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Howard C, Zari S, Li S, Huang H, Kim E, Park SR, Purohit T, Miao H, Zhang X, Nikolaidis C, Li H, Ndoj J, Cho H, Grembecka J, Cierpicki T. Abstract 3274: Targeting NSD family histone methyltransferase activity with irreversible inhibitors. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3274] [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
Nuclear SET domain containing (NSD) family member proteins are histone methyltransferases that mono- and di-methylate histone 3 at lysine 36 (H3K36) to alter gene expression in a context-dependent manner. NSD1 and NSD3 are two members of this family which share greater than 80 percent sequence similarity in the catalytic SET domain. NSD1 is found as a fusion with NUP98 in aggressive cases of pediatric leukemia, and the lysine methyltransferase (KMTase) activity of NUP98-NSD1 drives bone marrow progenitor proliferation. Similarly, high levels of enzymatically active NSD3 mRNA are correlated with reduced disease-free survival in breast cancer and catalytic NSD3 expression is sufficient to rescue tumor growth in a xenograft model of triple negative breast cancer. Selective and potent inhibitors of NSD1 and NSD3 KMTase activity are needed to further investigate the therapeutic potential of targeting this function in leukemia and/or solid cancers. Here, we report the development of irreversible small molecule inhibitors of the NSD1 and NSD3 SET domains. We utilized a NMR-based fragment screen of the NSD1 SET domain to identify the hit BT1, which binds reversibly to the SET domain of NSD1. BT1 was extensively optimized into a series of potent irreversible ligands. Mass spectrometry and structural studies revealed that these compounds react with a cysteine near the autoinhibitory loop, providing a rational for the strong inhibition of KMTase activity we observe in biochemical assays. These inhibitors also bind to the NSD1 and NSD3 SET domains in cells and exhibit potent anti-proliferative effects against leukemia cells containing NUP98-NSD1 and breast cancer cells with high levels of NSD3 expression. In summary, we present novel irreversible inhibitors of NSD1 and NSD3 KMTase activity which represent important chemical probes that can be used to investigate the therapeutic potential of targeting NSD family member catalytic activity in cancers.
Citation Format: Christina Howard, Sergei Zari, Shuangjiang Li, Huang Huang, EunGi Kim, Se Ra Park, Trupta Purohit, Hongzhi Miao, Xiaotian Zhang, Caroline Nikolaidis, Hao Li, Juliano Ndoj, HyoJe Cho, Jolanta Grembecka, Tomasz Cierpicki. Targeting NSD family histone methyltransferase activity with irreversible inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3274.
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Affiliation(s)
| | | | | | | | - EunGi Kim
- 1University of Michigan, Ann Arbor, MI
| | | | | | | | | | | | - Hao Li
- 1University of Michigan, Ann Arbor, MI
| | | | - HyoJe Cho
- 1University of Michigan, Ann Arbor, MI
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2
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Shukla S, Ying W, Gray F, Yao Y, Simes ML, Zhao Q, Miao H, Cho HJ, González-Alonso P, Winkler A, Lund G, Purohit T, Kim E, Zhang X, Ray JM, He S, Nikolaidis C, Ndoj J, Wang J, Jaremko Ł, Jaremko M, Ryan RJH, Guzman ML, Grembecka J, Cierpicki T. Small-molecule inhibitors targeting Polycomb repressive complex 1 RING domain. Nat Chem Biol 2021; 17:784-793. [PMID: 34155404 PMCID: PMC8238916 DOI: 10.1038/s41589-021-00815-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 04/21/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022]
Abstract
Polycomb repressive complex 1 (PRC1) is an essential chromatin-modifying complex that monoubiquitinates histone H2A and is involved in maintaining the repressed chromatin state. Emerging evidence suggests PRC1 activity in various cancers, rationalizing the need for small-molecule inhibitors with well-defined mechanisms of action. Here, we describe the development of compounds that directly bind to RING1B-BMI1, the heterodimeric complex constituting the E3 ligase activity of PRC1. These compounds block the association of RING1B-BMI1 with chromatin and inhibit H2A ubiquitination. Structural studies demonstrate that these inhibitors bind to RING1B by inducing the formation of a hydrophobic pocket in the RING domain. Our PRC1 inhibitor, RB-3, decreases the global level of H2A ubiquitination and induces differentiation in leukemia cell lines and primary acute myeloid leukemia (AML) samples. In summary, we demonstrate that targeting the PRC1 RING domain with small molecules is feasible, and RB-3 represents a valuable chemical tool to study PRC1 biology.
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Affiliation(s)
- Shirish Shukla
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Weijiang Ying
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Felicia Gray
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yiwu Yao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Miranda L Simes
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Qingjie Zhao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Alyssa Winkler
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - George Lund
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - EunGi Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaotian Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Joshua M Ray
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shihan He
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Juliano Ndoj
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jingya Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- MedImmune, LLC, Gaithersburg, MD, USA
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Russell J H Ryan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Monica L Guzman
- Division of Hematology and Medical Oncology, Leukemia Program, Weill Cornell Medicine/New York-Presbyterian Hospital, New York, NY, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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3
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Jiménez JA, Apfelbaum AA, Hawkins AG, Svoboda LK, Kumar A, Ruiz RO, Garcia AX, Haarer E, Nwosu ZC, Bradin J, Purohit T, Chen D, Cierpicki T, Grembecka J, Lyssiotis CA, Lawlor ER. EWS-FLI1 and Menin Converge to Regulate ATF4 Activity in Ewing Sarcoma. Mol Cancer Res 2021; 19:1182-1195. [PMID: 33741715 PMCID: PMC8462528 DOI: 10.1158/1541-7786.mcr-20-0679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 08/05/2020] [Revised: 01/15/2021] [Accepted: 03/11/2021] [Indexed: 11/16/2022]
Abstract
Ewing sarcomas are driven by EWS-ETS fusions, most commonly EWS-FLI1, which promotes widespread metabolic reprogramming, including activation of serine biosynthesis. We previously reported that serine biosynthesis is also activated in Ewing sarcoma by the scaffolding protein menin through as yet undefined mechanisms. Here, we investigated whether EWS-FLI1 and/or menin orchestrate serine biosynthesis via modulation of ATF4, a stress-response gene that acts as a master transcriptional regulator of serine biosynthesis in other tumors. Our results show that in Ewing sarcoma, ATF4 levels are high and that ATF4 modulates transcription of core serine synthesis pathway (SSP) genes. Inhibition of either EWS-FLI1 or menin leads to loss of ATF4, and this is associated with diminished expression of SSP transcripts and proteins. We identified and validated an EWS-FLI1 binding site at the ATF4 promoter, indicating that the fusion can directly activate ATF4 transcription. In contrast, our results suggest that menin-dependent regulation of ATF4 is mediated by transcriptional and post-transcriptional mechanisms. Importantly, our data also reveal that the downregulation of SSP genes that occurs in the context of EWS-FLI1 or menin loss is indicative of broader inhibition of ATF4-dependent transcription. Moreover, we find that menin inhibition similarly leads to loss of ATF4 and the ATF4-dependent transcriptional signature in MLL-rearranged B-cell acute lymphoblastic leukemia, extending our findings to another cancer in which menin serves an oncogenic role. IMPLICATIONS: These studies provide new insights into metabolic reprogramming in Ewing sarcoma and also uncover a previously undescribed role for menin in the regulation of ATF4.
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Affiliation(s)
- Jennifer A Jiménez
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - April A Apfelbaum
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Pediatrics, University of Washington, Seattle, Washington
- Seattle Children's Research Institute, Seattle, Washington
| | - Allegra G Hawkins
- New York Genome Center, New York, New York
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | | | - Abhijay Kumar
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Ramon Ocadiz Ruiz
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Alessandra X Garcia
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Elena Haarer
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Zeribe C Nwosu
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joshua Bradin
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Trupta Purohit
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Dong Chen
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Elizabeth R Lawlor
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan.
- Department of Pediatrics, University of Washington, Seattle, Washington
- Seattle Children's Research Institute, Seattle, Washington
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
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4
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Rogawski DS, Deng J, Li H, Miao H, Borkin D, Purohit T, Song J, Chase J, Li S, Ndoj J, Klossowski S, Kim E, Mao F, Zhou B, Ropa J, Krotoska MZ, Jin Z, Ernst P, Feng X, Huang G, Nishioka K, Kelly S, He M, Wen B, Sun D, Muntean A, Dou Y, Maillard I, Cierpicki T, Grembecka J. Discovery of first-in-class inhibitors of ASH1L histone methyltransferase with anti-leukemic activity. Nat Commun 2021; 12:2792. [PMID: 33990599 PMCID: PMC8121805 DOI: 10.1038/s41467-021-23152-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
ASH1L histone methyltransferase plays a crucial role in the pathogenesis of different diseases, including acute leukemia. While ASH1L represents an attractive drug target, developing ASH1L inhibitors is challenging, as the catalytic SET domain adapts an inactive conformation with autoinhibitory loop blocking the access to the active site. Here, by applying fragment-based screening followed by medicinal chemistry and a structure-based design, we developed first-in-class small molecule inhibitors of the ASH1L SET domain. The crystal structures of ASH1L-inhibitor complexes reveal compound binding to the autoinhibitory loop region in the SET domain. When tested in MLL leukemia models, our lead compound, AS-99, blocks cell proliferation, induces apoptosis and differentiation, downregulates MLL fusion target genes, and reduces the leukemia burden in vivo. This work validates the ASH1L SET domain as a druggable target and provides a chemical probe to further study the biological functions of ASH1L as well as to develop therapeutic agents.
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Affiliation(s)
- David S Rogawski
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jing Deng
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hao Li
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Dmitry Borkin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jiho Song
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer Chase
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Shuangjiang Li
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Juliano Ndoj
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - EunGi Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Bo Zhou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - James Ropa
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Marta Z Krotoska
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Zhuang Jin
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Patricia Ernst
- Department of Pediatrics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Xiaomin Feng
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Gang Huang
- Department of Pathology and Laboratory Medicine, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Kenichi Nishioka
- Department of Internal Medicine Musashimurayama Hospital, Enoki 1-1-5, Musashimurayama, Tokyo, Japan
| | - Samantha Kelly
- Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Miao He
- College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Bo Wen
- College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Duxin Sun
- College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Andrew Muntean
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Ivan Maillard
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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5
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Miao H, Kim E, Chen D, Purohit T, Kempinska K, Ropa J, Klossowski S, Trotman W, Danet-Desnoyers G, Cierpicki T, Grembecka J. Combinatorial treatment with menin and FLT3 inhibitors induces complete remission in AML models with activating FLT3 mutations. Blood 2020; 136:2958-2963. [PMID: 33331926 PMCID: PMC7751359 DOI: 10.1182/blood.2020006575] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/24/2020] [Indexed: 12/18/2022] Open
Affiliation(s)
- Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - EunGi Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Dong Chen
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | | | - James Ropa
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, IN; and
| | | | - Winifred Trotman
- Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gwenn Danet-Desnoyers
- Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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6
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Huang H, Howard CA, Zari S, Cho HJ, Shukla S, Li H, Ndoj J, González-Alonso P, Nikolaidis C, Abbott J, Rogawski DS, Potopnyk MA, Kempinska K, Miao H, Purohit T, Henderson A, Mapp A, Sulis ML, Ferrando A, Grembecka J, Cierpicki T. Covalent inhibition of NSD1 histone methyltransferase. Nat Chem Biol 2020; 16:1403-1410. [PMID: 32868895 PMCID: PMC7669657 DOI: 10.1038/s41589-020-0626-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [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: 08/30/2019] [Accepted: 06/29/2020] [Indexed: 11/09/2022]
Abstract
The nuclear receptor-binding SET domain (NSD) family of histone methyltransferases is associated with various malignancies, including aggressive acute leukemia with NUP98-NSD1 translocation. While NSD proteins represent attractive drug targets, their catalytic SET domains exist in autoinhibited conformation, presenting notable challenges for inhibitor development. Here, we employed a fragment-based screening strategy followed by chemical optimization, which resulted in the development of the first-in-class irreversible small-molecule inhibitors of the nuclear receptor-binding SET domain protein 1 (NSD1) SET domain. The crystal structure of NSD1 in complex with covalently bound ligand reveals a conformational change in the autoinhibitory loop of the SET domain and formation of a channel-like pocket suitable for targeting with small molecules. Our covalent lead-compound BT5-demonstrates on-target activity in NUP98-NSD1 leukemia cells, including inhibition of histone H3 lysine 36 dimethylation and downregulation of target genes, and impaired colony formation in an NUP98-NSD1 patient sample. This study will facilitate the development of the next generation of potent and selective inhibitors of the NSD histone methyltransferases.
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Affiliation(s)
- Huang Huang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Christina A Howard
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sergei Zari
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shirish Shukla
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hao Li
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Juliano Ndoj
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Joshua Abbott
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - David S Rogawski
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Andrew Henderson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Anna Mapp
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Maria Luisa Sulis
- Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
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7
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Klossowski S, Miao H, Kempinska K, Wu T, Purohit T, Kim E, Linhares BM, Chen D, Jih G, Perkey E, Huang H, He M, Wen B, Wang Y, Yu K, Lee SCW, Danet-Desnoyers G, Trotman W, Kandarpa M, Cotton A, Abdel-Wahab O, Lei H, Dou Y, Guzman M, Peterson L, Gruber T, Choi S, Sun D, Ren P, Li LS, Liu Y, Burrows F, Maillard I, Cierpicki T, Grembecka J. Menin inhibitor MI-3454 induces remission in MLL1-rearranged and NPM1-mutated models of leukemia. J Clin Invest 2020; 130:981-997. [PMID: 31855575 DOI: 10.1172/jci129126] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [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: 03/26/2019] [Accepted: 11/06/2019] [Indexed: 12/31/2022] Open
Abstract
The protein-protein interaction between menin and mixed lineage leukemia 1 (MLL1) plays a critical role in acute leukemias with translocations of the MLL1 gene or with mutations in the nucleophosmin 1 (NPM1) gene. As a step toward clinical translation of menin-MLL1 inhibitors, we report development of MI-3454, a highly potent and orally bioavailable inhibitor of the menin-MLL1 interaction. MI-3454 profoundly inhibited proliferation and induced differentiation in acute leukemia cells and primary patient samples with MLL1 translocations or NPM1 mutations. When applied as a single agent, MI-3454 induced complete remission or regression of leukemia in mouse models of MLL1-rearranged or NPM1-mutated leukemia, including patient-derived xenograft models, through downregulation of key genes involved in leukemogenesis. We also identified MEIS1 as a potential pharmacodynamic biomarker of treatment response with MI-3454 in leukemia, and demonstrated that this compound is well tolerated and did not impair normal hematopoiesis in mice. Overall, this study demonstrates, for the first time to our knowledge, profound activity of the menin-MLL1 inhibitor as a single agent in clinically relevant PDX models of leukemia. These data provide a strong rationale for clinical translation of MI-3454 or its analogs for leukemia patients with MLL1 rearrangements or NPM1 mutations.
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Affiliation(s)
- Szymon Klossowski
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Tao Wu
- Wellspring Biosciences, Inc., San Diego, California, USA
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - EunGi Kim
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Brian M Linhares
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Dong Chen
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Huang Huang
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Miao He
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Bo Wen
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Yi Wang
- Wellspring Biosciences, Inc., San Diego, California, USA
| | - Ke Yu
- Wellspring Biosciences, Inc., San Diego, California, USA
| | | | - Gwenn Danet-Desnoyers
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Winifred Trotman
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Malathi Kandarpa
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Hongwei Lei
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Luke Peterson
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Tanja Gruber
- Saint Jude Children's Hospital, Memphis, Tennessee, USA
| | - Sarah Choi
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Duxin Sun
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Pingda Ren
- Wellspring Biosciences, Inc., San Diego, California, USA.,Kura Oncology, Inc., San Diego, California, USA
| | - Lian-Sheng Li
- Wellspring Biosciences, Inc., San Diego, California, USA
| | - Yi Liu
- Wellspring Biosciences, Inc., San Diego, California, USA
| | | | - Ivan Maillard
- Life Sciences Institute and.,Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
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8
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Borkin D, Klossowski S, Pollock J, Miao H, Linhares BM, Kempinska K, Jin Z, Purohit T, Wen B, He M, Sun D, Cierpicki T, Grembecka J. Complexity of Blocking Bivalent Protein-Protein Interactions: Development of a Highly Potent Inhibitor of the Menin-Mixed-Lineage Leukemia Interaction. J Med Chem 2018; 61:4832-4850. [PMID: 29738674 PMCID: PMC7029623 DOI: 10.1021/acs.jmedchem.8b00071] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The protein-protein interaction between menin and mixed-lineage leukemia 1 (MLL1) plays an important role in development of acute leukemia with translocations of the MLL1 gene and in solid tumors. Here, we report the development of a new generation of menin-MLL1 inhibitors identified by structure-based optimization of the thienopyrimidine class of compounds. This work resulted in compound 28 (MI-1481), which showed very potent inhibition of the menin-MLL1 interaction (IC50 = 3.6 nM), representing the most potent reversible menin-MLL1 inhibitor reported to date. The crystal structure of the menin-28 complex revealed a hydrogen bond with Glu366 and hydrophobic interactions, which contributed to strong inhibitory activity of 28. Compound 28 also demonstrates pronounced activity in MLL leukemia cells and in vivo in MLL leukemia models. Thus, 28 is a valuable menin-MLL1 inhibitor that can be used for potential therapeutic applications and in further studies regarding the role of menin in cancer.
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Affiliation(s)
- Dmitry Borkin
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Szymon Klossowski
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jonathan Pollock
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brian M. Linhares
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Zhuang Jin
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bo Wen
- College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miao He
- College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Duxin Sun
- College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA,Corresponding author; Jolanta Grembecka, PhD, Associate Professor, Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI, 48108, , Tel. 734-615-9319
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9
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Quan T, Qin Z, Purohit T, Shao Y, Baldassare J, Voorhees J, Fisher G. 861 CCN2/Connective tissue growth factor regulates G1 to S phase cell cycle progression in human skin fibroblasts. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.872] [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: 11/25/2022]
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10
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Shukla S, Gray F, Ying W, Cho H, Zhao Q, Miao H, Miao H, Purohit T, Guzman M, Grembecka J, Cierpicki T. Abstract 50: Small molecule Ring1B-Bmi1 inhibitor attenuates PRC1 E3 ligase activity and targets leukemia stem cells self-renewal. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.hemmal17-50] [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
Polycomb group proteins, Ring1B and Bmi1 constitute catalytic component of Poly-comb Repressive Complex 1(PRC1) and execute gene silencing through histone H2A lysine119 ubiquitination (H2AK119ub). Bmi1 is overexpressed in a wide range of human cancers and has been implicated in regulation of leukemic stem cells (LSCs) self-renewal capacity. LSCs are refractory to the conventional therapies and eventually lead to the disease relapse. Small-molecule inhibitors of the Ring1B-Bmi1 E3 ligase activity have not been reported to date, but are highly desired as potential therapeutic agents to target LSCs. In the present study, employing fragment-based screening and extensive medicinal chemistry optimization, we developed WY332 that binds to Ring1B-Bmi1 with low micromolar affinity. Extensive characterization of the WY332 demonstrated selective reduction in Ring1B-Bmi1 mediated H2AK119ub levels in vitro and in leukemic cells whereas structurally similar and less potent compound displayed similar effect at much higher concentrations. Treatment of model cell lines, TEX and M9:ENL1, enriched in leukemia initiating cells show that the reduction in H2AK119ub levels is associated with induction of cellular differentiation and altered colony-forming potential. Further, gene expression analysis of TEX cells treated with WY332 indicated reprogramming of CD34+ cells and revealed significant increase in expression of genes suppressed in LSCs. In addition, WY332 treatment led to a marked increase in CD11b expression and significantly decreased CD34 expression in TEX cells. Evaluation of WY332 in patients' derived primary AML cells further revealed reprogramming of gene expression profile and phenotypic markers associated with LSCs self-renewal property. Overall, these compounds represent the novel small-molecule inhibitors of Ring1B-Bmi1 which inhibit E3 ubiquitin ligase activity and impair leukemic stem cell self-renewal capacity.
Citation Format: Shirish Shukla, Felicia Gray, Weijiang Ying, Hyoje Cho, Qingjie Zhao, Hongzhi Miao, Hongzhi Miao, Trupta Purohit, Monica Guzman, Jolanta Grembecka, Tomasz Cierpicki. Small molecule Ring1B-Bmi1 inhibitor attenuates PRC1 E3 ligase activity and targets leukemia stem cells self-renewal [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr 50.
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Affiliation(s)
| | | | | | - Hyoje Cho
- 1University of Michigan, Ann Arbor, MI,
| | | | | | | | | | - Monica Guzman
- 2Weill Cornell Medical College, Cornell University, New York, NY
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11
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Jedwabny W, Kłossowski S, Purohit T, Cierpicki T, Grembecka J, Dyguda-Kazimierowicz E. Theoretical models of inhibitory activity for inhibitors of protein-protein interactions: targeting menin-mixed lineage leukemia with small molecules. Medchemcomm 2017; 8:2216-2227. [PMID: 29456828 PMCID: PMC5774433 DOI: 10.1039/c7md00170c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/06/2017] [Indexed: 12/28/2022]
Abstract
A computationally affordable, non-empirical model based on electrostatic multipole and dispersion terms successfully predicts the binding affinity of inhibitors of menin–MLL protein–protein interactions.
Development and binding affinity predictions of inhibitors targeting protein–protein interactions (PPI) still represent a major challenge in drug discovery efforts. This work reports application of a predictive non-empirical model of inhibitory activity for PPI inhibitors, exemplified here for small molecules targeting the menin–mixed lineage leukemia (MLL) interaction. Systematic ab initio analysis of menin–inhibitor complexes was performed, revealing the physical nature of these interactions. Notably, the non-empirical protein–ligand interaction energy comprising electrostatic multipole and approximate dispersion terms (E(10)El,MTP + EDas) produced a remarkable correlation with experimentally measured inhibitory activities and enabled accurate activity prediction for new menin–MLL inhibitors. Importantly, this relatively simple and computationally affordable non-empirical interaction energy model outperformed binding affinity predictions derived from commonly used empirical scoring functions. This study demonstrates high relevance of the non-empirical model we developed for binding affinity prediction of inhibitors targeting protein–protein interactions that are difficult to predict using empirical scoring functions.
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Affiliation(s)
- Wiktoria Jedwabny
- Department of Chemistry , Wrocław University of Science and Technology , Wyb. Wyspiańskiego 27 , 50-370 Wrocław , Poland . ; Tel: +48 71 320 3200
| | - Szymon Kłossowski
- Department of Pathology , University of Michigan , 1150 W. Medical Center Dr, MSRBI, Rm 4510D , Ann Arbor , MI 48109 , USA . ; ; Tel: +734 615 9319
| | - Trupta Purohit
- Department of Pathology , University of Michigan , 1150 W. Medical Center Dr, MSRBI, Rm 4510D , Ann Arbor , MI 48109 , USA . ; ; Tel: +734 615 9319
| | - Tomasz Cierpicki
- Department of Pathology , University of Michigan , 1150 W. Medical Center Dr, MSRBI, Rm 4510D , Ann Arbor , MI 48109 , USA . ; ; Tel: +734 615 9319
| | - Jolanta Grembecka
- Department of Pathology , University of Michigan , 1150 W. Medical Center Dr, MSRBI, Rm 4510D , Ann Arbor , MI 48109 , USA . ; ; Tel: +734 615 9319
| | - Edyta Dyguda-Kazimierowicz
- Department of Chemistry , Wrocław University of Science and Technology , Wyb. Wyspiańskiego 27 , 50-370 Wrocław , Poland . ; Tel: +48 71 320 3200
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12
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Purohit T, Qin Z, Quan C, Lin Z, Quan T. Smad3-dependent CCN2 mediates fibronectin expression in human skin dermal fibroblasts. PLoS One 2017; 12:e0173191. [PMID: 28267785 PMCID: PMC5340390 DOI: 10.1371/journal.pone.0173191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/16/2017] [Indexed: 01/12/2023] Open
Abstract
The potential involvement of connective tissue growth factor (CCN2/CTGF) in extracellular matrix (ECM) production is recognized. However, the role CCN2 in fibronectin (FN) gene expression has remained incompletely understood and even controversial. Here we report that CCN2 is absolutely necessary for FN expression in primary human skin dermal fibroblasts, the major cells responsible for ECM production in skin. Gain- and loss-of-function approaches demonstrate that CCN2 is an essential component of FN expression in both basal and stimulation by TGF-β signaling, the major regulator of FN expression. CCN2 is significantly induced by Smad3, a critical mediator of TGF-β signaling. CCN2 acts as a downstream mediator of TGF-β/Smad signaling and acting synergistically with TGF-β to regulate FN gene expression. Finally, we observed that CCN2 and FN predominantly expressed in the dermis of normal human skin, stromal tissues of skin squamous cell carcinoma (SCC), and simultaneously induced in wounded human skin in vivo. These findings provide evidence that CCN2 is responsible for mediating the stimulatory effects of TGF-β/Smad on FN gene expression, and attenuation of CCN2 expression may benefit to reduce fibrotic ECM microenvironment in disease skin.
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Affiliation(s)
- Trupta Purohit
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Zhaoping Qin
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Chunji Quan
- Department of Pathology & Cancer Research Center, Yanbian University Medical College, Yanji, China
| | - Zhenhua Lin
- Department of Pathology & Cancer Research Center, Yanbian University Medical College, Yanji, China
| | - Taihao Quan
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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13
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Kessler L, Wu T, Grembecka J, Cierpicki T, Purohit T, Miao H, Kempinska K, Ely T, Hensen R, Li S, Patricelli M, Li S, Kucharski J, Zhang J, Yao Y, Yu K, Wang Y, Li L, Ren P, Liu Y. Discovery of novel menin-MLL small molecule inhibitors that display high potency and selectivity in vitro and in vivo. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32859-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Borkin D, Pollock J, Kempinska K, Purohit T, Li X, Wen B, Zhao T, Miao H, Shukla S, He M, Sun D, Cierpicki T, Grembecka J. Property Focused Structure-Based Optimization of Small Molecule Inhibitors of the Protein-Protein Interaction between Menin and Mixed Lineage Leukemia (MLL). J Med Chem 2016; 59:892-913. [PMID: 26744767 PMCID: PMC5092235 DOI: 10.1021/acs.jmedchem.5b01305] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [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: 12/19/2022]
Abstract
Development of potent small molecule inhibitors of protein-protein interactions with optimized druglike properties represents a challenging task in lead optimization process. Here, we report synthesis and structure-based optimization of new thienopyrimidine class of compounds, which block the protein-protein interaction between menin and MLL fusion proteins that plays an important role in acute leukemias with MLL translocations. We performed simultaneous optimization of both activity and druglike properties through systematic exploration of substituents introduced to the indole ring of lead compound 1 (MI-136) to identify compounds suitable for in vivo studies in mice. This work resulted in the identification of compound 27 (MI-538), which showed significantly increased activity, selectivity, polarity, and pharmacokinetic profile over 1 and demonstrated a pronounced effect in a mouse model of MLL leukemia. This study, which reports detailed structure-activity and structure-property relationships for the menin-MLL inhibitors, demonstrates challenges in optimizing inhibitors of protein-protein interactions for potential therapeutic applications.
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MESH Headings
- Animals
- Caco-2 Cells
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Female
- Histone-Lysine N-Methyltransferase/chemistry
- Histone-Lysine N-Methyltransferase/metabolism
- Humans
- Injections, Intraventricular
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, SCID
- Models, Molecular
- Molecular Structure
- Myeloid-Lymphoid Leukemia Protein/chemistry
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Protein Binding/drug effects
- Proto-Oncogene Proteins/chemistry
- Proto-Oncogene Proteins/metabolism
- Pyrimidines/administration & dosage
- Pyrimidines/chemistry
- Pyrimidines/pharmacology
- Small Molecule Libraries/administration & dosage
- Small Molecule Libraries/chemistry
- Small Molecule Libraries/pharmacology
- Structure-Activity Relationship
- Thiophenes/administration & dosage
- Thiophenes/chemistry
- Thiophenes/pharmacology
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Affiliation(s)
- Dmitry Borkin
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Jonathan Pollock
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Katarzyna Kempinska
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Trupta Purohit
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Xiaoqin Li
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bo Wen
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ting Zhao
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hongzhi Miao
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Shirish Shukla
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Miao He
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Duxin Sun
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States
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15
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Pollock J, Borkin D, Lund G, Purohit T, Dyguda-Kazimierowicz E, Grembecka J, Cierpicki T. Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes. J Med Chem 2015; 58:7465-74. [PMID: 26288158 PMCID: PMC4584387 DOI: 10.1021/acs.jmedchem.5b00975] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [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: 12/30/2022]
Abstract
![]()
Multipolar interactions involving
fluorine and the protein backbone
have been frequently observed in protein–ligand complexes.
Such fluorine–backbone interactions may substantially contribute
to the high affinity of small molecule inhibitors. Here we found that
introduction of trifluoromethyl groups into two different sites in
the thienopyrimidine class of menin–MLL inhibitors considerably
improved their inhibitory activity. In both cases, trifluoromethyl
groups are engaged in short interactions with the backbone of menin.
In order to understand the effect of fluorine, we synthesized a series
of analogues by systematically changing the number of fluorine atoms,
and we determined high-resolution crystal structures of the complexes
with menin. We found that introduction of fluorine at favorable geometry
for interactions with backbone carbonyls may improve the activity
of menin–MLL inhibitors as much as 5- to 10-fold. In order
to facilitate the design of multipolar fluorine–backbone interactions
in protein–ligand complexes, we developed a computational algorithm
named FMAP, which calculates fluorophilic sites in proximity to the
protein backbone. We demonstrated that FMAP could be used to rationalize
improvement in the activity of known protein inhibitors upon introduction
of fluorine. Furthermore, FMAP may also represent a valuable tool
for designing new fluorine substitutions and support ligand optimization
in drug discovery projects. Analysis of the menin–MLL inhibitor
complexes revealed that the backbone in secondary structures is particularly
accessible to the interactions with fluorine. Considering that secondary
structure elements are frequently exposed at protein interfaces, we
postulate that multipolar fluorine–backbone interactions may
represent a particularly attractive approach to improve inhibitors
of protein–protein interactions.
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Affiliation(s)
- Jonathan Pollock
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Dmitry Borkin
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - George Lund
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Trupta Purohit
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Edyta Dyguda-Kazimierowicz
- Molecular Modeling and Quantum Chemistry Group, Department of Chemistry, Wrocław University of Technology , Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan , Ann Arbor, Michigan 48109, United States
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16
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Singh D, Purohit T, Batke M, Dixit PK, Cappell MS. Durable hemostasis after embolization for massive arterial bleeding after percutaneous radiologic gastrostomy: salvage of original gastrostomy tube for enteral feeding for eight months after embolization. MINERVA GASTROENTERO 2015; 61:175-178. [PMID: 26161572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- D Singh
- Department of Internal Medicine, William Beaumont Hospital, Royal Oak, MI, USA -
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17
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Borkin D, He S, Miao H, Kempinska K, Pollock J, Chase J, Purohit T, Malik B, Zhao T, Wang J, Wen B, Zong H, Jones M, Danet-Desnoyers G, Guzman ML, Talpaz M, Bixby DL, Sun D, Hess JL, Muntean AG, Maillard I, Cierpicki T, Grembecka J. Pharmacologic inhibition of the Menin-MLL interaction blocks progression of MLL leukemia in vivo. Cancer Cell 2015; 27:589-602. [PMID: 25817203 PMCID: PMC4415852 DOI: 10.1016/j.ccell.2015.02.016] [Citation(s) in RCA: 260] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/11/2014] [Accepted: 02/27/2015] [Indexed: 12/22/2022]
Abstract
Chromosomal translocations affecting mixed lineage leukemia gene (MLL) result in acute leukemias resistant to therapy. The leukemogenic activity of MLL fusion proteins is dependent on their interaction with menin, providing basis for therapeutic intervention. Here we report the development of highly potent and orally bioavailable small-molecule inhibitors of the menin-MLL interaction, MI-463 and MI-503, and show their profound effects in MLL leukemia cells and substantial survival benefit in mouse models of MLL leukemia. Finally, we demonstrate the efficacy of these compounds in primary samples derived from MLL leukemia patients. Overall, we demonstrate that pharmacologic inhibition of the menin-MLL interaction represents an effective treatment for MLL leukemias in vivo and provide advanced molecular scaffold for clinical lead identification.
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Affiliation(s)
- Dmitry Borkin
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shihan He
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jonathan Pollock
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Graduate Program in Molecular and Cellular Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer Chase
- Center for Stem Cell Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bhavna Malik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ting Zhao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jingya Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hongliang Zong
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Morgan Jones
- Center for Stem Cell Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gwenn Danet-Desnoyers
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Monica L Guzman
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Moshe Talpaz
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dale L Bixby
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jay L Hess
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Andrew G Muntean
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ivan Maillard
- Center for Stem Cell Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
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18
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Grembecka JE, He S, Senter TJ, Borkin D, Pollock J, Han C, Upadhyay SK, Purohit T, Miao H, Gogliotti RDGD, Lindsley CW, Cierpicki T, Stauffer SR. Abstract 2534: High-affinity small molecule inhibitors of the menin-MLL interaction reverse oncogenic transformation mediated by MLL fusion proteins in leukemia. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2534] [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
The protein-protein interaction (PPI) between menin and Mixed Lineage Leukemia (MLL) plays a critical role in acute leukemias with translocations of MLL gene, and inhibition of this interaction with small molecules represents a new potential therapeutic strategy for the MLL leukemia patients. We identified novel small molecule inhibitors of the menin-MLL interaction with distinct molecular scaffolds by performing a High Throughput Screening (HTS) of over 300,000 compounds. Extensive medicinal chemistry efforts performed for two lead classes to improve inhibitory activity of these compounds resulted in menin-MLL inhibitors with low nanomolar binding affinities. The menin-inhibitor co-crystal structures revealed that these compounds directly bind to menin and closely mimic the key interactions of MLL with menin, resulting in their high binding affinity. Interestingly, the hydroxymethylpiperidine class of the menin-MLL inhibitors extends beyond the MLL binding region on menin, providing additional opportunity for their optimization. We combined extensive crystallography studies with structure-based design to perform rational optimization and scaffold modification to rapidly improve activity and modulate physicochemical properties of the menin-MLL inhibitors. Treatment of MLL leukemia cells with the most potent menin-MLL inhibitors we developed resulted in very effective and selective inhibition of cell proliferation, induced apoptosis and differentiation of these cells. These effects were associated with downregulation of Hoxa9 and Meis1 expression, the downstream targets of MLL fusion proteins required for their leukemogenicity, demonstrating a very specific mechanism of action for these newly developed menin-MLL inhibitors. In vivo studies are currently undergoing to assess the effect of these compounds on leukemia progression in animal models of MLL leukemia. Our studies provide a novel and very attractive scaffolds for further development as a new potential therapeutic approach for the MLL leukemia patients.
Citation Format: Jolanta E. Grembecka, Shihan He, Timothy J. Senter, Dmitry Borkin, Jonathan Pollock, Changho Han, Sunil Kumar Upadhyay, Trupta Purohit, Hongzhi Miao, Rocco D. Gogliotti D. Gogliotti, Craig W. Lindsley, Tomasz Cierpicki, Shaun R. Stauffer. High-affinity small molecule inhibitors of the menin-MLL interaction reverse oncogenic transformation mediated by MLL fusion proteins in leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2534. doi:10.1158/1538-7445.AM2014-2534
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Affiliation(s)
| | - Shihan He
- 1University of Michigan, Ann Arbor, MI
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Cierpicki T, Murai MJ, Pollock J, Purohit T, He S, Yokom A, Hess JL, Muntean AG, Grembecka J. Abstract 3225: LEDGF IBD domain represents therapeutic target for MLL leukemia and HIV. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Lens epithelium-derived growth factor (LEDGF) is a chromatin associated protein implicated in cell survival, cancer, autoimmune diseases and HIV pathogenesis. LEDGF is also involved in recurring chromosomal translocations with nucleoporin NUP98 in acute leukemia, and the LEDGF/p75 isoform is consistently upregulated in a subset of acute myeloid leukemias (AML) resistant to chemotherapy. Moreover, it has been established that LEDGF is an essential co-factor required for oncogenic activity of MLL fusion proteins in leukemia. LEDGF interacts simultaneously with MLL and menin and is necessary for up-regulation of HOXA9 gene and for leukemogenic transformation by MLL fusion proteins in vivo. Therefore, LEDGF represent a valuable molecular target for therapeutic intervention as a novel targeted therapy for MLL leukemia patients. Furthermore, targeting LEDGF may represent an attractive alternative to inhibition of the menin-MLL interaction as it will allow preserving the function of menin, a known tumor suppressor in endocrine tissues.
We determined the solution structure of MLL fragment bound to LEDGF IBD domain and identified a novel hydrophobic motif within MLL, which we called IBM2, that is required for high affinity interaction with LEDGF. Point mutations within IBM2 abolished leukemogenic activity of MLL-AF9, indicating that IBM2 represents a critical site for formation of a high affinity menin-MLL-LEDGF complex. Furthermore, we found that short peptide corresponding to IBM2 binds to IBD domain and disrupts the interaction of LEDGF with the menin-MLL complex, providing a proof of concept that the novel interface on IBD domain we identified represents a druggable site for small molecule intervention.
LEDGF plays also an essential role in pathogenesis of HIV-1 virus and is required for integration of viral cDNA. Targeting HIV integrase to disrupt the interaction with LEDGF has been recognized as an attractive approach to develop new anti-viral agents. Importantly, the new MLL binding site on IBD domain we found overlaps with the binding site of HIV integrase. Therefore, targeting the IBM2 site on IBD may represent a novel approach to target the LEDGF-integrase interaction. In summary, our findings pave the way towards development of new therapeutic agents with dual applications for both MLL leukemias and HIV.
Citation Format: Tomasz Cierpicki, Marcelo J. Murai, Jonathan Pollock, Trupta Purohit, Shihan He, Adam Yokom, Jay L. Hess, Andrew G. Muntean, Jolanta Grembecka. LEDGF IBD domain represents therapeutic target for MLL leukemia and HIV. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3225. doi:10.1158/1538-7445.AM2014-3225
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Affiliation(s)
| | | | | | | | - Shihan He
- University of Michigan, Ann Arbor, MI
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He S, Senter TJ, Pollock J, Han C, Upadhyay SK, Purohit T, Gogliotti RD, Lindsley CW, Cierpicki T, Stauffer SR, Grembecka J. High-affinity small-molecule inhibitors of the menin-mixed lineage leukemia (MLL) interaction closely mimic a natural protein-protein interaction. J Med Chem 2014; 57:1543-56. [PMID: 24472025 PMCID: PMC3983337 DOI: 10.1021/jm401868d] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [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: 12/05/2013] [Indexed: 12/14/2022]
Abstract
The protein-protein interaction (PPI) between menin and mixed lineage leukemia (MLL) plays a critical role in acute leukemias, and inhibition of this interaction represents a new potential therapeutic strategy for MLL leukemias. We report development of a novel class of small-molecule inhibitors of the menin-MLL interaction, the hydroxy- and aminomethylpiperidine compounds, which originated from HTS of ∼288000 small molecules. We determined menin-inhibitor co-crystal structures and found that these compounds closely mimic all key interactions of MLL with menin. Extensive crystallography studies combined with structure-based design were applied for optimization of these compounds, resulting in MIV-6R, which inhibits the menin-MLL interaction with IC50 = 56 nM. Treatment with MIV-6 demonstrated strong and selective effects in MLL leukemia cells, validating specific mechanism of action. Our studies provide novel and attractive scaffold as a new potential therapeutic approach for MLL leukemias and demonstrate an example of PPI amenable to inhibition by small molecules.
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Affiliation(s)
- Shihan He
- Department
of Pathology, University of Michigan, Ann Arbor, 1150 West
Medical Center Drive, MSRBI, Room 4510D, Michigan, 48109, United States
| | - Timothy J. Senter
- Department
of Pharmacology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Specialized Chemistry Center for Probe Development (MLPCN), Nashville, Tennessee 37232, United States
- Vanderbilt
Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jonathan Pollock
- Department
of Pathology, University of Michigan, Ann Arbor, 1150 West
Medical Center Drive, MSRBI, Room 4510D, Michigan, 48109, United States
| | - Changho Han
- Department
of Pharmacology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Specialized Chemistry Center for Probe Development (MLPCN), Nashville, Tennessee 37232, United States
- Vanderbilt
Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Sunil Kumar Upadhyay
- Department
of Pathology, University of Michigan, Ann Arbor, 1150 West
Medical Center Drive, MSRBI, Room 4510D, Michigan, 48109, United States
| | - Trupta Purohit
- Department
of Pathology, University of Michigan, Ann Arbor, 1150 West
Medical Center Drive, MSRBI, Room 4510D, Michigan, 48109, United States
| | - Rocco D. Gogliotti
- Department
of Pharmacology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Specialized Chemistry Center for Probe Development (MLPCN), Nashville, Tennessee 37232, United States
- Vanderbilt
Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Craig W. Lindsley
- Department
of Pharmacology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Specialized Chemistry Center for Probe Development (MLPCN), Nashville, Tennessee 37232, United States
- Vanderbilt
Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Tomasz Cierpicki
- Department
of Pathology, University of Michigan, Ann Arbor, 1150 West
Medical Center Drive, MSRBI, Room 4510D, Michigan, 48109, United States
| | - Shaun R. Stauffer
- Department
of Pharmacology, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
- Vanderbilt
Specialized Chemistry Center for Probe Development (MLPCN), Nashville, Tennessee 37232, United States
- Vanderbilt
Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jolanta Grembecka
- Department
of Pathology, University of Michigan, Ann Arbor, 1150 West
Medical Center Drive, MSRBI, Room 4510D, Michigan, 48109, United States
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Grembecka J, He S, Shi A, Purohit T, Muntean AG, Sorenson RJ, Showalter HD, Murai MJ, Belcher AM, Hartley T, Hess JL, Cierpicki T. Menin-MLL inhibitors reverse oncogenic activity of MLL fusion proteins in leukemia. Nat Chem Biol 2012; 8:277-84. [PMID: 22286128 DOI: 10.1038/nchembio.773] [Citation(s) in RCA: 307] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 11/02/2011] [Indexed: 12/12/2022]
Abstract
Translocations involving the mixed lineage leukemia (MLL) gene result in human acute leukemias with very poor prognosis. The leukemogenic activity of MLL fusion proteins is critically dependent on their direct interaction with menin, a product of the multiple endocrine neoplasia (MEN1) gene. Here we present what are to our knowledge the first small-molecule inhibitors of the menin-MLL fusion protein interaction that specifically bind menin with nanomolar affinities. These compounds effectively reverse MLL fusion protein-mediated leukemic transformation by downregulating the expression of target genes required for MLL fusion protein oncogenic activity. They also selectively block proliferation and induce both apoptosis and differentiation of leukemia cells harboring MLL translocations. Identification of these compounds provides a new tool for better understanding MLL-mediated leukemogenesis and represents a new approach for studying the role of menin as an oncogenic cofactor of MLL fusion proteins. Our findings also highlight a new therapeutic strategy for aggressive leukemias with MLL rearrangements.
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Affiliation(s)
- Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
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Fisher GJ, Quan T, Purohit T, Shao Y, Cho MK, He T, Varani J, Kang S, Voorhees JJ. Collagen fragmentation promotes oxidative stress and elevates matrix metalloproteinase-1 in fibroblasts in aged human skin. Am J Pathol 2008; 174:101-14. [PMID: 19116368 DOI: 10.2353/ajpath.2009.080599] [Citation(s) in RCA: 290] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aged human skin is fragile because of fragmentation and loss of type I collagen fibrils, which confer strength and resiliency. We report here that dermal fibroblasts express increased levels of collagen-degrading matrix metalloproteinases-1 (MMP-1) in aged (>80 years old) compared with young (21 to 30 years old) human skin in vivo. Transcription factor AP-1 and alpha2beta1 integrin, which are key regulators of MMP-1 expression, are also elevated in fibroblasts in aged human skin in vivo. MMP-1 treatment of young skin in organ culture causes fragmentation of collagen fibrils and reduces fibroblast stretch, consistent with reduced mechanical tension, as observed in aged human skin. Limited fragmentation of three-dimensional collagen lattices with exogenous MMP-1 also reduces fibroblast stretch and mechanical tension. Furthermore, fibroblasts cultured in fragmented collagen lattices express elevated levels of MMP-1, AP-1, and alpha2beta1 integrin. Importantly, culture in fragmented collagen raises intracellular oxidant levels and treatment with antioxidant MitoQ(10) significantly reduces MMP-1 expression. These data identify positive feedback regulation that couples age-dependent MMP-1-catalyzed collagen fragmentation and oxidative stress. We propose that this self perpetuating cycle promotes human skin aging. These data extend the current understanding of the oxidative theory of aging beyond a cellular-centric view to include extracellular matrix and the critical role that connective tissue microenvironment plays in the biology of aging.
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Affiliation(s)
- Gary J Fisher
- Department of Dermatology, Medical School, University of Michigan, Ann Arbor, Michigan 48109-5609, USA.
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Neogy D, Chatterji A, Purohit T. Erratum: Magnetic susceptibility of Nd(BrO3)3 ⋅ 9H2O single crystal: Effects of the crystal field and calculation of the electrostatic crystal field parameters [J. Chem. Phys. 80, 3753 (1984)]. J Chem Phys 1986. [DOI: 10.1063/1.450858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Neogy D, Chatterji A, Purohit T. Magnetic susceptibility of Nd (BrO3)3⋅9H2O single crystal: Effects of the crystal field and calculation of the electrostatic crystal field parameters. J Chem Phys 1984. [DOI: 10.1063/1.447153] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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