HS2ST1 is required for the feedback activation of the MAPK pathway that occurs downstream and in response to MEK or KRAS G12C inhibition via genetic validations studies. Knockout of HS2ST1 results in reduced feedback activation via FGFR1 and reduced MAPK pathway signaling. This reduced signaling leads to a reduction in cell growth in the presence of a MEK inhibitor, such as trametinib or selumetinib, or a KRAS G12C inhibitor like sotorasib. Our screen results reiterate the findings of others which indicate that effective MAPK suppression is key to inhibiting KRAS-mutant NSCLC cell growth. We find that HS2ST1 blockade would aid in maintaining the suppression of MAPK pathway signaling in KRAS-mutant NSCLC, leading to reduced cell viability and growth suppression. While others have described pairing receptor tyrosine kinase inhibitors with MAPK pathway inhibitors, this would be a novel approach to reducing upstream MAPK pathway feedback that may lead to reduced toxicity in patients.
Citation Format: Leanne G. Ahronian, Silvia Fenoglio, Nikitha Das, Daniel Aird, David Guerin, Douglas Whittington, Haris Jahic, Erin Brophy, Patrick McCarren, Brian McMillan, James Tepper, Michaela Mentzer, Fang Li, Hongxiang Zhang, Xuewen Pan, John Maxwell, Jannik Andersen, Alan Huang, Robert Tjin Tham Sjin. Loss of HS2ST1 cooperates with MAPK inhibition to impair growth of mesenchymal KRAS mutant NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P146.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Fang Li
- Tango Therapeutics, Cambridge, MA
| | | | | | | | | | | | | |
Collapse
|
3
|
McKinney DC, McMillan BJ, Ranaghan MJ, Moroco JA, Brousseau M, Mullin-Bernstein Z, O'Keefe M, McCarren P, Mesleh MF, Mulvaney KM, Robinson F, Singh R, Bajrami B, Wagner FF, Hilgraf R, Drysdale MJ, Campbell AJ, Skepner A, Timm DE, Porter D, Kaushik VK, Sellers WR, Ianari A. Discovery of a First-in-Class Inhibitor of the PRMT5-Substrate Adaptor Interaction. J Med Chem 2021; 64:11148-11168. [PMID: 34342224 DOI: 10.1021/acs.jmedchem.1c00507] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PRMT5 and its substrate adaptor proteins (SAPs), pICln and Riok1, are synthetic lethal dependencies in MTAP-deleted cancer cells. SAPs share a conserved PRMT5 binding motif (PBM) which mediates binding to a surface of PRMT5 distal to the catalytic site. This interaction is required for methylation of several PRMT5 substrates, including histone and spliceosome complexes. We screened for small molecule inhibitors of the PRMT5-PBM interaction and validated a compound series which binds to the PRMT5-PBM interface and directly inhibits binding of SAPs. Mode of action studies revealed the formation of a covalent bond between a halogenated pyridazinone group and cysteine 278 of PRMT5. Optimization of the starting hit produced a lead compound, BRD0639, which engages the target in cells, disrupts PRMT5-RIOK1 complexes, and reduces substrate methylation. BRD0639 is a first-in-class PBM-competitive inhibitor that can support studies of PBM-dependent PRMT5 activities and the development of novel PRMT5 inhibitors that selectively target these functions.
Collapse
Affiliation(s)
- David C McKinney
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Brian J McMillan
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Matthew J Ranaghan
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Jamie A Moroco
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Merissa Brousseau
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Zachary Mullin-Bernstein
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Meghan O'Keefe
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Patrick McCarren
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Michael F Mesleh
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Kathleen M Mulvaney
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Foxy Robinson
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Ritu Singh
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Besnik Bajrami
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Florence F Wagner
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Robert Hilgraf
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Martin J Drysdale
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Arthur J Campbell
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Adam Skepner
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - David E Timm
- Department of Biochemistry, University of Utah, 1390 Presidents Circle, Salt Lake City, Utah 84112, United States
| | - Dale Porter
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Virendar K Kaushik
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - William R Sellers
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02215, United States
| | - Alessandra Ianari
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
4
|
Michalska K, Chang C, Maltseva NI, Jedrzejczak R, Robertson GT, Gusovsky F, McCarren P, Schreiber SL, Nag PP, Joachimiak A. Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase. Protein Sci 2020; 29:779-788. [PMID: 31930594 PMCID: PMC7020977 DOI: 10.1002/pro.3825] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 10/30/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Global dispersion of multidrug resistant bacteria is very common and evolution of antibiotic-resistance is occurring at an alarming rate, presenting a formidable challenge for humanity. The development of new therapeuthics with novel molecular targets is urgently needed. Current drugs primarily affect protein, nucleic acid, and cell wall synthesis. Metabolic pathways, including those involved in amino acid biosynthesis, have recently sparked interest in the drug discovery community as potential reservoirs of such novel targets. Tryptophan biosynthesis, utilized by bacteria but absent in humans, represents one of the currently studied processes with a therapeutic focus. It has been shown that tryptophan synthase (TrpAB) is required for survival of Mycobacterium tuberculosis in macrophages and for evading host defense, and therefore is a promising drug target. Here we present crystal structures of TrpAB with two allosteric inhibitors of M. tuberculosis tryptophan synthase that belong to sulfolane and indole-5-sulfonamide chemical scaffolds. We compare our results with previously reported structural and biochemical studies of another, azetidine-containing M. tuberculosis tryptophan synthase inhibitor. This work shows how structurally distinct ligands can occupy the same allosteric site and make specific interactions. It also highlights the potential benefit of targeting more variable allosteric sites of important metabolic enzymes.
Collapse
Affiliation(s)
- Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Changsoo Chang
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Natalia I. Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Gregory T. Robertson
- Colorado State UniversityMycobacteria Research Laboratories, Department of Microbiology, Immunology and PathologyFort CollinsColorado
| | | | | | | | - Partha P. Nag
- Broad Institute of MIT and HarvardCambridgeMassachusetts
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinois
| |
Collapse
|
5
|
Corsello SM, Bittker JA, Liu Z, Gould J, McCarren P, Hirschman JE, Johnston SE, Vrcic A, Wong B, Khan M, Asiedu J, Narayan R, Mader CC, Subramanian A, Golub TR. The Drug Repurposing Hub: a next-generation drug library and information resource. Nat Med 2019; 23:405-408. [PMID: 28388612 DOI: 10.1038/nm.4306] [Citation(s) in RCA: 501] [Impact Index Per Article: 100.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Steven M Corsello
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua A Bittker
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Zihan Liu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Joshua Gould
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Patrick McCarren
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jodi E Hirschman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Anita Vrcic
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Bang Wong
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mariya Khan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jacob Asiedu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rajiv Narayan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| |
Collapse
|
6
|
Over B, Matsson P, Tyrchan C, Artursson P, Doak BC, Foley MA, Hilgendorf C, Johnston SE, Lee MD, Lewis RJ, McCarren P, Muncipinto G, Norinder U, Perry MWD, Duvall JR, Kihlberg J. Erratum: Structural and conformational determinants of macrocycle cell permeability. Nat Chem Biol 2017; 13:922. [PMID: 28853740 DOI: 10.1038/nchembio0817-922a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
7
|
Wagner FF, Lundh M, Kaya T, McCarren P, Zhang YL, Chattopadhyay S, Gale JP, Galbo T, Fisher SL, Meier BC, Vetere A, Richardson S, Morgan NG, Christensen DP, Gilbert TJ, Hooker JM, Leroy M, Walpita D, Mandrup-Poulsen T, Wagner BK, Holson EB. An Isochemogenic Set of Inhibitors To Define the Therapeutic Potential of Histone Deacetylases in β-Cell Protection. ACS Chem Biol 2016; 11:363-74. [PMID: 26640968 DOI: 10.1021/acschembio.5b00640] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Modulation of histone deacetylase (HDAC) activity has been implicated as a potential therapeutic strategy for multiple diseases. However, it has been difficult to dissect the role of individual HDACs due to a lack of selective small-molecule inhibitors. Here, we report the synthesis of a series of highly potent and isoform-selective class I HDAC inhibitors, rationally designed by exploiting minimal structural changes to the clinically experienced HDAC inhibitor CI-994. We used this toolkit of isochemogenic or chemically matched inhibitors to probe the role of class I HDACs in β-cell pathobiology and demonstrate for the first time that selective inhibition of an individual HDAC isoform retains beneficial biological activity and mitigates mechanism-based toxicities. The highly selective HDAC3 inhibitor BRD3308 suppressed pancreatic β-cell apoptosis induced by inflammatory cytokines, as expected, or now glucolipotoxic stress, and increased functional insulin release. In addition, BRD3308 had no effect on human megakaryocyte differentiation, while inhibitors of HDAC1 and 2 were toxic. Our findings demonstrate that the selective inhibition of HDAC3 represents a potential path forward as a therapy to protect pancreatic β-cells from inflammatory cytokines and nutrient overload in diabetes.
Collapse
Affiliation(s)
- Florence F. Wagner
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Morten Lundh
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department
of Biomedical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Taner Kaya
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Patrick McCarren
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Yan-Ling Zhang
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Shrikanta Chattopadhyay
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Jennifer P. Gale
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Thomas Galbo
- Department
of Internal Medicine, Yale University, New Haven, Connecticut 06520, United States
| | - Stewart L. Fisher
- SL Fisher Consulting, LLC, PO Box 3052, Framingham, Massachusetts 01701, United States
| | - Bennett C. Meier
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Amedeo Vetere
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Sarah Richardson
- University of Exeter Medical School, RD&E Hospital, Wonford EX2 5DW, U.K
| | - Noel G. Morgan
- University of Exeter Medical School, RD&E Hospital, Wonford EX2 5DW, U.K
| | - Dan Ploug Christensen
- Department
of Biomedical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Tamara J. Gilbert
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Jacob M. Hooker
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Athinoula
A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital,
Department of Radiology, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Mélanie Leroy
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Deepika Walpita
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Thomas Mandrup-Poulsen
- Department
of Biomedical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
- Department
of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Bridget K. Wagner
- Center
for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Edward B. Holson
- Stanley
Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
8
|
Wagner FF, Zhang YL, Fass DM, Joseph N, Gale JP, Weïwer M, McCarren P, Fisher SL, Kaya T, Zhao WN, Reis SA, Hennig KM, Thomas M, Lemercier BC, Lewis MC, Guan JS, Moyer MP, Scolnick E, Haggarty SJ, Tsai LH, Holson EB. Kinetically Selective Inhibitors of Histone Deacetylase 2 (HDAC2) as Cognition Enhancers. Chem Sci 2015; 6:804-815. [PMID: 25642316 PMCID: PMC4310013 DOI: 10.1039/c4sc02130d] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Kinetically selective inhibitors of HDAC2 enhanced learning and memory in a CK-p25 mouse model of neurodegeneration.
Aiming towards the development of novel nootropic therapeutics to address the cognitive impairment common to a range of brain disorders, we set out to develop highly selective small molecule inhibitors of HDAC2, a chromatin modifying histone deacetylase implicated in memory formation and synaptic plasticity. Novel ortho-aminoanilide inhibitors were designed and evaluated for their ability to selectively inhibit HDAC2 versus the other Class I HDACs. Kinetic and thermodynamic binding properties were essential elements of our design strategy and two novel classes of ortho-aminoanilides, that exhibit kinetic selectivity (biased residence time) for HDAC2 versus the highly homologous isoform HDAC1, were identified. These kinetically selective HDAC2 inhibitors (BRD6688 and BRD4884) increased H4K12 and H3K9 histone acetylation in primary mouse neuronal cell culture assays, in the hippocampus of CK-p25 mice, a model of neurodegenerative disease, and rescued the associated memory deficits of these mice in a cognition behavioural model. These studies demonstrate for the first time that selective pharmacological inhibition of HDAC2 is feasible and that inhibition of the catalytic activity of this enzyme may serve as a therapeutic approach towards enhancing the learning and memory processes that are affected in many neurological and psychiatric disorders.
Collapse
Affiliation(s)
- F F Wagner
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - Y-L Zhang
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - D M Fass
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA ; SL Fisher Consulting, LLC, PO Box 3052, Framingham, Massachusetts, USA
| | - N Joseph
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA ; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
| | - J P Gale
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - M Weïwer
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - P McCarren
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - S L Fisher
- SL Fisher Consulting, LLC, PO Box 3052, Framingham, Massachusetts, USA
| | - T Kaya
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - W-N Zhao
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA ; Chemical Neurobiology Laboratory, Center for Human Genetic Research, Massachusetts General Hospital, Department of Neurology and Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - S A Reis
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA ; Chemical Neurobiology Laboratory, Center for Human Genetic Research, Massachusetts General Hospital, Department of Neurology and Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - K M Hennig
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA ; Chemical Neurobiology Laboratory, Center for Human Genetic Research, Massachusetts General Hospital, Department of Neurology and Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - M Thomas
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - B C Lemercier
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - M C Lewis
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - J S Guan
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA ; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
| | - M P Moyer
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - E Scolnick
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| | - S J Haggarty
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA ; Chemical Neurobiology Laboratory, Center for Human Genetic Research, Massachusetts General Hospital, Department of Neurology and Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - L-H Tsai
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA ; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, Massachusetts, USA
| | - E B Holson
- Stanley Center for Psychiatric Research; Broad Institute of Harvard and MIT; 7 Cambridge Center, Cambridge, Massachusetts, USA
| |
Collapse
|
9
|
Fang C, D’Souza B, Thompson CF, Clifton MC, Fairman JW, Fulroth B, Leed A, McCarren P, Wang L, Wang Y, Feau C, Kaushik VK, Palmer M, Wei G, Golub TR, Hubbard BK, Serrano-Wu MH. Single Diastereomer of a Macrolactam Core Binds Specifically to Myeloid Cell Leukemia 1 (MCL1). ACS Med Chem Lett 2014; 5:1308-12. [PMID: 25516789 DOI: 10.1021/ml500388q] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/02/2014] [Indexed: 01/02/2023] Open
Abstract
A direct binding screen of 100 000 sp(3)-rich molecules identified a single diastereomer of a macrolactam core that binds specifically to myeloid cell leukemia 1 (MCL1). A comprehensive toolbox of biophysical methods was applied to validate the original hit and subsequent analogues and also established a binding mode competitive with NOXA BH3 peptide. X-ray crystallography of ligand bound to MCL1 reveals a remarkable ligand/protein shape complementarity that diverges from previously disclosed MCL1 inhibitor costructures.
Collapse
Affiliation(s)
- Chao Fang
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Brendan D’Souza
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | | | | | - James W. Fairman
- Beryllium, 3 Preston Court, Bedford, Massachusetts 01730, United States
| | - Ben Fulroth
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Alison Leed
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Patrick McCarren
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Lili Wang
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Yikai Wang
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Clementine Feau
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Virendar K. Kaushik
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Michelle Palmer
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Guo Wei
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Todd R. Golub
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Dana-Farber Cancer Institute and Howard Hughes Medical Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Brian K. Hubbard
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | | |
Collapse
|
10
|
Olson D, Udeshi ND, Wolfson NA, Pitcairn CA, Sullivan ED, Jaffe JD, Svinkina T, Natoli T, Lu X, Paulk J, McCarren P, Wagner FF, Barker D, Howe E, Lazzaro F, Gale JP, Zhang YL, Subramanian A, Fierke CA, Carr SA, Holson EB. An unbiased approach to identify endogenous substrates of "histone" deacetylase 8. ACS Chem Biol 2014; 9:2210-6. [PMID: 25089360 PMCID: PMC4201337 DOI: 10.1021/cb500492r] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/04/2014] [Indexed: 12/24/2022]
Abstract
Despite being extensively characterized structurally and biochemically, the functional role of histone deacetylase 8 (HDAC8) has remained largely obscure due in part to a lack of known cellular substrates. Herein, we describe an unbiased approach using chemical tools in conjunction with sophisticated proteomics methods to identify novel non-histone nuclear substrates of HDAC8, including the tumor suppressor ARID1A. These newly discovered substrates of HDAC8 are involved in diverse biological processes including mitosis, transcription, chromatin remodeling, and RNA splicing and may help guide therapeutic strategies that target the function of HDAC8.
Collapse
Affiliation(s)
- David
E. Olson
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Namrata D. Udeshi
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Noah A. Wolfson
- Department of Biological
Chemistry, Interdepartmental
Program in Chemical Biology, and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carol Ann Pitcairn
- Department of Biological
Chemistry, Interdepartmental
Program in Chemical Biology, and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Eric D. Sullivan
- Department of Biological
Chemistry, Interdepartmental
Program in Chemical Biology, and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jacob D. Jaffe
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Tanya Svinkina
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Ted Natoli
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Xiaodong Lu
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Joshiawa Paulk
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Patrick McCarren
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Florence F. Wagner
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Doug Barker
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Eleanor Howe
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Fanny Lazzaro
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Jennifer P. Gale
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Yan-Ling Zhang
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Aravind Subramanian
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Carol A. Fierke
- Department of Biological
Chemistry, Interdepartmental
Program in Chemical Biology, and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Steven A. Carr
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Edward B. Holson
- Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the
Science of Therapeutics, Broad Institute
of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
11
|
Over B, McCarren P, Artursson P, Foley M, Giordanetto F, Grönberg G, Hilgendorf C, Lee MD, Matsson P, Muncipinto G, Pellisson M, Perry MWD, Svensson R, Duvall JR, Kihlberg J. Impact of stereospecific intramolecular hydrogen bonding on cell permeability and physicochemical properties. J Med Chem 2014; 57:2746-54. [PMID: 24524242 PMCID: PMC3968888 DOI: 10.1021/jm500059t] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Indexed: 01/17/2023]
Abstract
Profiling of eight stereoisomeric T. cruzi growth inhibitors revealed vastly different in vitro properties such as solubility, lipophilicity, pKa, and cell permeability for two sets of four stereoisomers. Using computational chemistry and NMR spectroscopy, we identified the formation of an intramolecular NH→NR3 hydrogen bond in the set of stereoisomers displaying lower solubility, higher lipophilicity, and higher cell permeability. The intramolecular hydrogen bond resulted in a significant pKa difference that accounts for the other structure-property relationships. Application of this knowledge could be of particular value to maintain the delicate balance of size, solubility, and lipophilicity required for cell penetration and oral administration for chemical probes or therapeutics with properties at, or beyond, Lipinski's rule of 5.
Collapse
Affiliation(s)
- Björn Over
- CVMD
iMed, AstraZeneca R&D Mölndal, SE-431 83 Mölndal, Sweden
| | - Patrick McCarren
- Center
for the Science of Therapeutics, Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Per Artursson
- Department
of Pharmacy, BMC, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
- Uppsala
Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), a
Node at the Chemical Biology Consortium Sweden and the Drug Discovery
and Development Platform, Science for Life Laboratory, Department
of Pharmacy, BMC, Uppsala Univerisity, Box 580, SE-751 23 Uppsala, Sweden
| | - Michael Foley
- Center
for the Science of Therapeutics, Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Fabrizio Giordanetto
- Medicinal
Chemistry, Taros Chemicals GmbH & Co.
KG, Emil-Figge-Strasse
76a, 44227 Dortmund, Germany
| | - Gunnar Grönberg
- RIA
iMed, AstraZeneca R&D Mölndal, SE-431 83 Mölndal, Sweden
| | - Constanze Hilgendorf
- Drug
Safety and Metabolism, DMPK, AstraZeneca
R&D Mölndal, SE-431 83 Mölndal, Sweden
| | - Maurice D. Lee
- Center
for the Science of Therapeutics, Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Pär Matsson
- Department
of Pharmacy, BMC, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
- Uppsala
Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), a
Node at the Chemical Biology Consortium Sweden and the Drug Discovery
and Development Platform, Science for Life Laboratory, Department
of Pharmacy, BMC, Uppsala Univerisity, Box 580, SE-751 23 Uppsala, Sweden
| | - Giovanni Muncipinto
- Center
for the Science of Therapeutics, Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Mélanie Pellisson
- Center
for the Science of Therapeutics, Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | | | - Richard Svensson
- Uppsala
Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), a
Node at the Chemical Biology Consortium Sweden and the Drug Discovery
and Development Platform, Science for Life Laboratory, Department
of Pharmacy, BMC, Uppsala Univerisity, Box 580, SE-751 23 Uppsala, Sweden
| | - Jeremy R. Duvall
- Center
for the Science of Therapeutics, Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Jan Kihlberg
- Department
of Chemistry, BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| |
Collapse
|
12
|
McCarren P, Hall ML, Whitehead L. The Chemical Tuning of a Weak Zinc Binding Motif for Histone Deacetylase Using Electronic Effects. Chem Biol Drug Des 2012; 80:203-14. [DOI: 10.1111/j.1747-0285.2012.01382.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
13
|
McCarren P, Springer C, Whitehead L. An investigation into pharmaceutically relevant mutagenicity data and the influence on Ames predictive potential. J Cheminform 2011; 3:51. [PMID: 22107807 PMCID: PMC3277490 DOI: 10.1186/1758-2946-3-51] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 11/22/2011] [Indexed: 11/29/2022] Open
Abstract
Background In drug discovery, a positive Ames test for bacterial mutation presents a significant hurdle to advancing a drug to clinical trials. In a previous paper, we discussed success in predicting the genotoxicity of reagent-sized aryl-amines (ArNH2), a structure frequently found in marketed drugs and in drug discovery, using quantum mechanics calculations of the energy required to generate the DNA-reactive nitrenium intermediate (ArNH:+). In this paper we approach the question of what molecular descriptors could improve these predictions and whether external data sets are appropriate for further training. Results In trying to extend and improve this model beyond this quantum mechanical reaction energy, we faced considerable difficulty, which was surprising considering the long history and success of QSAR model development for this test. Other quantum mechanics descriptors were compared to this reaction energy including AM1 semi-empirical orbital energies, nitrenium formation with alternative leaving groups, nitrenium charge, and aryl-amine anion formation energy. Nitrenium formation energy, regardless of the starting species, was found to be the most useful single descriptor. External sets used in other QSAR investigations did not present the same difficulty using the same methods and descriptors. When considering all substructures rather than just aryl-amines, we also noted a significantly lower performance for the Novartis set. The performance gap between Novartis and external sets persists across different descriptors and learning methods. The profiles of the Novartis and external data are significantly different both in aryl-amines and considering all substructures. The Novartis and external data sets are easily separated in an unsupervised clustering using chemical fingerprints. The chemical differences are discussed and visualized using Kohonen Self-Organizing Maps trained on chemical fingerprints, mutagenic substructure prevalence, and molecular weight. Conclusions Despite extensive work in the area of predicting this particular toxicity, work in designing and publishing more relevant test sets for compounds relevant to drug discovery is still necessary. This work also shows that great care must be taken in using QSAR models to replace experimental evidence. When considering all substructures, a random forest model, which can inherently cover distinct neighborhoods, built on Novartis data and previously reported external data provided a suitable model.
Collapse
Affiliation(s)
- Patrick McCarren
- Novartis Institutes for Biomedical Research, 100 Technology Square, Cambridge, MA 02139, USA.
| | | | | |
Collapse
|
14
|
Nigsch F, Lounkine E, McCarren P, Cornett B, Glick M, Azzaoui K, Urban L, Marc P, Müller A, Hahne F, Heard DJ, Jenkins JL. Computational methods for early predictive safety assessment from biological and chemical data. Expert Opin Drug Metab Toxicol 2011; 7:1497-511. [DOI: 10.1517/17425255.2011.632632] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
15
|
McCarren P, Bebernitz GR, Gedeck P, Glowienke S, Grondine MS, Kirman LC, Klickstein J, Schuster HF, Whitehead L. Avoidance of the Ames test liability for aryl-amines via computation. Bioorg Med Chem 2011; 19:3173-82. [PMID: 21524589 DOI: 10.1016/j.bmc.2011.03.066] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 03/25/2011] [Accepted: 03/30/2011] [Indexed: 11/19/2022]
Abstract
Aryl-amines are commonly used synthons in modern drug discovery, however a minority of these chemical templates have the potential to cause toxicity through mutagenicity. The toxicity mostly arises through a series of metabolic steps leading to a reactive electrophilic nitrenium cation intermediate that reacts with DNA nucleotides causing mutation. Highly detailed in silico calculations of the energetics of chemical reactions involved in the metabolic formation of nitrenium cations have been performed. This allowed a critical assessment of the accuracy and reliability of using a theoretical formation energy of the DNA-reactive nitrenium intermediate to correlate with the Ames test response. This study contains the largest data set reported to date, and presents the in silico calculations versus the in vitro Ames response data in the form of beanplots commonly used in statistical analysis. A comparison of this quantum mechanical approach to QSAR and knowledge-based methods is also reported, as well as the calculated formation energies of nitrenium ions for thousands of commercially available aryl-amines generated as a watch-list for medicinal chemists in their synthetic optimization strategies.
Collapse
Affiliation(s)
- Patrick McCarren
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Liu P, McCarren P, Cheong PHY, Jamison TF, Houk KN. Origins of regioselectivity and alkene-directing effects in nickel-catalyzed reductive couplings of alkynes and aldehydes. J Am Chem Soc 2010; 132:2050-7. [PMID: 20095609 PMCID: PMC2830786 DOI: 10.1021/ja909562y] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The origins of reactivity and regioselectivity in nickel-catalyzed reductive coupling reactions of alkynes and aldehydes were investigated with density functional calculations. The regioselectivities of reactions of simple alkynes are controlled by steric effects, while conjugated enynes and diynes are predicted to have increased reactivity and very high regioselectivities, placing alkenyl or alkynyl groups distal to the forming C-C bond. The reactions of enynes and diynes involve 1,4-attack of the Ni-carbonyl complex on the conjugated enyne or diyne. The consequences of these conclusions on reaction design are discussed.
Collapse
Affiliation(s)
- Peng Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Patrick McCarren
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Paul Ha-Yeon Cheong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Timothy F. Jamison
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| |
Collapse
|
17
|
Natarajan A, Tsai CK, Khan SI, McCarren P, Houk KN, Garcia-Garibay MA. The Photoarrangement of α-Santonin is a Single-Crystal-to-Single-Crystal Reaction: A Long Kept Secret in Solid-State Organic Chemistry Revealed. J Am Chem Soc 2007; 129:9846-7. [PMID: 17645337 DOI: 10.1021/ja073189o] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Arunkumar Natarajan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90024-1569, USA
| | | | | | | | | | | |
Collapse
|