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Sen S, Spasic A, Sinha A, Wang J, Bush M, Li J, Nešić D, Zhou Y, Angiulli G, Morgan P, Salas-Estrada L, Takagi J, Walz T, Coller BS, Filizola M. Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVβ3. J Chem Inf Model 2022; 62:5607-5621. [PMID: 36279366 DOI: 10.1021/acs.jcim.2c00999] [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: 12/13/2022]
Abstract
Inhibitors of integrin αVβ3 have therapeutic promise for a variety of diseases. Most αVβ3-targeting small molecules patterned after the RGD motif are partial agonists because they induce a high-affinity, ligand-binding conformation and prime the receptor to bind the ligand without an activating stimulus, in part via a charge-charge interaction between their aspartic acid carboxyl group and the metal ion in the metal-ion-dependent adhesion site (MIDAS). Building upon our previous studies on the related integrin αIIbβ3, we searched for pure αVβ3 antagonists that lack this typical aspartic acid carboxyl group and instead engage through direct binding to one of the coordinating residues of the MIDAS metal ion, specifically β3 E220. By in silico screening of two large chemical libraries for compounds interacting with β3 E220, we indeed discovered a novel molecule that does not contain an acidic carboxyl group and does not induce the high-affinity, ligand-binding state of the receptor. Functional and structural characterization of a chemically optimized version of this compound led to the discovery of a novel small-molecule pure αVβ3 antagonist that (i) does not prime the receptor to bind the ligand and does not induce hybrid domain swing-out or receptor extension as judged by antibody binding and negative-stain electron microscopy, (ii) binds at the RGD-binding site as predicted by metadynamics rescoring of induced-fit docking poses and confirmed by a cryo-electron microscopy structure of the compound-bound integrin, and (iii) coordinates the MIDAS metal ion via a quinoline moiety instead of an acidic carboxyl group.
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Affiliation(s)
- Soumyo Sen
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Aleksandar Spasic
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Anjana Sinha
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, The Rockefeller University, 1230 York Avenue, P.O. Box 309, New York, New York10065, United States
| | - Jialing Wang
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, P.O. Box 219, New York, New York10065, United States
| | - Martin Bush
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, P.O. Box 219, New York, New York10065, United States
| | - Jihong Li
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, The Rockefeller University, 1230 York Avenue, P.O. Box 309, New York, New York10065, United States
| | - Dragana Nešić
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, The Rockefeller University, 1230 York Avenue, P.O. Box 309, New York, New York10065, United States
| | - Yuchen Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Gabriella Angiulli
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, P.O. Box 219, New York, New York10065, United States
| | - Paul Morgan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka565-0871, Japan
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, 1230 York Avenue, P.O. Box 219, New York, New York10065, United States
| | - Barry S Coller
- Allen and Frances Adler Laboratory of Blood and Vascular Biology, The Rockefeller University, 1230 York Avenue, P.O. Box 309, New York, New York10065, United States
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1677, New York, New York10029, United States
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Pinger J, Nešić D, Ali L, Aresta-Branco F, Lilic M, Chowdhury S, Kim HS, Verdi J, Raper J, Ferguson MAJ, Papavasiliou FN, Stebbins CE. African trypanosomes evade immune clearance by O-glycosylation of the VSG surface coat. Nat Microbiol 2018; 3:932-938. [PMID: 29988048 PMCID: PMC6108419 DOI: 10.1038/s41564-018-0187-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/04/2018] [Indexed: 11/09/2022]
Abstract
The African trypanosome Trypanosoma brucei spp. is a paradigm for antigenic variation, the orchestrated alteration of cell surface molecules to evade host immunity. The parasite elicits robust antibody-mediated immune responses to its variant surface glycoprotein (VSG) coat, but evades immune clearance by repeatedly accessing a large genetic VSG repertoire and 'switching' to antigenically distinct VSGs. This persistent immune evasion has been ascribed exclusively to amino-acid variance on the VSG surface presented by a conserved underlying protein architecture. We establish here that this model does not account for the scope of VSG structural and biochemical diversity. The 1.4-Å-resolution crystal structure of the variant VSG3 manifests divergence in the tertiary fold and oligomeric state. The structure also reveals an O-linked carbohydrate on the top surface of VSG3. Mass spectrometric analysis indicates that this O-glycosylation site is heterogeneously occupied in VSG3 by zero to three hexose residues and is also present in other VSGs. We demonstrate that this O-glycosylation increases parasite virulence by impairing the generation of protective immunity. These data alter the paradigm of antigenic variation by the African trypanosome, expanding VSG variability beyond amino-acid sequence to include surface post-translational modifications with immunomodulatory impact.
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Affiliation(s)
- Jason Pinger
- The Rockefeller University, Laboratory of Lymphocyte Biology, New York, NY, USA
| | - Dragana Nešić
- The Rockefeller University, Laboratory of Structural Microbiology, New York, NY, USA.,The Rockefeller University, Allen and Frances Adler Laboratory of Blood and Vascular Biology, New York, NY, USA
| | - Liaqat Ali
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - Francisco Aresta-Branco
- Division of Immune Diversity, German Cancer Research Center, Heidelberg, Germany.,Division of Structural Biology of Infection and Immunity, German Cancer Research Center, Heidelberg, Germany
| | - Mirjana Lilic
- The Rockefeller University, Laboratory of Structural Microbiology, New York, NY, USA.,The Rockefeller University, Laboratory of Molecular Biophysics, New York, NY, USA
| | - Shanin Chowdhury
- The Rockefeller University, Laboratory of Lymphocyte Biology, New York, NY, USA
| | - Hee-Sook Kim
- The Rockefeller University, Laboratory of Lymphocyte Biology, New York, NY, USA
| | - Joseph Verdi
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Jayne Raper
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Michael A J Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK.
| | - F Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center, Heidelberg, Germany.
| | - C Erec Stebbins
- Division of Structural Biology of Infection and Immunity, German Cancer Research Center, Heidelberg, Germany.
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Abachi S, Abbott B, Abolins M, Acharya BS, Adam I, Adams DL, Adams M, Ahn S, Aihara H, Alitti J, Álvarez G, Alves GA, Amidi E, Amos N, Anderson EW, Aronson SH, Astur R, Avery RE, Baden A, Balamurali V, Balderston J, Baldin B, Bantly J, Bartlett JF, Bazizi K, Bendich J, Beri SB, Bertram I, Bezzubov VA, Bhat PC, Bhatnagar V, Bhattacharjee M, Bischoff A, Biswas N, Blazey G, Blessing S, Bloom P, Boehnlein A, Bojko NI, Borcherding F, Borders J, Boswell C, Brandt A, Brock R, Bross A, Buchholz D, Burtovoi VS, Butler JM, Casey D, Castilla-Valdez H, Chakraborty D, Chang SM, Chekulaev SV, Chen LP, Chen W, Chevalier L, Chopra S, Choudhary BC, Christenson JH, Chung M, Claes D, Clark AR, Cobau WG, Cochran J, Cooper WE, Cretsinger C, Cullen-Vidal D, Cummings MAC, Cutts D, Dahl OI, De K, Demarteau M, Demina R, Denisenko K, Denisenko N, Denisov D, Denisov SP, Dharmaratna W, Diehl HT, Diesburg M, Di Loreto G, Dixon R, Draper P, Drinkard J, Ducros Y, Dugad SR, Durston-Johnson S, Edmunds D, Ellison J, Elvira VD, Engelmann R, Eno S, Eppley G, Ermolov P, Eroshin OV, Evdokimov VN, Fahey S, Fahland T, Fatyga M, Fatyga MK, Featherly J, Feher S, Fein D, Ferbel T, Finocchiaro G, Fisk HE, Fisyak Y, Flattum E, Forden GE, Fortner M, Frame KC, Franzini P, Fuess S, Galjaev AN, Gallas E, Gao CS, Gao S, Geld TL, Genik RJ, Genser K, Gerber CE, Gibbard B, Glaubman M, Glebov V, Glenn S, Gobbi B, Goforth M, Goldschmidt A, Gómez B, Goncharov PI, Gordon H, Goss LT, Graf N, Grannis PD, Green DR, Green J, Greenlee H, Griffin G, Grossman N, Grudberg P, Grünendahl S, Gu W, Guida JA, Guida JM, Guryn W, Gurzhiev SN, Gutnikov YE, Hadley NJ, Haggerty H, Hagopian S, Hagopian V, Hahn KS, Hall RE, Hansen S, Hatcher R, Hauptman JM, Hedin D, Heinson AP, Heintz U, Hernández-Montoya R, Heuring T, Hirosky R, Hobbs JD, Hoeneisen B, Hoftun JS, Hsieh F, Hu T, Hu T, Huehn T, Igarashi S, Ito AS, James E, Jaques J, Jerger SA, Jiang JZY, Joffe-Minor T, Johari H, Johns K, Johnson M, Johnstad H, Jonckheere A, Jones M, Jöstlein H, Jun SY, Jung CK, Kahn S, Kang JS, Kehoe R, Kelly ML, Kernan A, Kerth L, Kim CL, Kim SK, Klatchko A, Klima B, Klochkov BI, Klopfenstein C, Klyukhin VI, Kochetkov VI, Kohli JM, Koltick D, Kostritskiy AV, Kotcher J, Kourlas J, Kozelov AV, Kozlovski EA, Krishnaswamy MR, Krzywdzinski S, Kunori S, Lami S, Landsberg G, Lanou RE, Lebrat JF, Leflat A, Li H, Li J, Li YK, Li-Demarteau QZ, Lima JGR, Lincoln D, Linn SL, Linnemann J, Lipton R, Liu YC, Lobkowicz F, Loken SC, Lökös S, Lueking L, Lyon AL, Maciel AKA, Madaras RJ, Madden R, Mandrichenko IV, Mangeot P, Mani S, Mansoulié B, Mao HS, Margulies S, Markeloff R, Markosky L, Marshall T, Martin MI, Marx M, May B, Mayorov AA, McCarthy R, McKibben T, McKinley J, Melanson HL, de Mello Neto JRT, Merritt KW, Miettinen H, Milder A, Mincer A, de Miranda JM, Mishra CS, Mohammadi-Baarmand M, Mokhov N, Mondal NK, Montgomery HE, Mooney P, Mudan M, Murphy C, Murphy CT, Nang F, Narain M, Narasimham VS, Narayanan A, Neal HA, Negret JP, Neis E, Nemethy P, Nešić D, Norman D, Oesch L, Oguri V, Oltman E, Oshima N, Owen D, Padley P, Pang M, Para A, Park CH, Park YM, Partridge R, Parua N, Paterno M, Perkins J, Peryshkin A, Peters M, Piekarz H, Pischalnikov Y, Pluquet A, Podstavkov VM, Pope BG, Prosper HB, Protopopescu S, Pušeljić D, Qian J, Quintas PZ, Raja R, Rajagopalan S, Ramirez O, Rao MVS, Rapidis PA, Rasmussen L, Read AL, Reucroft S, Rijssenbeek M, Rockwell T, Roe NA, Rubinov P, Ruchti R, Rusin S, Rutherfoord J, Santoro A, Sawyer L, Schamberger RD, Schellman H, Sculli J, Shabalina E, Shaffer C, Shankar HC, Shivpuri RK, Shupe M, Singh JB, Sirotenko V, Smart W, Smith A, Smith RP, Snihur R, Snow GR, Snyder S, Solomon J, Sood PM, Sosebee M, Souza M, Spadafora AL, Stephens RW, Stevenson ML, Stewart D, Stoianova DA, Stoker D, Streets K, Strovink M, Taketani A, Tamburello P, Tarazi J, Tartaglia M, Taylor TL, Teiger J, Thompson J, Trippe TG, Tuts PM, Varelas N, Varnes EW, Virador PRG, Vititoe D, Volkov AA, Vorobiev AP, Wahl HD, Wang J, Wang LZ, Warchol J, Wayne M, Weerts H, Wenzel WA, White A, White JT, Wightman JA, Wilcox J, Willis S, Wimpenny SJ, Wirjawan JVD, Womersley J, Won E, Wood DR, Xu H, Yamada R, Yamin P, Yanagisawa C, Yang J, Yasuda T, Yoshikawa C, Youssef S, Yu J, Yu Y, Zhang Y, Zhou YH, Zhu Q, Zhu YS, Zhu ZH, Zieminska D, Zieminski A, Zylberstejn A. Top quark search with the D0 1992-1993 data sample. Phys Rev D Part Fields 1995; 52:4877-4919. [PMID: 10019713 DOI: 10.1103/physrevd.52.4877] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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