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Miller EB, Hwang H, Shelley M, Placzek A, Rodrigues JPGLM, Suto RK, Wang L, Akinsanya K, Abel R. Enabling structure-based drug discovery utilizing predicted models. Cell 2024; 187:521-525. [PMID: 38306979 DOI: 10.1016/j.cell.2023.12.034] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 02/04/2024]
Abstract
High-quality predicted structures enable structure-based approaches to an expanding number of drug discovery programs. We propose that by utilizing free energy perturbation (FEP), predicted structures can be confidently employed to achieve drug design goals. We use structure-based modeling of hERG inhibition to illustrate this value of FEP.
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Affiliation(s)
- Edward B Miller
- Schrödinger New York, 1540 Broadway, 24th Floor, New York, NY 10036, USA.
| | - Howook Hwang
- Schrödinger New York, 1540 Broadway, 24th Floor, New York, NY 10036, USA
| | - Mee Shelley
- Schrödinger Portland, 101 SW Main Street, Suite 1300, Portland, OR 97204, USA
| | - Andrew Placzek
- Schrödinger Portland, 101 SW Main Street, Suite 1300, Portland, OR 97204, USA
| | | | - Robert K Suto
- Schrödinger Framingham, 200 Staples Drive, Suite 210, Framingham, MA 01702, USA
| | - Lingle Wang
- Schrödinger New York, 1540 Broadway, 24th Floor, New York, NY 10036, USA
| | - Karen Akinsanya
- Schrödinger New York, 1540 Broadway, 24th Floor, New York, NY 10036, USA
| | - Robert Abel
- Schrödinger New York, 1540 Broadway, 24th Floor, New York, NY 10036, USA
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2
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Cole AG, Kultgen SG, Mani N, Ardzinski A, Fan KY, Thi EP, Dorsey BD, Stever K, Chiu T, Tang S, Daly O, Phelps JR, Harasym T, Olland A, Suto RK, Sofia MJ. The identification of highly efficacious functionalised tetrahydrocyclopenta[ c]pyrroles as inhibitors of HBV viral replication through modulation of HBV capsid assembly. RSC Med Chem 2022; 13:343-349. [PMID: 35434625 PMCID: PMC8942244 DOI: 10.1039/d1md00318f] [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] [Received: 09/30/2021] [Accepted: 01/17/2022] [Indexed: 01/21/2023] Open
Abstract
Disruption of the HBV viral life cycle with small molecules that prevent the encapsidation of pregenomic RNA and viral polymerase through binding to HBV core protein is a clinically validated approach to inhibiting HBV viral replication. Herein we report the further optimisation of clinical candidate AB-506 through core modification with a focus on increasing oral exposure and oral half-life. Maintenance of high levels of anti-HBV cellular potency in conjunction with improvements in pharmacokinetic properties led to multi-log10 reductions in serum HBV DNA following low, once-daily oral dosing for key analogues in a preclinical animal model of HBV replication.
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Affiliation(s)
- Andrew G. Cole
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | | | - Nagraj Mani
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | | | - Kristi Yi Fan
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | - Emily P. Thi
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | - Bruce D. Dorsey
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | - Kim Stever
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | - Tim Chiu
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | - Sunny Tang
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | - Owen Daly
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | - Janet R. Phelps
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | - Troy Harasym
- Arbutus Biopharma, Inc.701 Veterans CircleWarminsterPA 18974USA
| | - Andrea Olland
- Xtal BioStructures Inc.12 Michigan DriveNatickMA 01760USA
| | - Robert K. Suto
- Xtal BioStructures Inc.12 Michigan DriveNatickMA 01760USA
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3
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Park JJ, Thi EP, Carpio VH, Bi Y, Cole AG, Dorsey BD, Fan K, Harasym T, Iott CL, Kadhim S, Kim JH, Lee ACH, Nguyen D, Paratala BS, Qiu R, White A, Lakshminarasimhan D, Leo C, Suto RK, Rijnbrand R, Tang S, Sofia MJ, Moore CB. Checkpoint inhibition through small molecule-induced internalization of programmed death-ligand 1. Nat Commun 2021; 12:1222. [PMID: 33619272 PMCID: PMC7900207 DOI: 10.1038/s41467-021-21410-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 01/26/2021] [Indexed: 12/19/2022] Open
Abstract
Programmed death-ligand 1 is a glycoprotein expressed on antigen presenting cells, hepatocytes, and tumors which upon interaction with programmed death-1, results in inhibition of antigen-specific T cell responses. Here, we report a mechanism of inhibiting programmed death-ligand 1 through small molecule-induced dimerization and internalization. This represents a mechanism of checkpoint inhibition, which differentiates from anti-programmed death-ligand 1 antibodies which function through molecular disruption of the programmed death 1 interaction. Testing of programmed death ligand 1 small molecule inhibition in a humanized mouse model of colorectal cancer results in a significant reduction in tumor size and promotes T cell proliferation. In addition, antigen-specific T and B cell responses from patients with chronic hepatitis B infection are significantly elevated upon programmed death ligand 1 small molecule inhibitor treatment. Taken together, these data identify a mechanism of small molecule-induced programmed death ligand 1 internalization with potential therapeutic implications in oncology and chronic viral infections.
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Affiliation(s)
| | | | | | - Yingzhi Bi
- Arbutus Biopharma Inc, Warminster, PA, USA
| | | | | | - Kristi Fan
- Arbutus Biopharma Inc, Warminster, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sunny Tang
- Arbutus Biopharma Inc, Warminster, PA, USA
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4
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Vicens Q, Mondragón E, Reyes FE, Coish P, Aristoff P, Berman J, Kaur H, Kells KW, Wickens P, Wilson J, Gadwood RC, Schostarez HJ, Suto RK, Blount KF, Batey RT. Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch. ACS Chem Biol 2018; 13:2908-2919. [PMID: 30107111 DOI: 10.1021/acschembio.8b00533] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The flavin mononucleotide (FMN) riboswitch is an emerging target for the development of novel RNA-targeting antibiotics. We previously discovered an FMN derivative, 5FDQD, that protects mice against diarrhea-causing Clostridium difficile bacteria. Here, we present the structure-based drug design strategy that led to the discovery of this fluoro-phenyl derivative with antibacterial properties. This approach involved the following stages: (1) structural analysis of all available free and bound FMN riboswitch structures; (2) design, synthesis, and purification of derivatives; (3) in vitro testing for productive binding using two chemical probing methods; (4) in vitro transcription termination assays; and (5) resolution of the crystal structures of the FMN riboswitch in complex with the most mature candidates. In the process, we delineated principles for productive binding to this riboswitch, thereby demonstrating the effectiveness of a coordinated structure-guided approach to designing drugs against RNA.
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Affiliation(s)
- Quentin Vicens
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Estefanía Mondragón
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Francis E. Reyes
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Philip Coish
- BioRelix Inc., 124 Washington Street, Foxborough, Massachusetts 02035, United States
| | - Paul Aristoff
- Aristoff Consulting LLC, 3726 Green Spring Drive, Fort Collins, Colorado 80528, United States
| | - Judd Berman
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Harpreet Kaur
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Kevin W. Kells
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Phil Wickens
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Jeffery Wilson
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Robert C. Gadwood
- Kalexsyn, Inc., 4502 Campus Drive, Kalamazoo, Michigan 49008, United States
| | | | - Robert K. Suto
- Xtal BioStructures, Inc., 12 Michigan Drive, Natick, Massachusetts 01760, United States
| | - Kenneth F. Blount
- BioRelix Inc., 124 Washington Street, Foxborough, Massachusetts 02035, United States
| | - Robert T. Batey
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
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5
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Kharenko OA, Gesner EM, Patel RG, Norek K, White A, Fontano E, Suto RK, Young PR, McLure KG, Hansen HC. RVX-297- a novel BD2 selective inhibitor of BET bromodomains. Biochem Biophys Res Commun 2016; 477:62-67. [PMID: 27282480 DOI: 10.1016/j.bbrc.2016.06.021] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/05/2016] [Indexed: 11/26/2022]
Abstract
Bromodomains are epigenetic readers that specifically bind to the acetyl lysine residues of histones and transcription factors. Small molecule BET bromodomain inhibitors can disrupt this interaction which leads to potential modulation of several disease states. Here we describe the binding properties of a novel BET inhibitor RVX-297 that is structurally related to the clinical compound RVX-208, currently undergoing phase III clinical trials for the treatment of cardiovascular diseases, but is distinctly different in its biological and pharmacokinetic profiles. We report that RVX-297 preferentially binds to the BD2 domains of the BET bromodomain and Extra Terminal (BET) family of protein. We demonstrate the differential binding modes of RVX-297 in BD1 and BD2 domains of BRD4 and BRD2 using X-ray crystallography, and describe the structural differences driving the BD2 selective binding of RVX-297. The isothermal titration calorimetry (ITC) data illustrate the related differential thermodynamics of binding of RVX-297 to single as well as dual BET bromodomains.
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Affiliation(s)
- Olesya A Kharenko
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada.
| | - Emily M Gesner
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Reena G Patel
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Karen Norek
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Andre White
- Xtal BioStructures, Inc., 12 Michigan Dr., Natick, MA 01760, USA
| | - Eric Fontano
- Xtal BioStructures, Inc., 12 Michigan Dr., Natick, MA 01760, USA
| | - Robert K Suto
- Xtal BioStructures, Inc., 12 Michigan Dr., Natick, MA 01760, USA
| | - Peter R Young
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Kevin G McLure
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
| | - Henrik C Hansen
- Zenith Epigenetics, Suite 300, 4820 Richard Road SW, Calgary, Alberta, T3E 6L1, Canada
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6
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Duffy BC, Liu S, Martin GS, Wang R, Hsia MM, Zhao H, Guo C, Ellis M, Quinn JF, Kharenko OA, Norek K, Gesner EM, Young PR, McLure KG, Wagner GS, Lakshminarasimhan D, White A, Suto RK, Hansen HC, Kitchen DB. Discovery of a new chemical series of BRD4(1) inhibitors using protein-ligand docking and structure-guided design. Bioorg Med Chem Lett 2015; 25:2818-23. [PMID: 26022843 DOI: 10.1016/j.bmcl.2015.04.107] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 12/12/2022]
Abstract
Bromodomains are key transcriptional regulators that are thought to be druggable epigenetic targets for cancer, inflammation, diabetes and cardiovascular therapeutics. Of particular importance is the first of two bromodomains in bromodomain containing 4 protein (BRD4(1)). Protein-ligand docking in BRD4(1) was used to purchase a small, focused screening set of compounds possessing a large variety of core structures. Within this set, a small number of weak hits each contained a dihydroquinoxalinone ring system. We purchased other analogs with this ring system and further validated the new hit series and obtained improvement in binding inhibition. Limited exploration by new analog synthesis showed that the binding inhibition in a FRET assay could be improved to the low μM level making this new core a potential hit-to-lead series. Additionally, the predicted geometries of the initial hit and an improved analog were confirmed by X-ray co-crystallography with BRD4(1).
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Affiliation(s)
- Bryan C Duffy
- Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
| | - Shuang Liu
- Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
| | - Gregory S Martin
- Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
| | - Ruifang Wang
- Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
| | - Ming Min Hsia
- Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
| | - He Zhao
- Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
| | - Cheng Guo
- Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
| | - Michael Ellis
- Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA
| | - John F Quinn
- JFQuinn Consulting, 113 Jay St., Albany, NY 12210, USA
| | - Olesya A Kharenko
- Zenith Epigenetics Corp., Suite 300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | - Karen Norek
- Zenith Epigenetics Corp., Suite 300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | - Emily M Gesner
- Zenith Epigenetics Corp., Suite 300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | - Peter R Young
- Zenith Epigenetics Corp., Suite 300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | - Kevin G McLure
- Zenith Epigenetics Corp., Suite 300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | - Gregory S Wagner
- Zenith Epigenetics Corp., Suite 300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | | | - Andre White
- Xtal BioStructures, Inc., 12 Michigan Dr., Natick, MA 01760, USA
| | - Robert K Suto
- Xtal BioStructures, Inc., 12 Michigan Dr., Natick, MA 01760, USA
| | - Henrik C Hansen
- Zenith Epigenetics Corp., Suite 300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | - Douglas B Kitchen
- Albany Molecular Research (AMRI), 26 Corporate Circle, PO Box 15098, Albany, NY 12212-5098, USA.
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7
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McLure KG, Gesner EM, Tsujikawa L, Kharenko OA, Attwell S, Campeau E, Wasiak S, Stein A, White A, Fontano E, Suto RK, Wong NCW, Wagner GS, Hansen HC, Young PR. RVX-208, an inducer of ApoA-I in humans, is a BET bromodomain antagonist. PLoS One 2013; 8:e83190. [PMID: 24391744 PMCID: PMC3877016 DOI: 10.1371/journal.pone.0083190] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [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: 07/06/2013] [Accepted: 11/09/2013] [Indexed: 12/19/2022] Open
Abstract
Increased synthesis of Apolipoprotein A-I (ApoA-I) and HDL is believed to provide a new approach to treating atherosclerosis through the stimulation of reverse cholesterol transport. RVX-208 increases the production of ApoA-I in hepatocytes in vitro, and in vivo in monkeys and humans, which results in increased HDL-C, but the molecular target was not previously reported. Using binding assays and X-ray crystallography, we now show that RVX-208 selectively binds to bromodomains of the BET (Bromodomain and Extra Terminal) family, competing for a site bound by the endogenous ligand, acetylated lysine, and that this accounts for its pharmacological activity. siRNA experiments further suggest that induction of ApoA-I mRNA is mediated by BET family member BRD4. These data indicate that RVX-208 increases ApoA-I production through an epigenetic mechanism and suggests that BET inhibition may be a promising new approach to the treatment of atherosclerosis.
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Affiliation(s)
- Kevin G McLure
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Emily M Gesner
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Laura Tsujikawa
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Olesya A Kharenko
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Sarah Attwell
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Eric Campeau
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Sylwia Wasiak
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Adam Stein
- Xtal BioStructures Inc., Natick, Maryland, United States of America
| | - Andre White
- Xtal BioStructures Inc., Natick, Maryland, United States of America
| | - Eric Fontano
- Xtal BioStructures Inc., Natick, Maryland, United States of America
| | - Robert K Suto
- Xtal BioStructures Inc., Natick, Maryland, United States of America
| | - Norman C W Wong
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Gregory S Wagner
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Henrik C Hansen
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
| | - Peter R Young
- Resverlogix Corp., Calgary, Alberta, Canada, or San Francisco, California, United States of America
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8
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Abstract
The last five years have seen exciting advances in our understanding of the structure of the nucleosome core particle, the basic repeating unit in all eukaryotic chromatin. A picture emerges in which nucleosomal DNA, while distorted and compacted fivefold by tight interactions with the histone octamer core, is at the same time highly dynamic and adaptable. Here, we summarize the salient features from recent structural studies of nucleosome core particles (both published and unpublished) that concern the structure and dynamics of nucleosomal DNA, and the nature of protein-DNA interactions. Current mechanisms for chromatin remodeling and nucleosome sliding are discussed in light of new structural evidence. Finally, techniques to study nucleosome stability and ultimately dynamics are introduced.
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Affiliation(s)
- Uma M Muthurajan
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523-1870, USA
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9
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Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K. Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands. J Mol Biol 2003; 326:371-80. [PMID: 12559907 DOI: 10.1016/s0022-2836(02)01407-9] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [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: 01/08/2023]
Abstract
We determined the crystal structures of three nucleosome core particles in complex with site-specific DNA-binding ligands, the pyrrole-imidazole polyamides. While the structure of the histone octamer and its interaction with the DNA remain unaffected by ligand binding, nucleosomal DNA undergoes significant structural changes at the ligand-binding sites and in adjacent regions to accommodate the ligands. Our findings suggest that twist diffusion occurs over long distances through tightly bound nucleosomal DNA. This may be relevant to the mechanism of ATP-dependent and spontaneous nucleosome translocation, and to the effect of bound factors on nucleosome dynamics.
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Affiliation(s)
- Robert K Suto
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
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10
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Abstract
Chromatin is composed of nucleosomes, the universally repeating protein-DNA complex in eukaryotic cells. The crystal structure of the nucleosome core particle from Saccharomyces cerevisiae reveals that the structure and function of this fundamental complex is conserved between single-cell organisms and metazoans. Our results show that yeast nucleosomes are likely to be subtly destabilized as compared with nucleosomes from higher eukaryotes, consistent with the idea that much of the yeast genome remains constitutively open during much of its life cycle. Importantly, minor sequence variations lead to dramatic changes in the way in which nucleosomes pack against each other within the crystal lattice. This has important implications for our understanding of the formation of higher order chromatin structure and its modulation by post-translational modifications. Finally, the yeast nucleosome core particle provides a structural context by which to interpret genetic data obtained from yeast. Coordinates have been deposited with the Protein Data Bank under accession number 1ID3.
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Affiliation(s)
| | | | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
Corresponding author e-mail:
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11
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Gottesfeld JM, Melander C, Suto RK, Raviol H, Luger K, Dervan PB. Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides. J Mol Biol 2001; 309:615-29. [PMID: 11397084 DOI: 10.1006/jmbi.2001.4694] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [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: 11/22/2022]
Abstract
The ability of DNA-binding proteins to recognize their cognate sites in chromatin is restricted by the structure and dynamics of nucleosomal DNA, and by the translational and rotational positioning of the histone octamer. Here, we use six different pyrrole-imidazole polyamides as sequence-specific molecular probes for DNA accessibility in nucleosomes. We show that sites on nucleosomal DNA facing away from the histone octamer, or even partially facing the histone octamer, are fully accessible and that nucleosomes remain fully folded upon ligand binding. Polyamides only failed to bind where sites are completely blocked by interactions with the histone octamer. Removal of the amino-terminal tails of either histone H3 or histone H4 allowed these polyamides to bind. These results demonstrate that much of the DNA in the nucleosome is freely accessible for molecular recognition in the minor groove, and also support a role for the amino-terminal tails of H3 and H4 in modulating accessibility of nucleosomal DNA.
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Affiliation(s)
- J M Gottesfeld
- Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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12
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Suto RK, Brasch NE, Anderson OP, Finke RG. Synthesis, Characterization, Solution Stability, and X-ray Crystal Structure of the Thiolatocobalamin γ-Glutamylcysteinylcobalamin, a Dipeptide Analogue of Glutathionylcobalamin: Insights into the Enhanced Co−S Bond Stability of the Natural Product Glutathionylcobalamin. Inorg Chem 2001; 40:2686-92. [PMID: 11375680 DOI: 10.1021/ic001365n] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [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
Glutathionylcobalamin (gamma-glutamylcysteinylglycinylcobalamin; gamma-GluCysGly-Cbl) is a natural product which functions as an intermediate in the biosynthesis of the active B(12) coenzymes adenosylcobalamin and methylcobalamin. Of interest to the present studies is glutathionylcobalamin's unique stability in comparison to other thiolatocobalamins, notably the > or =6 x 10(4) fold less stable cysteinylcobalamin, Cys-Cbl. In order to determine which parts of the glutathione tripeptide contribute to the overall stability of glutathionylcobalamin, two cysteine-containing dipeptides, which are truncated versions of glutathione, were used to synthesize their corresponding cobalamins, specifically gamma-glutamylcysteinylCbl (gamma-GluCys-Cbl) and cysteinylglycinylcobalamin (CysGly-Cbl). As with glutathionylCbl, the dipeptide gamma-GluCys-Cbl forms a stable thiolatocobalamin. However and most interestingly, CysGly-Cbl is observed to be unstable much like Cys-Cbl. The results require that the extra stability of glutathionylcobalamin and its congeners, compared to cysteinylcobalamin and its analogues, must be derived from destabilization by the gamma-NH(3)(+) group in cysteinylcobalamin, or stabilization by the gamma-NHC(=O)- amide linkage in glutathionylcobalamin, or both. To probe any ground-state structural basis for the possible stabilization in gamma-GluCys-containing cobalamins, gamma-GluCys-Cbl was crystallized and yielded the first X-ray structural determination of a true thiolatocobalamin, and only the second structure of a cobalamin containing a Co-S bond, the first example being Randaccio and co-workers' 1999 structure of the thioketone complex, thioureacobalamin, (NH(2))(2)CSCbl. Key features of the structure of gamma-glutamylcysteinylcobalamin include (i) a normal Co-S bond length of 2.267(2) A, (ii) a Co-N(axial) bond length of 2.049(6) A, (iii) two alternate conformations of the gamma-glutamylcysteinyl moiety, and (iv) folding of the corrin ring upward by 24.2 degrees, the highest degree of folding yet observed for a cobalamin. These results do not show any strong stabilization (e.g., no shortened Co-S bond), although it is not clear for certain what the effect is (stabilizing or destabilizing) of the elongated Co-N(axial) bond; instead, the crystallographic results suggest that the metastable Cys-Cbl probably has a Co-S cleavage transition state that is stabilized (along with, possibly, any ground-state destabilization of the Co-S bond). Overall, the results strongly suggest that placing a positive charge on the gamma-NH(3)(+) stabilizes the Co-S bond cleavage transition state, thereby setting the stage for the needed full thermolysis product and kinetic studies-as a function of the axial-base on-off equilibrium-that will be required to understand in even greater detail the unique stability of glutathionyl- (gamma-glutamylcysteinylglycinyl-) and gamma-glutamylcysteinylcobalamins.
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Affiliation(s)
- R K Suto
- Department of Biochemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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Suto RK, Clarkson MJ, Tremethick DJ, Luger K. Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat Struct Biol 2000; 7:1121-4. [PMID: 11101893 DOI: 10.1038/81971] [Citation(s) in RCA: 397] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Activation of transcription within chromatin has been correlated with the incorporation of the essential histone variant H2A.Z into nucleosomes. H2A.Z and other histone variants may establish structurally distinct chromosomal domains; however, the molecular mechanism by which they function is largely unknown. Here we report the 2.6 A crystal structure of a nucleosome core particle containing the histone variant H2A.Z. The overall structure is similar to that of the previously reported 2.8 A nucleosome structure containing major histone proteins. However, distinct localized changes result in the subtle destabilization of the interaction between the (H2A.Z-H2B) dimer and the (H3-H4)(2) tetramer. Moreover, H2A.Z nucleosomes have an altered surface that includes a metal ion. This altered surface may lead to changes in higher order structure, and/or could result in the association of specific nuclear proteins with H2A.Z. Finally, incorporation of H2A.Z and H2A within the same nucleosome is unlikely, due to significant changes in the interface between the two H2A.Z-H2B dimers.
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Affiliation(s)
- R K Suto
- Department of Biochemistry Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870 USA
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Suto RK, Whalen MA, Finke RG. Adenosylcobalamin-dependent ribonucleoside triphosphate reductase from Lactobacillus leichmannii. Rapid, improved purification involving dGTP-based affinity chromatography plus biophysical characterization studies demonstrating enhanced, "crystallographic level" purity. Prep Biochem Biotechnol 1999; 29:273-309. [PMID: 10431931 DOI: 10.1080/10826069908544929] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [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: 10/22/2022]
Abstract
Ribonucleoside triphosphate reductase (RTPR, EC 1.17.4.2) from Lactobacillus leichmannii is a 5'-deoxyadenosylcobalamin-dependent (AdoCbl; Coenzyme B12) enzyme. RTPR is also a prototypical adenosylcobalamin-dependent ribonucleotide reductase, one that, as its name indicates, converts ribonucleoside triphosphates (NTP) to deoxyribonucleoside triphosphates (dNTP). Upon substrate binding to RTPR, AdoCbl's cobalt-carbon bond is cleaved to generate cob(II)alamin, 5'-deoxyadenosine, and the cysteine (C408) derived thiyl radical. Five key cysteines (Cys 119, 408, 419, 731, and 736), from among the ten total cysteines, are involved in RTPR's catalytic mechanism. A critical examination of the RTPR isolation and purification literature suggested that the purification protocol currently used results in RTPR which contains 2040% microheterogeneity, along with minor contamination by other proteins. In addition, no report of crystalline RTPR has ever appeared. The literature indicates that irreversible cysteine oxidation (e.g., to -SO2H or -SO3H) is one highly plausible reason for the microheterogeneity of RTPR. The literature also indicates that improvement in the level of enzyme purity is the most effective next step in coaxing enzymes to crystallize that have previously failed to do so. A shortened, improved purification of RTPR has been developed, one involving a shorter purification time, a lower pH, a higher concentration of the more effective reductant DTT (all designed to help protect the cysteines from oxidation), and a final step utilizing our recently reported, improved dGTP-based affinity chromatography resin. The resultant RTPR is approximately 20-30% higher in both specific activity and in its ability to undergo single turnovers, and is homogeneous by mass spectrometry and dynamic light scattering. Additionally, the revised purification procedure eliminates > 30 proteins present in 2-3% amounts along with damaged RTPR that does not bind properly (i.e. tightly) to the dGTP-affinity resin. Finally, dGTP-based affinity chromatography purified RTPR has yielded the first reported, albeit small, single crystals of RTPR.
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Affiliation(s)
- R K Suto
- Department of Biochemistry, Colorado State University, Fort Collins 80523, USA
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Suto RK, Whalen MA, Bender BR, Finke RG. Synthesis of gamma-phosphate-linked nucleoside affinity chromatography resins for protein purification, including ribonucleoside triphosphate reductase. Nucleosides Nucleotides 1998; 17:1453-71. [PMID: 9672704 DOI: 10.1080/07328319808003480] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Seven nucleotides linked through the gamma-phosphate to diamine hydrocarbons were synthesized and coupled to Sepharose for use in protein purification affinity chromatography. The synthesis involved converting the nucleotides to nucleoside-5'- trimetaphosphates using dicyclohexyl carbodiimide, followed by nucleophilic ring opening of the trimetaphosphate with an alpha, omega-diamino hydrocarbon to generate a gamma-phosphoamide linkage in each nucleotide.
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Affiliation(s)
- R K Suto
- Department of Biochemistry, Colorado State University, Fort Collins 80523, USA
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Loewus FA, Saito K, Suto RK, Maring E. Conversion of D-arabinose to D-erythroascorbic acid and oxalic acid in Sclerotinia sclerotiorum. Biochem Biophys Res Commun 1995; 212:196-203. [PMID: 7612007 DOI: 10.1006/bbrc.1995.1956] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
D-glycero-Pent-2-enono-1,4-lactone (trivial name: D-erythroascorbic acid) occurs in the phytopathogen, Sclerotinia sclerotiorum (Lib.) de Bary, where it has a potential role as precursor of oxalic acid. On Glc/yeast/malt medium, S. sclerotiorum produces only nominal amounts of D-erythroascorbic acid but even partial replacement of Glc by D-Ara increases production of erythroascorbic acid and oxalic acid. Use of D-[1-14C]-, -[3-14C]-, or -[6-14C]Glc and D-[5-3H]-, -[2-14C,5-3H]-, or -[UL-14C]Ara provide additional information on erythroascorbic acid biosynthesis and cleavage. The latter process resembles that obtained by peroxygenation of erythroascorbic acid in alkaline solution. An unknown erythroascorbic acid-like compound also occurs in both Glc- and Ara-based cultures.
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Affiliation(s)
- F A Loewus
- Institute of Biological Chemistry, Washington State University, Pullman 99164-6340, USA
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