1
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Mykura R, Sánchez-Bento R, Matador E, Duong VK, Varela A, Angelini L, Carbajo RJ, Llaveria J, Ruffoni A, Leonori D. Synthesis of polysubstituted azepanes by dearomative ring expansion of nitroarenes. Nat Chem 2024; 16:771-779. [PMID: 38273027 DOI: 10.1038/s41557-023-01429-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
The synthesis of functionalized nitrogen heterocycles is integral to discovering, manufacturing and evolving high-value materials. The availability of effective strategies for heterocycle synthesis often biases the frequency of specific ring systems over others in the core structures of bioactive leads. For example, while the six- and five-membered piperidine and pyrrolidine are widespread in medicinal chemistry libraries, the seven-membered azepane is essentially absent and this leaves open a substantial area of three-dimensional chemical space. Here we report a strategy to prepare complex azepanes from simple nitroarenes by photochemical dearomative ring expansion centred on the conversion of the nitro group into a singlet nitrene. This process is mediated by blue light, occurs at room temperature and transforms the six-membered benzenoid framework into a seven-membered ring system. A following hydrogenolysis provides the azepanes in just two steps. We have demonstrated the utility of the strategy with the synthesis of several azepane analogues of piperidine drugs.
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Affiliation(s)
- Rory Mykura
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | | | - Esteban Matador
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
- Departamento de Química Orgánica, Universidad de Sevilla and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Sevilla, Spain
| | - Vincent K Duong
- Department of Chemistry, University of Manchester, Manchester, UK
| | - Ana Varela
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | | | - Rodrigo J Carbajo
- In Silico Discovery, Therapeutics Discovery, Janssen Research & Development, Janssen-Cilag S.A., Toledo, Spain
| | - Josep Llaveria
- Global Discovery Chemistry, Therapeutics Discovery, Janssen Research & Development, Janssen-Cilag S.A., Toledo, Spain
| | - Alessandro Ruffoni
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany.
| | - Daniele Leonori
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany.
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2
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Yu X, Abeywickrema P, Bonneux B, Behera I, Anson B, Jacoby E, Fung A, Adhikary S, Bhaumik A, Carbajo RJ, De Bruyn S, Miller R, Patrick A, Pham Q, Piassek M, Verheyen N, Shareef A, Sutto-Ortiz P, Ysebaert N, Van Vlijmen H, Jonckers THM, Herschke F, McLellan JS, Decroly E, Fearns R, Grosse S, Roymans D, Sharma S, Rigaux P, Jin Z. Structural and mechanistic insights into the inhibition of respiratory syncytial virus polymerase by a non-nucleoside inhibitor. Commun Biol 2023; 6:1074. [PMID: 37865687 PMCID: PMC10590419 DOI: 10.1038/s42003-023-05451-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023] Open
Abstract
The respiratory syncytial virus polymerase complex, consisting of the polymerase (L) and phosphoprotein (P), catalyzes nucleotide polymerization, cap addition, and cap methylation via the RNA dependent RNA polymerase, capping, and Methyltransferase domains on L. Several nucleoside and non-nucleoside inhibitors have been reported to inhibit this polymerase complex, but the structural details of the exact inhibitor-polymerase interactions have been lacking. Here, we report a non-nucleoside inhibitor JNJ-8003 with sub-nanomolar inhibition potency in both antiviral and polymerase assays. Our 2.9 Å resolution cryo-EM structure revealed that JNJ-8003 binds to an induced-fit pocket on the capping domain, with multiple interactions consistent with its tight binding and resistance mutation profile. The minigenome and gel-based de novo RNA synthesis and primer extension assays demonstrated that JNJ-8003 inhibited nucleotide polymerization at the early stages of RNA transcription and replication. Our results support that JNJ-8003 binding modulates a functional interplay between the capping and RdRp domains, and this molecular insight could accelerate the design of broad-spectrum antiviral drugs.
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Affiliation(s)
- Xiaodi Yu
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA.
| | - Pravien Abeywickrema
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Brecht Bonneux
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Ishani Behera
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA
| | - Brandon Anson
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA
| | - Edgar Jacoby
- Johnson & Johnson Innovative Medicine, Beerse, Belgium
| | - Amy Fung
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA
| | - Suraj Adhikary
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Anusarka Bhaumik
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Rodrigo J Carbajo
- Johnson & Johnson Innovative Medicine, Janssen-Cilag, Discovery Chemistry S.A. Río Jarama, 75A, 45007, Toledo, Spain
| | | | - Robyn Miller
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Aaron Patrick
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Quyen Pham
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA
| | - Madison Piassek
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Nick Verheyen
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
| | - Afzaal Shareef
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | | | - Nina Ysebaert
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
| | | | | | | | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Etienne Decroly
- Aix Marseille Université, CNRS, AFMB, UMR 7257, Marseille, France
| | - Rachel Fearns
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | | | - Dirk Roymans
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
| | - Sujata Sharma
- Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, PA, 19477, USA
| | - Peter Rigaux
- Janssen Infectious Diseases and Vaccines, 2340, Beerse, Belgium
| | - Zhinan Jin
- Johnson & Johnson Innovative Medicine, Brisbane, CA, 94005, USA.
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3
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Hargreaves D, Carbajo RJ, Bodnarchuk MS, Embrey K, Rawlins PB, Packer M, Degorce SL, Hird AW, Johannes JW, Chiarparin E, Schade M. Design of rigid protein-protein interaction inhibitors enables targeting of undruggable Mcl-1. Proc Natl Acad Sci U S A 2023; 120:e2221967120. [PMID: 37186857 PMCID: PMC10214187 DOI: 10.1073/pnas.2221967120] [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: 12/30/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
The structure-based design of small-molecule inhibitors targeting protein-protein interactions (PPIs) remains a huge challenge as the drug must bind typically wide and shallow protein sites. A PPI target of high interest for hematological cancer therapy is myeloid cell leukemia 1 (Mcl-1), a prosurvival guardian protein from the Bcl-2 family. Despite being previously considered undruggable, seven small-molecule Mcl-1 inhibitors have recently entered clinical trials. Here, we report the crystal structure of the clinical-stage inhibitor AMG-176 bound to Mcl-1 and analyze its interaction along with clinical inhibitors AZD5991 and S64315. Our X-ray data reveal high plasticity of Mcl-1 and a remarkable ligand-induced pocket deepening. Nuclear Magnetic Resonance (NMR)-based free ligand conformer analysis demonstrates that such unprecedented induced fit is uniquely achieved by designing highly rigid inhibitors, preorganized in their bioactive conformation. By elucidating key chemistry design principles, this work provides a roadmap for targeting the largely untapped PPI class more successfully.
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Affiliation(s)
- David Hargreaves
- Discovery Sciences, AstraZeneca, CambridgeCB4 0WG, United Kingdom
| | | | | | - Kevin Embrey
- Discovery Sciences, AstraZeneca, CambridgeCB4 0WG, United Kingdom
| | | | - Martin Packer
- Chemistry, Oncology R&D, AstraZeneca, CambridgeCB4 0WG, United Kingdom
| | | | | | | | | | - Markus Schade
- Chemistry, Oncology R&D, AstraZeneca, CambridgeCB4 0WG, United Kingdom
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4
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Scott JS, Stead D, Barlaam B, Breed J, Carbajo RJ, Chiarparin E, Cureton N, Davey PRJ, Fisher DI, Gangl ET, Grebe T, Greenwood RD, Hande S, Hatoum-Mokdad H, Hughes SJ, Hunt TA, Johnson T, Kavanagh SL, Klinowska TCM, Larner CJB, Lawson M, Lister AS, Longmire D, Marden S, McGuire TM, McMillan C, McMurray L, Morrow CJ, Nissink JWM, Moss TA, O'Donovan DH, Polanski R, Stokes S, Thakur K, Trueman D, Truman C, Tucker MJ, Wang H, Whalley N, Wu D, Wu Y, Yang B, Yang W. Discovery of a Potent and Orally Bioavailable Zwitterionic Series of Selective Estrogen Receptor Degrader-Antagonists. J Med Chem 2023; 66:2918-2945. [PMID: 36727211 DOI: 10.1021/acs.jmedchem.2c01964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Herein, we report the optimization of a meta-substituted series of selective estrogen receptor degrader (SERD) antagonists for the treatment of ER+ breast cancer. Structure-based design together with the use of modeling and NMR to favor the bioactive conformation led to a highly potent series of basic SERDs with promising physicochemical properties. Issues with hERG activity resulted in a strategy of zwitterion formation and ultimately in the identification of 38. This compound was shown to be a highly potent SERD capable of effectively degrading ERα in both MCF-7 and CAMA-1 cell lines. The low lipophilicity and zwitterionic nature led to a SERD with a clean secondary pharmacology profile and no hERG activity. Favorable physicochemical properties resulted in good oral bioavailability in preclinical species and potent in vivo activity in a mouse xenograft model.
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Affiliation(s)
- James S Scott
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Darren Stead
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Bernard Barlaam
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Jason Breed
- Discovery Sciences R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | | | - Natalie Cureton
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Paul R J Davey
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - David I Fisher
- Discovery Sciences R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Eric T Gangl
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Tyler Grebe
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Sudhir Hande
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Holia Hatoum-Mokdad
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Thomas A Hunt
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Tony Johnson
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Stefan L Kavanagh
- Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB2 OAA, United Kingdom
| | | | - Carrie J B Larner
- Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB2 OAA, United Kingdom
| | - Mandy Lawson
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Andrew S Lister
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - David Longmire
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Stacey Marden
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, Boston, Massachusetts 02451, United States
| | | | | | | | | | | | - Thomas A Moss
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | - Radoslaw Polanski
- Discovery Sciences R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Stephen Stokes
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Kumar Thakur
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Dawn Trueman
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Caroline Truman
- Discovery Sciences R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | - Haixia Wang
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Nicky Whalley
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Dedong Wu
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, Boston, Massachusetts 02451, United States
| | - Ye Wu
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Bin Yang
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Wenzhan Yang
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, Boston, Massachusetts 02451, United States
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5
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Kettle JG, Bagal SK, Bickerton S, Bodnarchuk MS, Boyd S, Breed J, Carbajo RJ, Cassar DJ, Chakraborty A, Cosulich S, Cumming I, Davies M, Davies NL, Eatherton A, Evans L, Feron L, Fillery S, Gleave ES, Goldberg FW, Hanson L, Harlfinger S, Howard M, Howells R, Jackson A, Kemmitt P, Lamont G, Lamont S, Lewis HJ, Liu L, Niedbala MJ, Phillips C, Polanski R, Raubo P, Robb G, Robinson DM, Ross S, Sanders MG, Tonge M, Whiteley R, Wilkinson S, Yang J, Zhang W. Discovery of AZD4625, a Covalent Allosteric Inhibitor of the Mutant GTPase KRAS G12C. J Med Chem 2022; 65:6940-6952. [PMID: 35471939 DOI: 10.1021/acs.jmedchem.2c00369] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
KRAS is an archetypal high-value intractable oncology drug target. The glycine to cysteine mutation at codon 12 represents an Achilles heel that has now rendered this important GTPase druggable. Herein, we report our structure-based drug design approach that led to the identification of 21, AZD4625, a clinical development candidate for the treatment of KRASG12C positive tumors. Highlights include a quinazoline tethering strategy to lock out a bio-relevant binding conformation and an optimization strategy focused on the reduction of extrahepatic clearance mechanisms seen in preclinical species. Crystallographic analysis was also key in helping to rationalize unusual structure-activity relationship in terms of ring size and enantio-preference. AZD4625 is a highly potent and selective inhibitor of KRASG12C with an anticipated low clearance and high oral bioavailability profile in humans.
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Affiliation(s)
| | | | | | | | - Scott Boyd
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Jason Breed
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | | | | | - Iain Cumming
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | | | - Laura Evans
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Lyman Feron
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Emma S Gleave
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | | | | | | | - Anne Jackson
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Paul Kemmitt
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Scott Lamont
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Libin Liu
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | | | | | - Radek Polanski
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Piotr Raubo
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Graeme Robb
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Sarah Ross
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Michael Tonge
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Junsheng Yang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
| | - Wenman Zhang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P. R. China
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6
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Weerakoon D, Carbajo RJ, De Maria L, Tyrchan C, Zhao H. Impact of PROTAC Linker Plasticity on the Solution Conformations and Dissociation of the Ternary Complex. J Chem Inf Model 2022; 62:340-349. [PMID: 35018781 DOI: 10.1021/acs.jcim.1c01036] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The conformational behavior of a small molecule free in solution is important to understand the free energy of binding to its target. This could be of special interest for proteolysis-targeting chimeras (PROTACs) due to their often flexible and lengthy linkers and the need to induce a ternary complex. Here, we report on the molecular dynamics (MD) simulations of two PROTACs, MZ1 and dBET6, revealing different linker conformational behaviors. The simulation of MZ1 in dimethyl sulfoxide (DMSO) agrees well with the nuclear magnetic resonance study, providing strong support for the relevance of our simulations. To further understand the role of linker plasticity in the formation of a ternary complex, the dissociation of the complex von Hippel-Lindau-MZ1-BRD4 is investigated in detail by steered simulations and is shown to follow a two-step pathway. Interestingly, both MZ1 and dBET6 display in water, a tendency toward an intramolecular lipophilic interaction between the two warheads. The hydrophobic contact of the two warheads would prevent them from binding to their respective proteins and might have an effect on the efficacy of induced cellular protein degradation. However, conformations featuring this hydrophobic contact of the two warheads are calculated to be marginally more favorable.
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Affiliation(s)
- Dhanushka Weerakoon
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Rodrigo J Carbajo
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0QA, United Kingdom
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
| | - Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 43183, Sweden
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7
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Linclau B, Wang Z, Jeffries B, Graton J, Carbajo RJ, Sinnaeve D, Le Questel J, Scott JS, Chiarparin E. Relating Conformational Equilibria to Conformer‐Specific Lipophilicities: New Opportunities in Drug Discovery. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202114862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bruno Linclau
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
- Department of Organic and Macromolecular Chemistry, Ghent University Campus Sterre, S4 Krijgslaan 281 9000 Ghent Belgium
| | - Zhong Wang
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
| | - Benjamin Jeffries
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
| | - Jérôme Graton
- CEISAM UMR CNRS 6230 Université de Nantes CNRS CEISAM UMR 6230 44000 Nantes France
| | | | - Davy Sinnaeve
- Univ. Lille Inserm Institut Pasteur de Lille CHU Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 59000 Lille France
- CNRS ERL9002—Integrative Structural Biology 59000 Lille France
| | - Jean‐Yves Le Questel
- CEISAM UMR CNRS 6230 Université de Nantes CNRS CEISAM UMR 6230 44000 Nantes France
| | - James S. Scott
- Medicinal Chemistry, Oncology R&D AstraZeneca Cambridge CB4 0WG UK
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8
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Linclau B, Wang Z, Jeffries B, Graton J, Carbajo RJ, Sinnaeve D, Le Questel JY, Scott JS, Chiarparin E. Relating Conformational Equilibria to Conformer-Specific Lipophilicities: New Opportunities in Drug Discovery. Angew Chem Int Ed Engl 2021; 61:e202114862. [PMID: 34913249 PMCID: PMC9304282 DOI: 10.1002/anie.202114862] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 11/10/2022]
Abstract
Efficient drug discovery is based on a concerted effort in optimizing bioactivity and compound properties such as lipophilicity, and is guided by efficiency metrics that reflect both aspects. While conformation–activity relationships and ligand conformational control are known strategies to improve bioactivity, the use of conformer‐specific lipophilicities (logp) is much less explored. Here we show how conformer‐specific logp values can be obtained from knowledge of the macroscopic logP value, and of the equilibrium constants between the individual species in water and in octanol. This is illustrated with fluorinated amide rotamers, with integration of rotamer 19F NMR signals as a facile, direct method to obtain logp values. The difference between logp and logP optimization is highlighted, giving rise to a novel avenue for lipophilicity control in drug discovery.
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.,Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, S4, Krijgslaan 281, 9000, Ghent, Belgium
| | - Zhong Wang
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Benjamin Jeffries
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France
| | - Rodrigo J Carbajo
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Davy Sinnaeve
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167-RID-AGE-Risk Factors and Molecular, Determinants of Aging-Related Diseases, 59000, Lille, France.,CNRS, ERL9002-Integrative Structural Biology, 59000, Lille, France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France
| | - James S Scott
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, UK
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9
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Fumagalli G, Carbajo RJ, Nissink JWM, Tart J, Dou R, Thomas AP, Spring DR. Targeting a Novel KRAS Binding Site: Application of One-Component Stapling of Small (5-6-mer) Peptides. J Med Chem 2021; 64:17287-17303. [PMID: 34787423 DOI: 10.1021/acs.jmedchem.1c01334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RAS proteins are central in the proliferation of many types of cancer, but a general approach toward the identification of pan-mutant RAS inhibitors has remained unresolved. In this work, we describe the application of a binding pharmacophore identified from analysis of known RAS binding peptides to the design of novel peptides. Using a chemically divergent approach, we generated a library of small stapled peptides from which we identified compounds with weak binding activity. Exploration of structure-activity relationships (SARs) and optimization of these early compounds led to low-micromolar binders of KRAS that block nucleotide exchange.
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Affiliation(s)
- Gabriele Fumagalli
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K.,Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Jonathan Tart
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Rongxuan Dou
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Andrew P Thomas
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - David R Spring
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
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10
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Balazs AYS, Carbajo RJ, Davies NL, Dong Y, Hird AW, Johannes JW, Lamb ML, McCoull W, Raubo P, Robb GR, Packer MJ, Chiarparin E. Correction to "Free Ligand 1D NMR Conformational Signatures To Enhance Structure Based Drug Design of a Mcl-1 Inhibitor (AZD5991) and Other Synthetic Macrocycles". J Med Chem 2021; 64:2849. [PMID: 33646774 DOI: 10.1021/acs.jmedchem.1c00273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Raubo P, Carbajo RJ, McCoull W, Raubo J, Thomas M. Diversity-orientated synthesis of macrocyclic heterocycles using a double S NAr approach. Org Biomol Chem 2021; 19:6274-6290. [PMID: 34195728 DOI: 10.1039/d1ob00612f] [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: 11/21/2022]
Abstract
An efficient macrocyclisation approach based on the double aromatic nucleophilic substitution (SNACK) was developed. This methodology allows a facile incorporation of heterocyclic motifs into macrocyclic rings and rapid synthesis of a significant number of structurally diverse macrocycles. SNACK macrocyclisation enables preparation of stable diastereoisomers of conformationally restricted macrocycles (atropisomers). Practical application of SNACK macrocyclisation in a drug discovery project was exemplified by the identification of high affinity macrocyclic binders of B-cell lymphoma 6 (BCL6).
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Affiliation(s)
- Piotr Raubo
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - Rodrigo J Carbajo
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - William McCoull
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - Joanna Raubo
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - Morgan Thomas
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK.
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12
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Scott JS, Moss TA, Balazs A, Barlaam B, Breed J, Carbajo RJ, Chiarparin E, Davey PRJ, Delpuech O, Fawell S, Fisher DI, Gagrica S, Gangl ET, Grebe T, Greenwood RD, Hande S, Hatoum-Mokdad H, Herlihy K, Hughes S, Hunt TA, Huynh H, Janbon SLM, Johnson T, Kavanagh S, Klinowska T, Lawson M, Lister AS, Marden S, McGinnity DF, Morrow CJ, Nissink JWM, O'Donovan DH, Peng B, Polanski R, Stead DS, Stokes S, Thakur K, Throner SR, Tucker MJ, Varnes J, Wang H, Wilson DM, Wu D, Wu Y, Yang B, Yang W. Discovery of AZD9833, a Potent and Orally Bioavailable Selective Estrogen Receptor Degrader and Antagonist. J Med Chem 2020; 63:14530-14559. [PMID: 32910656 DOI: 10.1021/acs.jmedchem.0c01163] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein we report the optimization of a series of tricyclic indazoles as selective estrogen receptor degraders (SERD) and antagonists for the treatment of ER+ breast cancer. Structure based design together with systematic investigation of each region of the molecular architecture led to the identification of N-[1-(3-fluoropropyl)azetidin-3-yl]-6-[(6S,8R)-8-methyl-7-(2,2,2-trifluoroethyl)-6,7,8,9-tetrahydro-3H-pyrazolo[4,3-f]isoquinolin-6-yl]pyridin-3-amine (28). This compound was demonstrated to be a highly potent SERD that showed a pharmacological profile comparable to fulvestrant in its ability to degrade ERα in both MCF-7 and CAMA-1 cell lines. A stringent control of lipophilicity ensured that 28 had favorable physicochemical and preclinical pharmacokinetic properties for oral administration. This, combined with demonstration of potent in vivo activity in mouse xenograft models, resulted in progression of this compound, also known as AZD9833, into clinical trials.
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Affiliation(s)
- James S Scott
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Thomas A Moss
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Amber Balazs
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Bernard Barlaam
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Jason Breed
- Discovery Sciences R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | | | - Paul R J Davey
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Oona Delpuech
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Stephen Fawell
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - David I Fisher
- Discovery Sciences R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | - Eric T Gangl
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Tyler Grebe
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Sudhir Hande
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Holia Hatoum-Mokdad
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Kara Herlihy
- Discovery Sciences R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Samantha Hughes
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Thomas A Hunt
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Hoan Huynh
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sophie L M Janbon
- Early Chemical Development, Pharmaceutical Sciences, R&D, Macclesfield, United Kingdom
| | - Tony Johnson
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Stefan Kavanagh
- Oncology Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Mandy Lawson
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Andrew S Lister
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Stacey Marden
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, Boston, Massachusetts, United States
| | | | | | | | | | - Bo Peng
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Radoslaw Polanski
- Discovery Sciences R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Darren S Stead
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Stephen Stokes
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Kumar Thakur
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Scott R Throner
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Jeffrey Varnes
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Haixia Wang
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - David M Wilson
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Dedong Wu
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, Boston, Massachusetts, United States
| | - Ye Wu
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Bin Yang
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Wenzhan Yang
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, Boston, Massachusetts, United States
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13
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Guéret SM, Thavam S, Carbajo RJ, Potowski M, Larsson N, Dahl G, Dellsén A, Grossmann TN, Plowright AT, Valeur E, Lemurell M, Waldmann H. Macrocyclic Modalities Combining Peptide Epitopes and Natural Product Fragments. J Am Chem Soc 2020; 142:4904-4915. [PMID: 32058716 PMCID: PMC7307906 DOI: 10.1021/jacs.0c00269] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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] [Indexed: 12/11/2022]
Abstract
![]()
“Hot
loop” protein segments have variable structure
and conformation and contribute crucially to protein–protein
interactions. We describe a new hot loop mimicking modality, termed
PepNats, in which natural product (NP)-inspired structures are incorporated
as conformation-determining and -restricting structural elements into
macrocyclic hot loop-derived peptides. Macrocyclic PepNats representing
hot loops of inducible nitric oxide synthase (iNOS) and human agouti-related
protein (AGRP) were synthesized on solid support employing macrocyclization
by imine formation and subsequent stereoselective 1,3-dipolar cycloaddition
as key steps. PepNats derived from the iNOS DINNN hot loop and the
AGRP RFF hot spot sequence yielded novel and potent ligands of the
SPRY domain-containing SOCS box protein 2 (SPSB2) that binds to iNOS,
and selective ligands for AGRP-binding melanocortin (MC) receptors.
NP-inspired fragment absolute configuration determines the conformation
of the peptide part responsible for binding. These results demonstrate
that combination of NP-inspired scaffolds with peptidic epitopes enables
identification of novel hot loop mimics with conformationally constrained
and biologically relevant structure.
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Affiliation(s)
- Stéphanie M Guéret
- Department of Chemical Biology, AstraZeneca-Max Planck Institute Satellite Unit, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Sasikala Thavam
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Rodrigo J Carbajo
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - Marco Potowski
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Niklas Larsson
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Göran Dahl
- Structure, Biophysics & Fragment Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Anita Dellsén
- Mechanistic Biology & Profiling, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Eric Valeur
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
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14
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Kettle JG, Bagal SK, Bickerton S, Bodnarchuk MS, Breed J, Carbajo RJ, Cassar DJ, Chakraborty A, Cosulich S, Cumming I, Davies M, Eatherton A, Evans L, Feron L, Fillery S, Gleave ES, Goldberg FW, Harlfinger S, Hanson L, Howard M, Howells R, Jackson A, Kemmitt P, Kingston JK, Lamont S, Lewis HJ, Li S, Liu L, Ogg D, Phillips C, Polanski R, Robb G, Robinson D, Ross S, Smith JM, Tonge M, Whiteley R, Yang J, Zhang L, Zhao X. Structure-Based Design and Pharmacokinetic Optimization of Covalent Allosteric Inhibitors of the Mutant GTPase KRASG12C. J Med Chem 2020; 63:4468-4483. [DOI: 10.1021/acs.jmedchem.9b01720] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | | | | | | | - Jason Breed
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | | | | | - Iain Cumming
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Laura Evans
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Lyman Feron
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Emma S. Gleave
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | | | | | | | - Anne Jackson
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Paul Kemmitt
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Scott Lamont
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Songlei Li
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176 P. R. China
| | - Libin Liu
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176 P. R. China
| | - Derek Ogg
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Radek Polanski
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Graeme Robb
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Sarah Ross
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Michael Tonge
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Junsheng Yang
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176 P. R. China
| | - Longfei Zhang
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176 P. R. China
| | - Xiliang Zhao
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176 P. R. China
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15
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Barlaam B, Breed J, Carbajo RJ, Gangl E, Hughes S, Morrow CJ, Moss TA, Polanski R, Nissink WM, O'Donovan D, Varnes J, Yang B, Scott JS. Abstract A107: Small Molecule Degraders of the Estrogen Receptor (SERDs): Optimization of the tricyclic indole scaffold beyond AZD9496. Mol Cancer Ther 2019. [DOI: 10.1158/1535-7163.targ-19-a107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The estrogen receptor alpha (ERα) is expressed in >70% of breast cancers and is a clinically validated target in oncology.1 Anti-hormonal therapies that directly block ER function (e.g., tamoxifen) or therapies that block the production of estrogen itself (e.g., aromatase inhibitors) have proven to be effective treatments of the disease. Further advances have been made with the development of SERDs (Selective Estrogen Receptor Degraders) such as fulvestrant which both antagonise ERα-driven tumor cell growth and cause degradation of the ERα receptor.2 We previously disclosed the identification of a tricyclic indole scaffold that led to the orally active clinical candidate AZD9496.3 Additional work to identify novel chemotypes including phenol 14 and indazole 25 was also disclosed together. The work previously disclosed relied on the presence of the acrylic acid for efficient degradation of the estrogen receptor. In this poster we will discuss the replacement of the acrylic acid on the tricyclic indole scaffold with amines (e.g. compound 3). Compound 3 is a degrader of the estrogen receptor in the MCF-7 cell line (pIC50 8.4). Further optimisation of lead structure 3 led to more potent selective degraders of the estrogen receptor in multiple cell lines (e.g. pIC50 >10 in MCF-7) with suitable properties for oral absorption (e.g. oral AUC 44 μM.h in mice at 20 mg/kg). We will discuss some of the medicinal chemistry challenges that were faced along the way and the optimisation strategy (use of NMR derived solution phase conformations, understanding of the binding mode in the estrogen receptor by X-ray crystallography). ol>
Citation Format: Bernard Barlaam, Jason Breed, Rodrigo J Carbajo, Eric Gangl, Samantha Hughes, Christopher J Morrow, Thomas A Moss, Radoslaw Polanski, Willem M Nissink, Daniel O'Donovan, Jeffrey Varnes, Bin Yang, James S Scott. Small Molecule Degraders of the Estrogen Receptor (SERDs): Optimization of the tricyclic indole scaffold beyond AZD9496 [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A107. doi:10.1158/1535-7163.TARG-19-A107
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16
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Degorce SL, Anjum R, Bloecher A, Carbajo RJ, Dillman KS, Drew L, Halsall CT, Lenz EM, Lindsay NA, Mayo MF, Pink JH, Robb GR, Rosen A, Scott JS, Xue Y. Discovery of a Series of 5-Azaquinazolines as Orally Efficacious IRAK4 Inhibitors Targeting MyD88L265P Mutant Diffuse Large B Cell Lymphoma. J Med Chem 2019; 62:9918-9930. [DOI: 10.1021/acs.jmedchem.9b01346] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sébastien L. Degorce
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, U.K
| | - Rana Anjum
- Bioscience, Oncology R&D, AstraZeneca, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Andrew Bloecher
- Bioscience, Oncology R&D, AstraZeneca, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Rodrigo J. Carbajo
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, U.K
| | - Keith S. Dillman
- Bioscience, Oncology R&D, AstraZeneca, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Lisa Drew
- Bioscience, Oncology R&D, AstraZeneca, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Christopher T. Halsall
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, U.K
| | - Eva M. Lenz
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, U.K
| | - Nicola A. Lindsay
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, U.K
| | - Michele F. Mayo
- Bioscience, Oncology R&D, AstraZeneca, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jennifer H. Pink
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, U.K
| | - Graeme R. Robb
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, U.K
| | - Alan Rosen
- Bioscience, Oncology R&D, AstraZeneca, Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - James S. Scott
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, U.K
| | - Yafeng Xue
- Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Mölndal, Sweden
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17
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Scott JS, Breed J, Carbajo RJ, Davey PR, Greenwood R, Huynh HK, Klinowska T, Morrow CJ, Moss TA, Polanski R, Nissink JWM, Varnes J, Yang B. Building Bridges in a Series of Estrogen Receptor Degraders: An Application of Metathesis in Medicinal Chemistry. ACS Med Chem Lett 2019; 10:1492-1497. [PMID: 31620239 DOI: 10.1021/acsmedchemlett.9b00370] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/23/2019] [Indexed: 11/30/2022] Open
Abstract
Herein we report the use of metathesis to construct a novel tetracyclic core in a series of estrogen receptor degraders. This improved the chemical stability, as assessed using an NMR-MS based assay, and gave a molecule with excellent physicochemical properties and pharmacokinetics in rat. X-ray crystallography established minimal perturbation of the bridged compounds relative to the unbridged analogues in the receptor binding pocket. Unfortunately, despite retaining excellent binding to ERα, this adversely affected the ability of the compounds to degrade the receptor.
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Affiliation(s)
- James S. Scott
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Jason Breed
- Discovery Sciences, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | - Paul R. Davey
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Ryan Greenwood
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Hoan K. Huynh
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | | | - Thomas A. Moss
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | | | - Jeffrey Varnes
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Bin Yang
- Oncology R&D, AstraZeneca, R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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18
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Schlagnitweit J, Friebe Sandoz S, Jaworski A, Guzzetti I, Aussenac F, Carbajo RJ, Chiarparin E, Pell AJ, Petzold K. Observing an Antisense Drug Complex in Intact Human Cells by in-Cell NMR Spectroscopy. Chembiochem 2019; 20:2474-2478. [PMID: 31206961 DOI: 10.1002/cbic.201900297] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Gaining insight into the uptake, trafficking and target engagement of drugs in cells can enhance understanding of a drug's function and efficiency. However, there are currently no reliable methods for studying untagged biomolecules in macromolecular complexes in intact human cells. Here we have studied an antisense oligonucleotide (ASO) drug in HEK 293T and HeLa cells by NMR spectroscopy. Using a combination of transfection, cryoprotection and dynamic nuclear polarization (DNP), we were able to detect the drug directly in intact frozen cells. Activity of the drug was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). By applying DNP NMR to frozen cells, we overcame limitations both of solution-state in-cell NMR spectroscopy (e.g., size, stability and sensitivity) and of visualization techniques, in which (e.g., fluorescent) tagging of the ASO decreases its activity. The capability to detect an untagged, active drug, interacting in its natural environment, represents a first step towards studying molecular mechanisms in intact cells.
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Affiliation(s)
- Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 17165, Solna, Sweden
| | - Sarah Friebe Sandoz
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 17165, Solna, Sweden
| | - Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, 106 91, Stockholm, Sweden
| | - Ileana Guzzetti
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 17165, Solna, Sweden
| | - Fabien Aussenac
- Bruker BioSpin, 34 Rue de l'Industrie, 67160, Wissembourg, France
| | - Rodrigo J Carbajo
- Analytical and Structural Chemistry Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Elisabetta Chiarparin
- Analytical and Structural Chemistry Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Andrew J Pell
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, 106 91, Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 17165, Solna, Sweden
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19
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Balazs AYS, Carbajo RJ, Davies NL, Dong Y, Hird AW, Johannes JW, Lamb ML, McCoull W, Raubo P, Robb GR, Packer MJ, Chiarparin E. Free Ligand 1D NMR Conformational Signatures To Enhance Structure Based Drug Design of a Mcl-1 Inhibitor (AZD5991) and Other Synthetic Macrocycles. J Med Chem 2019; 62:9418-9437. [PMID: 31361481 DOI: 10.1021/acs.jmedchem.9b00716] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The three-dimensional conformations adopted by a free ligand in solution impact bioactivity and physicochemical properties. Solution 1D NMR spectra inherently contain information on ligand conformational flexibility and three-dimensional shape, as well as the propensity of the free ligand to fully preorganize into the bioactive conformation. Herein we discuss some key learnings, distilled from our experience developing potent and selective synthetic macrocyclic inhibitors, including Mcl-1 clinical candidate AZD5991. Case studies have been selected from recent oncology research projects, demonstrating how 1D NMR conformational signatures can complement X-ray protein-ligand structural information to guide medicinal chemistry optimization. Learning to extract free ligand conformational information from routinely available 1D NMR signatures has proven to be fast enough to guide medicinal chemistry decisions within design cycles for compound optimization.
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Affiliation(s)
- Amber Y S Balazs
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - Rodrigo J Carbajo
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Nichola L Davies
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Yu Dong
- Pharmaron Beijing Co., Ltd. , Beijing 100176 , China
| | - Alexander W Hird
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - Jeffrey W Johannes
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - Michelle L Lamb
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - William McCoull
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Piotr Raubo
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Graeme R Robb
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Martin J Packer
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
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Scott JS, Bailey A, Buttar D, Carbajo RJ, Curwen J, Davey PRJ, Davies RDM, Degorce SL, Donald C, Gangl E, Greenwood R, Groombridge SD, Johnson T, Lamont S, Lawson M, Lister A, Morrow CJ, Moss TA, Pink JH, Polanski R. Tricyclic Indazoles-A Novel Class of Selective Estrogen Receptor Degrader Antagonists. J Med Chem 2019; 62:1593-1608. [PMID: 30640465 DOI: 10.1021/acs.jmedchem.8b01837] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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
Herein, we report the identification and synthesis of a series of tricyclic indazoles as a novel class of selective estrogen receptor degrader antagonists. Replacement of a phenol, present in our previously reported tetrahydroisoquinoline scaffold, with an indazole group led to the removal of a reactive metabolite signal in an in vitro glutathione trapping assay. Further optimization, guided by X-ray crystal structures and NMR conformational work, varied the alkyl side chain and pendant aryl group and resulted in compounds with low turnover in human hepatocytes and enhanced chemical stability. Compound 9 was profiled as a representative of the series in terms of pharmacology and demonstrated the desired estrogen receptor α degrader-antagonist profile and demonstrated activity in a xenograft model of breast cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Eric Gangl
- Oncology IMED Biotech Unit , AstraZeneca, R&D Boston , 35 Gatehouse Drive , Waltham , Massachusetts 02451 , United States
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21
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McCoull W, Cheung T, Anderson E, Barton P, Burgess J, Byth K, Cao Q, Castaldi MP, Chen H, Chiarparin E, Carbajo RJ, Code E, Cowan S, Davey PR, Ferguson AD, Fillery S, Fuller NO, Gao N, Hargreaves D, Howard MR, Hu J, Kawatkar A, Kemmitt PD, Leo E, Molina DM, O’Connell N, Petteruti P, Rasmusson T, Raubo P, Rawlins PB, Ricchiuto P, Robb GR, Schenone M, Waring MJ, Zinda M, Fawell S, Wilson DM. Development of a Novel B-Cell Lymphoma 6 (BCL6) PROTAC To Provide Insight into Small Molecule Targeting of BCL6. ACS Chem Biol 2018; 13:3131-3141. [DOI: 10.1021/acschembio.8b00698] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- William McCoull
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Tony Cheung
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Erica Anderson
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Peter Barton
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Jonathan Burgess
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Kate Byth
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Qing Cao
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - M. Paola Castaldi
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Huawei Chen
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Elisabetta Chiarparin
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Rodrigo J. Carbajo
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Erin Code
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Suzanna Cowan
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Paul R. Davey
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Andrew D. Ferguson
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Shaun Fillery
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Nathan O. Fuller
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Ning Gao
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - David Hargreaves
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Martin R. Howard
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Jun Hu
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Aarti Kawatkar
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Paul D. Kemmitt
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Elisabetta Leo
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | | | - Nichole O’Connell
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Philip Petteruti
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Timothy Rasmusson
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Piotr Raubo
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Philip B. Rawlins
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Piero Ricchiuto
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Graeme R. Robb
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Monica Schenone
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Michael J. Waring
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Michael Zinda
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Stephen Fawell
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - David M. Wilson
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
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McCoull W, Abrams RD, Anderson E, Blades K, Barton P, Box M, Burgess J, Byth K, Cao Q, Chuaqui C, Carbajo RJ, Cheung T, Code E, Ferguson AD, Fillery S, Fuller NO, Gangl E, Gao N, Grist M, Hargreaves D, Howard MR, Hu J, Kemmitt PD, Nelson JE, O'Connell N, Prince DB, Raubo P, Rawlins PB, Robb GR, Shi J, Waring MJ, Whittaker D, Wylot M, Zhu X. Correction to Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors. J Med Chem 2017; 60:6459. [PMID: 28714680 DOI: 10.1021/acs.jmedchem.7b00962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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McCoull W, Abrams RD, Anderson E, Blades K, Barton P, Box M, Burgess J, Byth K, Cao Q, Chuaqui C, Carbajo RJ, Cheung T, Code E, Ferguson AD, Fillery S, Fuller NO, Gangl E, Gao N, Grist M, Hargreaves D, Howard MR, Hu J, Kemmitt PD, Nelson JE, O'Connell N, Prince DB, Raubo P, Rawlins PB, Robb GR, Shi J, Waring MJ, Whittaker D, Wylot M, Zhu X. Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors. J Med Chem 2017; 60:4386-4402. [PMID: 28485934 DOI: 10.1021/acs.jmedchem.7b00359] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Inhibition of the protein-protein interaction between B-cell lymphoma 6 (BCL6) and corepressors has been implicated as a therapeutic target in diffuse large B-cell lymphoma (DLBCL) cancers and profiling of potent and selective BCL6 inhibitors are critical to test this hypothesis. We identified a pyrazolo[1,5-a]pyrimidine series of BCL6 binders from a fragment screen in parallel with a virtual screen. Using structure-based drug design, binding affinity was increased 100000-fold. This involved displacing crystallographic water, forming new ligand-protein interactions and a macrocyclization to favor the bioactive conformation of the ligands. Optimization for slow off-rate constant kinetics was conducted as well as improving selectivity against an off-target kinase, CK2. Potency in a cellular BCL6 assay was further optimized to afford highly selective probe molecules. Only weak antiproliferative effects were observed across a number of DLBCL lines and a multiple myeloma cell line without a clear relationship to BCL6 potency. As a result, we conclude that the BCL6 hypothesis in DLBCL cancer remains unproven.
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Affiliation(s)
- William McCoull
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Roman D Abrams
- IMED Oncology, AstraZeneca , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Erica Anderson
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Kevin Blades
- IMED Oncology, AstraZeneca , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Peter Barton
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Matthew Box
- IMED Oncology, AstraZeneca , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Jonathan Burgess
- IMED Oncology, AstraZeneca , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Kate Byth
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Qing Cao
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Claudio Chuaqui
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Rodrigo J Carbajo
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Tony Cheung
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Erin Code
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Andrew D Ferguson
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Shaun Fillery
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Nathan O Fuller
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Eric Gangl
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Ning Gao
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Matthew Grist
- IMED Oncology, AstraZeneca , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - David Hargreaves
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Martin R Howard
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Jun Hu
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Paul D Kemmitt
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Jennifer E Nelson
- IMED Oncology, AstraZeneca , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Nichole O'Connell
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - D Bryan Prince
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Piotr Raubo
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Philip B Rawlins
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Graeme R Robb
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Junjie Shi
- Pharmaron Beijing Co., Ltd. 6 Taihe Road BDA, Beijing 100176 P. R. China
| | - Michael J Waring
- IMED Oncology, AstraZeneca , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - David Whittaker
- IMED Oncology, AstraZeneca , Mereside, Alderley Park, Macclesfield, SK10 4TG, U.K
| | - Marta Wylot
- IMED Oncology and Discovery Sciences, AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K
| | - Xiahui Zhu
- IMED Oncology and Discovery Sciences, AstraZeneca , Gatehouse Park, Waltham, Massachusetts 02451, United States
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Simões RV, Muñoz-Moreno E, Carbajo RJ, González-Tendero A, Illa M, Sanz-Cortés M, Pineda-Lucena A, Gratacós E. In Vivo Detection of Perinatal Brain Metabolite Changes in a Rabbit Model of Intrauterine Growth Restriction (IUGR). PLoS One 2015. [PMID: 26208165 PMCID: PMC4514800 DOI: 10.1371/journal.pone.0131310] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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] [Indexed: 01/08/2023] Open
Abstract
Background Intrauterine growth restriction (IUGR) is a risk factor for abnormal neurodevelopment. We studied a rabbit model of IUGR by magnetic resonance imaging (MRI) and spectroscopy (MRS), to assess in vivo brain structural and metabolic consequences, and identify potential metabolic biomarkers for clinical translation. Methods IUGR was induced in 3 pregnant rabbits at gestational day 25, by 40–50% uteroplacental vessel ligation in one horn; the contralateral horn was used as control. Fetuses were delivered at day 30 and weighted. A total of 6 controls and 5 IUGR pups underwent T2-w MRI and localized proton MRS within the first 8 hours of life, at 7T. Changes in brain tissue volumes and respective contributions to each MRS voxel were estimated by semi-automated registration of MRI images with a digital atlas of the rabbit brain. MRS data were used for: (i) absolute metabolite quantifications, using linear fitting; (ii) local temperature estimations, based on the water chemical shift; and (iii) classification, using spectral pattern analysis. Results Lower birth weight was associated with (i) smaller brain sizes, (ii) slightly lower brain temperatures, and (iii) differential metabolite profile changes in specific regions of the brain parenchyma. Specifically, we found estimated lower levels of aspartate and N-acetylaspartate (NAA) in the cerebral cortex and hippocampus (suggesting neuronal impairment), and higher glycine levels in the striatum (possible marker of brain injury). Our results also suggest that the metabolic changes in cortical regions are more prevalent than those detected in hippocampus and striatum. Conclusions IUGR was associated with brain metabolic changes in vivo, which correlate well with the neurostructural changes and neurodevelopment problems described in IUGR. Metabolic parameters could constitute non invasive biomarkers for the diagnosis and abnormal neurodevelopment of perinatal origin.
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Affiliation(s)
- Rui V. Simões
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Emma Muñoz-Moreno
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Rodrigo J. Carbajo
- Structural Biochemistry Laboratory, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Anna González-Tendero
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Miriam Illa
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Magdalena Sanz-Cortés
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Antonio Pineda-Lucena
- Structural Biochemistry Laboratory, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Eduard Gratacós
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
- * E-mail:
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25
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Mosulén S, Pineda-Lucena A, Carbajo RJ. Chemical shift assignments and secondary structure of the surrogate domain for drug discovery studies of human heparanase. Biomol NMR Assign 2015; 9:15-19. [PMID: 24395156 DOI: 10.1007/s12104-013-9536-9] [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] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 12/17/2013] [Indexed: 06/03/2023]
Abstract
Heparanase is an endoglycosidase that specifically degrades heparan sulfate, one of the main components of the extracellular matrix. Heparanase is implicated in cancer processes such as tumour formation, angiogenesis and metastasis, making it a very attractive target in drug discovery. Its active form is a heterodimer constituted by a 45 kDa glycosylated subunit (Lys158-Ile543) non-covalently bound to a smaller 8 kDa polypeptide (Gln36-Glu109). Residues Glu225 and Glu343 are critical in its catalytic mechanism and two heparan sulfate binding sites (Lys158-Asp171 and Gln270-Lys280) have been identified in the enzyme. Here we report the (1)H, (13)C and (15)N chemical shift assignments, secondary structure and chemical shift deviations from random coil of the domain of human heparanase comprising residues Lys158-Lys417, a construct that has been validated as surrogate of the full length protein in the search of novel inhibitors for this enzyme.
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Affiliation(s)
- Silvia Mosulén
- Laboratory of Structural Biochemistry, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012, Valencia, Spain
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26
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Carbajo RJ, Sanz L, Perez A, Calvete JJ. NMR structure of bitistatin – a missing piece in the evolutionary pathway of snake venom disintegrins. FEBS J 2014; 282:341-60. [PMID: 25363287 DOI: 10.1111/febs.13138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/13/2014] [Accepted: 10/29/2014] [Indexed: 11/28/2022]
Abstract
Extant disintegrins, as found in the venoms of Viperidae and Crotalidae snakes (vipers and rattlesnakes, represent a family of polypeptides that block the function of β1 and β3 integrin receptors, both potently and with a high degree of selectivity. This toxin family owes its origin to the neofunctionalization of the extracellular region of an ADAM (a disintegrin and metalloprotease) molecule recruited into the snake venom gland proteome in the Jurassic. The evolutionary structural diversification of the disintegrin scaffold, from the ancestral long disintegrins to the more recently evolved medium-sized, dimeric and short disintegrins, involved the stepwise loss of pairs of class-specific disulfide linkages and the processing of the N-terminal region. NMR and crystal structures of medium-sized, dimeric and short disintegrins have been solved. However, the structure of a long disintegrin remained unknown. The present study reports the NMR solution structures of two disulfide bond conformers of the long disintegrin bitistatin from the African puff adder Bitis arietans. The findings provide insight into how a structural domain of the extracellular region of an ADAM molecule, recruited into and selectively expressed in the snake venom gland proteome as a PIII metalloprotease in the Jurassic, has subsequently been tranformed into a family of integrin receptor antagonists.
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Affiliation(s)
- Rodrigo J Carbajo
- Laboratory of Structural Biochemistry, Centro de Investigación Príncipe Felipe, Valencia, Spain
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27
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Orzáez M, Sancho M, Marchán S, Mondragón L, Montava R, Valero JG, Landeta O, Basañez G, Carbajo RJ, Pineda-Lucena A, Bujons J, Moure A, Messeguer A, Lagunas C, Herrero C, Pérez-Payá E. Apaf-1 inhibitors protect from unwanted cell death in in vivo models of kidney ischemia and chemotherapy induced ototoxicity. PLoS One 2014; 9:e110979. [PMID: 25330150 PMCID: PMC4203855 DOI: 10.1371/journal.pone.0110979] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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: 07/02/2014] [Accepted: 09/18/2014] [Indexed: 12/21/2022] Open
Abstract
Background Excessive apoptosis induces unwanted cell death and promotes pathological conditions. Drug discovery efforts aimed at decreasing apoptotic damage initially targeted the inhibition of effector caspases. Although such inhibitors were effective, safety problems led to slow pharmacological development. Therefore, apoptosis inhibition is still considered an unmet medical need. Methodology and Principal Findings The interaction between Apaf-1 and the inhibitors was confirmed by NMR. Target specificity was evaluated in cellular models by siRNa based approaches. Cell recovery was confirmed by MTT, clonogenicity and flow cytometry assays. The efficiency of the compounds as antiapoptotic agents was tested in cellular and invivo models of protection upon cisplatin induced ototoxicity in a zebrafish model and from hypoxia and reperfusion kidney damage in a rat model of hot ischemia. Conclusions Apaf-1 inhibitors decreased Cytc release and apoptosome-mediated activation of procaspase-9 preventing cell and tissue damage in exvivo experiments and invivo animal models of apoptotic damage. Our results provide evidence that Apaf-1 pharmacological inhibition has therapeutic potential for the treatment of apoptosis-related diseases.
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Affiliation(s)
- Mar Orzáez
- Laboratory of Peptide and Protein Chemistry, Centro de Investigación Príncipe Felipe, Valencia, Spain
- * E-mail:
| | - Mónica Sancho
- Laboratory of Peptide and Protein Chemistry, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Sandra Marchán
- Laboratorios SALVAT S.A., Esplugues de Llobregat, Barcelona, Spain
| | - Laura Mondragón
- Laboratory of Peptide and Protein Chemistry, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Rebeca Montava
- Laboratory of Peptide and Protein Chemistry, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | | | | | | | - Rodrigo J. Carbajo
- Laboratory of Structural Biochemistry, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Antonio Pineda-Lucena
- Laboratory of Structural Biochemistry, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Jordi Bujons
- Department of Chemical and Biomolecular Nanotechnology and Department of Biological Chemistry and Molecular Modeling, Instituto de Química Avanzada de Cataluña (CSIC), Barcelona, Spain
| | - Alejandra Moure
- Department of Chemical and Biomolecular Nanotechnology and Department of Biological Chemistry and Molecular Modeling, Instituto de Química Avanzada de Cataluña (CSIC), Barcelona, Spain
| | - Angel Messeguer
- Department of Chemical and Biomolecular Nanotechnology and Department of Biological Chemistry and Molecular Modeling, Instituto de Química Avanzada de Cataluña (CSIC), Barcelona, Spain
| | - Carmen Lagunas
- Laboratorios SALVAT S.A., Esplugues de Llobregat, Barcelona, Spain
| | - Carmen Herrero
- Laboratorios SALVAT S.A., Esplugues de Llobregat, Barcelona, Spain
| | - Enrique Pérez-Payá
- Laboratory of Peptide and Protein Chemistry, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Instituto de Biomedicina de Valencia (CSIC), Valencia, Spain
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Filipiak K, Hidalgo M, Silvan JM, Fabre B, Carbajo RJ, Pineda-Lucena A, Ramos A, de Pascual-Teresa B, de Pascual-Teresa S. Dietary gallic acid and anthocyanin cytotoxicity on human fibrosarcoma HT1080 cells. A study on the mode of action. Food Funct 2014; 5:381-9. [PMID: 24413695 DOI: 10.1039/c3fo60465a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Gallic acid and anthocyanins are abundant plant food bioactives present in many fruits and vegetables, being especially important in the composition of berries. Gallic acid has been shown to possess cytotoxic properties in several cancer cell lines and to inhibit carcinogenesis in animal models. However, its mechanism of action is not yet fully understood. The aim of this study was to elucidate whether the observed inhibitory activity of gallic acid against gelatinases corresponds to its cytotoxic activity in HT1080 cells and to determine if anthocyanins could exhibit a similar behavior. Gallic acid and delphinidin-3-glucoside have shown selective cytotoxicity towards HT1080 cells. Further analysis by a migration and invasion assay showed anti-invasive activities of gallic acid, delphinidin and pelargonidin-3-glucosides. Zymographic analysis demonstrated the inhibitory activity of gallic acid at the level of secreted and activated gelatinases. Moreover, gallic acid inhibited MMP-2 and MMP-9 proteolytic activity with very similar potency. NMR and molecular modelling experiments confirmed the interaction of gallic acid with MMP-2, and suggested that it takes place within the catalytic center. In this work we give some new experimental data supporting the role of these compounds in the inhibition of metalloproteases as the mechanism for their cytotoxic activity against fibrosarcoma.
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Affiliation(s)
- Kamila Filipiak
- Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo, Urbanización Monteprincipe, 28668 Madrid, Spain
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Fabre B, Filipiak K, Coderch C, Zapico JM, Carbajo RJ, Schott AK, Pineda-Lucena A, de Pascual-Teresa B, Ramos A. New clicked thiirane derivatives as gelatinase inhibitors: the relevance of the P1′ segment. RSC Adv 2014. [DOI: 10.1039/c3ra46402d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Gozalbes R, Mosulén S, Ortí L, Rodríguez-Díaz J, Carbajo RJ, Melnyk P, Pineda-Lucena A. Hit identification of novel heparanase inhibitors by structure- and ligand-based approaches. Bioorg Med Chem 2013; 21:1944-51. [PMID: 23415087 DOI: 10.1016/j.bmc.2013.01.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 01/09/2013] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
Abstract
Heparanase is a key enzyme involved in the dissemination of metastatic cancer cells. In this study a combination of in silico techniques and experimental methods was used to identify new potential inhibitors against this target. A 3D model of heparanase was built from sequence homology and applied to the virtual screening of a library composed of 27 known heparanase inhibitors and a commercial collection of drugs and drug-like compounds. The docking results from this campaign were combined with those obtained from a pharmacophore model recently published based in the same set of chemicals. Compounds were then ranked according to their theoretical binding affinity, and the top-rated commercial drugs were selected for further experimental evaluation. Biophysical methods (NMR and SPR) were applied to assess experimentally the interaction of the selected compounds with heparanase. The binding site was evaluated via competition experiments, using a known inhibitor of heparanase. Three of the selected drugs were found to bind to the active site of the protein and their KD values were determined. Among them, the antimalarial drug amodiaquine presented affinity towards the protein in the low-micromolar range, and was singled out for a SAR study based on its chemical scaffold. A subset of fourteen 4-arylaminoquinolines from a global set of 249 analogues of amodiaquine was selected based on the application of in silico models, a QSAR solubility prediction model and a chemical diversity analysis. Some of these compounds displayed binding affinities in the micromolar range.
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Affiliation(s)
- Rafael Gozalbes
- Structural Biochemistry Laboratory, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
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Fabre B, Filipiak K, Zapico JM, Díaz N, Carbajo RJ, Schott AK, Martínez-Alcázar MP, Suárez D, Pineda-Lucena A, Ramos A, de Pascual-Teresa B. Progress towards water-soluble triazole-based selective MMP-2 inhibitors. Org Biomol Chem 2013; 11:6623-41. [DOI: 10.1039/c3ob41046c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Roldós V, Carbajo RJ, Schott AK, Pineda-Lucena A, Ochoa-Callejero L, Martínez A, Ramos A, de Pascual-Teresa B. Identification of first proadrenomedullin N-terminal 20 peptide (PAMP) modulator by means of virtual screening and NMR interaction experiments. Eur J Med Chem 2012; 55:262-72. [DOI: 10.1016/j.ejmech.2012.07.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 07/06/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
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Sancho M, Herrera AE, Gortat A, Carbajo RJ, Pineda-Lucena A, Orzáez M, Pérez-Payá E. Minocycline inhibits cell death and decreases mutant Huntingtin aggregation by targeting Apaf-1. Hum Mol Genet 2011; 20:3545-53. [DOI: 10.1093/hmg/ddr271] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Carbajo RJ, Sanz L, Mosulén S, Pérez A, Marcinkiewicz C, Pineda-Lucena A, Calvete JJ. NMR structure and dynamics of recombinant wild type and mutated jerdostatin, a selective inhibitor of integrin α1
β1. Proteins 2011; 79:2530-42. [DOI: 10.1002/prot.23076] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/26/2011] [Accepted: 04/27/2011] [Indexed: 11/06/2022]
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Zapico JM, Serra P, García-Sanmartín J, Filipiak K, Carbajo RJ, Schott AK, Pineda-Lucena A, Martínez A, Martín-Santamaría S, de Pascual-Teresa B, Ramos A. Potent “Clicked” MMP2 Inhibitors: Synthesis, Molecular Modeling and Biological Exploration. Org Biomol Chem 2011; 9:4587-99. [DOI: 10.1039/c0ob00852d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Deacon SPE, Apostolovic B, Carbajo RJ, Schott AK, Beck K, Vicent MJ, Pineda-Lucena A, Klok HA, Duncan R. Polymer Coiled-Coil Conjugates: Potential for Development as a New Class of Therapeutic “Molecular Switch”. Biomacromolecules 2010; 12:19-27. [DOI: 10.1021/bm100843e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Samuel P. E. Deacon
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, United Kingdom, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015, Lausanne, Switzerland, Structural Biology Laboratory and Medicinal Chemistry Unit, Polymer Therapeutics Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del
| | - Bojana Apostolovic
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, United Kingdom, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015, Lausanne, Switzerland, Structural Biology Laboratory and Medicinal Chemistry Unit, Polymer Therapeutics Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del
| | - Rodrigo J. Carbajo
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, United Kingdom, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015, Lausanne, Switzerland, Structural Biology Laboratory and Medicinal Chemistry Unit, Polymer Therapeutics Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del
| | - Anne-Kathrin Schott
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, United Kingdom, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015, Lausanne, Switzerland, Structural Biology Laboratory and Medicinal Chemistry Unit, Polymer Therapeutics Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del
| | - Konrad Beck
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, United Kingdom, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015, Lausanne, Switzerland, Structural Biology Laboratory and Medicinal Chemistry Unit, Polymer Therapeutics Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del
| | - María J. Vicent
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, United Kingdom, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015, Lausanne, Switzerland, Structural Biology Laboratory and Medicinal Chemistry Unit, Polymer Therapeutics Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del
| | - Antonio Pineda-Lucena
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, United Kingdom, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015, Lausanne, Switzerland, Structural Biology Laboratory and Medicinal Chemistry Unit, Polymer Therapeutics Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del
| | - Harm-Anton Klok
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, United Kingdom, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015, Lausanne, Switzerland, Structural Biology Laboratory and Medicinal Chemistry Unit, Polymer Therapeutics Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del
| | - Ruth Duncan
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, United Kingdom, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Matériaux, and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Bâtiment MXD, Station 12, CH-1015, Lausanne, Switzerland, Structural Biology Laboratory and Medicinal Chemistry Unit, Polymer Therapeutics Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Avda. Autopista del
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Díaz MD, Palomino-Schätzlein M, Corzana F, Andreu C, Carbajo RJ, del Olmo M, Canales-Mayordomo A, Pineda-Lucena A, Asensio G, Jiménez-Barbero J. Antimicrobial Peptides and Their Superior Fluorinated Analogues: Structure-Activity Relationships as Revealed by NMR Spectroscopy and MD Calculations. Chembiochem 2010; 11:2424-32. [DOI: 10.1002/cbic.201000424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mosulén S, Ortí L, Bas E, Carbajo RJ, Pineda-Lucena A. Production of heparanase constructs suitable for nuclear magnetic resonance and drug discovery studies. Biopolymers 2010; 95:151-60. [PMID: 20882536 DOI: 10.1002/bip.21549] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 08/24/2010] [Accepted: 09/14/2010] [Indexed: 11/09/2022]
Abstract
Heparanase is an endo-β-D-glucosidase capable of specifically degrading heparan sulphate, one of the main components of the extracellular matrix. This 65 kDa polypeptide is implicated in cancer processes such as tumour formation, angiogenesis and metastasis, making it a very attractive target in antitumour treatments. Structure-based approaches to find inhibitors of heparanase have been historically hampered by the lack of success in crystallizing the protein. With the aim to undertake the NMR structural characterisation of heparanase, we have designed and produced, using recombinant methods, smaller constructs of heparanase containing the catalytically active glutamic acids and the two binding sites for heparan sulphate. An extensive range of expression and purification conditions were evaluated to alleviate the intrinsic low solubility and aggregation propensity of heparanase, allowing the obtention of the enzyme in milligram quantities, both unlabelled and ¹⁵N-labelled for NMR studies. Using the smallest of the designed constructs and applying NMR and SPR methodologies, we have demonstrated that known inhibitors of heparanase bind to this construct specifically and selectively with K(D) values in the range of those reported for human heparanase, validating it for future drug discovery projects focused on the identification of novel inhibitors of this enzyme.
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Affiliation(s)
- Silvia Mosulén
- Medicinal Chemistry Department, Structural Biology Laboratory, Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, E-46012 Valencia, Spain
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Gozalbes R, J. Carbajo R, Pineda-Lucena A. Contributions of Computational Chemistry and Biophysical Techniques to Fragment-Based Drug Discovery. Curr Med Chem 2010; 17:1769-94. [DOI: 10.2174/092986710791111224] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 03/17/2010] [Indexed: 11/22/2022]
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Olano C, Gómez C, Pérez M, Palomino M, Pineda-Lucena A, Carbajo RJ, Braña AF, Méndez C, Salas JA. Deciphering Biosynthesis of the RNA Polymerase Inhibitor Streptolydigin and Generation of Glycosylated Derivatives. ACTA ACUST UNITED AC 2009; 16:1031-44. [DOI: 10.1016/j.chembiol.2009.09.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 09/15/2009] [Accepted: 09/18/2009] [Indexed: 11/29/2022]
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Sánchez C, Salas AP, Braña AF, Palomino M, Pineda-Lucena A, Carbajo RJ, Méndez C, Moris F, Salas JA. Generation of potent and selective kinase inhibitors by combinatorial biosynthesis of glycosylated indolocarbazoles. Chem Commun (Camb) 2009:4118-20. [PMID: 19568652 DOI: 10.1039/b905068j] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report the generation of novel glycosylated indolocarbazoles by combinatorial biosynthesis, and the identification of two novel potent and selective compounds inhibitors of JAK2 and Ikkb kinases.
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Affiliation(s)
- César Sánchez
- Department Biología Funcional & Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
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Gozalbes R, Mosulén S, Carbajo RJ, Pineda-Lucena A. Development and NMR validation of minimal pharmacophore hypotheses for the generation of fragment libraries enriched in heparanase inhibitors. J Comput Aided Mol Des 2009; 23:555-69. [PMID: 19421720 DOI: 10.1007/s10822-009-9269-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
Abstract
A combined strategy based on the development of pharmacophore hypotheses and NMR approaches is reported for the identification of novel inhibitors of heparanase, a key enzyme involved in tumor metastasis through the remodeling of the subepithelial and subendothelial basement membranes, resulting in the dissemination of metastatic cancer cells. Several pharmacophore hypotheses were initially developed from the most active heparanase inhibitors known to date and, after their application to a pool of 27 known heparanase inhibitors and a database of 1,120 compounds approved by the FDA, a four-point pharmacophore model was selected as the most predictive. This model was subsequently applied to a database of 686 chemical fragments, and a subset of 100 fragments accomplishing completely or partially the four-point model was selected to perform nuclear magnetic resonance experiments to validate the hypothesis. The experimental studies confirmed the reliability of our pharmacophore model, its applicability to in silico databases in order to reduce the number of compounds to be experimentally screened, and the possibility of generating fragment libraries enriched in heparanase inhibitors.
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Affiliation(s)
- Rafael Gozalbes
- Structural Biology Laboratory, Department of Medicinal Chemistry, Centro de Investigación Príncipe Felipe, Avenida Autopista del Saler 16, 46012, Valencia, Spain
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Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA. A kernel for open source drug discovery in tropical diseases. PLoS Negl Trop Dis 2009; 3:e418. [PMID: 19381286 PMCID: PMC2667270 DOI: 10.1371/journal.pntd.0000418] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 03/23/2009] [Indexed: 01/28/2023] Open
Abstract
Background Conventional patent-based drug development incentives work badly for the developing world, where commercial markets are usually small to non-existent. For this reason, the past decade has seen extensive experimentation with alternative R&D institutions ranging from private–public partnerships to development prizes. Despite extensive discussion, however, one of the most promising avenues—open source drug discovery—has remained elusive. We argue that the stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. Historically, open source software collaborations have almost never succeeded without such “kernels”. Methodology/Principal Findings Here, we use a computational pipeline for: (i) comparative structure modeling of target proteins, (ii) predicting the localization of ligand binding sites on their surfaces, and (iii) assessing the similarity of the predicted ligands to known drugs. Our kernel currently contains 143 and 297 protein targets from ten pathogen genomes that are predicted to bind a known drug or a molecule similar to a known drug, respectively. The kernel provides a source of potential drug targets and drug candidates around which an online open source community can nucleate. Using NMR spectroscopy, we have experimentally tested our predictions for two of these targets, confirming one and invalidating the other. Conclusions/Significance The TDI kernel, which is being offered under the Creative Commons attribution share-alike license for free and unrestricted use, can be accessed on the World Wide Web at http://www.tropicaldisease.org. We hope that the kernel will facilitate collaborative efforts towards the discovery of new drugs against parasites that cause tropical diseases. Open source drug discovery, a promising alternative avenue to conventional patent-based drug development, has so far remained elusive with few exceptions. A major stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. This paper introduces the results from a newly assembled computational pipeline for identifying protein targets for drug discovery in ten organisms that cause tropical diseases. We have also experimentally tested two promising targets for their binding to commercially available drugs, validating one and invalidating the other. The resulting kernel provides a base of drug targets and lead candidates around which an open source community can nucleate. We invite readers to donate their judgment and in silico and in vitro experiments to develop these targets to the point where drug optimization can begin.
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Affiliation(s)
- Leticia Ortí
- Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Structural Biology Laboratory, Medicinal Chemistry Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Rodrigo J. Carbajo
- Structural Biology Laboratory, Medicinal Chemistry Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
| | - Narayanan Eswar
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
| | - Stephen M. Maurer
- Gould School of Law, University of Southern California, Los Angeles, California, United States of America
| | - Arti K. Rai
- School of Law, Duke University, Durham, North Carolina, United States of America
| | - Ginger Taylor
- The Synaptic Leap, San Ramon, California, United States of America
| | - Matthew H. Todd
- School of Chemistry, University of Sydney, Sydney, New South Wales, Australia
| | - Antonio Pineda-Lucena
- Structural Biology Laboratory, Medicinal Chemistry Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (AS); (MAM-R)
| | - Marc A. Marti-Renom
- Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
- * E-mail: (AS); (MAM-R)
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Vicent MJ, Dieudonné L, Carbajo RJ, Pineda-Lucena A. Polymer conjugates as therapeutics: future trends, challenges and opportunities. Expert Opin Drug Deliv 2008; 5:593-614. [DOI: 10.1517/17425247.5.5.593] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Duncan R, Gilbert HRP, Carbajo RJ, Vicent MJ. Polymer Masked−Unmasked Protein Therapy. 1. Bioresponsive Dextrin−Trypsin and −Melanocyte Stimulating Hormone Conjugates Designed for α-Amylase Activation. Biomacromolecules 2008; 9:1146-54. [DOI: 10.1021/bm701073n] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ruth Duncan
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3XF, U.K., and Polymer Therapeutics Laboratory and Laboratory of Structural Biology, Centro de Investigación Príncipe Felipe, Av. Autopista del Saler 16, E-46012 Valencia, Spain
| | - Helena R. P. Gilbert
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3XF, U.K., and Polymer Therapeutics Laboratory and Laboratory of Structural Biology, Centro de Investigación Príncipe Felipe, Av. Autopista del Saler 16, E-46012 Valencia, Spain
| | - Rodrigo J. Carbajo
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3XF, U.K., and Polymer Therapeutics Laboratory and Laboratory of Structural Biology, Centro de Investigación Príncipe Felipe, Av. Autopista del Saler 16, E-46012 Valencia, Spain
| | - María J. Vicent
- Centre for Polymer Therapeutics, Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3XF, U.K., and Polymer Therapeutics Laboratory and Laboratory of Structural Biology, Centro de Investigación Príncipe Felipe, Av. Autopista del Saler 16, E-46012 Valencia, Spain
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Mora P, Carbajo RJ, Pineda-Lucena A, Sánchez del Pino MM, Pérez-Payá E. Solvent-exposed residues located in the β-sheet modulate the stability of the tetramerization domain of p53-A structural and combinatorial approach. Proteins 2007; 71:1670-85. [DOI: 10.1002/prot.21854] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Fustero S, Fernández B, Sanz-Cervera JF, Mateu N, Mosulén S, Carbajo RJ, Pineda-Lucena A, Ramírez de Arellano C. Asymmetric Synthesis of Fluorinated Amino Macrolactones through Ring-Closing Metathesis. J Org Chem 2007; 72:8716-23. [DOI: 10.1021/jo701484w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Santos Fustero
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain, and Laboratorio de Moléculas Orgánicas and Laboratorio de Biología Estructural, Centro de Investigación Príncipe Felipe, E-46013 Valencia, Spain
| | - Begoña Fernández
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain, and Laboratorio de Moléculas Orgánicas and Laboratorio de Biología Estructural, Centro de Investigación Príncipe Felipe, E-46013 Valencia, Spain
| | - Juan F. Sanz-Cervera
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain, and Laboratorio de Moléculas Orgánicas and Laboratorio de Biología Estructural, Centro de Investigación Príncipe Felipe, E-46013 Valencia, Spain
| | - Natalia Mateu
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain, and Laboratorio de Moléculas Orgánicas and Laboratorio de Biología Estructural, Centro de Investigación Príncipe Felipe, E-46013 Valencia, Spain
| | - Silvia Mosulén
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain, and Laboratorio de Moléculas Orgánicas and Laboratorio de Biología Estructural, Centro de Investigación Príncipe Felipe, E-46013 Valencia, Spain
| | - Rodrigo J. Carbajo
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain, and Laboratorio de Moléculas Orgánicas and Laboratorio de Biología Estructural, Centro de Investigación Príncipe Felipe, E-46013 Valencia, Spain
| | - Antonio Pineda-Lucena
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain, and Laboratorio de Moléculas Orgánicas and Laboratorio de Biología Estructural, Centro de Investigación Príncipe Felipe, E-46013 Valencia, Spain
| | - Carmen Ramírez de Arellano
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain, and Laboratorio de Moléculas Orgánicas and Laboratorio de Biología Estructural, Centro de Investigación Príncipe Felipe, E-46013 Valencia, Spain
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Carbajo RJ, Kellas FA, Yang JC, Runswick MJ, Montgomery MG, Walker JE, Neuhaus D. How the N-terminal Domain of the OSCP Subunit of Bovine F1Fo-ATP Synthase Interacts with the N-terminal Region of an Alpha Subunit. J Mol Biol 2007; 368:310-8. [PMID: 17355883 DOI: 10.1016/j.jmb.2007.02.059] [Citation(s) in RCA: 27] [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] [Received: 12/21/2006] [Revised: 02/13/2007] [Accepted: 02/15/2007] [Indexed: 11/23/2022]
Abstract
The peripheral stalk of ATP synthase acts as a stator holding the alpha(3)beta(3) catalytic subcomplex and the membrane subunit a against the torque of the rotating central stalk and attached c ring. In bovine mitochondria, the N-terminal domain of the oligomycin sensitivity conferral protein (OSCP-NT; residues 1-120) anchors one end of the peripheral stalk to the N-terminal tails of one or more alpha subunits of the F(1) subcomplex. Here, we present an NMR characterisation of the interaction between OSCP-NT and a peptide corresponding to residues 1-25 of the alpha-subunit of bovine F(1)-ATPase. The interaction site contains adjoining hydrophobic surfaces of helices 1 and 5 of OSCP-NT binding to hydrophobic side-chains of the alpha-peptide.
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