1
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Yuan T, Kumar S, Skinner M, Victor-Joseph R, Abuaita M, Keijer J, Zhang J, Kunkel TJ, Liu Y, Petrunak EM, Saunders TL, Lieberman AP, Stuckey JA, Neamati N, Al-Murshedi F, Alfadhel M, Spelbrink JN, Rodenburg R, de Boer VCJ, Lombard DB. SIRT5 variants from patients with mitochondrial disease are associated with reduced SIRT5 stability and activity, but not with neuropathology. bioRxiv 2023:2023.12.06.570371. [PMID: 38105987 PMCID: PMC10723467 DOI: 10.1101/2023.12.06.570371] [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] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
SIRT5 is a sirtuin deacylase that represents the major activity responsible for removal of negatively-charged lysine modifications, in the mitochondrial matrix and elsewhere in the cell. In benign cells and mouse models, under basal non-stressed conditions, the phenotypes of SIRT5 deficiency are generally quite subtle. Here, we identify two homozygous SIRT5 variants in human patients suffering from severe mitochondrial disease. Both variants, P114T and L128V, are associated with reduced SIRT5 protein stability and impaired biochemical activity, with no evidence of neomorphic or dominant negative properties. The crystal structure of the P114T enzyme was solved and shows only subtle deviations from wild-type. Via CRISPR-Cas9, we generate a mouse model that recapitulates the human P114T mutation; homozygotes show reduced SIRT5 levels and activity, but no obvious metabolic abnormalities, neuropathology or other gross evidence of severe disease. We conclude that these human SIRT5 variants most likely represent severe hypomorphs, and are likely not the primary pathogenic cause of the neuropathology observed in the patients.
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Affiliation(s)
- Taolin Yuan
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen, The Netherlands
| | - Surinder Kumar
- Department of Pathology & Laboratory Medicine, Miller School of Medicine, and Sylvester Comprehensive Cancer Center, University of Miami, Miami FL 33136
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Mary Skinner
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | | | - Majd Abuaita
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen, The Netherlands
| | - Jessica Zhang
- Department of Pathology & Laboratory Medicine, Miller School of Medicine, and Sylvester Comprehensive Cancer Center, University of Miami, Miami FL 33136
| | | | - Yanghan Liu
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109
| | - Elyse M. Petrunak
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas L. Saunders
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | | | - Jeanne A. Stuckey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109
| | - Fathiya Al-Murshedi
- Genetic and Developmental Medicine Clinic, Department of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Majid Alfadhel
- Medical Genomic Research Department, King Abdullah International Medical Research Center(KAIMRC), King Saud Bin Abdulaziz University for Health Sciences(KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- Genetics and Precision Medicine department (GPM), King Abdullah Specialized Children’s Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Johannes N. Spelbrink
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richard Rodenburg
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vincent C. J. de Boer
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen, The Netherlands
| | - David B. Lombard
- Department of Pathology & Laboratory Medicine, Miller School of Medicine, and Sylvester Comprehensive Cancer Center, University of Miami, Miami FL 33136
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
- Miami VA Healthcare System, Miami FL 33125
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2
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Yuan X, Jiang H, Fu D, Rech JC, Robida A, Rajanayake K, Yuan H, He M, Wen B, Sun D, Liu C, Chinnaswamy K, Stuckey JA, Paczesny S, Yang CY. Prophylactic Mitigation of Acute Graft versus Host Disease by Novel 2-(Pyrrolidin-1-ylmethyl)pyrrole-Based Stimulation-2 (ST2) Inhibitors. ACS Pharmacol Transl Sci 2023; 6:1275-1287. [PMID: 37705593 PMCID: PMC10496145 DOI: 10.1021/acsptsci.3c00122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 09/15/2023]
Abstract
Hematopoietic cell transplantation (HCT) is a proven and potentially curable therapy for hematological malignancies and inherited hematological disease. The main risk of HCT is the development of graft versus host disease (GVHD) acquired in up to 50% of patients. Upregulation of soluble ST2 (sST2) is a key clinical biomarker for GVHD prognosis and was shown to be a potential therapeutic target for GVHD. Agents targeting sST2 to reduce the sST2 level after HCT have the potential to mitigate GVHD progression. Here, we report 32 (or XY52) as the lead ST2 inhibitor from our optimization campaign. XY52 had improved inhibitory activity and metabolic stability in vitro and in vivo. XY52 suppressed proinflammatory T-cell proliferation while increasing regulatory T cells in vitro. In a clinically relevant GVHD model, a 21-day prophylactic regimen of XY52 reduced plasma sST2 and IFN-γ levels and GVHD score and extended survival in mice. XY52 represented a significant improvement over our previous compound, iST2-1, and further optimization of XY52 is warranted. The small-molecule ST2 inhibitors can potentially be used as a biomarker-guided therapy for mitigating GVHD in future clinical applications.
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Affiliation(s)
- Xinrui Yuan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Hua Jiang
- Department
of Microbiology & Immunology, Medical
University of South Carolina, Charleston, South Carolina 29425-2503, United States
| | - Denggang Fu
- Department
of Microbiology & Immunology, Medical
University of South Carolina, Charleston, South Carolina 29425-2503, United States
| | - Jason C. Rech
- Michigan Center for Therapeutic Innovation, Department
of Internal
Medicine, Life Sciences Institute, Department of Pharmaceutical Sciences, College of
Pharmacy, and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aaron Robida
- Michigan Center for Therapeutic Innovation, Department
of Internal
Medicine, Life Sciences Institute, Department of Pharmaceutical Sciences, College of
Pharmacy, and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Krishani Rajanayake
- Michigan Center for Therapeutic Innovation, Department
of Internal
Medicine, Life Sciences Institute, Department of Pharmaceutical Sciences, College of
Pharmacy, and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hebao Yuan
- Michigan Center for Therapeutic Innovation, Department
of Internal
Medicine, Life Sciences Institute, Department of Pharmaceutical Sciences, College of
Pharmacy, and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Miao He
- Michigan Center for Therapeutic Innovation, Department
of Internal
Medicine, Life Sciences Institute, Department of Pharmaceutical Sciences, College of
Pharmacy, and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bo Wen
- Michigan Center for Therapeutic Innovation, Department
of Internal
Medicine, Life Sciences Institute, Department of Pharmaceutical Sciences, College of
Pharmacy, and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Duxin Sun
- Michigan Center for Therapeutic Innovation, Department
of Internal
Medicine, Life Sciences Institute, Department of Pharmaceutical Sciences, College of
Pharmacy, and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chen Liu
- Department
of Pathology, Yale University, New Haven, Connecticut 06520, United States
| | - Krishnapriya Chinnaswamy
- Michigan Center for Therapeutic Innovation, Department
of Internal
Medicine, Life Sciences Institute, Department of Pharmaceutical Sciences, College of
Pharmacy, and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne A. Stuckey
- Michigan Center for Therapeutic Innovation, Department
of Internal
Medicine, Life Sciences Institute, Department of Pharmaceutical Sciences, College of
Pharmacy, and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sophie Paczesny
- Department
of Microbiology & Immunology, Medical
University of South Carolina, Charleston, South Carolina 29425-2503, United States
| | - Chao-Yie Yang
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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3
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Kaneshige A, Bai L, Wang M, McEachern D, Meagher JL, Xu R, Wang Y, Jiang W, Metwally H, Kirchhoff PD, Zhao L, Jiang H, Wang M, Wen B, Sun D, Stuckey JA, Wang S. A selective small-molecule STAT5 PROTAC degrader capable of achieving tumor regression in vivo. Nat Chem Biol 2023; 19:703-711. [PMID: 36732620 DOI: 10.1038/s41589-022-01248-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 03/23/2022] [Accepted: 12/21/2022] [Indexed: 02/04/2023]
Abstract
Signal transducer and activator of transcription 5 (STAT5) is an attractive therapeutic target, but successful targeting of STAT5 has proved to be difficult. Here we report the development of AK-2292 as a first, potent and selective small-molecule degrader of both STAT5A and STAT5B isoforms. AK-2292 induces degradation of STAT5A/B proteins with an outstanding selectivity over all other STAT proteins and more than 6,000 non-STAT proteins, leading to selective inhibition of STAT5 activity in cells. AK-2292 effectively induces STAT5 depletion in normal mouse tissues and human chronic myeloid leukemia (CML) xenograft tissues and achieves tumor regression in two CML xenograft mouse models at well-tolerated dose schedules. AK-2292 is not only a powerful research tool with which to investigate the biology of STAT5 and the therapeutic potential of selective STAT5 protein depletion and inhibition but also a promising lead compound toward ultimate development of a STAT5-targeted therapy.
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Affiliation(s)
- Atsunori Kaneshige
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Longchuan Bai
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Mi Wang
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Donna McEachern
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | | | - Renqi Xu
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Yu Wang
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Wei Jiang
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Hoda Metwally
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Paul D Kirchhoff
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Lijie Zhao
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Hui Jiang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Meilin Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Shaomeng Wang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.
- Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
- Department of Pharmacology, Medical School, University of Michigan, Ann Arbor, MI, USA.
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4
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Yuan X, Howie KL, Kazemi Sabzvar M, Chinnaswamy K, Stuckey JA, Yang CY. Correction to "Profiling the Binding Activities of Peptides and Inhibitors to the U2 Auxiliary Factor Homology Motif (UHM) Domains". ACS Med Chem Lett 2023; 14:681. [PMID: 37197465 PMCID: PMC10184150 DOI: 10.1021/acsmedchemlett.3c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Indexed: 05/19/2023] Open
Abstract
[This corrects the article DOI: 10.1021/acsmedchemlett.2c00537.].
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5
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Wubben TJ, Chaudhury S, Watch BT, Stuckey JA, Weh E, Fernando R, Goswami M, Pawar M, Rech JC, Besirli CG. Development of Novel Small-Molecule Activators of Pyruvate Kinase Muscle Isozyme 2, PKM2, to Reduce Photoreceptor Apoptosis. Pharmaceuticals (Basel) 2023; 16:ph16050705. [PMID: 37242488 DOI: 10.3390/ph16050705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Treatment options are lacking to prevent photoreceptor death and subsequent vision loss. Previously, we demonstrated that reprogramming metabolism via the pharmacologic activation of PKM2 is a novel photoreceptor neuroprotective strategy. However, the features of the tool compound used in those studies, ML-265, preclude its advancement as an intraocular, clinical candidate. This study sought to develop the next generation of small-molecule PKM2 activators, aimed specifically for delivery into the eye. Compounds were developed that replaced the thienopyrrolopyridazinone core of ML-265 and modified the aniline and methyl sulfoxide functional groups. Compound 2 demonstrated that structural changes to the ML-265 scaffold are tolerated from a potency and efficacy standpoint, allow for a similar binding mode to the target, and circumvent apoptosis in models of outer retinal stress. To overcome the low solubility and problematic functional groups of ML-265, compound 2's efficacious and versatile core structure for the incorporation of diverse functional groups was then utilized to develop novel PKM2 activators with improved solubility, lack of structural alerts, and retained potency. No other molecules are in the pharmaceutical pipeline for the metabolic reprogramming of photoreceptors. Thus, this study is the first to cultivate the next generation of novel, structurally diverse, small-molecule PKM2 activators for delivery into the eye.
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Affiliation(s)
- Thomas J Wubben
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
| | - Sraboni Chaudhury
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
| | - Brennan T Watch
- Department of Internal Medicine, Hematology and Oncology, Michigan Center for Therapeutic Innovation, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeanne A Stuckey
- Departments of Biological Chemistry and Biophysics, Center for Structural Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eric Weh
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
| | - Roshini Fernando
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
| | - Moloy Goswami
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
| | - Mercy Pawar
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
| | - Jason C Rech
- Department of Internal Medicine, Hematology and Oncology, Michigan Center for Therapeutic Innovation, University of Michigan, Ann Arbor, MI 48109, USA
| | - Cagri G Besirli
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
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6
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Yuan X, Howie KL, Kazemi Sabzvar M, Chinnaswamy K, Stuckey JA, Yang CY. Profiling the Binding Activities of Peptides and Inhibitors to the U2 Auxiliary Factor Homology Motif (UHM) Domains. ACS Med Chem Lett 2023; 14:450-457. [PMID: 37077390 PMCID: PMC10107908 DOI: 10.1021/acsmedchemlett.2c00537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/17/2023] [Indexed: 04/21/2023] Open
Abstract
RNA splicing is a biological process to generate mature mRNA (mRNA) by removing introns and annexing exons in the nascent RNA transcript and is executed by a multiprotein complex called spliceosome. To aid RNA splicing, a class of splicing factors use an atypical RNA recognition domain (UHM) to bind with U2AF ligand motifs (ULMs) in proteins to form modules that recognize splice sites and splicing regulatory elements on mRNA. Mutations of UHM containing splicing factors have been found frequently in myeloid neoplasms. To profile the selectivity of UHMs for inhibitor development, we established binding assays to measure the binding activities between UHM domains and ULM peptides and a set of small-molecule inhibitors. Additionally, we computationally analyzed the targeting potential of the UHM domains by small-molecule inhibitors. Our study provided the binding assessment of UHM domains to diverse ligands that may guide development of selective UHM domain inhibitors in the future.
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Affiliation(s)
- Xinrui Yuan
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Kathryn L. Howie
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Mona Kazemi Sabzvar
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | | | - Jeanne A. Stuckey
- Life
Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- Departments
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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7
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Kaneshige A, Bai L, Wang M, McEachern D, Meagher JL, Xu R, Kirchhoff PD, Wen B, Sun D, Stuckey JA, Wang S. Discovery of a Potent and Selective STAT5 PROTAC Degrader with Strong Antitumor Activity In Vivo in Acute Myeloid Leukemia. J Med Chem 2023; 66:2717-2743. [PMID: 36735833 DOI: 10.1021/acs.jmedchem.2c01665] [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: 02/05/2023]
Abstract
STAT5 is an attractive therapeutic target for human cancers. We report herein the discovery of a potent and selective STAT5 degrader with strong antitumor activity in vivo. We first obtained small-molecule ligands with sub-micromolar to low micromolar binding affinities to STAT5 and STAT6 SH2 domains and determined co-crystal structures of three such ligands in complex with STAT5A. We successfully transformed these ligands into potent and selective STAT5 degraders using the PROTAC technology with AK-2292 as the best compound. AK-2292 effectively induces degradation of STAT5A, STAT5B, and phosphorylated STAT5 proteins in a concentration- and time-dependent manner in acute myeloid leukemia (AML) cell lines and demonstrates excellent degradation selectivity for STAT5 over all other STAT members. It exerts potent and specific cell growth inhibitory activity in AML cell lines with high levels of phosphorylated STAT5. AK-2292 effectively reduces STAT5 protein in vivo and achieves strong antitumor activity in mice at well-tolerated dose schedules.
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Affiliation(s)
- Atsunori Kaneshige
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Longchuan Bai
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mi Wang
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Donna McEachern
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer L Meagher
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Renqi Xu
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul D Kirchhoff
- Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne A Stuckey
- Life Science Institute, University of Michigan, Ann Arbor, Michigan 48109, United States.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Pharmacology, Medical School, University of Michigan, Ann Arbor, Michigan 48109, United States.,Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
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8
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Deng J, Paulus A, Fang DD, Manna A, Wang G, Wang H, Zhu S, Chen J, Min P, Yin Y, Dutta N, Halder N, Ciccio G, Copland JA, Miller J, Han B, Bai L, Liu L, Wang M, McEachern D, Przybranowski S, Yang CY, Stuckey JA, Wu D, Li C, Ryan J, Letai A, Ailawadhi S, Yang D, Wang S, Chanan-Khan A, Zhai Y. Lisaftoclax (APG-2575) Is a Novel BCL-2 Inhibitor with Robust Antitumor Activity in Preclinical Models of Hematologic Malignancy. Clin Cancer Res 2022; 28:5455-5468. [PMID: 36048524 DOI: 10.1158/1078-0432.ccr-21-4037] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/01/2022] [Accepted: 08/30/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Development of B-cell lymphoma 2 (BCL-2)-specific inhibitors poses unique challenges in drug design because of BCL-2 homology domain 3 (BH3) shared homology between BCL-2 family members and the shallow surface of their protein-protein interactions. We report herein discovery and extensive preclinical investigation of lisaftoclax (APG-2575). EXPERIMENTAL DESIGN Computational modeling was used to design "lead" compounds. Biochemical binding, mitochondrial BH3 profiling, and cell-based viability or apoptosis assays were used to determine the selectivity and potency of BCL-2 inhibitor lisaftoclax. The antitumor effects of lisaftoclax were also evaluated in several xenograft models. RESULTS Lisaftoclax selectively binds BCL-2 (Ki < 0.1 nmol/L), disrupts BCL-2:BIM complexes, and compromises mitochondrial outer membrane potential, culminating in BAX/BAK-dependent, caspase-mediated apoptosis. Lisaftoclax exerted strong antitumor activity in hematologic cancer cell lines and tumor cells from patients with chronic lymphocytic leukemia, multiple myeloma, or Waldenström macroglobulinemia. After lisaftoclax treatment, prodeath proteins BCL-2‒like protein 11 (BIM) and Noxa increased, and BIM translocated from cytosol to mitochondria. Consistent with these apoptotic activities, lisaftoclax entered malignant cells rapidly, reached plateau in 2 hours, and significantly downregulated mitochondrial respiratory function and ATP production. Furthermore, lisaftoclax inhibited tumor growth in xenograft models, correlating with caspase activation, poly (ADP-ribose) polymerase 1 cleavage, and pharmacokinetics of the compound. Lisaftoclax combined with rituximab or bendamustine/rituximab enhanced antitumor activity in vivo. CONCLUSIONS These findings demonstrate that lisaftoclax is a novel, orally bioavailable BH3 mimetic BCL-2-selective inhibitor with considerable potential for the treatment of certain hematologic malignancies.
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Affiliation(s)
- Jing Deng
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Aneel Paulus
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, Florida
| | - Douglas D Fang
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Alak Manna
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Guangfeng Wang
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Hengbang Wang
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Saijie Zhu
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Jianyong Chen
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Ping Min
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Yan Yin
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Navnita Dutta
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Nabanita Halder
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Gina Ciccio
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - John A Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - James Miller
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Bing Han
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
| | - Longchuan Bai
- Department of Internal Medicine, Pharmacology and Medicinal Chemistry, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Liu Liu
- Department of Internal Medicine, Pharmacology and Medicinal Chemistry, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Mi Wang
- Department of Internal Medicine, Pharmacology and Medicinal Chemistry, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Donna McEachern
- Department of Internal Medicine, Pharmacology and Medicinal Chemistry, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Sally Przybranowski
- Department of Internal Medicine, Pharmacology and Medicinal Chemistry, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Chao-Yie Yang
- Department of Internal Medicine, Pharmacology and Medicinal Chemistry, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Jeanne A Stuckey
- Department of Internal Medicine, Pharmacology and Medicinal Chemistry, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Depei Wu
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Caixia Li
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jeremy Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Dajun Yang
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Ascentage Pharma Group, Rockville, Maryland
| | - Shaomeng Wang
- Department of Internal Medicine, Pharmacology and Medicinal Chemistry, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Asher Chanan-Khan
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida
- Mayo Clinic Cancer Center at St. Vincent's Medical Center Riverside, Jacksonville, Florida
| | - Yifan Zhai
- Ascentage Pharma (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
- Ascentage Pharma Group, Rockville, Maryland
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9
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Yuan X, Jiang H, Fu D, Robida A, Rajanayake K, Yuan H, Wen B, Sun D, Watch BT, Chinnaswamy K, Stuckey JA, Paczesny S, Rech JC, Yang CY. Structure-Activity relationship of 1-(Furan-2ylmethyl)Pyrrolidine-Based Stimulation-2 (ST2) inhibitors for treating graft versus host disease. Bioorg Med Chem 2022; 71:116942. [PMID: 35930851 PMCID: PMC9451522 DOI: 10.1016/j.bmc.2022.116942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 11/20/2022]
Abstract
An elevated plasma level of soluble ST2 (sST2) is a risk biomarker for graft-versus-host disease (GVHD) and death in patients receiving hematopoietic cell transplantation (HCT). sST2 functions as a trap for IL-33 and amplifies the pro-inflammatory type 1 and 17 response while suppressing the tolerogenic type 2 and regulatory T cells activation during GVHD development. We previously identified small-molecule ST2 inhibitors particularly iST2-1 that reduces plasma sST2 levels and improved survival in two animal models. Here, we reported the structure-activity relationship of the furanylmethylpyrrolidine-based ST2 inhibitors based on iST2-1. Based on the biochemical AlphaLISA assay, we improved the activity of iST2-1 by 6-fold (∼6 μM in IC50 values) in the inhibition of ST2/IL-33 and confirmed the activities of the compounds in a cellular reporter assay. To determine the inhibition of the alloreactivity in vitro, we used the mixed lymphocyte reaction assay to demonstrate that our ST2 inhibitors decreased CD4+ and CD8+ T cells proliferation and increased Treg population. The data presented in this work are critical to the development of ST2 inhibitors in future.
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Affiliation(s)
- Xinrui Yuan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Hua Jiang
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, United States
| | - Denggang Fu
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, United States
| | - Aaron Robida
- Life Sciences Institute, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Krishani Rajanayake
- Rogel Cancer Center, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States; Pharmaceutical Sciences, College of Pharmacy, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Hebao Yuan
- Rogel Cancer Center, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States; Pharmaceutical Sciences, College of Pharmacy, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Bo Wen
- Rogel Cancer Center, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States; Pharmaceutical Sciences, College of Pharmacy, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Duxin Sun
- Rogel Cancer Center, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States; Pharmaceutical Sciences, College of Pharmacy, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Brennan T Watch
- Michigan Center for Therapeutic Innovation, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Krishnapriya Chinnaswamy
- Life Sciences Institute, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States; Rogel Cancer Center, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Jeanne A Stuckey
- Life Sciences Institute, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States; Rogel Cancer Center, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Sophie Paczesny
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC, United States
| | - Jason C Rech
- Michigan Center for Therapeutic Innovation, Departments of Internal Medicine, University of Michigan, Ann Arbor, MI, United States.
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, United States.
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10
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Yuan X, Chinnaswamy K, Stuckey JA, Yang CY. Computational Cosolvent Mapping Analysis Leads to Identify Salicylic Acid Analogs as Weak Inhibitors of ST2 and IL33 Binding. J Phys Chem B 2022; 126:2394-2406. [PMID: 35294837 PMCID: PMC9354565 DOI: 10.1021/acs.jpcb.2c00341] [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] [Indexed: 11/28/2022]
Abstract
Cytokine signaling initiated by the binding of the cytokine receptors to cytokines plays important roles in immune regulation and diseases. Structurally, cytokine receptors interact with cytokines via an extensive, rugged interface that represents a challenge in inhibitor development. Our computational analysis has previously indicated that butyric acid, mimicking acidic residues, preferentially binds to sites in ST2 (Stimulation-2) that interact with acidic residues of IL33, the endogenous cytokine for ST2. To investigate if a charged group in small molecules facilitates ligand binding to ST2, we developed a biochemical homogeneous time resolved fluorescence assay to determine the inhibition of ST2/IL33 binding by five molecules containing an aromatic ring and a charged group. Three molecules, including niacin, salicylic acid, and benzamidine, exhibit inhibition activities at millimolar concentrations. We further employed the computational cosolvent mapping analysis to identify a shared mode of interaction between niacin, salicylic acid, and ST2. The mode of interaction was further confirmed by four analogous compounds that exhibited similar or improved activities. Our study provided the evidence of inhibition of ST2 and IL33 binding by salicylic acid and analogs. The results suggest that biological activity of salicylic acid may be partly mediated through modulating extracellular cytokine receptors and cytokine interaction.
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Affiliation(s)
- Xinrui Yuan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | | | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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11
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Rej RK, Wang C, Lu J, Wang M, Petrunak E, Zawacki KP, McEachern D, Yang CY, Wang L, Li R, Chinnaswamy K, Wen B, Sun D, Stuckey JA, Zhou Y, Chen J, Tang G, Wang S. Discovery of EEDi-5273 as an Exceptionally Potent and Orally Efficacious EED Inhibitor Capable of Achieving Complete and Persistent Tumor Regression. J Med Chem 2021; 64:14540-14556. [PMID: 34613724 DOI: 10.1021/acs.jmedchem.1c01059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Embryonic ectoderm development (EED) is a promising therapeutic target for human cancers and other diseases. We report herein the discovery of exceptionally potent and efficacious EED inhibitors. By conformational restriction of a previously reported EED inhibitor, we obtained a potent lead compound. Further optimization of the lead yielded exceptionally potent EED inhibitors. The best compound EEDi-5273 binds to EED with an IC50 value of 0.2 nM and inhibits the KARPAS422 cell growth with an IC50 value of 1.2 nM. It demonstrates an excellent PK and ADME profile, and its oral administration leads to complete and persistent tumor regression in the KARPAS422 xenograft model with no signs of toxicity. Co-crystal structures of two potent EED inhibitors with EED provide a solid structural basis for their high-affinity binding. EEDi-5273 is a promising EED inhibitor for further advanced preclinical development for the treatment of human cancer and other human diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | | | | | | | | | | | | | - Yunlong Zhou
- Ascentage Pharma Group, Suzhou, Jiangsu 215216, China
| | - Jianyong Chen
- Ascentage Pharma Group, Suzhou, Jiangsu 215216, China
| | - Guozhi Tang
- Ascentage Pharma Group, Suzhou, Jiangsu 215216, China
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12
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Pinter TBJ, Ruckthong L, Stuckey JA, Deb A, Penner-Hahn JE, Pecoraro VL. Open Reading Frame 1 Protein of the Human Long Interspersed Nuclear Element 1 Retrotransposon Binds Multiple Equivalents of Lead. J Am Chem Soc 2021; 143:15271-15278. [PMID: 34494819 DOI: 10.1021/jacs.1c06461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The human long interspersed nuclear element 1 (LINE1) has been implicated in numerous diseases and has been suggested to play a significant role in genetic evolution. Open reading frame 1 protein (ORF1p) is one of the two proteins encoded in this self-replicating mobile genetic element, both of which are essential for retrotransposition. The structure of the three-stranded coiled-coil domain of ORF1p was recently solved and showed the presence of tris-cysteine layers in the interior of the coiled-coil that could function as metal binding sites. Here, we demonstrate that ORF1p binds Pb(II). We designed a model peptide, GRCSL16CL23C, to mimic two of the ORF1p Cys3 layers and crystallized the peptide both as the apo-form and in the presence of Pb(II). Structural comparison of the ORF1p with apo-(GRCSL16CL23C)3 shows very similar Cys3 layers, preorganized for Pb(II) binding. We propose that exposure to heavy metals, such as lead, could influence directly the structural parameters of ORF1p and thus impact the overall LINE1 retrotransposition frequency, directly relating heavy metal exposure to genetic modification.
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Affiliation(s)
- Tyler B J Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Leela Ruckthong
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bang Mod, Thung Khru, Bangkok 10140, Thailand
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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13
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Zhou H, Bai L, Xu R, McEachern D, Chinnaswamy K, Li R, Wen B, Wang M, Yang CY, Meagher JL, Sun D, Stuckey JA, Wang S. SD-91 as A Potent and Selective STAT3 Degrader Capable of Achieving Complete and Long-Lasting Tumor Regression. ACS Med Chem Lett 2021; 12:996-1004. [PMID: 34141084 DOI: 10.1021/acsmedchemlett.1c00155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/05/2021] [Indexed: 11/30/2022] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) is an attractive cancer therapeutic target. We report herein our extensive in vitro and in vivo evaluations of SD-91, the product of the hydrolysis of our previously reported STAT3 degrader SD-36. SD-91 binds to STAT3 protein with a high affinity and displays >300-fold selectivity over other STAT family protein members. SD-91 potently and effectively induces degradation of STAT3 protein and displays a high selectivity over other STAT members and >7000 non-STAT proteins in cells. A single administration of SD-91 selectively depletes STAT3 protein in tumor tissues with a persistent effect. SD-91 achieves complete and long-lasting tumor regression in the MOLM-16 xenograft model in mice even with weekly administration. Hence, SD-91 is a potent, highly selective, and efficacious STAT3 degrader for extensive evaluations for the treatment of human cancers and other diseases for which STAT3 plays a key role.
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14
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Covés-Datson EM, King SR, Legendre M, Swanson MD, Gupta A, Claes S, Meagher JL, Boonen A, Zhang L, Kalveram B, Raglow Z, Freiberg AN, Prichard M, Stuckey JA, Schols D, Markovitz DM. Targeted disruption of pi-pi stacking in Malaysian banana lectin reduces mitogenicity while preserving antiviral activity. Sci Rep 2021; 11:656. [PMID: 33436903 PMCID: PMC7804308 DOI: 10.1038/s41598-020-80577-7] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/21/2020] [Indexed: 11/23/2022] Open
Abstract
Lectins, carbohydrate-binding proteins, have been regarded as potential antiviral agents, as some can bind glycans on viral surface glycoproteins and inactivate their functions. However, clinical development of lectins has been stalled by the mitogenicity of many of these proteins, which is the ability to stimulate deleterious proliferation, especially of immune cells. We previously demonstrated that the mitogenic and antiviral activities of a lectin (banana lectin, BanLec) can be separated via a single amino acid mutation, histidine to threonine at position 84 (H84T), within the third Greek key. The resulting lectin, H84T BanLec, is virtually non-mitogenic but retains antiviral activity. Decreased mitogenicity was associated with disruption of pi-pi stacking between two aromatic amino acids. To examine whether we could provide further proof-of-principle of the ability to separate these two distinct lectin functions, we identified another lectin, Malaysian banana lectin (Malay BanLec), with similar structural features as BanLec, including pi-pi stacking, but with only 63% amino acid identity, and showed that it is both mitogenic and potently antiviral. We then engineered an F84T mutation expected to disrupt pi-pi stacking, analogous to H84T. As predicted, F84T Malay BanLec (F84T) was less mitogenic than wild type. However, F84T maintained strong antiviral activity and inhibited replication of HIV, Ebola, and other viruses. The F84T mutation disrupted pi-pi stacking without disrupting the overall lectin structure. These findings show that pi-pi stacking in the third Greek key is a conserved mitogenic motif in these two jacalin-related lectins BanLec and Malay BanLec, and further highlight the potential to rationally engineer antiviral lectins for therapeutic purposes.
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Affiliation(s)
- Evelyn M Covés-Datson
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Steven R King
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maureen Legendre
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Michael D Swanson
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
- Predictive and Clinical Immunogenicity, Merck and Co., Inc, Kenilworth, NJ, 07033, USA
| | - Auroni Gupta
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sandra Claes
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, University of Leuven, 3000, Leuven, Belgium
| | - Jennifer L Meagher
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arnaud Boonen
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, University of Leuven, 3000, Leuven, Belgium
| | - Lihong Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Birte Kalveram
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Zoe Raglow
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alexander N Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Mark Prichard
- University of Alabama Health Services Foundation Diagnostic Virology Laboratory, University of Alabama, Birmingham, AL, 35294, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, University of Leuven, 3000, Leuven, Belgium
| | - David M Markovitz
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
- Cancer Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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15
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Kump KJ, Miao L, Mady AA, Ansari NH, Shrestha UK, Yang Y, Pal M, Liao C, Perdih A, Abulwerdi FA, Chinnaswamy K, Meagher JL, Carlson JM, Khanna M, Stuckey JA, Nikolovska-Coleska Z. Abstract LB-226: Discovery of small molecule Mcl-1 and Bfl-1 inhibitors. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-lb-226] [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
Anti-apoptotic Bcl-2 family proteins are frequently overexpressed in various cancers and are established therapeutic targets. Cancer cells can either display dependence on individual or subsets of these pro-survival proteins, which gives therapeutic relevance to both selective and multimodal inhibitors. Selective Bcl-2, Bcl-xL, and Mcl-1 inhibitors are being evaluated clinically in a wide spectrum of cancers. Bfl-1 is another homologous anti-apoptotic protein with closest structural relation to Mcl-1, but drug discovery efforts on this protein have been limited to peptide inhibitors. There is increasing evidence of Bfl-1 being a viable therapeutic target, particularly in the context of drug resistance. Both Mcl-1 and Bfl-1 share the selective endogenous binding partner, Noxa, which highlights the relevance of these proteins being therapeutically co-inhibited, especially in cancers where they are commonly overexpressed together. Mcl-1 and Bfl-1 have emerged as key players in melanoma, associated with poor clinical responses to BRAF/MEK pathway inhibitors and cell death resistance, thus representing attractive new therapeutic targets.We report herein the structure-based design, synthesis, SAR, and biological characterization of dual inhibitors displaying equipotent binding to Mcl-1 and Bfl-1. This class of inhibitors was designed based on the validated hit molecule identified in our recently reported integrated high throughput and virtual screening study. Several co-crystal structures of these molecules were solved, which guided the structure-based design efforts and led to the optimization of compounds that bind both Mcl-1 and Bfl-1 with Ki values in the 100 nM range and >250-fold selectivity over Bcl-2/Bcl-xL. Direct binding of optimized inhibitors to the Mcl-1 and Bfl-1 proteins was validated by several biophysical methods, including HSQC-NMR, and bio-layer interferometry (BLI). Selectivity over Bcl-2/Bcl-xL was demonstrated on the cellular level by the ability to selectively bind endogenous Mcl-1 and Bfl-1 and disrupt interactions with Bim. On-target cellular activity was further confirmed using Eµ-Myc lymphoma cell lines, which stably overexpress individual anti-apoptotic Bcl-2 proteins with a strong survival dependence on each of these targets. Eµ-Myc cells overexpressing Mcl-1 and Bfl-1 showed dose-dependent cell death in response to treatment with the most potent compounds, while cells overexpressing Bcl-2 and Bcl-xL were not affected even at the highest tested concentration, further demonstrating the selective targeting of Mcl-1 and Bfl-1. With a selective set of chemical tools, we employed the BH3 profiling assay across a panel of melanoma cell lines in order to functionally dissect survival dependence. The obtained data suggests that melanoma cell lines mainly rely on Bcl-xL and Mcl-1, with certain cell lines displaying increased involvement of Bfl-1. Importantly, the vemurafenib resistant SK-MEL-239 melanoma cell line showed increased functional Mcl-1 and Bfl-1 dependence compared to the parental line. Overall, this work contributes to the drug discovery efforts of Bcl-2 family inhibitors and provides novel dual Mcl-1/Bfl-1 selective inhibitors. Further optimization of these dual inhibitors may provide valuable therapeutics to help combat acquired resistance in melanoma, where Mcl-1 and Bfl-1 play prominent functional roles, as determined by BH3 profiling.
Citation Format: Karson J. Kump, Lei Miao, Ahmed A. Mady, Nurul H. Ansari, Uttar K. Shrestha, Yuting Yang, Mohan Pal, Chenzhong Liao, Andrej Perdih, Fardokht A. Abulwerdi, Krishnapriya Chinnaswamy, Jennifer L. Meagher, Jacob M. Carlson, May Khanna, Jeanne A. Stuckey, Zaneta Nikolovska-Coleska. Discovery of small molecule Mcl-1 and Bfl-1 inhibitors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-226.
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Affiliation(s)
| | - Lei Miao
- 1University of Michigan, Ann Arbor, MI
| | | | | | | | | | - Mohan Pal
- 1University of Michigan, Ann Arbor, MI
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16
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Chern TR, Liu L, Petrunak E, Stuckey JA, Wang M, Bernard D, Zhou H, Lee S, Dou Y, Wang S. Discovery of Potent Small-Molecule Inhibitors of MLL Methyltransferase. ACS Med Chem Lett 2020; 11:1348-1352. [PMID: 32551023 DOI: 10.1021/acsmedchemlett.0c00229] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
The mixed-lineage leukemia (MLL) protein, also known as MLL1, is a lysine methyltransferase specifically responsible for methylation of histone 3 lysine 4. MLL has been pursued as an attractive therapeutic target for the treatment of acute leukemia carrying the MLL fusion gene or MLL leukemia. Herein, we report the design, synthesis, and evaluation of an S-adenosylmethionine-based focused chemical library which led to the discovery of potent small-molecule inhibitors directly targeting the MLL SET domain. Determination of cocrystal structures for a number of these MLL inhibitors reveals that they adopt a unique binding mode that locks the MLL SET domain in an open, inactive conformation.
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17
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Tolbert AE, Ervin CS, Ruckthong L, Paul TJ, Jayasinghe-Arachchige VM, Neupane KP, Stuckey JA, Prabhakar R, Pecoraro VL. Heteromeric three-stranded coiled coils designed using a Pb(II)(Cys) 3 template mediated strategy. Nat Chem 2020; 12:405-411. [PMID: 32123337 DOI: 10.1038/s41557-020-0423-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/19/2020] [Indexed: 11/09/2022]
Abstract
Three-stranded coiled coils are peptide structures constructed from amphipathic heptad repeats. Here we show that it is possible to form pure heterotrimeric three-stranded coiled coils by combining three distinct characteristics: (1) a cysteine sulfur layer for metal coordination, (2) a thiophilic, trigonal pyramidal metalloid (Pb(II)) that binds to these sulfurs and (3) an adjacent layer of reduced steric bulk generating a cavity where water can hydrogen bond to the cysteine sulfur atoms. Cysteine substitution in an a site yields Pb(II)A2B heterotrimers, while d sites provide pure Pb(II)C2D or Pb(II)CD2 scaffolds. Altering the metal from Pb(II) to Hg(II) or shifting the relative position of the sterically less demanding layer removes heterotrimer specificity. Because only two of the eight or ten hydrophobic layers are perturbed, catalytic sites can be introduced at other regions of the scaffold. A Zn(II)(histidine)3(H2O) centre can be incorporated at a remote location without perturbing the heterotrimer selectivity, suggesting a unique strategy to prepare dissymmetric catalytic sites within self-assembling de novo-designed proteins.
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Affiliation(s)
- Audrey E Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Leela Ruckthong
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok, Thailand
| | - Thomas J Paul
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | | | - Kosh P Neupane
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA. .,Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
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18
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Kump KJ, Miao L, Mady ASA, Ansari NH, Shrestha UK, Yang Y, Pal M, Liao C, Perdih A, Abulwerdi FA, Chinnaswamy K, Meagher JL, Carlson JM, Khanna M, Stuckey JA, Nikolovska-Coleska Z. Discovery and Characterization of 2,5-Substituted Benzoic Acid Dual Inhibitors of the Anti-apoptotic Mcl-1 and Bfl-1 Proteins. J Med Chem 2020; 63:2489-2510. [PMID: 31971799 DOI: 10.1021/acs.jmedchem.9b01442] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Anti-apoptotic Bcl-2 family proteins are overexpressed in a wide spectrum of cancers and have become well validated therapeutic targets. Cancer cells display survival dependence on individual or subsets of anti-apoptotic proteins that could be effectively targeted by multimodal inhibitors. We designed a 2,5-substituted benzoic acid scaffold that displayed equipotent binding to Mcl-1 and Bfl-1. Structure-based design was guided by several solved cocrystal structures with Mcl-1, leading to the development of compound 24, which binds both Mcl-1 and Bfl-1 with Ki values of 100 nM and shows appreciable selectivity over Bcl-2/Bcl-xL. The selective binding profile of 24 was translated to on-target cellular activity in model lymphoma cell lines. These studies lay a foundation for developing more advanced dual Mcl-1/Bfl-1 inhibitors that have potential to provide greater single agent efficacy and broader coverage to combat resistance in several types of cancer than selective Mcl-1 inhibitors alone.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Andrej Perdih
- National Institute of Chemistry, Ljubljana 1000, Slovenia
| | | | | | | | - Jacob M Carlson
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States.,Center for Innovation in Brain Science, Tucson, Arizona 85721, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States.,Center for Innovation in Brain Science, Tucson, Arizona 85721, United States
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19
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Zhou H, Bai L, Xu R, Zhao Y, Chen J, McEachern D, Chinnaswamy K, Wen B, Dai L, Kumar P, Yang CY, Liu Z, Wang M, Liu L, Meagher JL, Yi H, Sun D, Stuckey JA, Wang S. Structure-Based Discovery of SD-36 as a Potent, Selective, and Efficacious PROTAC Degrader of STAT3 Protein. J Med Chem 2019; 62:11280-11300. [PMID: 31747516 DOI: 10.1021/acs.jmedchem.9b01530] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Signal transducer and activator of transcription 3 (STAT3) is a transcription factor and an attractive therapeutic target for cancer and other human diseases. Despite 20 years of persistent research efforts, targeting STAT3 has been very challenging. We report herein the structure-based discovery of potent small-molecule STAT3 degraders based upon the proteolysis targeting chimera (PROTAC) concept. We first designed SI-109 as a potent, small-molecule inhibitor of the STAT3 SH2 domain. Employing ligands for cereblon/cullin 4A E3 ligase and SI-109, we obtained a series of potent PROTAC STAT3 degraders, exemplified by SD-36. SD-36 induces rapid STAT3 degradation at low nanomolar concentrations in cells and fails to degrade other STAT proteins. SD-36 achieves nanomolar cell growth inhibitory activity in leukemia and lymphoma cell lines with high levels of phosphorylated STAT3. A single dose of SD-36 results in complete STAT3 protein degradation in xenograft tumor tissue and normal mouse tissues. SD-36 achieves complete and long-lasting tumor regression in the Molm-16 xenograft tumor model at well-tolerated dose-schedules. SD-36 is a potent, selective, and efficacious STAT3 degrader.
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20
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Bai L, Zhou H, Xu R, Zhao Y, Chinnaswamy K, McEachern D, Chen J, Yang CY, Liu Z, Wang M, Liu L, Jiang H, Wen B, Kumar P, Meagher JL, Sun D, Stuckey JA, Wang S. A Potent and Selective Small-Molecule Degrader of STAT3 Achieves Complete Tumor Regression In Vivo. Cancer Cell 2019; 36:498-511.e17. [PMID: 31715132 PMCID: PMC6880868 DOI: 10.1016/j.ccell.2019.10.002] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/14/2019] [Accepted: 10/07/2019] [Indexed: 01/21/2023]
Abstract
Signal transducer and activator of transcription 3 (STAT3) is an attractive cancer therapeutic target. Here we report the discovery of SD-36, a small-molecule degrader of STAT3. SD-36 potently induces the degradation of STAT3 protein in vitro and in vivo and demonstrates high selectivity over other STAT members. Induced degradation of STAT3 results in a strong suppression of its transcription network in leukemia and lymphoma cells. SD-36 inhibits the growth of a subset of acute myeloid leukemia and anaplastic large-cell lymphoma cell lines by inducing cell-cycle arrest and/or apoptosis. SD-36 achieves complete and long-lasting tumor regression in multiple xenograft mouse models at well-tolerated dose schedules. Degradation of STAT3 protein, therefore, is a promising cancer therapeutic strategy.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Apoptosis/drug effects
- Apoptosis/genetics
- Cell Cycle Checkpoints/drug effects
- Cell Cycle Checkpoints/genetics
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Lymphoma, Large-Cell, Anaplastic/drug therapy
- Lymphoma, Large-Cell, Anaplastic/genetics
- Lymphoma, Large-Cell, Anaplastic/pathology
- Mice
- Proteolysis/drug effects
- STAT3 Transcription Factor/antagonists & inhibitors
- STAT3 Transcription Factor/metabolism
- Tumor Burden/drug effects
- Tumor Burden/genetics
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Longchuan Bai
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Haibin Zhou
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Renqi Xu
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yujun Zhao
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Donna McEachern
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianyong Chen
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chao-Yie Yang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhaomin Liu
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mi Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liu Liu
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui Jiang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bo Wen
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Praveen Kumar
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer L Meagher
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Duxin Sun
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeanne A Stuckey
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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21
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Ruckthong L, Stuckey JA, Pecoraro VL. How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation. Chemistry 2019; 25:6773-6787. [PMID: 30861211 PMCID: PMC6510599 DOI: 10.1002/chem.201806040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Indexed: 11/06/2022]
Abstract
A challenging objective of de novo metalloprotein design is to control of the outer coordination spheres of an active site to fine tune metal properties. The well-defined three stranded coiled coils, TRI and CoilSer peptides, are used to address this question. Substitution of Cys for Leu yields a thiophilic site within the core. Metals such as HgII , PbII , and AsIII result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies have shown that CdII forms three-, four- or five-coordinate CdII S3 (OH2 )x (in which x=0-2) when the outer coordination spheres are perturbed. Unfortunately, there has been little crystallographic examination of these proteins to explain the observations. Here, the high-resolution X-ray structures of apo- and mercurated proteins are compared to explain the modifications that lead to metal coordination number and geometry variation. It reveals that Ala substitution for Leu opens a cavity above the Cys site allowing for water excess, facilitating CdII S3 (OH2 ). Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal-binding plane, which displaces water, forming CdII S3 . Residue d-Leu, above the Cys site, reorients the side chain towards the Cys layer, diminishing the space for water accommodation yielding CdII S3 , whereas d-Leu below opens more space, allowing for equal CdII S3 (OH2 ) and CdII S3 (OH2 )2 . These studies provide insights into how to control desired metal geometries in metalloproteins by using coded and non-coded amino acids.
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Affiliation(s)
- Leela Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology, Thonburi (KMUTT), Bang Mod, Thung Khru, Bangkok, 10140, Thailand
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
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22
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Dai W, Samanta S, Xue D, Petrunak EM, Stuckey JA, Han Y, Sun D, Wu Y, Neamati N. Structure-Based Design of N-(5-Phenylthiazol-2-yl)acrylamides as Novel and Potent Glutathione S-Transferase Omega 1 Inhibitors. J Med Chem 2019; 62:3068-3087. [PMID: 30735370 DOI: 10.1021/acs.jmedchem.8b01960] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Weiyang Dai
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, No. 17 People’s South Road, Chengdu 610041, P. R. China
| | | | | | - Elyse M. Petrunak
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne A. Stuckey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | - Yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, No. 17 People’s South Road, Chengdu 610041, P. R. China
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23
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Penumutchu S, Chiu LY, Meagher JL, Hansen AL, Stuckey JA, Tolbert BS. Differential Conformational Dynamics Encoded by the Linker between Quasi RNA Recognition Motifs of Heterogeneous Nuclear Ribonucleoprotein H. J Am Chem Soc 2018; 140:11661-11673. [PMID: 30122033 PMCID: PMC6648666 DOI: 10.1021/jacs.8b05366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 01/07/2023]
Abstract
Members of the heterogeneous nuclear ribonucleoprotein (hnRNP) F/H family are multipurpose RNA binding proteins that participate in most stages of RNA metabolism. Despite having similar RNA sequence preferences, hnRNP F/H proteins function in overlapping and, in some cases, distinct cellular processes. The domain organization of hnRNP F/H proteins is modular, consisting of N-terminal tandem quasi-RNA recognition motifs (F/HqRRM1,2) and a third C-terminal qRRM3 embedded between glycine-rich repeats. The tandem qRRMs are connected through a 10-residue linker, with several amino acids strictly conserved between hnRNP H and F. A significant difference occurs at position 105 of the linker, where hnRNP H contains a proline and hnRNP F an alanine. To investigate the influence of P105 on the conformational properties of hnRNP H, we probed the structural dynamics of its HqRRM1,2 domain with X-ray crystallography, NMR spectroscopy, and small-angle X-ray scattering. The collective results best describe that HqRRM1,2 exists in a conformational equilibrium between compact and extended structures. The compact structure displays an electropositive surface formed at the qRRM1-qRRM2 interface. Comparison of NMR relaxation parameters, including Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion, between HqRRM1,2 and FqRRM1,2 indicates that FqRRM1,2 primarily adopts a more extended and flexible conformation. Introducing the P105A mutation into HqRRM1,2 alters its conformational dynamics to favor an extended structure. Thus, our work demonstrates that the linker compositions confer different structural properties between hnRNP F/H family members that might contribute to their functional diversity.
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Affiliation(s)
- Srinivasa
R. Penumutchu
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Liang-Yuan Chiu
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Jennifer L. Meagher
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexandar L. Hansen
- Campus
Chemical Instrument Center, The Ohio State
University, Columbus, Ohio 43210, United States
| | - Jeanne A. Stuckey
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Blanton S. Tolbert
- Department
of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States,
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24
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Koebke KJ, Ruckthong L, Meagher JL, Mathieu E, Harland J, Deb A, Lehnert N, Policar C, Tard C, Penner-Hahn JE, Stuckey JA, Pecoraro VL. Clarifying the Copper Coordination Environment in a de Novo Designed Red Copper Protein. Inorg Chem 2018; 57:12291-12302. [PMID: 30226758 DOI: 10.1021/acs.inorgchem.8b01989] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cupredoxins are copper-dependent electron-transfer proteins that can be categorized as blue, purple, green, and red depending on the spectroscopic properties of the Cu(II) bound forms. Interestingly, despite significantly different first coordination spheres and nuclearity, all cupredoxins share a common Greek Key β-sheet fold. We have previously reported the design of a red copper protein within a completely distinct three-helical bundle protein, α3DChC2. (1) While this design demonstrated that a β-barrel fold was not requisite to recapitulate the properties of a native cupredoxin center, the parent peptide α3D was not sufficiently stable to allow further study through additional mutations. Here we present the design of an elongated protein GRANDα3D (GRα3D) with Δ Gu = -11.4 kcal/mol compared to the original design's -5.1 kcal/mol. Diffraction quality crystals were grown of GRα3D (a first for an α3D peptide) and solved to a resolution of 1.34 Å. Examination of this structure suggested that Glu41 might interact with the Cu in our previously reported red copper protein. The previous bis(histidine)(cysteine) site (GRα3DChC2) was designed into this new scaffold and a series of variant constructs were made to explore this hypothesis. Mutation studies around Glu41 not only prove the proposed interaction, but also enabled tuning of the constructs' hyperfine coupling constant from 160 to 127 × 10-4 cm-1. X-ray absorption spectroscopy analysis is consistent with these hyperfine coupling differences being the result of variant 4p mixing related to coordination geometry changes. These studies not only prove that an Glu41-Cu interaction leads to the α3DChC2 construct's red copper protein like spectral properties, but also exemplify the exact control one can have in a de novo construct to tune the properties of an electron-transfer Cu site.
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Affiliation(s)
| | | | | | - Emilie Mathieu
- Laboratoire des biomolécules, LBM, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | | | | | | | - Clotilde Policar
- Laboratoire des biomolécules, LBM, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Cédric Tard
- LCM, CNRS, Ecole Polytechnique , Université Paris-Saclay , 91128 Palaiseau Cedex , France
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25
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Ramadan AM, Daguindau E, Rech JC, Chinnaswamy K, Zhang J, Hura GL, Griesenauer B, Bolten Z, Robida A, Larsen M, Stuckey JA, Yang CY, Paczesny S. From proteomics to discovery of first-in-class ST2 inhibitors active in vivo. JCI Insight 2018; 3:99208. [PMID: 30046004 DOI: 10.1172/jci.insight.99208] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 12/11/2017] [Accepted: 06/12/2018] [Indexed: 12/19/2022] Open
Abstract
Soluble cytokine receptors function as decoy receptors to attenuate cytokine-mediated signaling and modulate downstream cellular responses. Dysregulated overproduction of soluble receptors can be pathological, such as soluble ST2 (sST2), a prognostic biomarker in cardiovascular diseases, ulcerative colitis, and graft-versus-host disease (GVHD). Although intervention using an ST2 antibody improves survival in murine GVHD models, sST2 is a challenging target for drug development because it binds to IL-33 via an extensive interaction interface. Here, we report the discovery of small-molecule ST2 inhibitors through a combination of high-throughput screening and computational analysis. After in vitro and in vivo toxicity assessment, 3 compounds were selected for evaluation in 2 experimental GVHD models. We show that the most effective compound, iST2-1, reduces plasma sST2 levels, alleviates disease symptoms, improves survival, and maintains graft-versus-leukemia activity. Our data suggest that iST2-1 warrants further optimization to develop treatment for inflammatory diseases mediated by sST2.
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Affiliation(s)
- Abdulraouf M Ramadan
- Department of Pediatrics and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Etienne Daguindau
- Department of Pediatrics and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jason C Rech
- Department of Internal Medicine, Hematology and Oncology Division, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Jilu Zhang
- Department of Pediatrics and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Greg L Hura
- Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Brad Griesenauer
- Department of Pediatrics and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Zachary Bolten
- Department of Pediatrics and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Aaron Robida
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Martha Larsen
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Chao-Yie Yang
- Department of Internal Medicine, Hematology and Oncology Division, University of Michigan, Ann Arbor, Michigan, USA
| | - Sophie Paczesny
- Department of Pediatrics and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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26
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Zhao Y, Zhou B, Bai L, Liu L, Yang CY, Meagher JL, Stuckey JA, McEachern D, Przybranowski S, Wang M, Ran X, Aguilar A, Hu Y, Kampf JW, Li X, Zhao T, Li S, Wen B, Sun D, Wang S. Structure-Based Discovery of CF53 as a Potent and Orally Bioavailable Bromodomain and Extra-Terminal (BET) Bromodomain Inhibitor. J Med Chem 2018; 61:6110-6120. [PMID: 30015487 DOI: 10.1021/acs.jmedchem.8b00483] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the structure-based discovery of CF53 (28) as a highly potent and orally active inhibitor of bromodomain and extra-terminal (BET) proteins. By the incorporation of a NH-pyrazole group into the 9H-pyrimido[4,5- b]indole core, we identified a series of compounds that bind to BRD4 BD1 protein with Ki values of <1 nM and achieve low nanomolar potencies in the cell growth inhibition of leukemia and breast cancer cells. The most-promising compound, CF53, possesses excellent oral pharmacokinetic properties and achieves significant antitumor activity in both triple-negative breast cancer and acute leukemia xenograft models in mice. Determination of the co-crystal structure of CF53 with the BRD4 BD1 protein provides a structural basis for its high binding affinity to BET proteins. CF53 is very selective over non-BET bromodomain-containing proteins. These data establish CF53 as a potent, selective, and orally active BET inhibitor, which warrants further evaluation for advanced preclinical development.
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27
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Mady ASA, Liao C, Bajwa N, Kump KJ, Abulwerdi FA, Lev KL, Miao L, Grigsby SM, Perdih A, Stuckey JA, Du Y, Fu H, Nikolovska-Coleska Z. Discovery of Mcl-1 inhibitors from integrated high throughput and virtual screening. Sci Rep 2018; 8:10210. [PMID: 29976942 PMCID: PMC6033896 DOI: 10.1038/s41598-018-27899-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 03/09/2018] [Accepted: 06/05/2018] [Indexed: 02/06/2023] Open
Abstract
Protein-protein interactions (PPIs) represent important and promising therapeutic targets that are associated with the regulation of various molecular pathways, particularly in cancer. Although they were once considered “undruggable,” the recent advances in screening strategies, structure-based design, and elucidating the nature of hot spots on PPI interfaces, have led to the discovery and development of successful small-molecule inhibitors. In this report, we are describing an integrated high-throughput and computational screening approach to enable the discovery of small-molecule PPI inhibitors of the anti-apoptotic protein, Mcl-1. Applying this strategy, followed by biochemical, biophysical, and biological characterization, nineteen new chemical scaffolds were discovered and validated as Mcl-1 inhibitors. A novel series of Mcl-1 inhibitors was designed and synthesized based on the identified difuryl-triazine core scaffold and structure-activity studies were undertaken to improve the binding affinity to Mcl-1. Compounds with improved in vitro binding potency demonstrated on-target activity in cell-based studies. The obtained results demonstrate that structure-based analysis complements the experimental high-throughput screening in identifying novel PPI inhibitor scaffolds and guides follow-up medicinal chemistry efforts. Furthermore, our work provides an example that can be applied to the analysis of available screening data against numerous targets in the PubChem BioAssay Database, leading to the identification of promising lead compounds, fuelling drug discovery pipelines.
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Affiliation(s)
- Ahmed S A Mady
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Interdepartmental Graduate Program in Medicinal Chemistry, University of Michigan, College of Pharmacy, Ann Arbor, MI, USA
| | - Chenzhong Liao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,School of Medical Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China
| | - Naval Bajwa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Pfizer Inc, Lake Forest, IL, 60045, USA
| | - Karson J Kump
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Fardokht A Abulwerdi
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Interdepartmental Graduate Program in Medicinal Chemistry, University of Michigan, College of Pharmacy, Ann Arbor, MI, USA.,Basic Research Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Katherine L Lev
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lei Miao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sierrah M Grigsby
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Andrej Perdih
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Yuhong Du
- Department of Pharmacology, Emory University, Atlanta, GA, USA
| | - Haian Fu
- Department of Pharmacology, Emory University, Atlanta, GA, USA
| | - Zaneta Nikolovska-Coleska
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA. .,Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA. .,Interdepartmental Graduate Program in Medicinal Chemistry, University of Michigan, College of Pharmacy, Ann Arbor, MI, USA. .,Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.
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28
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Madak JT, Cuthbertson CR, Miyata Y, Tamura S, Petrunak EM, Stuckey JA, Han Y, He M, Sun D, Showalter HD, Neamati N. Design, Synthesis, and Biological Evaluation of 4-Quinoline Carboxylic Acids as Inhibitors of Dihydroorotate Dehydrogenase. J Med Chem 2018; 61:5162-5186. [PMID: 29727569 DOI: 10.1021/acs.jmedchem.7b01862] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We pursued a structure-guided approach toward the development of improved dihydroorotate dehydrogenase (DHODH) inhibitors with the goal of forming new interactions between DHODH and the brequinar class of inhibitors. Two potential residues, T63 and Y356, suitable for novel H-bonding interactions, were identified in the brequinar-binding pocket. Analogues were designed to maintain the essential pharmacophore and form new electrostatic interactions through strategically positioned H-bond accepting groups. This effort led to the discovery of potent quinoline-based analogues 41 (DHODH IC50 = 9.71 ± 1.4 nM) and 43 (DHODH IC50 = 26.2 ± 1.8 nM). A cocrystal structure between 43 and DHODH depicts a novel water mediated H-bond interaction with T63. Additional optimization led to the 1,7-naphthyridine 46 (DHODH IC50 = 28.3 ± 3.3 nM) that forms a novel H-bond with Y356. Importantly, compound 41 possesses significant oral bioavailability ( F = 56%) and an elimination t1/2 = 2.78 h (PO dosing). In conclusion, the data supports further preclinical studies of our lead compounds toward selection of a candidate for early-stage clinical development.
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Affiliation(s)
| | | | | | | | - Elyse M Petrunak
- Life Sciences Institute and Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Jeanne A Stuckey
- Life Sciences Institute and Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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29
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Moody RR, Lo MC, Meagher JL, Lin CC, Stevers NO, Tinsley SL, Jung I, Matvekas A, Stuckey JA, Sun D. Probing the interaction between the histone methyltransferase/deacetylase subunit RBBP4/7 and the transcription factor BCL11A in epigenetic complexes. J Biol Chem 2018; 293:2125-2136. [PMID: 29263092 PMCID: PMC5808772 DOI: 10.1074/jbc.m117.811463] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [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: 08/10/2017] [Revised: 12/14/2017] [Indexed: 01/07/2023] Open
Abstract
The transcription factor BCL11A has recently been reported to be a driving force in triple-negative breast cancer (TNBC), contributing to the maintenance of a chemoresistant breast cancer stem cell (BCSC) population. Although BCL11A was shown to suppress γ-globin and p21 and to induce MDM2 expression in the hematopoietic system, its downstream targets in TNBC are still unclear. For its role in transcriptional repression, BCL11A was found to interact with several corepressor complexes; however, the mechanisms underlying these interactions remain unknown. Here, we reveal that BCL11A interacts with histone methyltransferase (PRC2) and histone deacetylase (NuRD and SIN3A) complexes through their common subunit, RBBP4/7. In fluorescence polarization assays, we show that BCL11A competes with histone H3 for binding to the negatively charged top face of RBBP4. To define that interaction, we solved the crystal structure of RBBP4 in complex with an N-terminal peptide of BCL11A (residues 2-16, BCL11A(2-16)). The crystal structure identifies novel interactions between BCL11A and the side of the β-propeller of RBBP4 that are not seen with histone H3. We next show that BCL11A(2-16) pulls down RBBP4, RBBP7, and other components of PRC2, NuRD, and SIN3A from the cell lysate of the TNBC cell line SUM149. Furthermore, we demonstrate the therapeutic potential of targeting the RBBP4-BCL11A binding by showing that a BCL11A peptide can decrease aldehyde dehydrogenase-positive BCSCs and mammosphere formation capacity in SUM149. Together, our findings have uncovered a previously unidentified mechanism that BCL11A may use to recruit epigenetic complexes to regulate transcription and promote tumorigenesis.
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Affiliation(s)
- Rebecca Reed Moody
- From the Chemical Biology Program, ,Department of Pharmaceutical Sciences, College of Pharmacy
| | - Miao-Chia Lo
- Department of Pharmaceutical Sciences, College of Pharmacy, , To whom correspondence may be addressed. Tel.:
858-784-1624; Fax:
734-936-7675; E-mail:
| | | | | | | | | | - Inkyung Jung
- Department of Pharmaceutical Sciences, College of Pharmacy
| | | | - Jeanne A. Stuckey
- Life Sciences Institute, and ,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Duxin Sun
- From the Chemical Biology Program, ,Department of Pharmaceutical Sciences, College of Pharmacy, , To whom correspondence may be addressed. Tel.:
734-615-8740; Fax:
734-936-7675; E-mail:
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30
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Stevers NO, Tinsley SL, Moody R, Lin CC, Meagher J, Stuckey JA, Lo MC, Sun D. Abstract 4495: Elucidating BCL11A’s function in triple negative breast cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4495] [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
It has been recently shown that the B-cell CLL/lymphoma 11A (BCL11A) transcription factor is highly expressed in triple-negative breast cancer (TNBC) and has critical functions in promoting tumor growth and mammary stem cell maintenance. Studies in our group have found that the first twelve amino acids (aa 1-12) of BCL11A are a conserved sequence that allows binding to retinoblastoma binding protein 4 (RBBP4). RBBP4, a histone binding protein, is involved in many epigenetic complexes, including the Polycomb repressive complex 2 (PRC2), the nucleosome remodeling and deacetylase (NuRD) complex, and SIN3A complex. Through these interactions BCL11A may exert transcriptional and epigenetic regulation.
Herein we investigate the importance of BCL11A’s interaction with RBBP4 and its function in TNBC. BCL11A-complex interactions were observed through pull-down experiments of TNBC cell lysate utilizing aa 2-16 of BCL11A and a scramble control sequence. Our results demonstrate that this 16-amino acid sequence is sufficient to bind to RBBP4 and pull down the PRC2, NuRD, and SIN3A complexes. Furthermore, the NuRD and Sin3a complexes pulled down by BCL11A aa 2-16 retained their functionality as observed through post pull-down histone deacetylase (HDAC) activity assays. These results indicate significantly higher HDAC activity in the wildtype sequence as compared to the scrambled sequence. To further investigate this interaction, protein crystallization was conducted, the results of which validate the binding between BCL11A and RBBP4. Additionally, a BCL11A peptide (aa 2-12) and a scramble control were transfected into the TNBC cell line SUM149. Analysis via flow cytometry shows a reduction of the ALDH+ cell population in the BCL11A peptide transfected cells versus scramble control. We are currently investigating the necessity of this 12-amino acid sequence in interactions with RBBP4, PRC2, NuRD and SIN3A via co-Immunoprecipitation experiments using an N-terminal truncated BCL11A protein (del 2-12). The effects of full-length BCL11A and del 2-12 on the ALDH+ cell population are also being examined. These experiments will further delineate this sequence’s importance in BCL11A-RBBP4 interactions.
Citation Format: Nicholas O. Stevers, Samantha L. Tinsley, Rebecca Moody, Chang-Ching Lin, Jennifer Meagher, Jeanne A. Stuckey, Miao-Chia Lo, Duxin Sun. Elucidating BCL11A’s function in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4495. doi:10.1158/1538-7445.AM2017-4495
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31
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Karatas H, Li Y, Liu L, Ji J, Lee S, Chen Y, Yang J, Huang L, Bernard D, Xu J, Townsend EC, Cao F, Ran X, Li X, Wen B, Sun D, Stuckey JA, Lei M, Dou Y, Wang S. Discovery of a Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (MM-589) Targeting the WD Repeat Domain 5 Protein (WDR5)-Mixed Lineage Leukemia (MLL) Protein-Protein Interaction. J Med Chem 2017; 60:4818-4839. [PMID: 28603984 DOI: 10.1021/acs.jmedchem.6b01796] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report herein the design, synthesis, and evaluation of macrocyclic peptidomimetics that bind to WD repeat domain 5 (WDR5) and block the WDR5-mixed lineage leukemia (MLL) protein-protein interaction. Compound 18 (MM-589) binds to WDR5 with an IC50 value of 0.90 nM (Ki value <1 nM) and inhibits the MLL H3K4 methyltransferase (HMT) activity with an IC50 value of 12.7 nM. Compound 18 potently and selectively inhibits cell growth in human leukemia cell lines harboring MLL translocations and is >40 times better than the previously reported compound MM-401. Cocrystal structures of 16 and 18 complexed with WDR5 provide structural basis for their high affinity binding to WDR5. Additionally, we have developed and optimized a new AlphaLISA-based MLL HMT functional assay to facilitate the functional evaluation of these designed compounds. Compound 18 represents the most potent inhibitor of the WDR5-MLL interaction reported to date, and further optimization of 18 may yield a new therapy for acute leukemia.
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Affiliation(s)
- Hacer Karatas
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Yangbing Li
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Liu Liu
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jiao Ji
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Shirley Lee
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Yong Chen
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jiuling Yang
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Liyue Huang
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Denzil Bernard
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jing Xu
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Elizabeth C Townsend
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Fang Cao
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Xu Ran
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Xiaoqin Li
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Bo Wen
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Duxin Sun
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jeanne A Stuckey
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Ming Lei
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Yali Dou
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- Department of Medicinal Chemistry, ‡Department of Internal Medicine, §Comprehensive Cancer Center, ∥Department of Pathology, ⊥Howard Hughes Medical Institute, #Department of Biological Chemistry, ∇Department of Pharmaceutical Sciences, ○Department of Pharmacology, and ¶Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
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32
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Ruckthong L, Peacock AFA, Pascoe CE, Hemmingsen L, Stuckey JA, Pecoraro VL. d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils. Chemistry 2017; 23:8232-8243. [PMID: 28384393 DOI: 10.1002/chem.201700660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Indexed: 12/31/2022]
Abstract
Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by X-ray crystallography that d-Cys side chains are preorganized within a suitable geometry to bind such a ligand. This is confirmed by comparison of the structure of ZnII Cl(CSL16D C)32- to the published structure of ZnII (H2 O)(GRAND-CSL12AL16L C)3- . Moreover, spectroscopic analysis indicates that the CdII geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate CdII ) is altered to a single four-coordinate species when d-Cys is present. This work opens a new avenue for the control of the metal site environment in man-made proteins, by simply altering the binding ligand with its mirror-imaged d configuration. Thus, the use of non-coded amino acids in the coordination sphere of a metal promises to be a powerful tool for controlling the properties of future metalloproteins.
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Affiliation(s)
- Leela Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: Department Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bang Mod, ThungKhru, Bangkok, 10140, Thailand
| | - Anna F A Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Cherilyn E Pascoe
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
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33
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Zhao Y, Bai L, Liu L, McEachern D, Stuckey JA, Meagher JL, Yang CY, Ran X, Zhou B, Hu Y, Li X, Wen B, Zhao T, Li S, Sun D, Wang S. Structure-Based Discovery of 4-(6-Methoxy-2-methyl-4-(quinolin-4-yl)-9H-pyrimido[4,5-b]indol-7-yl)-3,5-dimethylisoxazole (CD161) as a Potent and Orally Bioavailable BET Bromodomain Inhibitor. J Med Chem 2017; 60:3887-3901. [PMID: 28463487 DOI: 10.1021/acs.jmedchem.7b00193] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have designed and synthesized 9H-pyrimido[4,5-b]indole-containing compounds to obtain potent and orally bioavailable BET inhibitors. By incorporation of an indole or a quinoline moiety to the 9H-pyrimido[4,5-b]indole core, we identified a series of small molecules showing high binding affinities to BET proteins and low nanomolar potencies in inhibition of cell growth in acute leukemia cell lines. One such compound, 4-(6-methoxy-2-methyl-4-(quinolin-4-yl)-9H-pyrimido[4,5-b]indol-7-yl)-3,5-dimethylisoxazole (31) has excellent microsomal stability and good oral pharmacokinetics in rats and mice. Orally administered, 31 achieves significant antitumor activity in the MV4;11 leukemia and MDA-MB-231 triple-negative breast cancer xenograft models in mice. Determination of the cocrystal structure of 31 with BRD4 BD2 provides a structural basis for its high binding affinity to BET proteins. Testing its binding affinities against other bromodomain-containing proteins shows that 31 is a highly selective inhibitor of BET proteins. Our data show that 31 is a potent, selective, and orally active BET inhibitor.
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Affiliation(s)
- Yujun Zhao
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Longchuan Bai
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Liu Liu
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Donna McEachern
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jeanne A Stuckey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jennifer L Meagher
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Xu Ran
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Bing Zhou
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Yang Hu
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Xiaoqin Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Ting Zhao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Siwei Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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34
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Won SJ, Davda D, Labby KJ, Hwang SY, Pricer R, Majmudar JD, Armacost KA, Rodriguez LA, Rodriguez CL, Chong FS, Torossian KA, Palakurthi J, Hur ES, Meagher JL, Brooks CL, Stuckey JA, Martin BR. Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2). ACS Chem Biol 2016; 11:3374-3382. [PMID: 27748579 DOI: 10.1021/acschembio.6b00720] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Post-translational S-palmitoylation directs the trafficking and membrane localization of hundreds of cellular proteins, often involving a coordinated palmitoylation cycle that requires both protein acyl transferases (PATs) and acyl protein thioesterases (APTs) to actively redistribute S-palmitoylated proteins toward different cellular membrane compartments. This process is necessary for the trafficking and oncogenic signaling of S-palmitoylated Ras isoforms, and potentially many peripheral membrane proteins. The depalmitoylating enzymes APT1 and APT2 are separately conserved in all vertebrates, suggesting unique functional roles for each enzyme. The recent discovery of the APT isoform-selective inhibitors ML348 and ML349 has opened new possibilities to probe the function of each enzyme, yet it remains unclear how each inhibitor achieves orthogonal inhibition. Herein, we report the high-resolution structure of human APT2 in complex with ML349 (1.64 Å), as well as the complementary structure of human APT1 bound to ML348 (1.55 Å). Although the overall peptide backbone structures are nearly identical, each inhibitor adopts a distinct conformation within each active site. In APT1, the trifluoromethyl group of ML348 is positioned above the catalytic triad, but in APT2, the sulfonyl group of ML349 forms hydrogen bonds with active site resident waters to indirectly engage the catalytic triad and oxyanion hole. Reciprocal mutagenesis and activity profiling revealed several differing residues surrounding the active site that serve as critical gatekeepers for isoform accessibility and dynamics. Structural and biochemical analysis suggests the inhibitors occupy a putative acyl-binding region, establishing the mechanism for isoform-specific inhibition, hydrolysis of acyl substrates, and structural orthogonality important for future probe development.
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Affiliation(s)
- Sang Joon Won
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Dahvid Davda
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Kristin J. Labby
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Sin Ye Hwang
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Rachel Pricer
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Jaimeen D. Majmudar
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Kira A. Armacost
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Laura A. Rodriguez
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Christina L. Rodriguez
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Fei San Chong
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Kristopher A. Torossian
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Jasmine Palakurthi
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Edward S. Hur
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Jennifer L. Meagher
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Charles L. Brooks
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Jeanne A. Stuckey
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Brent R. Martin
- Program
in Chemical Biology, ‡Department of Chemistry, §Department of Biophysics, and ∥Life Sciences
Institute, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, United States
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35
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Yang CY, Phillips JG, Stuckey JA, Bai L, Sun H, Delproposto J, Brown WC, Chinnaswamy K. Buried Hydrogen Bond Interactions Contribute to the High Potency of Complement Factor D Inhibitors. ACS Med Chem Lett 2016; 7:1092-1096. [PMID: 27994744 DOI: 10.1021/acsmedchemlett.6b00299] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 08/01/2016] [Accepted: 09/13/2016] [Indexed: 01/16/2023] Open
Abstract
Aberrant activation of the complement system is associated with diseases, including paroxysmal nocturnal hemoglobinuria and age-related macular degeneration. Complement factor D is the rate-limiting enzyme for activating the alternative pathway in the complement system. Recent development led to a class of potent amide containing pyrrolidine derived factor D inhibitors. Here, we used biochemical enzymatic and biolayer interferometry assays to demonstrate that the amide group improves the inhibitor potency by more than 80-fold. Our crystal structures revealed buried hydrogen bond interactions are important. Molecular orbital analysis from quantum chemistry calculations dissects the chemical groups participating in these interactions. Free energy calculation supports the differential contributions of the amide group to the binding affinities of these inhibitors. Cell-based hemolysis assay confirmed these compounds inhibit factor D mediated complement activation via the alternative pathway. Our study highlights the important interactions contributing to the high potency of factor D inhibitors reported recently.
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Affiliation(s)
| | - James G. Phillips
- Department
of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | | | | | - Haiying Sun
- Jiansu
Key Laboratory of Drug Design and Optimization, Department of Medicinal
Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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Gathiaka S, Liu S, Chiu M, Yang H, Stuckey JA, Kang YN, Delproposto J, Kubish G, Dunbar JB, Carlson HA, Burley SK, Walters WP, Amaro RE, Feher VA, Gilson MK. D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J Comput Aided Mol Des 2016; 30:651-668. [PMID: 27696240 DOI: 10.1007/s10822-016-9946-8] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [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: 07/09/2016] [Accepted: 08/18/2016] [Indexed: 11/26/2022]
Abstract
The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (1) HSP90, donated by AbbVie and the Community Structure Activity Resource (CSAR), and (2) MAP4K4, donated by Genentech. The challenges for both target datasets were conducted in two stages, with the first stage testing pose predictions and the capacity to rank compounds by affinity with minimal structural data; and the second stage testing methods for ranking compounds with knowledge of at least a subset of the ligand-protein poses. An additional sub-challenge provided small groups of chemically similar HSP90 compounds amenable to alchemical calculations of relative binding free energy. Unlike previous blinded Challenges, we did not provide cognate receptors or receptors prepared with hydrogens and likewise did not require a specified crystal structure to be used for pose or affinity prediction in Stage 1. Given the freedom to select from over 200 crystal structures of HSP90 in the PDB, participants employed workflows that tested not only core docking and scoring technologies, but also methods for addressing water-mediated ligand-protein interactions, binding pocket flexibility, and the optimal selection of protein structures for use in docking calculations. Nearly 40 participating groups submitted over 350 prediction sets for Grand Challenge 2015. This overview describes the datasets and the organization of the challenge components, summarizes the results across all submitted predictions, and considers broad conclusions that may be drawn from this collaborative community endeavor.
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Affiliation(s)
- Symon Gathiaka
- Drug Design Data Resource, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Shuai Liu
- Drug Design Data Resource, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Michael Chiu
- Drug Design Data Resource, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Huanwang Yang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Jeanne A Stuckey
- Center for Structural Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - You Na Kang
- Center for Structural Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Jim Delproposto
- Center for Structural Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Ginger Kubish
- Center for Structural Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - James B Dunbar
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI, 48109-1065, USA
| | - Heather A Carlson
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI, 48109-1065, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ, 08854, USA
- Department of Pharmacy, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | | | - Rommie E Amaro
- Drug Design Data Resource, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Victoria A Feher
- Drug Design Data Resource, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Schrodinger, Inc., New York, NY, USA.
| | - Michael K Gilson
- Drug Design Data Resource, Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Department of Pharmacy, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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Ruckthong L, Zastrow ML, Stuckey JA, Pecoraro VL. A Crystallographic Examination of Predisposition versus Preorganization in de Novo Designed Metalloproteins. J Am Chem Soc 2016; 138:11979-88. [PMID: 27532255 DOI: 10.1021/jacs.6b07165] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Preorganization and predisposition are important molecular recognition concepts exploited by nature to obtain site-specific and selective metal binding to proteins. While native structures containing an MS3 core are often unavailable in both apo- and holo-forms, one can use designed three-stranded coiled coils (3SCCs) containing tris-thiolate sites to evaluate these concepts. We show that the preferred metal geometry dictates the degree to which the cysteine rotamers change upon metal complexation. The Cys ligands in the apo-form are preorganized for binding trigonal pyramidal species (Pb(II)S3 and As(III)S3) in an endo conformation oriented toward the 3SCC C-termini, whereas the cysteines are predisposed for trigonal planar Hg(II)S3 and 4-coordinate Zn(II)S3O structures, requiring significant thiol rotation for metal binding. This study allows assessment of the importance of protein fold and side-chain reorientation for achieving metal selectivity in human retrotransposons and metalloregulatory proteins.
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Affiliation(s)
- Leela Ruckthong
- Department of Chemistry, ‡Biophysics Program, and §Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Melissa L Zastrow
- Department of Chemistry, ‡Biophysics Program, and §Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jeanne A Stuckey
- Department of Chemistry, ‡Biophysics Program, and §Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Vincent L Pecoraro
- Department of Chemistry, ‡Biophysics Program, and §Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
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Pereira PR, Meagher JL, Winter HC, Goldstein IJ, Paschoalin VMF, Silva JT, Stuckey JA. High-resolution crystal structures of Colocasia esculenta tarin lectin. Glycobiology 2016; 27:50-56. [PMID: 27558840 DOI: 10.1093/glycob/cww083] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 08/10/2015] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 01/24/2023] Open
Abstract
Tarin, the Colocasia esculenta lectin from the superfamily of α-d-mannose-specific plant bulb lectins, is a tetramer of 47 kDa composed of two heterodimers. Each heterodimer possesses homologous monomers of ~11.9 (A chain) and ~12.7 (B chain) kDa. The structures of apo and carbohydrate-bound tarin were solved to 1.7 Å and 1.91 Å, respectively. Each tarin monomer forms a canonical β-prism II fold, common to all members of Galanthus nivalis agglutinin (GNA) family, which is partially stabilized by a disulfide bond and a conserved hydrophobic core. The heterodimer is formed through domain swapping involving the C-terminal β-strand and the β-sheet on face I of the prism. The tetramer is assembled through the dimerization of the B chains from heterodimers involving face II of each prism. The 1.91 Å crystal structure of tarin bound to Manα(1,3)Manα(1,6)Man reveals an expanded carbohydrate-binding sequence (QxDxNxVxYx4/6WX) on face III of the β-prism. Both monomers possess a similar fold, except for the length of the loop, which begins after the conserved tyrosine and creates the binding pocket for the α(1,6)-terminal mannose. This loop differs in size and amino-acid composition from 10 other β-prism II domain proteins, and may confer carbohydrate-binding specificity among members of the GNA-related lectin family.
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Affiliation(s)
- Patricia R Pereira
- Centro de Tecnologia, Universidade Federal do Rio de Janeiro (UFRJ), Avenida Athos da Silveira Ramos, 149., Rio de Janeiro 21941-909, Brazil.,Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jennifer L Meagher
- Center for Structural Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109, USA
| | - Harry C Winter
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Irwin J Goldstein
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Vânia M F Paschoalin
- Centro de Tecnologia, Universidade Federal do Rio de Janeiro (UFRJ), Avenida Athos da Silveira Ramos, 149., Rio de Janeiro 21941-909, Brazil
| | - Joab T Silva
- Centro de Tecnologia, Universidade Federal do Rio de Janeiro (UFRJ), Avenida Athos da Silveira Ramos, 149., Rio de Janeiro 21941-909, Brazil
| | - Jeanne A Stuckey
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA .,Center for Structural Biology, Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI 48109, USA
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Ruckthong L, Stuckey JA, Pecoraro VL. Methods for Solving Highly Symmetric De Novo Designed Metalloproteins: Crystallographic Examination of a Novel Three-Stranded Coiled-Coil Structure Containing d-Amino Acids. Methods Enzymol 2016; 580:135-48. [PMID: 27586331 DOI: 10.1016/bs.mie.2016.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The core objective of de novo metalloprotein design is to define metal-protein relationships that control the structure and function of metal centers by using simplified proteins. An essential requirement to achieve this goal is to obtain high resolution structural data using either NMR or crystallographic studies in order to evaluate successful design. X-ray crystal structures have proven that a four heptad repeat scaffold contained in the three-stranded coiled coil (3SCC), called CoilSer (CS), provides an excellent motif for modeling a three Cys binding environment capable of chelating metals into geometries that resemble heavy metal sites in metalloregulatory systems. However, new generations of more complicated designs that feature, for example, a d-amino acid or multiple metal ligand sites in the helical sequence require a more stable construct. In doing so, an extra heptad was introduced into the original CS sequence, yielding a GRAND-CoilSer (GRAND-CS) to retain the 3SCC folding. An apo-(GRAND-CSL12DLL16C)3 crystal structure, designed for Cd(II)S3 complexation, proved to be a well-folded parallel 3SCC. Because this structure is novel, protocols for crystallization, structural determination, and refinements of the apo-(GRAND-CSL12DLL16C)3 are described. This report should be generally useful for future crystallographic studies of related coiled-coil designs.
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Affiliation(s)
- L Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - J A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States
| | - V L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States.
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Kwarcinski FE, Brandvold KR, Phadke S, Beleh OM, Johnson TK, Meagher JL, Seeliger MA, Stuckey JA, Soellner MB. Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity. ACS Chem Biol 2016; 11:1296-304. [PMID: 26895387 PMCID: PMC7306399 DOI: 10.1021/acschembio.5b01018] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the kinase field, there are many widely held tenets about conformation-selective inhibitors that have yet to be validated using controlled experiments. We have designed, synthesized, and characterized a series of kinase inhibitor analogues of dasatinib, an FDA-approved kinase inhibitor that binds the active conformation. This inhibitor series includes two Type II inhibitors that bind the DFG-out inactive conformation and two inhibitors that bind the αC-helix-out inactive conformation. Using this series of compounds, we analyze the impact that conformation-selective inhibitors have on target binding and kinome-wide selectivity.
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Affiliation(s)
- Frank E. Kwarcinski
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Sameer Phadke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Omar M. Beleh
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794
| | - Jeanne A. Stuckey
- Center for Structural Biology, University of Michigan, Ann Arbor, MI 48109
| | - Matthew B. Soellner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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Carlson HA, Smith RD, Damm-Ganamet KL, Stuckey JA, Ahmed A, Convery MA, Somers DO, Kranz M, Elkins PA, Cui G, Peishoff CE, Lambert MH, Dunbar JB. CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. J Chem Inf Model 2016; 56:1063-77. [PMID: 27149958 DOI: 10.1021/acs.jcim.5b00523] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 2014 CSAR Benchmark Exercise was the last community-wide exercise that was conducted by the group at the University of Michigan, Ann Arbor. For this event, GlaxoSmithKline (GSK) donated unpublished crystal structures and affinity data from in-house projects. Three targets were used: tRNA (m1G37) methyltransferase (TrmD), Spleen Tyrosine Kinase (SYK), and Factor Xa (FXa). A particularly strong feature of the GSK data is its large size, which lends greater statistical significance to comparisons between different methods. In Phase 1 of the CSAR 2014 Exercise, participants were given several protein-ligand complexes and asked to identify the one near-native pose from among 200 decoys provided by CSAR. Though decoys were requested by the community, we found that they complicated our analysis. We could not discern whether poor predictions were failures of the chosen method or an incompatibility between the participant's method and the setup protocol we used. This problem is inherent to decoys, and we strongly advise against their use. In Phase 2, participants had to dock and rank/score a set of small molecules given only the SMILES strings of the ligands and a protein structure with a different ligand bound. Overall, docking was a success for most participants, much better in Phase 2 than in Phase 1. However, scoring was a greater challenge. No particular approach to docking and scoring had an edge, and successful methods included empirical, knowledge-based, machine-learning, shape-fitting, and even those with solvation and entropy terms. Several groups were successful in ranking TrmD and/or SYK, but ranking FXa ligands was intractable for all participants. Methods that were able to dock well across all submitted systems include MDock,1 Glide-XP,2 PLANTS,3 Wilma,4 Gold,5 SMINA,6 Glide-XP2/PELE,7 FlexX,8 and MedusaDock.9 In fact, the submission based on Glide-XP2/PELE7 cross-docked all ligands to many crystal structures, and it was particularly impressive to see success across an ensemble of protein structures for multiple targets. For scoring/ranking, submissions that showed statistically significant achievement include MDock1 using ITScore1,10 with a flexible-ligand term,11 SMINA6 using Autodock-Vina,12,13 FlexX8 using HYDE,14 and Glide-XP2 using XP DockScore2 with and without ROCS15 shape similarity.16 Of course, these results are for only three protein targets, and many more systems need to be investigated to truly identify which approaches are more successful than others. Furthermore, our exercise is not a competition.
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Affiliation(s)
- Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Richard D Smith
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Kelly L Damm-Ganamet
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Jeanne A Stuckey
- Center for Structural Biology, University of Michigan , 3358E Life Sciences Institute, 210 Washtenaw Ave., Ann Arbor, Michigan 48109-2216, United States
| | - Aqeel Ahmed
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
| | - Maire A Convery
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Donald O Somers
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Michael Kranz
- Computational and Structural Sciences, Medicines Research Centre, GlaxoSmithKline Research & Development , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Patricia A Elkins
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Guanglei Cui
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Catherine E Peishoff
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Millard H Lambert
- Computational and Structural Sciences, GlaxoSmithKline Research & Development , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - James B Dunbar
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
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Yang CY, Delproposto J, Chinnaswamy K, Brown WC, Wang S, Stuckey JA, Wang X. Conformational Sampling and Binding Site Assessment of Suppression of Tumorigenicity 2 Ectodomain. PLoS One 2016; 11:e0146522. [PMID: 26735493 PMCID: PMC4703388 DOI: 10.1371/journal.pone.0146522] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 11/02/2015] [Accepted: 12/20/2015] [Indexed: 11/23/2022] Open
Abstract
Suppression of Tumorigenicity 2 (ST2), a member of the interleukin-1 receptor (IL-1R) family, activates type 2 immune responses to pathogens and tissue damage via binding to IL-33. Dysregulated responses contribute to asthma, graft-versus-host and autoinflammatory diseases and disorders. To study ST2 structure for inhibitor development, we performed the principal component (PC) analysis on the crystal structures of IL1-1R1, IL1-1R2, ST2 and the refined ST2 ectodomain (ST2ECD) models, constructed from previously reported small-angle X-ray scattering data. The analysis facilitates mapping of the ST2ECD conformations to PC subspace for characterizing structural changes. Extensive coverage of ST2ECD conformations was then obtained using the accelerated molecular dynamics simulations started with the IL-33 bound ST2ECD structure as instructed by their projected locations on the PC subspace. Cluster analysis of all conformations further determined representative conformations of ST2ECD ensemble in solution. Alignment of the representative conformations with the ST2/IL-33 structure showed that the D3 domain of ST2ECD (containing D1-D3 domains) in most conformations exhibits no clashes with IL-33 in the crystal structure. Our experimental binding data informed that the D1-D2 domain of ST2ECD contributes predominantly to the interaction between ST2ECD and IL-33 underscoring the importance of the D1-D2 domain in binding. Computational binding site assessment revealed one third of the total detected binding sites in the representative conformations may be suitable for binding to potent small molecules. Locations of these sites include the D1-D2 domain ST2ECD and modulation sites conformed to ST2ECD conformations. Our study provides structural models and analyses of ST2ECD that could be useful for inhibitor discovery.
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Affiliation(s)
- Chao-Yie Yang
- Department of Internal Medicine, Hematology and Oncology Division, University of Michigan, Ann Arbor, Michigan, 48109, United States of America
| | - James Delproposto
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States of America
| | - Krishnapriya Chinnaswamy
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States of America
| | - William Clay Brown
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States of America
| | - Shuying Wang
- Department of Microbiology and Immunology, National Cheng Kung University Medical College, Tainan 701, Taiwan; and Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - Jeanne A. Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States of America
- Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States of America
| | - Xinquan Wang
- Ministry of Education Key Laboratory of Protein Science, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Swanson MD, Boudreaux DM, Salmon L, Chugh J, Winter HC, Meagher JL, André S, Murphy PV, Oscarson S, Roy R, King S, Kaplan MH, Goldstein IJ, Tarbet EB, Hurst BL, Smee DF, de la Fuente C, Hoffmann HH, Xue Y, Rice CM, Schols D, Garcia JV, Stuckey JA, Gabius HJ, Al-Hashimi HM, Markovitz DM. Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity. Cell 2015; 163:746-58. [PMID: 26496612 DOI: 10.1016/j.cell.2015.09.056] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 06/05/2015] [Accepted: 09/29/2015] [Indexed: 10/22/2022]
Abstract
A key effector route of the Sugar Code involves lectins that exert crucial regulatory controls by targeting distinct cellular glycans. We demonstrate that a single amino-acid substitution in a banana lectin, replacing histidine 84 with a threonine, significantly reduces its mitogenicity, while preserving its broad-spectrum antiviral potency. X-ray crystallography, NMR spectroscopy, and glycocluster assays reveal that loss of mitogenicity is strongly correlated with loss of pi-pi stacking between aromatic amino acids H84 and Y83, which removes a wall separating two carbohydrate binding sites, thus diminishing multivalent interactions. On the other hand, monovalent interactions and antiviral activity are preserved by retaining other wild-type conformational features and possibly through unique contacts involving the T84 side chain. Through such fine-tuning, target selection and downstream effects of a lectin can be modulated so as to knock down one activity, while preserving another, thus providing tools for therapeutics and for understanding the Sugar Code.
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Affiliation(s)
- Michael D Swanson
- Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Division of Infectious Diseases, Department of Medicine and UNC AIDS Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel M Boudreaux
- Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Loïc Salmon
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeetender Chugh
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Harry C Winter
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer L Meagher
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sabine André
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Paul V Murphy
- School of Chemistry, National University of Ireland, Galway, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - René Roy
- Department of Chemistry, Université du Québec à Montréal, Montréal, Québec H3C 3P8, Canada
| | - Steven King
- Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark H Kaplan
- Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Irwin J Goldstein
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - E Bart Tarbet
- Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA
| | - Donald F Smee
- Institute for Antiviral Research, Utah State University, Logan, UT 84322, USA
| | | | | | - Yi Xue
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | | | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, University of Leuven, 3000 Leuven, Belgium
| | - J Victor Garcia
- Division of Infectious Diseases, Department of Medicine and UNC AIDS Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Hashim M Al-Hashimi
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biochemistry, Duke University, Durham, NC 27710, USA.
| | - David M Markovitz
- Division of Infectious Diseases, Department of Internal Medicine, Program in Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. J Chem Inf Model 2015; 56:1022-31. [PMID: 26419257 DOI: 10.1021/acs.jcim.5b00387] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Community Structure-Activity Resource (CSAR) conducted a benchmark exercise to evaluate the current computational methods for protein design, ligand docking, and scoring/ranking. The exercise consisted of three phases. The first phase required the participants to identify and rank order which designed sequences were able to bind the small molecule digoxigenin. The second phase challenged the community to select a near-native pose of digoxigenin from a set of decoy poses for two of the designed proteins. The third phase investigated the ability of current methods to rank/score the binding affinity of 10 related steroids to one of the designed proteins (pKd = 4.1 to 6.7). We found that 11 of 13 groups were able to correctly select the sequence that bound digoxigenin, with most groups providing the correct three-dimensional structure for the backbone of the protein as well as all atoms of the active-site residues. Eleven of the 14 groups were able to select the appropriate pose from a set of plausible decoy poses. The ability to predict absolute binding affinities is still a difficult task, as 8 of 14 groups were able to correlate scores to affinity (Pearson-r > 0.7) of the designed protein for congeneric steroids and only 5 of 14 groups were able to correlate the ranks of the 10 related ligands (Spearman-ρ > 0.7).
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Affiliation(s)
- Richard D Smith
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Kelly L Damm-Ganamet
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - James B Dunbar
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Aqeel Ahmed
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Krishnapriya Chinnaswamy
- Life Sciences Institute, University of Michigan , 210 Washtenaw Ave, Ann Arbor, Michigan 48109-2216, United States
| | - James E Delproposto
- Life Sciences Institute, University of Michigan , 210 Washtenaw Ave, Ann Arbor, Michigan 48109-2216, United States
| | - Ginger M Kubish
- Life Sciences Institute, University of Michigan , 210 Washtenaw Ave, Ann Arbor, Michigan 48109-2216, United States
| | | | | | | | - Lindsey Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center , 1100 Fairview Ave. N., Seattle, Washington 98109, United States
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan , 210 Washtenaw Ave, Ann Arbor, Michigan 48109-2216, United States
| | | | - Heather A Carlson
- Department of Medicinal Chemistry, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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45
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Ran X, Zhao Y, Liu L, Bai L, Yang CY, Zhou B, Meagher JL, Chinnaswamy K, Stuckey JA, Wang S. Structure-Based Design of γ-Carboline Analogues as Potent and Specific BET Bromodomain Inhibitors. J Med Chem 2015; 58:4927-39. [PMID: 26080064 DOI: 10.1021/acs.jmedchem.5b00613] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Small-molecule inhibitors of bromodomain and extra terminal proteins (BET), including BRD2, BRD3, and BRD4 proteins have therapeutic potential for the treatment of human cancers and other diseases and conditions. In this paper, we report the design, synthesis, and evaluation of γ-carboline-containing compounds as a new class of small-molecule BET inhibitors. The most potent inhibitor (compound 18, RX-37) obtained from this study binds to BET bromodomain proteins (BRD2, BRD3, and BRD4) with Ki values of 3.2-24.7 nM and demonstrates high selectivity over other non-BET bromodomain-containing proteins. Compound 18 potently and selectively inhibits cell growth in human acute leukemia cell lines harboring the rearranged mixed lineage leukemia 1 gene. We have determined a cocrystal structure of 18 in complex with BRD4 BD2 at 1.4 Å resolution, which provides a solid structural basis for the compound's high binding affinity and for its further structure-based optimization. Compound 18 represents a promising lead compound for the development of a new class of therapeutics for the treatment of human cancer and other conditions.
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Affiliation(s)
- Xu Ran
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yujun Zhao
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Liu Liu
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Longchuan Bai
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bing Zhou
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer L Meagher
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Krishnapriya Chinnaswamy
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne A Stuckey
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- †Departments of Medicinal Chemistry, ‡Internal Medicine, §Pharmacology, and ∥Biological Chemistry, ⊥Life Sciences Institute, and #Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
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Morgan CE, Meagher JL, Levengood JD, Delproposto J, Rollins C, Stuckey JA, Tolbert BS. The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein. J Mol Biol 2015; 427:3241-3257. [PMID: 26003924 DOI: 10.1016/j.jmb.2015.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 03/12/2015] [Revised: 04/29/2015] [Accepted: 05/15/2015] [Indexed: 01/01/2023]
Abstract
The heterogeneous nuclear ribonucleoprotein (hnRNP) A1 protein is a multifunctional RNA binding protein implicated in a wide range of biological functions. Mechanisms and putative hnRNP A1-RNA interactions have been inferred primarily from the crystal structure of its UP1 domain bound to ssDNA. RNA stem loops represent an important class of known hnRNP A1 targets, yet little is known about the structural basis of hnRNP A1-RNA recognition. Here, we report the first high-resolution structure (1.92Å) of UP1 bound to a 5'-AGU-3' trinucleotide that resembles sequence elements of several native hnRNP A1-RNA stem loop targets. UP1 interacts specifically with the AG dinucleotide sequence via a "nucleobase pocket" formed by the β-sheet surface of RRM1 and the inter-RRM linker; RRM2 does not contact the RNA. The inter-RRM linker forms the lid of the nucleobase pocket and we show using structure-guided mutagenesis that the conserved salt-bridge interactions (R75:D155 and R88:D157) on the α-helical side of the RNA binding surface stabilize the linker in a geometry poised to bind RNA. We further investigated the structural basis of UP1 binding HIViSL3(ESS3) by determining a structural model of the complex scored by small-angle X-ray scattering. UP1 docks on the apical loop of SL3(ESS3) using its RRM1 domain and inter-RRM linker only. The biophysical implications of the structural model were tested by measuring kinetic binding parameters, where mutations introduced within the apical loop reduce binding affinities by slowing down the rate of complex formation. Collectively, the data presented here provide the first insights into hnRNP A1-RNA interactions.
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Affiliation(s)
- Christopher E Morgan
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jennifer L Meagher
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey D Levengood
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - James Delproposto
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carrie Rollins
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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47
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Larsen MJ, Larsen SD, Fribley A, Grembecka J, Homan K, Mapp A, Haak A, Nikolovska-Coleska Z, Stuckey JA, Sun D, Sherman DH. The role of HTS in drug discovery at the University of Michigan. Comb Chem High Throughput Screen 2015; 17:210-30. [PMID: 24409957 DOI: 10.2174/1386207317666140109121546] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 11/05/2013] [Accepted: 01/07/2014] [Indexed: 12/17/2022]
Abstract
High throughput screening (HTS) is an integral part of a highly collaborative approach to drug discovery at the University of Michigan. The HTS lab is one of four core centers that provide services to identify, produce, screen and follow-up on biomedical targets for faculty. Key features of this system are: protein cloning and purification, protein crystallography, small molecule and siRNA HTS, medicinal chemistry and pharmacokinetics. Therapeutic areas that have been targeted include anti-bacterial, metabolic, neurodegenerative, cardiovascular, anti-cancer and anti-viral. The centers work in a coordinated, interactive environment to affordably provide academic investigators with the technology, informatics and expertise necessary for successful drug discovery. This review provides an overview of these centers at the University of Michigan, along with case examples of successful collaborations with faculty.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - David H Sherman
- Center for Chemical Genomics, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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48
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Buer B, Paul B, Das D, Stuckey JA, Marsh ENG. Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound. ACS Chem Biol 2014; 9:2584-93. [PMID: 25222710 PMCID: PMC4245163 DOI: 10.1021/cb500343j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [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: 05/02/2014] [Accepted: 09/02/2014] [Indexed: 11/28/2022]
Abstract
The nonheme diiron enzyme cyanobacterial aldehyde deformylating oxygenase, cADO, catalyzes the highly unusual deformylation of aliphatic aldehydes to alkanes and formate. We have determined crystal structures for the enzyme with a long-chain water-soluble aldehyde and medium-chain carboxylic acid bound to the active site. These structures delineate a hydrophobic channel that connects the solvent with the deeply buried active site and reveal a mode of substrate binding that is different from previously determined structures with long-chain fatty acids bound. The structures also identify a water channel leading to the active site that could facilitate the entry of protons required in the reaction. NMR studies examining 1-[(13)C]-octanal binding to cADO indicate that the enzyme binds the aldehyde form rather than the hydrated form. Lastly, the fortuitous cocrystallization of the metal-free form of the protein with aldehyde bound has revealed protein conformation changes that are involved in binding iron.
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Affiliation(s)
- Benjamin
C. Buer
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bishwajit Paul
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Debasis Das
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne A. Stuckey
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - E. Neil G. Marsh
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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49
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Pereira PR, Winter HC, Verícimo MA, Meagher JL, Stuckey JA, Goldstein IJ, Paschoalin VMF, Silva JT. Structural analysis and binding properties of isoforms of tarin, the GNA-related lectin from Colocasia esculenta. Biochim Biophys Acta 2014; 1854:20-30. [PMID: 25448725 DOI: 10.1016/j.bbapap.2014.10.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 01/15/2023]
Abstract
The lectins, a class of proteins that occur widely in animals, plants, fungi, lichens and microorganisms, are known for their ability to specifically bind to carbohydrates. Plant lectins can be classified into 12 families including the Galanthus nivalis agglutinin (GNA)-related lectin superfamily, which is widespread among monocotyledonous plants and binds specifically to mannose, a behavior that confers remarkable anti-tumor, anti-viral and insecticidal properties on these proteins. The present study characterized a mitogenic lectin from this family, called tarin, which was purified from the crude extract from taro (Colocasia esculenta). The results showed that tarin is a glycoprotein with 2-3% carbohydrate content, composed of least 10 isoforms with pIs ranging from 5.5 to 9.5. The intact protein is a heterotetramer of 47kDa composed of two non-identical and non-covalently associated polypeptides, with small subunits of 11.9kDa and large subunits of 12.6kDa. The tarin structure is stable and recovers or maintains its functional structure following treatments at different temperatures and pH. Tarin showed a complex carbohydrate specificity, binding with high affinity to high-mannose and complex N-glycans. Many of these ligands can be found in viruses, tumor cells and insects, as well as in hematopoietic progenitor cells. Chemical modifications confirmed that both conserved and non-conserved amino acids participate in this interaction. This study determined the structural and ligand binding characteristics of a GNA-related lectin that can be exploited for several different purposes, particularly as a proliferative therapeutic molecule that is able to enhance the immunological response.
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Affiliation(s)
- Patrícia R Pereira
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil.
| | - Harry C Winter
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Mauricio A Verícimo
- Instituto de Biologia, Universidade Federal Fluminense, Rio de Janeiro 4020141, Brazil.
| | - Jennifer L Meagher
- Center for Structural Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Jeanne A Stuckey
- Center for Structural Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Irwin J Goldstein
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Vânia M F Paschoalin
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil.
| | - Joab T Silva
- Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil.
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50
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Abulwerdi FA, Mady AS, Perdih A, Stuckey JA, Showalter HD, Nikolovska-Coleska Z. Abstract 1641: Structure-based design and development of pyrazolopyridine-based inhibitors of Mcl-1. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-1641] [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 anti-apoptotic myeloid cell leukemia protein Mcl-1, a member of the Bcl-2 family proteins, has emerged as a promising therapeutic target. Mcl-1 is overexpressed in many human cancers which has been associated with inferior survival, poor prognosis and resistance to chemotherapies. Disruption of Mcl-1 interaction with its pro-apoptotic partners through small molecules is a viable strategy to overcome Mcl-1 mediated resistance to apoptosis. Targeting Mcl-1 protein represents a promising strategy either alone or in combination with other therapies.
Applying an integrated screening approach through combining high throughput and virtual screenings, several novel chemical classes were identified as Mcl-1 inhibitors. Compound 38 with a pyrazolopyridine scaffold was selected as a promising high throughput lead for medicinal chemistry efforts. Using reported chemistry a focused library of analogs of 38 was generated. Through HSQC protein-observed NMR studies and chemical shift mapping, the binding of the lead compound 38 was characterized and confirmed to be the BH3 binding pocket of Mcl-1. Computational modeling guided by NMR studies was applied in lead optimization and rational design of more potent analogs. Structure-activity relationship was established utilizing two different competitive platforms of fluorescent polarization and surface plasmon resonance, and confirmed by HSQC NMR spectroscopy. The binding affinity of this class of compounds was improved more than twenty fold in comparison with the lead compound 38. In vitro binding, functional and cell-based assays were performed in order to determine selectivity profile against five members of Bcl-2 family, mechanism of action and cellular activity of analogs with improved potency. The obtained results show promise for further chemical modification and development of pyrazolopyridine-based inhibitors of Mcl-1.
Citation Format: Fardokht A. Abulwerdi, Ahmed S.A. Mady, Andrej Perdih, Jeanne A. Stuckey, Hollis D. Showalter, Zaneta Nikolovska-Coleska. Structure-based design and development of pyrazolopyridine-based inhibitors of Mcl-1. [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 1641. doi:10.1158/1538-7445.AM2014-1641
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Affiliation(s)
| | - Ahmed S.A. Mady
- 1Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | - Andrej Perdih
- 1Department of Pathology, University of Michigan Medical School, Ann Arbor, MI
| | | | - Hollis D. Showalter
- 3Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI
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