1
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Kim YY, Gryder BE, Sinniah R, Peach ML, Shern JF, Abdelmaksoud A, Pomella S, Woldemichael GM, Stanton BZ, Milewski D, Barchi JJ, Schneekloth JS, Chari R, Kowalczyk JT, Shenoy SR, Evans JR, Song YK, Wang C, Wen X, Chou HC, Gangalapudi V, Esposito D, Jones J, Procter L, O'Neill M, Jenkins LM, Tarasova NI, Wei JS, McMahon JB, O'Keefe BR, Hawley RG, Khan J. KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma. Nat Commun 2024; 15:1703. [PMID: 38402212 PMCID: PMC10894237 DOI: 10.1038/s41467-024-45902-y] [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: 11/21/2022] [Accepted: 02/07/2024] [Indexed: 02/26/2024] Open
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. Here, we screen 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, P3FI-63. RNA-seq, ATAC-seq, and docking analyses implicate histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirm the inhibition of multiple KDMs with the highest selectivity for KDM3B. Structural similarity search of P3FI-63 identifies P3FI-90 with improved solubility and potency. Biophysical binding of P3FI-90 to KDM3B is demonstrated using NMR and SPR. P3FI-90 suppresses the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopies P3FI-90 effects. Thus, we report KDM inhibitors P3FI-63 and P3FI-90 with the highest specificity for KDM3B. Their potent suppression of PAX3-FOXO1 activity indicates a possible therapeutic approach for FP-RMS and other transcriptionally addicted cancers.
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Affiliation(s)
| | - Berkley E Gryder
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Megan L Peach
- Basic Science Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD, USA
| | - Jack F Shern
- Pediatric Oncology Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Silvia Pomella
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Girma M Woldemichael
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Benjamin Z Stanton
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Nationwide Children's Hospital, Center for Childhood Cancer Research, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Biological Chemistry & Pharmacology, The Ohio State University College of Medicine, Columbus, OH, USA
| | | | | | | | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, FNLCR, Frederick, MD, USA
| | | | - Shilpa R Shenoy
- Leidos Biomed Res Inc, FNLCR, Basic Sci Program, Frederick, MD, USA
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
| | - Jason R Evans
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | | | - Chaoyu Wang
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | - Xinyu Wen
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | | | | | - Jane Jones
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Lauren Procter
- Protein Expression Laboratory, FNLCR, NIH, Frederick, MD, USA
| | - Maura O'Neill
- Protein Characterization Laboratory, FNLCR, NIH, Frederick, MD, USA
| | | | | | - Jun S Wei
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | | | - Barry R O'Keefe
- Molecular Targets Program, NCI, NIH, Frederick, MD, USA
- Natural Products Branch, NCI, NIH, Frederick, MD, USA
| | - Robert G Hawley
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Anatomy and Cell Biology, George Washington University, Washington, DC, USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
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2
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Takada K, Oku N, Peach ML, Ransom TT, Henrich CJ, Gustafson KR. Enigmazole Phosphomacrolides from the Marine Sponge Cinachyrella enigmatica. J Org Chem 2023; 88:10996-11002. [PMID: 37471139 DOI: 10.1021/acs.joc.3c00963] [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: 07/21/2023]
Abstract
Enigmazole B (1) and four new analogues, cis-enigmazole B (2), dehydroenigmazole B (3), enigmimide B (4), and enigmimide A (5), were isolated from the marine sponge Cinachyrella enigmatica. Their planar structures were elucidated by detailed NMR and MS data analyses, which established 1-3 to be oxazole-substituted 18-membered phosphomacrolides, while 4 and 5 were oxazole ring-opened congeners. The relative and absolute configurations in 1 were determined by a combination of chemical transformations and spectroscopic analyses. Photooxidation of the oxazole moiety in 1 gave enigmimide B (4), thus establishing that 4 has the same absolute configuration of 1. Enigmazole B (1) along with analogues 2 and 3 showed cytotoxicity against murine IC-2 mast cells with IC50 values of 3.6-7.0 μM. The enigmimides (4 and 5) and dephosphoenigmazoles did not show cytotoxicity (IC50 > 10 μM), implying that both the oxazole moiety and the phosphate group are necessary for the cytotoxicity of the enigmazole class macrolides.
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Affiliation(s)
- Kentaro Takada
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Naoya Oku
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Megan L Peach
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United States
| | - Tanya T Ransom
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Curtis J Henrich
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United States
| | - Kirk R Gustafson
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
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3
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DeLaitsch AT, Pridgen JR, Tytla A, Peach ML, Hu R, Farnsworth DW, McMillan AK, Flanagan N, Temme JS, Nicklaus MC, Gildersleeve JC. Selective Recognition of Carbohydrate Antigens by Germline Antibodies Isolated from AID Knockout Mice. J Am Chem Soc 2022; 144:4925-4941. [PMID: 35282679 PMCID: PMC10506689 DOI: 10.1021/jacs.1c12745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/29/2022]
Abstract
Germline antibodies, the initial set of antibodies produced by the immune system, are critical for host defense, and information about their binding properties can be useful for designing vaccines, understanding the origins of autoantibodies, and developing monoclonal antibodies. Numerous studies have found that germline antibodies are polyreactive with malleable, flexible binding pockets. While insightful, it remains unclear how broadly this model applies, as there are many families of antibodies that have not yet been studied. In addition, the methods used to obtain germline antibodies typically rely on assumptions and do not work well for many antibodies. Herein, we present a distinct approach for isolating germline antibodies that involves immunizing activation-induced cytidine deaminase (AID) knockout mice. This strategy amplifies antigen-specific B cells, but somatic hypermutation does not occur because AID is absent. Using synthetic haptens, glycoproteins, and whole cells, we obtained germline antibodies to an assortment of clinically important tumor-associated carbohydrate antigens, including Lewis Y, the Tn antigen, sialyl Lewis C, and Lewis X (CD15/SSEA-1). Through glycan microarray profiling and cell binding, we demonstrate that all but one of these germline antibodies had high selectivity for their glycan targets. Using molecular dynamics simulations, we provide insights into the structural basis of glycan recognition. The results have important implications for designing carbohydrate-based vaccines, developing anti-glycan monoclonal antibodies, and understanding antibody evolution within the immune system.
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Affiliation(s)
- Andrew T DeLaitsch
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jacey R Pridgen
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Avery Tytla
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Rayleen Hu
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - David W Farnsworth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Aislinn K McMillan
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Natalie Flanagan
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - J Sebastian Temme
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jeffrey C Gildersleeve
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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4
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Elhalem E, Bellomo A, Cooke M, Scravaglieri A, Pearce LV, Peach ML, Gandolfi Donadío L, Kazanietz MG, Comin MJ. Design, Synthesis, and Characterization of Novel sn-1 Heterocyclic DAG-Lactones as PKC Activators. J Med Chem 2021; 64:11418-11431. [PMID: 34279947 DOI: 10.1021/acs.jmedchem.1c00739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DAG-lactones represent useful templates for the design of potent and selective C1 domain ligands for PKC isozymes. The ester moiety at the sn-1 position, a common feature in this template, is relevant for C1 domain interactions, but it represents a labile group susceptible to endogenous esterases. An interesting challenge involves replacing the ester group of these ligands while still maintaining biological activity. Here, we present the synthesis and functional characterization of novel diacylglycerol-lactones containing heterocyclic ring substituents at the sn-1 position. Our results showed that the new compound 10B12, a DAG-lactone with an isoxazole ring, binds PKCα and PKCε with nanomolar affinity. Remarkably, 10B12 displays preferential selectivity for PKCε translocation in cells and induces a PKCε-dependent reorganization of the actin cytoskeleton into peripheral ruffles in lung cancer cells. We conclude that introducing a stable isoxazole ring as an ester surrogate in DAG-lactones emerges as a novel structural approach to achieve PKC isozyme selectivity.
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Affiliation(s)
- Eleonora Elhalem
- Departamento de Ingredientes Activos y Biorrefinerías, Instituto Nacional de Tecnología Industrial, Av. General Paz 5445, San Martín, Buenos Aires B1650WAB, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. General Paz 5445, San Martín, Buenos Aires B1650WAB, Argentina
| | - Ana Bellomo
- Departamento de Ingredientes Activos y Biorrefinerías, Instituto Nacional de Tecnología Industrial, Av. General Paz 5445, San Martín, Buenos Aires B1650WAB, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. General Paz 5445, San Martín, Buenos Aires B1650WAB, Argentina
| | - Mariana Cooke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Medicine, Einstein Medical Center Philadelphia, Philadelphia, Pennsylvania 19141, United States
| | - Antonella Scravaglieri
- Departamento de Ingredientes Activos y Biorrefinerías, Instituto Nacional de Tecnología Industrial, Av. General Paz 5445, San Martín, Buenos Aires B1650WAB, Argentina
| | - Larry V Pearce
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892-4255, United States
| | - Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Lucía Gandolfi Donadío
- Departamento de Ingredientes Activos y Biorrefinerías, Instituto Nacional de Tecnología Industrial, Av. General Paz 5445, San Martín, Buenos Aires B1650WAB, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. General Paz 5445, San Martín, Buenos Aires B1650WAB, Argentina
| | - Marcelo G Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - María J Comin
- Departamento de Ingredientes Activos y Biorrefinerías, Instituto Nacional de Tecnología Industrial, Av. General Paz 5445, San Martín, Buenos Aires B1650WAB, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. General Paz 5445, San Martín, Buenos Aires B1650WAB, Argentina
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5
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Peach ML, Beedie SL, Chau CH, Collins MK, Markolovic S, Luo W, Tweedie D, Steinebach C, Greig NH, Gütschow M, Vargesson N, Nicklaus MC, Figg WD. Antiangiogenic Activity and in Silico Cereblon Binding Analysis of Novel Thalidomide Analogs. Molecules 2020; 25:E5683. [PMID: 33276504 PMCID: PMC7730988 DOI: 10.3390/molecules25235683] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 09/18/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
Due to its antiangiogenic and anti-immunomodulatory activity, thalidomide continues to be of clinical interest despite its teratogenic actions, and efforts to synthesize safer, clinically active thalidomide analogs are continually underway. In this study, a cohort of 27 chemically diverse thalidomide analogs was evaluated for antiangiogenic activity in an ex vivo rat aorta ring assay. The protein cereblon has been identified as the target for thalidomide, and in silico pharmacophore analysis and molecular docking with a crystal structure of human cereblon were used to investigate the cereblon binding abilities of the thalidomide analogs. The results suggest that not all antiangiogenic thalidomide analogs can bind cereblon, and multiple targets and mechanisms of action may be involved.
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Affiliation(s)
- Megan L. Peach
- Basic Science Program, Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21701, USA;
| | - Shaunna L. Beedie
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
- School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Cindy H. Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
| | - Matthew K. Collins
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
| | - Suzana Markolovic
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
| | - Weiming Luo
- Drug Design & Development Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA; (W.L.); (D.T.); (N.H.G.)
| | - David Tweedie
- Drug Design & Development Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA; (W.L.); (D.T.); (N.H.G.)
| | - Christian Steinebach
- Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany; (C.S.); (M.G.)
| | - Nigel H. Greig
- Drug Design & Development Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA; (W.L.); (D.T.); (N.H.G.)
| | - Michael Gütschow
- Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany; (C.S.); (M.G.)
| | - Neil Vargesson
- School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Marc C. Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA;
| | - William D. Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
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6
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Patel H, Ihlenfeldt WD, Judson PN, Moroz YS, Pevzner Y, Peach ML, Delannée V, Tarasova NI, Nicklaus MC. SAVI, in silico generation of billions of easily synthesizable compounds through expert-system type rules. Sci Data 2020; 7:384. [PMID: 33177514 PMCID: PMC7658252 DOI: 10.1038/s41597-020-00727-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/16/2020] [Indexed: 01/08/2023] Open
Abstract
We have made available a database of over 1 billion compounds predicted to be easily synthesizable, called Synthetically Accessible Virtual Inventory (SAVI). They have been created by a set of transforms based on an adaptation and extension of the CHMTRN/PATRAN programming languages describing chemical synthesis expert knowledge, which originally stem from the LHASA project. The chemoinformatics toolkit CACTVS was used to apply a total of 53 transforms to about 150,000 readily available building blocks (enamine.net). Only single-step, two-reactant syntheses were calculated for this database even though the technology can execute multi-step reactions. The possibility to incorporate scoring systems in CHMTRN allowed us to subdivide the database of 1.75 billion compounds in sets according to their predicted synthesizability, with the most-synthesizable class comprising 1.09 billion synthetic products. Properties calculated for all SAVI products show that the database should be well-suited for drug discovery. It is being made publicly available for free download from https://doi.org/10.35115/37n9-5738.
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Affiliation(s)
- Hitesh Patel
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | | | - Philip N Judson
- Heather Lea, Bland Hill, Norwood, Harrogate, HG3 1TE, England
| | - Yurii S Moroz
- Enamine Ltd, 78 Chervonotkatska Street, Suite 1, Kyiv, 02094, Ukraine and Chemspace LLC, 85 Chervonotkatska Street, Suite 1, Kyiv, 02094, Ukraine
| | - Yuri Pevzner
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
- AbbVie, Inc., North Chicago, IL, 60064, USA
| | - Megan L Peach
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Victorien Delannée
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Nadya I Tarasova
- Synthetic Biologics and Drug Discovery Group, Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Marc C Nicklaus
- Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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7
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Byun JS, Park S, Yi DI, Shin JH, Hernandez SG, Hewitt SM, Nicklaus MC, Peach ML, Guasch L, Tang B, Wakefield LM, Yan T, Caban A, Jones A, Kabbout M, Vohra N, Nápoles AM, Singhal S, Yancey R, De Siervi A, Gardner K. Epigenetic re-wiring of breast cancer by pharmacological targeting of C-terminal binding protein. Cell Death Dis 2019; 10:689. [PMID: 31534138 PMCID: PMC6751206 DOI: 10.1038/s41419-019-1892-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 03/28/2019] [Revised: 07/17/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023]
Abstract
The C-terminal binding protein (CtBP) is an NADH-dependent dimeric family of nuclear proteins that scaffold interactions between transcriptional regulators and chromatin-modifying complexes. Its association with poor survival in several cancers implicates CtBP as a promising target for pharmacological intervention. We employed computer-assisted drug design to search for CtBP inhibitors, using quantitative structure-activity relationship (QSAR) modeling and docking. Functional screening of these drugs identified 4 compounds with low toxicity and high water solubility. Micro molar concentrations of these CtBP inhibitors produces significant de-repression of epigenetically silenced pro-epithelial genes, preferentially in the triple-negative breast cancer cell line MDA-MB-231. This epigenetic reprogramming occurs through eviction of CtBP from gene promoters; disrupted recruitment of chromatin-modifying protein complexes containing LSD1, and HDAC1; and re-wiring of activating histone marks at targeted genes. In functional assays, CtBP inhibition disrupts CtBP dimerization, decreases cell migration, abolishes cellular invasion, and improves DNA repair. Combinatorial use of CtBP inhibitors with the LSD1 inhibitor pargyline has synergistic influence. Finally, integrated correlation of gene expression in breast cancer patients with nuclear levels of CtBP1 and LSD1, reveals new potential therapeutic vulnerabilities. These findings implicate a broad role for this class of compounds in strategies for epigenetically targeted therapeutic intervention.
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Affiliation(s)
- Jung S Byun
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Samson Park
- Genetics Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Dae Ik Yi
- Genetics Branch, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jee-Hye Shin
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | | | - Stephen M Hewitt
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 20892, USA
| | - Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Laura Guasch
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 20892, USA
| | - Binwu Tang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Lalage M Wakefield
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Tingfen Yan
- National Human Genome Institute, Bethesda, MD, 20892, USA
| | - Ambar Caban
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Alana Jones
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Mohamed Kabbout
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Nasreen Vohra
- Brody School of Medicine at East Carolina University, Greenville, NC, 27834, USA
| | - Anna María Nápoles
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA
| | - Sandeep Singhal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Ryan Yancey
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Adriana De Siervi
- Laboratorio de Oncologıa Molecular y Nuevos Blancos Terapeuticos, Instituto de Biologıa y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Kevin Gardner
- National Institute on Minority Health and Health Disparities, Bethesda, MD, 20892, USA. .,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA.
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8
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Journey SN, Alden SL, Hewitt WM, Peach ML, Nicklaus MC, Schneekloth JS. Probing the hras-1 Y i-motif with small molecules. Medchemcomm 2018; 9:2000-2007. [PMID: 30647878 DOI: 10.1039/c8md00311d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/19/2018] [Indexed: 01/21/2023]
Abstract
Non-B DNA structures represent intriguing and challenging targets for small molecules. For example, the promoter of the HRAS oncogene contains multiple G-quadruplex and i-motif structures, atypical globular folds that serve as molecular switches for gene expression. Of the two, i-motif structures are far less studied. Here, we report the first example of small organic compounds that directly interact with the hras-1Y i-motif. We use a small molecule microarray screen to identify drug-like small molecules that bind to the hras-1Y i-motif but not to several other DNA or RNA secondary structures. Two different lead compounds, 1 and 2, were discovered to have 7.4 ± 5.3 μM and 5.9 ± 3.7 μM binding affinity by surface plasmon resonance and similar affinity by fluorescence titration. A structure-activity relationship (SAR) was developed and two improved analogues of 2 demonstrated submicromolar binding affinities. Both compounds display pH-dependent binding, indicating that they interact with the DNA only when the i-motif is properly folded. Chemical shift perturbation shows that 1 alters the structure of the i-motif, while 2 has no effect on the i-motif conformation, indicating different modes of interaction.
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Affiliation(s)
- Sara N Journey
- Chemical Biology Laboratory , National Cancer Institute , Frederick , MD , USA .
| | - Stephanie L Alden
- Chemical Biology Laboratory , National Cancer Institute , Frederick , MD , USA .
| | - Will M Hewitt
- Chemical Biology Laboratory , National Cancer Institute , Frederick , MD , USA .
| | - Megan L Peach
- Chemical Biology Laboratory , Basic Science Program , Frederick National Laboratory for Cancer Research , Leidos Biomedical Research Inc. , Frederick , MD , USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory , National Cancer Institute , Frederick , MD , USA .
| | - John S Schneekloth
- Chemical Biology Laboratory , National Cancer Institute , Frederick , MD , USA .
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9
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Ann J, Czikora A, Saini AS, Zhou X, Mitchell GA, Lewin NE, Peach ML, Blumberg PM, Lee J. α-Arylidene Diacylglycerol-Lactones (DAG-Lactones) as Selective Ras Guanine-Releasing Protein 3 (RasGRP3) Ligands. J Med Chem 2018; 61:6261-6276. [PMID: 29860841 DOI: 10.1021/acs.jmedchem.8b00661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diacylglycerol-lactones have proven to be a powerful template for the design of potent ligands targeting C1 domains, the recognition motif for the cellular second messenger diacylglycerol. A major objective has been to better understand the structure activity relations distinguishing the seven families of signaling proteins that contain such domains, of which the protein kinase C (PKC) and RasGRP families are of particular interest. Here, we synthesize a series of aryl- and alkyl-substituted diacylglycerol-lactones and probe their relative selectivities for RasGRP3 versus PKC. Compound 96 showed 73-fold selectivity relative to PKCα and 45-fold selectivity relative to PKCε for in vitro binding activity. Likewise, in intact cells, compound 96 induced Ras activation, a downstream response to RasGRP stimulation, with 8-29 fold selectivity relative to PKCδ S299 phosphorylation, a measure of PKCδ stimulation.
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Affiliation(s)
- Jihyae Ann
- Laboratory of Medicinal Chemistry, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Agnes Czikora
- Laboratory of Cancer Biology and Genetics , Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Amandeep S Saini
- Laboratory of Cancer Biology and Genetics , Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Xiaoling Zhou
- Laboratory of Cancer Biology and Genetics , Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Gary A Mitchell
- Laboratory of Cancer Biology and Genetics , Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Nancy E Lewin
- Laboratory of Cancer Biology and Genetics , Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Megan L Peach
- Basic Science Program, Leidos Biomedical Research Inc., Chemical Biology Laboratory , Frederick National Laboratory for Cancer Research, National Institutes of Health , Frederick , Maryland 21702 , United States
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics , Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
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10
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Sterner E, Peach ML, Nicklaus MC, Gildersleeve JC. Therapeutic Antibodies to Ganglioside GD2 Evolved from Highly Selective Germline Antibodies. Cell Rep 2018; 20:1681-1691. [PMID: 28813678 DOI: 10.1016/j.celrep.2017.07.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 05/15/2017] [Accepted: 07/19/2017] [Indexed: 12/11/2022] Open
Abstract
Antibodies play a crucial role in host defense and are indispensable research tools, diagnostics, and therapeutics. Antibody generation involves binding of genomically encoded germline antibodies followed by somatic hypermutation and in vivo selection to obtain antibodies with high affinity and selectivity. Understanding this process is critical for developing monoclonal antibodies, designing effective vaccines, and understanding autoantibody formation. Prior studies have found that antibodies to haptens, peptides, and proteins evolve from polyspecific germline antibodies. The immunological evolution of antibodies to mammalian glycans has not been studied. Using glycan microarrays, protein microarrays, cell binding studies, and molecular modeling, we demonstrate that therapeutic antibodies to the tumor-associated ganglioside GD2 evolved from highly specific germline precursors. The results have important implications for developing vaccines and monoclonal antibodies that target carbohydrate antigens. In addition, they demonstrate an alternative pathway for antibody evolution within the immune system that is distinct from the polyspecific germline pathway.
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Affiliation(s)
- Eric Sterner
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jeffrey C Gildersleeve
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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11
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Zlotkowski K, Hewitt WM, Yan P, Bokesch HR, Peach ML, Nicklaus MC, O'Keefe BR, McMahon JB, Gustafson KR, Schneekloth JS. Macrophilone A: Structure Elucidation, Total Synthesis, and Functional Evaluation of a Biologically Active Iminoquinone from the Marine Hydroid Macrorhynchia philippina. Org Lett 2017; 19:1726-1729. [PMID: 28345939 DOI: 10.1021/acs.orglett.7b00496] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A previously uncharacterized pyrroloiminoquinone natural product, macrophilone A, was isolated from the stinging hydroid Macrorhynchia philippina. The structure was assigned utilizing long-range NMR couplings and DFT calculations and proved by a concise, five-step total synthesis. Macrophilone A and a synthetic analogue displayed potent biological activity, including increased intracellular reactive oxygen species levels and submicromolar cytotoxicity toward lung adenocarcinoma cells.
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Affiliation(s)
| | | | - Pengcheng Yan
- School of Pharmaceutical Sciences, Wenzhou Medical University , Wenzhou, Zhejiang 325035, People's Republic of China
| | - Heidi R Bokesch
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Megan L Peach
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
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12
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Peach ML, Cachau RE, Nicklaus MC. Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding. J Mol Recognit 2017; 30. [PMID: 28233410 DOI: 10.1002/jmr.2618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 07/25/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 12/25/2022]
Abstract
In this review, we address a fundamental question: What is the range of conformational energies seen in ligands in protein-ligand crystal structures? This value is important biophysically, for better understanding the protein-ligand binding process; and practically, for providing a parameter to be used in many computational drug design methods such as docking and pharmacophore searches. We synthesize a selection of previously reported conflicting results from computational studies of this issue and conclude that high ligand conformational energies really are present in some crystal structures. The main source of disagreement between different analyses appears to be due to divergent treatments of electrostatics and solvation. At the same time, however, for many ligands, a high conformational energy is in error, due to either crystal structure inaccuracies or incorrect determination of the reference state. Aside from simple chemistry mistakes, we argue that crystal structure error may mainly be because of the heuristic weighting of ligand stereochemical restraints relative to the fit of the structure to the electron density. This problem cannot be fixed with improvements to electron density fitting or with simple ligand geometry checks, though better metrics are needed for evaluating ligand and binding site chemistry in addition to geometry during structure refinement. The ultimate solution for accurately determining ligand conformational energies lies in ultrahigh-resolution crystal structures that can be refined without restraints.
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Affiliation(s)
- Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Raul E Cachau
- Data Science and Information Technology Program, Advanced Biomedical Computing Center, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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13
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Guasch L, Yapamudiyansel W, Peach ML, Kelley JA, Barchi JJ, Nicklaus MC. Experimental and Chemoinformatics Study of Tautomerism in a Database of Commercially Available Screening Samples. J Chem Inf Model 2016; 56:2149-2161. [PMID: 27669079 PMCID: PMC5129033 DOI: 10.1021/acs.jcim.6b00338] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
We
investigated how many cases of the same chemical sold as different
products (at possibly different prices) occurred in a prototypical
large aggregated database and simultaneously tested the tautomerism
definitions in the chemoinformatics toolkit CACTVS. We applied the
standard CACTVS tautomeric transforms plus a set of recently developed
ring–chain transforms to the Aldrich Market Select (AMS) database
of 6 million screening samples and building blocks. In 30 000
cases, two or more AMS products were found to be just different tautomeric
forms of the same compound. We purchased and analyzed 166 such tautomer
pairs and triplets by 1H and 13C NMR to determine
whether the CACTVS transforms accurately predicted what is the same
“stuff in the bottle”. Essentially all prototropic transforms
with examples in the AMS were confirmed. Some of the ring–chain
transforms were found to be too “aggressive”, i.e. to
equate structures with one another that were different compounds.
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Affiliation(s)
- Laura Guasch
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Waruna Yapamudiyansel
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Inc., Frederick National Laboratory for Cancer Research , Frederick, Maryland 21702, United States
| | - James A Kelley
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Joseph J Barchi
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Frederick, Maryland 21702, United States
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14
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Baumann DO, McGowan KM, Kedei N, Peach ML, Blumberg PM, Keck GE. Synthesis and Biological Evaluation of Several Bryostatin Analogues Bearing a Diacylglycerol Lactone C-Ring. J Org Chem 2016; 81:7862-83. [PMID: 27494208 DOI: 10.1021/acs.joc.6b01516] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As an initial step in designing a simplified bryostatin hybrid molecule, three bryostatin analogues bearing a diacylglycerol lactone-based C-ring, which possessed the requisite pharmacophores for binding to protein kinase C (PKC) together with a modified bryostatin-like A- and B-ring region, were synthesized and evaluated. Merle 46 and Merle 47 exhibited binding affinity to PKC alpha with Ki values of 7000 ± 990 and 4940 ± 470 nM, respectively. Reinstallation of the trans-olefin and gem-dimethyl group present in bryostatin 1 in Merle 48 resulted in improved binding affinity, 363 ± 42 nM. While Merle 46 and 47 were only marginally active biologically, Merle 48 showed sufficient activity on the U937 cells to confirm that it was PMA-like for growth and attachment, as predicted by the substitution pattern of its A- and B-rings.
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Affiliation(s)
- David O Baumann
- Department of Chemistry, University of Utah , 315 S 1300 E, RM 2020, Salt Lake City, Utah 84112, United States
| | - Kevin M McGowan
- Department of Chemistry, University of Utah , 315 S 1300 E, RM 2020, Salt Lake City, Utah 84112, United States
| | - Noemi Kedei
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute , Bethesda, Maryland 20892-4255, United States
| | - Megan L Peach
- Basic Science Program, Leidos Biomedical Research, Inc., Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research , Frederick, Maryland 21702, United States
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute , Bethesda, Maryland 20892-4255, United States
| | - Gary E Keck
- Department of Chemistry, University of Utah , 315 S 1300 E, RM 2020, Salt Lake City, Utah 84112, United States
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15
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Czikora A, Lundberg DJ, Abramovitz A, Lewin NE, Kedei N, Peach ML, Zhou X, Merritt RC, Craft EA, Braun DC, Blumberg PM. Structural Basis for the Failure of the C1 Domain of Ras Guanine Nucleotide Releasing Protein 2 (RasGRP2) to Bind Phorbol Ester with High Affinity. J Biol Chem 2016; 291:11133-47. [PMID: 27022025 PMCID: PMC4900263 DOI: 10.1074/jbc.m116.725333] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/28/2016] [Indexed: 11/06/2022] Open
Abstract
The C1 domain represents the recognition module for diacylglycerol and phorbol esters in protein kinase C, Ras guanine nucleotide releasing protein (RasGRP), and related proteins. RasGRP2 is exceptional in that its C1 domain has very weak binding affinity (Kd = 2890 ± 240 nm for [(3)H]phorbol 12,13-dibutyrate. We have identified four amino acid residues responsible for this lack of sensitivity. Replacing Asn(7), Ser(8), Ala(19), and Ile(21) with the corresponding residues from RasGRP1/3 (Thr(7), Tyr(8), Gly(19), and Leu(21), respectively) conferred potent binding affinity (Kd = 1.47 ± 0.03 nm) in vitro and membrane translocation in response to phorbol 12-myristate 13-acetate in LNCaP cells. Mutant C1 domains incorporating one to three of the four residues showed intermediate behavior with S8Y making the greatest contribution. Binding activity for diacylglycerol was restored in parallel. The requirement for anionic phospholipid for [(3)H]phorbol 12,13-dibutyrate binding was determined; it decreased in going from the single S8Y mutant to the quadruple mutant. The full-length RasGRP2 protein with the mutated C1 domains also showed strong phorbol ester binding, albeit modestly weaker than that of the C1 domain alone (Kd = 8.2 ± 1.1 nm for the full-length protein containing all four mutations), and displayed translocation in response to phorbol ester. RasGRP2 is a guanyl exchange factor for Rap1. Consistent with the ability of phorbol ester to induce translocation of the full-length RasGRP2 with the mutated C1 domain, phorbol ester enhanced the ability of the mutated RasGRP2 to activate Rap1. Modeling confirmed that the four mutations helped the binding cleft maintain a stable conformation.
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Affiliation(s)
- Agnes Czikora
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel J Lundberg
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D. C. 20002, and
| | - Adelle Abramovitz
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Nancy E Lewin
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Noemi Kedei
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Megan L Peach
- Basic Science Program, Leidos Biomedical Research, Inc., Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
| | - Xiaoling Zhou
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Raymond C Merritt
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D. C. 20002, and
| | - Elizabeth A Craft
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D. C. 20002, and
| | - Derek C Braun
- Department of Science, Technology, and Mathematics, Gallaudet University, Washington, D. C. 20002, and
| | - Peter M Blumberg
- From the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892,
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16
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Abstract
Warfarin, an important anticoagulant drug, can exist in solution in 40 distinct tautomeric forms through both prototropic tautomerism and ring-chain tautomerism. We have investigated all warfarin tautomers with computational and NMR approaches. Relative energies calculated at the B3LYP/6-311G++(d,p) level of theory indicate that the 4-hydroxycoumarin cyclic hemiketal tautomer is the most stable tautomer in aqueous solution, followed by the 4-hydroxycoumarin open-chain tautomer. This is in agreement with our NMR experiments where the spectral assignments indicate that warfarin exists mainly as a mixture of cyclic hemiketal diastereomers, with an open-chain tautomer as a minor component. We present a diagram of the interconversion of warfarin created taking into account the calculated equilibrium constants (pK(T)) for all tautomeric reactions. These findings help with gaining further understanding of proton transfer and ring closure tautomerization processes. We also discuss the results in the context of chemoinformatics rules for handling tautomerism.
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Affiliation(s)
- Laura Guasch
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Megan L. Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Marc C. Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
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17
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Leyva MJ, Kim YS, Peach ML, Schneekloth JS. Synthetic derivatives of the SUMO consensus sequence provide a basis for improved substrate recognition. Bioorg Med Chem Lett 2015; 25:2146-51. [PMID: 25881829 PMCID: PMC6341477 DOI: 10.1016/j.bmcl.2015.03.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 01/30/2015] [Revised: 03/21/2015] [Accepted: 03/24/2015] [Indexed: 12/21/2022]
Abstract
Protein sumoylation is a dynamic posttranslational modification that regulates a diverse subset of the proteome. The mechanism by which sumoylation enzymes recognize their cognate substrates is unclear, and the consequences of sumoylation remain difficult to predict. While small molecule probes of the sumoylation process could be valuable for understanding SUMO biology, few small molecules that modulate this process exist. Here, we report the synthesis and evaluation of over 600 oxime-containing peptide sumoylation substrates. Our work demonstrates that higher modification efficiency can be achieved with non-natural side chains that deviate substantially from the consensus site requirement of a hydrophobic substituent. Furthermore, docking studies suggest that these improved substrates mimic binding interactions that are used by other endogenous protein sequences through tertiary interactions. The development of these high efficiency substrates provides key mechanistic insights toward specific recognition of low molecular weight species in the sumoylation pathway.
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Affiliation(s)
- Melissa J Leyva
- Chemical Biology Laboratory, National Cancer Institute, 376 Boyles St., Frederick, MD 21702, USA
| | - Yeong Sang Kim
- Chemical Biology Laboratory, National Cancer Institute, 376 Boyles St., Frederick, MD 21702, USA
| | - Megan L Peach
- Basic Science Program, Chemical Biology Laboratory, Leidos Biomedical Research, Inc., National Cancer Institute, 376 Boyles St., Frederick, MD 21702, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, 376 Boyles St., Frederick, MD 21702, USA.
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18
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Kraft MB, Poudel YB, Kedei N, Lewin NE, Peach ML, Blumberg PM, Keck GE. Synthesis of a des-B-ring bryostatin analogue leads to an unexpected ring expansion of the bryolactone core. J Am Chem Soc 2014; 136:13202-8. [PMID: 25207434 PMCID: PMC4183620 DOI: 10.1021/ja5078188] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 11/28/2022]
Abstract
![]()
A convergent synthesis of a des-B-ring bryostatin
analogue is described. This analogue was found to undergo an unexpected
ring expansion of the bryolactone core to generate the corresponding
21-membered macrocycle. The parent analogue and the ring-expanded
product both displayed nanomolar binding affinity for PKC. Despite
containing A-ring substitution identical to that of bryostatin 1 and
displaying bryostatin-like biological function, the des-B-ring analogues displayed a phorbol-like biological function in
cells. These studies shed new light on the role of the bryostatin
B-ring in conferring bryo-like biological function to bryostatin analogues.
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Affiliation(s)
- Matthew B Kraft
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
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19
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Andrews IP, Ketcham JM, Blumberg PM, Kedei N, Lewin NE, Peach ML, Krische MJ. Synthesis of seco-B-ring bryostatin analogue WN-1 via C-C bond-forming hydrogenation: critical contribution of the B-ring in determining bryostatin-like and phorbol 12-myristate 13-acetate-like properties. J Am Chem Soc 2014; 136:13209-16. [PMID: 25207655 PMCID: PMC4183601 DOI: 10.1021/ja507825s] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [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: 01/31/2023]
Abstract
![]()
The seco-B-ring
bryostatin analogue, macrodiolide WN-1, was prepared
in 17 steps (longest linear sequence) and
30 total steps with three bonds formed via hydrogen-mediated C–C
coupling. This synthetic route features a palladium-catalyzed alkoxycarbonylation
of a C2-symmetric diol to form the C9-deoxygenated
bryostatin A-ring. WN-1 binds to PKCα (Ki = 16.1 nM) and inhibits the growth of multiple
leukemia cell lines. Although structural features of the WN-1 A-ring and C-ring are shared by analogues that display bryostatin-like
behavior, WN-1 displays PMA-like behavior in U937 cell
attachment and proliferation assays, as well as in K562 and MV-4-11
proliferation assays. Molecular modeling studies suggest the pattern
of internal hydrogen bonds evident in bryostatin 1 is preserved in WN-1, and that upon docking WN-1 into the crystal
structure of the C1b domain of PKCδ, the binding mode of bryostatin
1 is reproduced. The collective data emphasize the critical contribution
of the B-ring to the function of the upper portion of the molecule
in conferring a bryostatin-like pattern of biological activity.
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Affiliation(s)
- Ian P Andrews
- Department of Chemistry and Biochemistry, University of Texas at Austin , Austin, Texas 78712, United States
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20
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Pu Y, Kang JH, Sigano DM, Peach ML, Lewin NE, Marquez VE, Blumberg PM. Diacylglycerol lactones targeting the structural features that distinguish the atypical C1 domains of protein kinase C ζ and ι from typical C1 domains. J Med Chem 2014; 57:3835-44. [PMID: 24684293 PMCID: PMC4310642 DOI: 10.1021/jm500165n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 01/25/2023]
Abstract
To explore the feasibility of developing ligands targeted to the atypical C1 domains of protein kinase C ζ and ι, we have prepared diacylglycerol lactones substituted with hydrophilic groups on their side chains, which potentially could interact with the arginine residues that distinguish the atypical C1 domains of PKCζ and PKCι from typical C1 domains, and we have measured their binding to mutated versions of the C1b domain of PKCδ that incorporate one or more of these arginine residues. The most selective of the diacylglycerol lactones showed only a 10-fold reduction in binding affinity with the triple arginine mutant (N7R/S10R/L20R) compared to the wild-type, whereas phorbol 12,13-dibutyrate showed a 6000-fold loss of affinity. Molecular modeling confirms that these ligands are indeed able to interact with the arginine residues. Our results show that dramatic changes in selectivity can be obtained through appropriate substitution of diacylglycerol lactones.
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Affiliation(s)
- Yongmei Pu
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
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21
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Abstract
![]()
We
describe a novel approach to RBF approximation, which combines
two new elements: (1) linear radial basis functions and (2) weighting
the model by each descriptor’s contribution. Linear radial
basis functions allow one to achieve more accurate predictions for
diverse data sets. Taking into account the contribution of each descriptor
produces more accurate similarity values used for model development.
The method was validated on 14 public data sets comprising nine physicochemical
properties and five toxicity endpoints. We also compared the new method
with five different QSAR methods implemented in the EPA T.E.S.T. program.
Our approach, implemented in the program GUSAR, showed a reasonable
accuracy of prediction and high coverage for all external test sets,
providing more accurate prediction results than the comparison methods
and even the consensus of these methods. Using our new method, we
have created models for physicochemical and toxicity endpoints, which
we have made freely available in the form of an online service at http://cactus.nci.nih.gov/chemical/apps/cap.
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Affiliation(s)
- Alexey V Zakharov
- CADD Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , DHHS, NCI-Frederick, , 376 Boyles St., Frederick, Maryland 21702, United States
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22
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Abstract
![]()
Many
of the structures in PubChem are annotated with activities
determined in high-throughput screening (HTS) assays. Because of the
nature of these assays, the activity data are typically strongly imbalanced,
with a small number of active compounds contrasting with a very large
number of inactive compounds. We have used several such imbalanced
PubChem HTS assays to test and develop strategies to efficiently build
robust QSAR models from imbalanced data sets. Different descriptor
types [Quantitative Neighborhoods of Atoms (QNA) and “biological”
descriptors] were used to generate a variety of QSAR models in the
program GUSAR. The models obtained were compared using external test
and validation sets. We also report on our efforts to incorporate
the most predictive of our models in the publicly available NCI/CADD
Group Web services (http://cactus.nci.nih.gov/chemical/apps/cap).
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Affiliation(s)
- Alexey V Zakharov
- CADD Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , DHHS, NCI-Frederick, 376 Boyles St., Frederick, Maryland 21702, United States
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23
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Sitzmann M, Weidlich IE, Filippov IV, Liao C, Peach ML, Ihlenfeldt WD, Karki RG, Borodina YV, Cachau RE, Nicklaus MC. PDB ligand conformational energies calculated quantum-mechanically. J Chem Inf Model 2012; 52:739-56. [PMID: 22303903 DOI: 10.1021/ci200595n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient (RSCC). We repeated these calculations with the solvent model IEFPCM, which yielded energy differences that were generally somewhat lower than the corresponding vacuum results but did not produce a qualitatively different picture. Torsional sampling around the crystal conformation at the molecular mechanics level using the MMFF94s force field typically led to an increase in energy.
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Affiliation(s)
- Markus Sitzmann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , DHHS, NCI-Frederick, 376 Boyles Street, Frederick, Maryland 21702, USA
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Geczy T, Peach ML, El Kazzouli S, Sigano DM, Kang JH, Valle CJ, Selezneva J, Woo W, Kedei N, Lewin NE, Garfield SH, Lim L, Mannan P, Marquez VE, Blumberg PM. Molecular basis for failure of "atypical" C1 domain of Vav1 to bind diacylglycerol/phorbol ester. J Biol Chem 2012; 287:13137-58. [PMID: 22351766 DOI: 10.1074/jbc.m111.320010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
C1 domains, the recognition motif of the second messenger diacylglycerol and of the phorbol esters, are classified as typical (ligand-responsive) or atypical (not ligand-responsive). The C1 domain of Vav1, a guanine nucleotide exchange factor, plays a critical role in regulation of Vav activity through stabilization of the Dbl homology domain, which is responsible for exchange activity of Vav. Although the C1 domain of Vav1 is classified as atypical, it retains a binding pocket geometry homologous to that of the typical C1 domains of PKCs. This study clarifies the basis for its failure to bind ligands. Substituting Vav1-specific residues into the C1b domain of PKCδ, we identified five crucial residues (Glu(9), Glu(10), Thr(11), Thr(24), and Tyr(26)) along the rim of the binding cleft that weaken binding potency in a cumulative fashion. Reciprocally, replacing these incompatible residues in the Vav1 C1 domain with the corresponding residues from PKCδ C1b (δC1b) conferred high potency for phorbol ester binding. Computer modeling predicts that these unique residues in Vav1 increase the hydrophilicity of the rim of the binding pocket, impairing membrane association and thereby preventing formation of the ternary C1-ligand-membrane binding complex. The initial design of diacylglycerol-lactones to exploit these Vav1 unique residues showed enhanced selectivity for C1 domains incorporating these residues, suggesting a strategy for the development of ligands targeting Vav1.
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Affiliation(s)
- Tamas Geczy
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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25
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Geczy T, Valle CJ, Selezneva JS, Kedei N, Lewin NE, Lim L, Mannam P, Garfield SH, Peach ML, Blumberg PM. Abstract 3854: Identification of crucial residues at the rim of the binding cleft of the C1 domain of Vav1 that determine its ligand sensitivity. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-3854] [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
Vav1 is a guanine exchange factor (GEF) for the Rho family of GTPases. It plays a pivotal role in T-cell maturation and development, cytoskeleton organization, and oncogenic transformation. The GEF activity of Vav1 is regulated by several factors, including interaction between its catalytic DH domain and its C1 domain. Its C1 domain shows homology with “typical” C1 domains that are sensitive to the second messenger diacylglycerol (DAG) and phorbol esters (PEs), but it is classified as “atypical” based on its unresponsiveness to these ligands. However, crystallographic analysis has shown that, unlike atypical C1 domains (e.g. Raf1) which possess a distorted structure, the Vav1 C1 retains the geometry of the binding cavity.
We hypothesized that residues in the vicinity of the binding pocket might interfere with ligand binding. Sequence alignment with typical C1 domains revealed six unique residues situated along the rim of the putative binding cleft in Vav1 C1: Glu9, Glu10, Pro11, Trp22, Thr24, Tyr26.To probe the role of these residues on DAG/PE sensitivity, we first mutated these sites in the potent PE-sensitive C1b domain of PKCΔ to that of the corresponding sites of Vav1 C1, and analyzed the potency of the mutants for PEs. In vitro binding assays showed that 5 of 6 single-site-mutations (except Trp22) caused significant but limited (10-15 fold) reduction in the binding affinity to phorbol 12,13-dibutyrate (PDBU). Introduction of multiple mutations further decreased the affinity, in a cumulative fashion, leading to no detectable binding in the quintuple mutant. Correspondingly, in vivo confocal microscopy revealed that double and triple GFP-tagged mutants showed much slower and weaker plasma membrane translocation in response to PE than did WT C1bΔ, whereas the quintuple mutation was completely unresponsive. Thus, the ligand-insensitivity of Vav1 C1 reflects the combined effects of Glu9, Glu10, Pro11, Thr24, Tyr26 rather than the effect of a single specific residue.
Conversely, introducing “reverse” mutations (corresponding to the residues of PKCΔ C1b) into Vav1 C1 generate binding activity. The quintuple (PKCΔ-like) mutation restored the phorbol-ester-sensitivity of Vav1 C1 to the level of the potent PKCΔ C1b both in vitro and in vivo. In addition, the quintuple mutation conferred PE-sensitivity to the full length Vav1, as revealed by translocation studies. Computer modeling suggests that the presence of these residues confers on Vav1 C1 a hydrophilic surface at the tip of the binding cavity (as opposed to the rather lipophilic surface of PKCΔ C1b), thus impeding interactions with the membrane bilayer and hindering the formation of the ternary binding complex of ligand, receptor (C1) and membrane lipid. We speculate that targeting those unique hydrophilic residues with specific DAG/PE analogs may provide a rationale for selectively manipulating Vav1 function.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3854. doi:10.1158/1538-7445.AM2011-3854
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Affiliation(s)
- Tamas Geczy
- 1Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | | | - Julia S. Selezneva
- 1Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Noemi Kedei
- 1Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Nancy E. Lewin
- 1Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Langston Lim
- 1Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Poonam Mannam
- 1Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Susan H. Garfield
- 1Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
| | - Megan L. Peach
- 2Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD
| | - Peter M. Blumberg
- 1Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD
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26
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Keck GE, Poudel YB, Rudra A, Stephens JC, Kedei N, Lewin NE, Peach ML, Blumberg PM. Molecular modeling, total synthesis, and biological evaluations of C9-deoxy bryostatin 1. Angew Chem Int Ed Engl 2010; 49:4580-4. [PMID: 20491108 DOI: 10.1002/anie.201001200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gary E Keck
- Department of Chemistry, University of Utah, 315 South 1400 East, Rm 2020, Salt Lake City, UT 84112, USA.
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Oku N, Takada K, Fuller RW, Wilson JA, Peach ML, Pannell LK, McMahon JB, Gustafson KR. Isolation, structural elucidation, and absolute stereochemistry of enigmazole A, a cytotoxic phosphomacrolide from the Papua New Guinea marine sponge Cinachyrella enigmatica. J Am Chem Soc 2010; 132:10278-85. [PMID: 20590096 PMCID: PMC3850515 DOI: 10.1021/ja1016766] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enigmazole A (1), a novel phosphate-containing macrolide, was isolated from a Papua New Guinea collection of the marine sponge Cinachyrella enigmatica. The structure of 1, including the absolute stereochemistry at all eight chiral centers, was determined by a combination of spectroscopic analyses and a series of microscale chemical derivatization studies. Compound 1 is comprised of an 18-membered phosphomacrolide that contains an embedded exomethylene-substituted tetrahydropyran ring and an acyclic portion that spans an embedded oxazole moiety. Two additional analogues, 15-O-methylenigmazole A and 13-hydroxy-15-O-methylenigmazole A, were also isolated and assigned. The enigmazoles are the first phosphomacrolides from a marine source and 1 exhibited significant cytotoxicity in the NCI 60-cell line antitumor screen, with a mean GI(50) of 1.7 microM.
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Affiliation(s)
- Naoya Oku
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Building 1052, Room 121, Frederick, Maryland 21701-1201
| | - Kentaro Takada
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Building 1052, Room 121, Frederick, Maryland 21701-1201
| | - Richard W. Fuller
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Building 1052, Room 121, Frederick, Maryland 21701-1201
| | - Jennifer A. Wilson
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Building 1052, Room 121, Frederick, Maryland 21701-1201
| | - Megan L. Peach
- Chemical Biology Laboratory, SAIC-Frederick, Inc., NCI-Frederick, Building 376, Frederick, Maryland, 21702
| | - Lewis K. Pannell
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, Bethesda, Maryland, 20892
| | - James B. McMahon
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Building 1052, Room 121, Frederick, Maryland 21701-1201
| | - Kirk R. Gustafson
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Building 1052, Room 121, Frederick, Maryland 21701-1201
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28
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Peach ML, Tan N, Choyke SJ, Giubellino A, Athauda G, Burke TR, Nicklaus MC, Bottaro DP. Directed discovery of agents targeting the Met tyrosine kinase domain by virtual screening. J Med Chem 2009; 52:943-51. [PMID: 19199650 DOI: 10.1021/jm800791f] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Hepatocyte growth factor (HGF) is an important regulator of normal development and homeostasis, and dysregulated signaling through the HGF receptor, Met, contributes to tumorigenesis, tumor progression, and metastasis in numerous human malignancies. The development of selective small-molecule inhibitors of oncogenic tyrosine kinases (TK) has led to well-tolerated, targeted therapies for a growing number of cancer types. To identify selective Met TK inhibitors, we used a high-throughput virtual screen of the 13.5 million compound ChemNavigator database to find compounds most likely to bind to the Met ATP binding site and to form several critical interactions with binding site residues predicted to stabilize the kinase domain in its inactive conformation. Subsequent biological screening of 70 in silico hit structures using cell-free and intact cell assays identified three active compounds with micromolar IC(50) values. The predicted binding modes and target selectivity of these compounds are discussed and compared to other known Met TK inhibitors.
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Affiliation(s)
- Megan L Peach
- Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA
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29
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Abstract
BACKGROUND Virtual screening is used to distinguish potential leads from inactive compounds in a database of chemical samples. One method for accomplishing this is by docking compounds into the structure of a receptor binding site in order to rank-order compounds by the quality of the interactions they form with the receptor. It is generally established that docking can be reasonably successful at generating good poses of a ligand in an active site. However, the scoring functions that are used with docking are typically not successful at correctly ranking ligands according to binding affinity or even distinguishing correct poses of a given ligand from incorrect ones. RESULTS We have developed a simple method for reducing the number of false positives in a virtual screen, meaning ligands which are scored highly by the docking program but do not bind well in reality. This method uses a docking program for pose generation without regard to scoring, followed by filtering with receptor-based pharmacophore searches. We applied it to three test-case targets: neuraminidase A, cyclin-dependent kinase 2, and the C1 domain of protein kinase C. CONCLUSION The pharmacophore filtering method can perform better than more traditional docking + scoring methods, and allows the advantages of both docking-based and pharmacophore-based approaches to virtual screening to be fully realized.
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Affiliation(s)
- Megan L Peach
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA.
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30
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Duan D, Sigano DM, Kelley JA, Lai CC, Lewin NE, Kedei N, Peach ML, Lee J, Abeyweera TP, Rotenberg SA, Kim H, Kim YH, El Kazzouli S, Chung JU, Young HA, Young MR, Baker A, Colburn NH, Haimovitz-Friedman A, Truman JP, Parrish DA, Deschamps JR, Perry NA, Surawski RJ, Blumberg PM, Marquez VE. Conformationally constrained analogues of diacylglycerol. 29. Cells sort diacylglycerol-lactone chemical zip codes to produce diverse and selective biological activities. J Med Chem 2008; 51:5198-220. [PMID: 18698758 DOI: 10.1021/jm8001907] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Diacylglycerol-lactone (DAG-lactone) libraries generated by a solid-phase approach using IRORI technology produced a variety of unique biological activities. Subtle differences in chemical diversity in two areas of the molecule, the combination of which generates what we have termed "chemical zip codes", are able to transform a relatively small chemical space into a larger universe of biological activities, as membrane-containing organelles within the cell appear to be able to decode these "chemical zip codes". It is postulated that after binding to protein kinase C (PKC) isozymes or other nonkinase target proteins that contain diacylglycerol responsive, membrane interacting domains (C1 domains), the resulting complexes are directed to diverse intracellular sites where different sets of substrates are accessed. Multiple cellular bioassays show that DAG-lactones, which bind in vitro to PKCalpha to varying degrees, expand their biological repertoire into a larger domain, eliciting distinct cellular responses.
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Affiliation(s)
- Dehui Duan
- Laboratory of Medicinal Chemistry, National Cancer Institute at Frederick, National Institutes of Health, 376 Boyles Street, Frederick, Maryland 21702, USA
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31
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Abstract
The diacylglycerol-responsive C1 domains of protein kinase C and of the related classes of signaling proteins represent highly attractive targets for drug development. The signaling functions that are regulated by C1 domains are central to cellular control, thereby impacting many pathological conditions. Our understanding of the diacylglycerol signaling pathways provides great confidence in the utility of intervention in these pathways for treatment of cancer and other conditions. Multiple compounds directed at these signaling proteins, including compounds directed at the C1 domains, are currently in clinical trials, providing strong validation for these targets. Extensive understanding of the structure and function of C1 domains, coupled with detailed insights into the molecular details of ligand - C1 domain interactions, provides a solid basis for rational and semi-rational drug design. Finally, the complexity of the factors contributing to ligand - C1 domain interactions affords abundant opportunities for manipulation of selectivity; indeed, substantially selective compounds have already been identified.
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Affiliation(s)
- P M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Center, Bethesda, MD 20892, USA.
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32
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Choi Y, Pu Y, Peach ML, Kang JH, Lewin NE, Sigano DM, Garfield SH, Blumberg PM, Marquez VE. Conformationally Constrained Analogues of Diacylglycerol (DAG). 28. DAG-dioxolanones Reveal a New Additional Interaction Site in the C1b Domain of PKCδ. J Med Chem 2007; 50:3465-81. [PMID: 17591763 DOI: 10.1021/jm0702579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [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
Diacylglycerol (DAG) lactones have provided a powerful platform for structural exploration of the interactions between ligands and the C1 domains of protein kinase C (PKC). In this study, we report that DAG-dioxolanones, novel derivatives of DAG-lactones, exploit an additional point of contact (glutamine 27) in their binding with the C1b domain of PKC delta. Mutation of this point of contact to glutamate selectively impairs binding of the DAG-dioxolanones compared to that of the corresponding DAG-lactones (1200- to 3000-fold versus 35- to 55-fold, respectively). The differential response of this mutated C1b domain to the DAG-dioxolanones relative to the DAG-lactones provides a unique tool to probe the role of the C1b domain in PKC delta function, where the response to the DAG-lactones affords a positive control for retained function. Using this approach, we show that the C1b domain of PKC delta plays the predominant role in the translocation of PKC delta to the membrane in the presence of DAG.
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Affiliation(s)
- Yongseok Choi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
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33
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Pu Y, Peach ML, Garfield SH, Wincovitch S, Marquez VE, Blumberg PM. Effects on Ligand Interaction and Membrane Translocation of the Positively Charged Arginine Residues Situated along the C1 Domain Binding Cleft in the Atypical Protein Kinase C Isoforms. J Biol Chem 2006; 281:33773-88. [PMID: 16950780 DOI: 10.1074/jbc.m606560200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The C1 domain zinc finger structure is highly conserved among the protein kinase C (PKC) superfamily members. As the interaction site for the second messenger sn-1,2-diacylglycerol (DAG) and for the phorbol esters, the C1 domain has been an important target for developing selective ligands for different PKC isoforms. However, the C1 domains of the atypical PKC members are DAG/phorbol ester-insensitive. Compared with the DAG/phorbol ester-sensitive C1 domains, the rim of the binding cleft of the atypical PKC C1 domains possesses four additional positively charged arginine residues (at positions 7, 10, 11, and 20). In this study, we showed that mutation to arginines of the four corresponding sites in the C1b domain of PKCdelta abolished its high potency for phorbol 12,13-dibutyrate in vitro, with only marginal remaining activity for phorbol 12-myristate 13-acetate in vivo. We also demonstrated both in vitro and in vivo that the loss of potency to ligands was cumulative with the introduction of the arginine residues along the rim of the binding cavity rather than the consequence of loss of a single, specific residue. Computer modeling reveals that these arginine residues reduce access of ligands to the binding cleft and change the electrostatic profile of the C1 domain surface, whereas the basic structure of the binding cleft is still maintained. Finally, mutation of the four arginine residues of the atypical PKC C1 domains to the corresponding residues in the deltaC1b domain conferred response to phorbol ester. We speculate that the arginine residues of the C1 domain of atypical PKCs may provide an opportunity for the design of ligands selective for the atypical PKCs.
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Affiliation(s)
- Yongmei Pu
- Laboratory of Cellular Carcinogenesis and Tumor Promotion, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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34
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Jiang S, Li P, Peach ML, Bindu L, Worthy KW, Fisher RJ, Burke TR, Nicklaus M, Roller PP. Structure-based design of potent Grb2–SH2 domain antagonists not relying on phosphotyrosine mimics. Biochem Biophys Res Commun 2006; 349:497-503. [PMID: 16945340 DOI: 10.1016/j.bbrc.2006.08.059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [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: 07/28/2006] [Accepted: 08/05/2006] [Indexed: 12/01/2022]
Abstract
Development of Grb2-SH2 domain antagonists is considered to be an effective and non-cytotoxic strategy to develop new antiproliferative agents because of their potential to shut down the Ras signaling pathway. We developed a concise route for the efficient synthesis of G1TE analogs on solid phase. Using this route, a series of cyclic peptides that do not rely on phosphotyrosine or its mimics were designed and synthesized based upon the phage library-derived cyclopeptide, G1TE. Considering that Gly7 plays prominent roles for G1TE binding to the Grb2-SH2 domain, we introduced different amino acids in the 7th position. The D-Ala7-containing peptide 3 demonstrates improved binding affinity by adopting favorable conformation for protein binding. This can be rationalized by molecular modeling. The optimization at the Leu2 position was also studied, and the resulting cyclopeptides exhibited remarkably improved binding affinity. Based upon these global modifications, a highly potent peptide ligand 9 was discovered with a Kd = 17 nM, evaluated by Biacore binding assay. This new analog is one of the most potent non-phosphorus-containing Grb2-SH2 antagonists reported to date. This potent peptidomimetic provides a new template for the development of non-pTyr containing Grb2-SH2 domain antagonists and acts as a chemotherapeutic lead for the treatment of erbB2-related cancer.
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Affiliation(s)
- Sheng Jiang
- Laboratory of Medicinal Chemistry, NCI, NIH, Frederick, MD 21702, USA
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35
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Kang JH, Benzaria S, Sigano DM, Lewin NE, Pu Y, Peach ML, Blumberg PM, Marquez VE. Conformationally constrained analogues of diacylglycerol. 26. Exploring the chemical space surrounding the C1 domain of protein kinase C with DAG-lactones containing aryl groups at the sn-1 and sn-2 positions. J Med Chem 2006; 49:3185-203. [PMID: 16722637 DOI: 10.1021/jm060011o] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [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: 11/30/2022]
Abstract
Diacylglycerol lactones (DAG-lactones) are known to operate as effective agonists of protein kinase C (PKC), surpassing in potency the activity of natural diacylglycerol (DAG). Localization of activated PKC isozymes in the cell is determined in part by the different cellular scaffolds, the lipid composition of the specific membranes, and the targeting information intrinsic to the individual isoforms bound to DAG. This multifaceted control of diversity suggests that, to develop effective DAG-lactones capable of honing in on a specific cellular target, we need to gain a better understanding of the chemical space surrounding its binding site. Seeking to augment the chemical repertoire of DAG-lactone side chains that could steer the translocation of PKC to specific cellular domains, we report herein the effects of incorporating simple or substituted phenyl residues. A combined series of n-alkyl and phenyl substitutions were used to explore the optimal location of the phenyl group on the side chains. The substantial differences in binding affinity between DAG-lactones with identical functionalized phenyl groups at either the sn-1 or sn-2 position are consistent with the proposed binding model in which the DAG-lactone binds to the C1 domain of PKC with the acyl chain oriented toward the interior of the membrane and the alpha-alkylidene or alpha-arylalkylidene chains directed to the surface of the C1 domain adjacent to the lipid interface. We conclude that DAG-lactones containing alpha-phenylalkylidene side chains at the sn-2 position represent excellent scaffolds upon which to explore further chemical diversity.
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Affiliation(s)
- Ji-Hye Kang
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
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36
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Song YL, Peach ML, Roller PP, Qiu S, Wang S, Long YQ. Discovery of a novel nonphosphorylated pentapeptide motif displaying high affinity for Grb2-SH2 domain by the utilization of 3'-substituted tyrosine derivatives. J Med Chem 2006; 49:1585-96. [PMID: 16509576 DOI: 10.1021/jm050910x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [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
The growth factor receptor-bound protein 2 (Grb2) is an SH2 domain-containing docking module that represents an attractive target for anticancer therapeutic intervention. An impressive number of synthetic Grb2-SH2 domain inhibitors have been identified; however, clinical agents operating by this mechanism are lacking, due in part to the unique requirement of anionic phosphate-mimicking functionality for high SH2 domain-binding affinity or the extended peptide nature of most inhibitors. In the current study, a new binding motif was successfully developed by the incorporation of 3'-substituted tyrosine derivatives into a simplified nonphosphorylated cyclic pentapeptide scaffold (4), which resulted in high affinity Grb2-SH2 inhibitors without any phosphotyrosine or phosphotyrosine mimetics. The new L-amino acid analogues bearing an additional nitro, amino, hydroxy, methoxy or carboxy group at the 3'-position of the phenol ring of tyrosine were prepared in an orthogonally protected form suitable for solid-phase peptide synthesis using Fmoc protocols. The incorporation of these residues into cyclic peptides composed of a five-amino acid sequence motif, Xx(1)-Leu-(3'-substituted-Tyr)-Ac6c-Asn, provided a brand new class of nonphosphorylated Grb2 SH2 domain inhibitors with reduced size, charge and peptidic character. The highest binding affinity was exhibited by the 3'-aminotyrosine (3'-NH2-Tyr)-containing (R)-sulfoxide-cyclized pentapeptide (10b) with an IC50 = 58 nM, the first example with low-nanomolar affinity for a five-amino acid long sequence binding to Grb2-SH2 domain free of any phosphotyrosine or phosphotyrosine mimics. However, the incorporation of 3'-NO2-Tyr, 3'-OH-Tyr or 3'-OCH3-Tyr surrogates in the pentapeptide scaffold is detrimental to Grb2-SH2 binding. These observations were rationalized using molecular modeling. More significantly, the best Grb2-SH2 inhibitor 10b showed excellent activity in inhibiting the growth of erbB2-dependent MDA-MB-453 tumor cell lines with an IC50 value of 19 nM. This study is the first attempt to identify novel nonphosphorylated high affinity Grb2 SH2 inhibitors by the utilization of 3'-substituted tyrosine derivatives, providing a promising new strategy and template for the development of non-pTyr-containing Grb2-SH2 domain antagonists with potent cellular activity, which potentially may find value in chemical therapeutics for erbB2-related cancers.
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Affiliation(s)
- Yan-Li Song
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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37
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Lung FDT, Chang CW, Chong MC, Liou CC, Li P, Peach ML, Nicklaus MC, Lou BS, Roller PP. Small nonphosphorylated Grb2-SH2 domain antagonists evaluated by surface plasmon resonance technology. Biopolymers 2005; 80:628-35. [PMID: 15660381 DOI: 10.1002/bip.20209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The growth factor receptor-binding protein-Src homology 2 (Grb2-SH2) domain plays an important role in the oncogenic Ras signal transduction pathway, which involves cell proliferation and differentiation. Therefore, the Grb2-SH2 domain has been chosen as our target for development of potential antiproliferative agents. Herein, we report the study of the inhibitory effects of small nonphosphorylated peptide analogs interacting with the Grb2-SH2 domain protein by surface plasmon resonance (SPR) technology. A set of 8 related peptide analogs were synthesized, purified, and characterized. Their inhibitory effects on Grb2-SH2 were evaluated by the SPR technology developed with the BIACORE X instrument. The lead peptide, Fmoc-Glu-Tyr-Aib-Asn-NH2 (Fmoc-E-Y-Aib-N; Fmoc: 9-fluorenylmethyoxycarbonyl; Aib=alpha-amino isobutyric acid) inhibited Grb2-SH2 domain function with an IC50 value of 8.7 microM. A molecular modeling study of the lead peptide indicated that the glutamate in the Fmoc peptide is ideally positioned to form a strong salt bridge to Arg 67 in the Grb2-SH2 domain, using both its backbone carbonyl and its acidic group. Residue Glu 89 in Grb2-SH2 flips inward to fill the binding site and partially replace the phosphate group as a hydrogen-bond acceptor. Results of these studies provide important information for further development of potent nonphosphorylated peptide inhibitors of the Grb2-SH2 domain.
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Affiliation(s)
- Feng-Di T Lung
- Department of Chemistry, Tunghai University, Taichung, Taiwan, Republic of China.
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38
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Lai WC, Peach ML, Lybrand TP, Hazelbauer GL. Diagnostic cross-linking of paired cysteine pairs demonstrates homologous structures for two chemoreceptor domains with low sequence identity. Protein Sci 2005; 15:94-101. [PMID: 16322572 PMCID: PMC2242362 DOI: 10.1110/ps.051802806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 10/25/2022]
Abstract
Hundreds of bacterial chemoreceptors from many species have periplasmic, ligand-recognition domains of approximately the same size, but little or no sequence identity. The only structure determined is for the periplasmic domain of chemoreceptor Tar from Salmonella and Escherichia coli. Do sequence-divergent but similarly sized chemoreceptor periplasmic domains have related structures? We addressed this issue for the periplasmic domain of chemoreceptor Trg(E) from E. coli, which has a low level of sequence similarity to Tar, by combining homology modeling and diagnostic cross-linking between pairs of introduced cysteines. A homology model of the Trg(E) domain was created using the homodimeric, four-helix bundle structure of the Tar(S) domain from Salmonella. In this model, we chose four pairs of positions at which introduced cysteines would be sufficiently close to form disulfides across each of four different helical interfaces. For each pair we chose a second pair, in which one cysteine of the original pair was shifted by one position around the helix and thus would be less favorably placed for disulfide formation. We created genes coding for proteins containing four such pairs of cysteine pairs and investigated disulfide formation in vivo as well as functional consequences of the substitutions and disulfides between neighboring helices. Results of the experimental tests provided strong support for the accuracy of the model, indicating that the Trg(E) periplasmic domain is very similar to the Tar(S) domain. Diagnostic cross-linking of paired pairs of introduced cysteines could be applied generally as a stringent test of homology models.
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Affiliation(s)
- Wing-Cheung Lai
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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39
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Kang JH, Peach ML, Pu Y, Lewin NE, Nicklaus MC, Blumberg PM, Marquez VE. Conformationally constrained analogues of diacylglycerol (DAG). 25. Exploration of the sn-1 and sn-2 carbonyl functionality reveals the essential role of the sn-1 carbonyl at the lipid interface in the binding of DAG-lactones to protein kinase C. J Med Chem 2005; 48:5738-48. [PMID: 16134942 PMCID: PMC2563800 DOI: 10.1021/jm050352m] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [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: 11/30/2022]
Abstract
Diacylglycerol (DAG) lactones with altered functionality (C=O --> CH(2) or C=O --> C=S) at the sn-1 and sn-2 carbonyl pharmacophores were synthesized and used as probes to dissect the individual role of each carbonyl in the binding to protein kinase C (PKC). The results suggest that the hydrated sn-1 carbonyl is engaged in very strong hydrogen-bonding interactions with the charged lipid headgroups and organized water molecules at the lipid interface. Conversely, the sn-2 carbonyl has a more modest contribution to the binding process as a result of its involvement with the receptor (C1 domain) via conventional hydrogen bonding to the protein. The parent DAG-lactones, E-6 and Z-7, were designed to bind exclusively in the sn-2 binding mode to ensure the correct orientation and disposition of pharmacophores at the binding site.
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Affiliation(s)
- Ji-Hye Kang
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Megan L. Peach
- Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702
| | - Yongmei Pu
- Laboratory of Cellular Carcinogenesis & Tumor Promotion, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Nancy E. Lewin
- Laboratory of Cellular Carcinogenesis & Tumor Promotion, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Marc C. Nicklaus
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
| | - Peter M. Blumberg
- Laboratory of Cellular Carcinogenesis & Tumor Promotion, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Victor E. Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702
- Author to whom correspondence should be addressed. Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702Tel: 301-846-5954. Fax: 301-846-6033.
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Simmons DP, Peach ML, Friedman JR, Green MMB, Nicklaus MC, De Luca LM. Evidence that sequence homologous region in LRAT-like proteins possesses anti-proliferative activity and DNA binding properties: translational implications and mechanism of action. Carcinogenesis 2005; 27:693-707. [PMID: 16234259 DOI: 10.1093/carcin/bgi235] [Citation(s) in RCA: 14] [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: 11/14/2022] Open
Abstract
LRAT (lecithin:retinol acyltransferase), an enzyme whose levels are modulated during malignant conversion, has been reported as the founder member of a new LRAT-like family that includes tumor suppressors TIG-3(1-164) and Ha-Rev107(1-162). The mechanisms that link these three proteins to carcinogenesis as well as the significance of a reported shared sequence homologous region remain unclear. This begs the question if the tumor suppressors possess enzyme properties and/or if the LRAT enzyme possesses tumor suppressor properties. We use the reported homologous region as a first approach to address the question from the perspective that all three proteins can possess tumor suppressor properties. We postulated that the homologous sequence harbors an anti-proliferation domain within the full-length proteins and that dodecapeptides of this sequence possess anti-proliferative activity. We report that H-TIG-3(111-123), H-Ha-Rev107-1(111-123) and H-LRAT160-171:C168L exhibited in vitro growth inhibitory activity in a human cutaneous melanoma (HCM) model and affected tumor growth in a nude mouse model. Further, in peptide-sensitive HCM cells, these peptides crossed the plasma membrane and localized to the nucleus, where they could bind and activate promoters of transcription factors involved in G1-->S transition. Moreover, peptide-induced abrogation of cyclin dependent kinase-2 expression was concomitant with sub-cellular re-distribution of cyclins E and A. Indeed, the sequence homologous region within each full-length wild-type protein as well as the growth inhibitory peptides can form alpha helices, a likely configuration for binding to DNA. This is the first report that this sequence homologous region (AA111-123) within these LRAT-like proteins harbors an anti-proliferative domain with DNA binding properties. Sequences from this sequence homologous region can be used as templates for anti-tumor drug design and as probes to investigate disease-related mechanisms and structure-activity relationships of the full-length proteins, TIG-3(1-164), Ha-Rev107(1-162) and LRAT160-171.
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Affiliation(s)
- Denise Perry Simmons
- Laboratory of Cellular Carcinogenesis and Tumor Promotion, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Tamamura H, Sigano DM, Lewin NE, Peach ML, Nicklaus MC, Blumberg PM, Marquez VE. Conformationally constrained analogues of diacylglycerol (DAG). 23. Hydrophobic ligand-protein interactions versus ligand-lipid interactions of DAG-lactones with protein kinase C (PK-C). J Med Chem 2004; 47:4858-64. [PMID: 15369389 DOI: 10.1021/jm049723+] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The constrained glycerol backbone of DAG-lactones, when combined with highly branched alkyl chains, has engendered a series of DAG-lactone ligands capable of binding protein kinase C (PK-C) with affinities that approximate those of phorbol esters. These branched chains not only appear to be involved in making important hydrophobic contacts with the protein (specific interactions) but also provide adequate lipophilicity to facilitate partitioning into the lipid-rich membrane environment (nonspecific interactions). With the idea of minimizing the nonspecific interactions without reducing lipophilicity, the present work explores the strategy of relocating lipophilicity from the side chain to the lactone "core". Such a transfer of lipophilicity, exemplified by compounds 1 and 3, was conceived to allow the new hydrophobic groups on the lactone to engage in specific hydrophobic contacts inside the binding pocket without any expectation of interfering with the hydrogen-bonding network of the DAG-lactone pharmacophore. Surprisingly, both (E)-3 and (Z)-3 showed a significant decrease in binding affinity. From the molecular docking studies performed with the new ligands, we conclude that the binding pocket of the C1 domain of PK-C is sterically restricted and prevents the methyl groups at the C-3 position of the lactone from engaging in productive hydrophobic contacts with the receptor.
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Affiliation(s)
- Hirokazu Tamamura
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Building 376, Room 104, Frederick, Maryland 21702, USA
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Li P, Zhang M, Peach ML, Liu H, Yang D, Roller PP. Concise and enantioselective synthesis of Fmoc-Pmp(But)2-OH and design of potent Pmp-containing Grb2-SH2 domain antagonists. Org Lett 2003; 5:3095-8. [PMID: 12916990 DOI: 10.1021/ol035078+] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] L-Phosphonomethylphenylalanine (L-Pmp) is an important phosphatase-resistant pTyr analogue. A most concise and stereoselective approach to the synthesis of the suitably protected Fmoc-Pmp(Bu(t))(2)-OH was developed in order to incorporate the functionally significant L-Pmp residue into peptides and peptidomimetics efficiently using standard Fmoc protocol. With this key building block, we are able to efficiently synthesize a series of potent Pmp-containing Grb2-SH2 domain antagonists, which can be used as chemotherapeutic leads for the treatment of erbB2-overexpressed breast cancer.
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Affiliation(s)
- Peng Li
- Laboratory of Medicinal Chemistry, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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43
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Li P, Zhang M, Peach ML, Zhang X, Liu H, Nicklaus M, Yang D, Roller PP. Structural basis for a non-phosphorus-containing cyclic peptide binding to Grb2-SH2 domain with high affinity. Biochem Biophys Res Commun 2003; 307:1038-44. [PMID: 12878216 DOI: 10.1016/s0006-291x(03)01291-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Blocking the interaction between phosphotyrosine (pTyr)-containing activated receptors and the Src homology 2 (SH2) domain of the growth factor receptor bound protein 2 (Grb2) is considered to be an effective and non-cytotoxic strategy to develop new anti-proliferative agents due to its potential to shut down the Ras activation pathway. Generally, the pTyr-X-Asn minimal binding motif is required for a high-affinity ligand binding to the Grb2-SH2 domain. Using phage-display techniques, we discovered a non-pTyr-containing cyclic peptide G1 with moderate binding affinity from 10(7) different sequences. To understand the structural basis for the high-affinity binding of these novel non-phosphorus-containing inhibitors to the Grb2-SH2 domain, we extensively studied herein the unique functional requirements of the acidic side chain in Tyr-2 position due to the absence of the phosphate group in these non-phosphorylated peptides. A comprehensive SAR study was also carried out to develop potent Grb2-SH2 domain antagonists based upon this novel template. With both the peptidomimetic optimization of the amino acid side-chains and the constraint of the backbone conformation guided by molecular modeling, we developed several potent antagonists with low nanomolar range binding affinity, such as cyclic peptide 20 with an IC(50)=0.026 microM, which is one of the most potent non-phosphorus-containing Grb2-SH2 antagonists reported to date. Whole cell assays indicate that peptide 20 can penetrate the cell membranes and inhibit the association of Grb2 with p185(erbB2) in erbB2-overexpressing MDA-MA-453 cancer cells at low micromolar concentrations.
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Affiliation(s)
- Peng Li
- Laboratory of Medicinal Chemistry, National Cancer Institute, National Institutes of Health, 376 Boyles Street, Frederick, MD 21702-1201, USA
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Li P, Zhang M, Long YQ, Peach ML, Liu H, Yang D, Nicklaus M, Roller PP. Potent Grb2-SH2 domain antagonists not relying on phosphotyrosine mimics. Bioorg Med Chem Lett 2003; 13:2173-7. [PMID: 12798329 DOI: 10.1016/s0960-894x(03)00385-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Development of Grb2-SH2 domain antagonists is an effective approach to inhibit the growth of malignant cells by modulating Grb2-related Ras signaling. We report here potent Grb2-SH2 domain antagonists that do not rely on phosphotyrosine or its mimics. These non-phosphorylated antagonists were developed and further modified by constraining the backbone conformation and optimizing amino acid side chains of a phage library-derived peptide, G1TE. After extensive SAR studies and structural optimization, non-phosphorylated peptide 12 was discovered with an IC(50) of 75 nM. This potent peptidomimetic provides a novel template for the development of non-pTyr containing Grb2-SH2 domain antagonists and acts as a chemotherapeutic lead for the treatment of erbB2-related cancer.
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Affiliation(s)
- Peng Li
- Laboratory of Medicinal Chemistry, National Cancer Institute, National Institutes of Health, 21702, Frederick, MD, USA
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45
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Sigano DM, Peach ML, Nacro K, Choi Y, Lewin NE, Nicklaus MC, Blumberg PM, Marquez VE. Differential binding modes of diacylglycerol (DAG) and DAG lactones to protein kinase C (PK-C). J Med Chem 2003; 46:1571-9. [PMID: 12699375 DOI: 10.1021/jm020476o] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diacylglycerol lactones (DAG lactones), analogous to highly potent diacylglycerols (DAGs) were synthesized to demonstrate the ability of PK-C to discriminate between two differential binding modes, sn-1 and sn-2. While both sn-1 and sn-2 binding modes are allowable in terms of hydrogen bonding, it has been found that in general, DAGs prefer to bind sn-1, while the corresponding analogous DAG lactones prefer to bind sn-2. However, this binding orientation can be directly influenced by the disposition and nature of the acyl substituent, particularly if it is highly branched. When the "binding driving force" (i.e., the larger branched acyl chain) is in the sn-2 position, a dramatic increase in binding affinity is observed in the DAG lactone as compared to its open chain DAG counterpart. As these analogous DAGs and DAG lactones have almost identical log P values, this difference in binding affinity is a direct result of the entropic advantage of constraining the glycerol backbone.
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Affiliation(s)
- Dina M Sigano
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
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46
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Li P, Peach ML, Zhang M, Liu H, Yang D, Nicklaus M, Roller PP. Structure-based design of thioether-bridged cyclic phosphopeptides binding to Grb2-SH2 domain. Bioorg Med Chem Lett 2003; 13:895-9. [PMID: 12617916 DOI: 10.1016/s0960-894x(03)00015-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A series of phosphotyrosine containing cyclic peptides was designed and synthesized based upon the phage library derived cyclopeptide, G1TE. Considering the type-I beta-turn feature of peptidic ligand binding to Grb2 SH2 domain, we introduce alpha,alpha-disubstituted cyclic amino acid, Ach, into the 4th position of the cyclic peptide to induce a local right handed 3(10) helical conformation. In order to stabilize the favorable binding conformation, the bulky and hydrophobic amino acids, neopentylglycine (NPG) and phenylalanine, were introduced into the 8th and 2nd positions of the peptide ligand, respectively. To facilitate the sidechain of pTyr3 reaching into the phosphotyrosine binding pocket, a less bulky alanine was preferred in position 1. Based upon these global modifications, a highly potent peptide ligand 12 was discovered with an IC(50)=1.68 nM, evaluated by ELISA binding essay. Ligand 12 is at least 10(5) more potent than the lead peptide, termed G1TE.
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Affiliation(s)
- Peng Li
- Laboratory of Medicinal Chemistry, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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Abstract
Bacterial chemoreceptors signal across the membrane by conformational changes that traverse a four-helix transmembrane domain. High-resolution structures are available for the chemoreceptor periplasmic domain and part of the cytoplasmic domain but not for the transmembrane domain. Thus, we constructed molecular models of the transmembrane domains of chemoreceptors Trg and Tar, using coordinates of an unrelated four-helix coiled coil as a template and the X-ray structure of a chemoreceptor periplasmic domain to establish register and positioning. We tested the models using the extensive data for cross-linking propensities between cysteines introduced into adjacent transmembrane helices, and we found that many aspects of the models corresponded with experimental observations. The one striking disparity, the register of transmembrane helix 2 (TM2) relative to its partner transmembrane helix 1, could be corrected by sliding TM2 along its long axis toward the periplasm. The correction implied that axial sliding of TM2, the signaling movement indicated by a large body of data, was of greater magnitude than previously thought. The refined models were used to assess effects of inter-helical disulfides on the two ligand-induced conformational changes observed in alternative crystal structures of periplasmic domains: axial sliding within a subunit and subunit rotation. Analyses using a measure of disulfide potential energy provided strong support for the helical sliding model of transmembrane signaling but indicated that subunit rotation could be involved in other ligand-induced effects. Those analyses plus modeled distances between diagnostic cysteine pairs indicated a magnitude for TM2 sliding in transmembrane signaling of several angstroms.
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Affiliation(s)
- Megan L Peach
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
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