1
|
Schnute ME, Wennerstål M, Alley J, Bengtsson M, Blinn JR, Bolten CW, Braden T, Bonn T, Carlsson B, Caspers N, Chen M, Choi C, Collis LP, Crouse K, Färnegårdh M, Fennell KF, Fish S, Flick AC, Goos-Nilsson A, Gullberg H, Harris PK, Heasley SE, Hegen M, Hromockyj AE, Hu X, Husman B, Janosik T, Jones P, Kaila N, Kallin E, Kauppi B, Kiefer JR, Knafels J, Koehler K, Kruger L, Kurumbail RG, Kyne RE, Li W, Löfstedt J, Long SA, Menard CA, Mente S, Messing D, Meyers MJ, Napierata L, Nöteberg D, Nuhant P, Pelc MJ, Prinsen MJ, Rhönnstad P, Backström-Rydin E, Sandberg J, Sandström M, Shah F, Sjöberg M, Sundell A, Taylor AP, Thorarensen A, Trujillo JI, Trzupek JD, Unwalla R, Vajdos FF, Weinberg RA, Wood DC, Xing L, Zamaratski E, Zapf CW, Zhao Y, Wilhelmsson A, Berstein G. Discovery of 3-Cyano-N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)benzamide: A Potent, Selective, and Orally Bioavailable Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonist. J Med Chem 2018; 61:10415-10439. [DOI: 10.1021/acs.jmedchem.8b00392] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Tomas Bonn
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Bo Carlsson
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Nicole Caspers
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Ming Chen
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Chulho Choi
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | | | | | - Andrew C. Flick
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | - Steven E. Heasley
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | - Bolette Husman
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Tomasz Janosik
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | | | | | | | - Björn Kauppi
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | | | - John Knafels
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Konrad Koehler
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Lars Kruger
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Ravi G. Kurumbail
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | - Robert E. Kyne
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | - Carol A. Menard
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | | | | | - Philippe Nuhant
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | | | | | | | | | - Maria Sjöberg
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | - Aron Sundell
- Karo Bio AB (now Karo Pharma AB), 111 48 Stockholm, Sweden
| | | | | | - John I. Trujillo
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | - Felix F. Vajdos
- Medicine Design, Pfizer Inc., Groton, Connecticut 06340, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Vazquez ML, Kaila N, Strohbach JW, Trzupek JD, Brown MF, Flanagan ME, Mitton-Fry MJ, Johnson TA, TenBrink RE, Arnold EP, Basak A, Heasley SE, Kwon S, Langille J, Parikh MD, Griffin SH, Casavant JM, Duclos BA, Fenwick AE, Harris TM, Han S, Caspers N, Dowty ME, Yang X, Banker ME, Hegen M, Symanowicz PT, Li L, Wang L, Lin TH, Jussif J, Clark JD, Telliez JB, Robinson RP, Unwalla R. Identification of N-{cis-3-[Methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl}propane-1-sulfonamide (PF-04965842): A Selective JAK1 Clinical Candidate for the Treatment of Autoimmune Diseases. J Med Chem 2018; 61:1130-1152. [DOI: 10.1021/acs.jmedchem.7b01598] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Michael L. Vazquez
- Medicine
Design, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Neelu Kaila
- Medicine
Design, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Joseph W. Strohbach
- Medicine
Design, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - John D. Trzupek
- Medicine
Design, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Matthew F. Brown
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark E. Flanagan
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark J. Mitton-Fry
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Timothy A. Johnson
- Veterinary
Medicine Research and Development, Pfizer Inc, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Ruth E. TenBrink
- Medicinal
Chemistry, Pfizer Inc, 700 Chesterfield Parkway West, Chesterfield, Missouri 63017, United States
| | - Eric P. Arnold
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Arindrajit Basak
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Steven E. Heasley
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Soojin Kwon
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jonathan Langille
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mihir D. Parikh
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Sarah H. Griffin
- Chemical
Research Development, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeffrey M. Casavant
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brian A. Duclos
- Veterinary
Medicine Research and Development, Pfizer Inc, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Ashley E. Fenwick
- Veterinary
Medicine Research and Development, Pfizer Inc, 333 Portage Street, Kalamazoo, Michigan 49007, United States
| | - Thomas M. Harris
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Seungil Han
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Nicole Caspers
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Martin E. Dowty
- Medicine
Design, Pfizer Inc, 1 Burtt Road, Andover, Massachusetts 01810, United States
| | - Xin Yang
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mary Ellen Banker
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Martin Hegen
- Inflammation
and Immunology, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Peter T. Symanowicz
- Inflammation
and Immunology, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Li Li
- Inflammation
and Immunology, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Lu Wang
- Inflammation
and Immunology, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Tsung H. Lin
- Inflammation
and Immunology, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jason Jussif
- Inflammation
and Immunology, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - James D. Clark
- Inflammation
and Immunology, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Jean-Baptiste Telliez
- Inflammation
and Immunology, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Ralph P. Robinson
- Medicine
Design, Pfizer Inc, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ray Unwalla
- Medicine
Design, Pfizer Inc, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
3
|
Lee KL, Ambler CM, Anderson DR, Boscoe BP, Bree AG, Brodfuehrer JI, Chang JS, Choi C, Chung S, Curran KJ, Day JE, Dehnhardt CM, Dower K, Drozda SE, Frisbie RK, Gavrin LK, Goldberg JA, Han S, Hegen M, Hepworth D, Hope HR, Kamtekar S, Kilty IC, Lee A, Lin LL, Lovering FE, Lowe MD, Mathias JP, Morgan HM, Murphy EA, Papaioannou N, Patny A, Pierce BS, Rao VR, Saiah E, Samardjiev IJ, Samas BM, Shen MWH, Shin JH, Soutter HH, Strohbach JW, Symanowicz PT, Thomason JR, Trzupek JD, Vargas R, Vincent F, Yan J, Zapf CW, Wright SW. Discovery of Clinical Candidate 1-{[(2S,3S,4S)-3-Ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide (PF-06650833), a Potent, Selective Inhibitor of Interleukin-1 Receptor Associated Kinase 4 (IRAK4), by Fragment-Based Drug Design. J Med Chem 2017; 60:5521-5542. [PMID: 28498658 DOI: 10.1021/acs.jmedchem.7b00231] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Through fragment-based drug design focused on engaging the active site of IRAK4 and leveraging three-dimensional topology in a ligand-efficient manner, a micromolar hit identified from a screen of a Pfizer fragment library was optimized to afford IRAK4 inhibitors with nanomolar potency in cellular assays. The medicinal chemistry effort featured the judicious placement of lipophilicity, informed by co-crystal structures with IRAK4 and optimization of ADME properties to deliver clinical candidate PF-06650833 (compound 40). This compound displays a 5-unit increase in lipophilic efficiency from the fragment hit, excellent kinase selectivity, and pharmacokinetic properties suitable for oral administration.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Heidi M Morgan
- Worldwide Medicinal Chemistry, Pfizer Inc. , 1070 Science Center Drive, San Diego, California 92121, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jiangli Yan
- Worldwide Medicinal Chemistry, Pfizer Inc. , 1070 Science Center Drive, San Diego, California 92121, United States
| | | | | |
Collapse
|
4
|
Gerstenberger BS, Trzupek JD, Tallant C, Fedorov O, Filippakopoulos P, Brennan PE, Fedele V, Martin S, Picaud S, Rogers C, Parikh M, Taylor A, Samas B, O'Mahony A, Berg E, Pallares G, Torrey AD, Treiber DK, Samardjiev IJ, Nasipak BT, Padilla-Benavides T, Wu Q, Imbalzano AN, Nickerson JA, Bunnage ME, Müller S, Knapp S, Owen DR. Identification of a Chemical Probe for Family VIII Bromodomains through Optimization of a Fragment Hit. J Med Chem 2016; 59:4800-11. [PMID: 27115555 DOI: 10.1021/acs.jmedchem.6b00012] [Citation(s) in RCA: 68] [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: 12/12/2022]
Abstract
The acetyl post-translational modification of chromatin at selected histone lysine residues is interpreted by an acetyl-lysine specific interaction with bromodomain reader modules. Here we report the discovery of the potent, acetyl-lysine-competitive, and cell active inhibitor PFI-3 that binds to certain family VIII bromodomains while displaying significant, broader bromodomain family selectivity. The high specificity of PFI-3 for family VIII was achieved through a novel bromodomain binding mode of a phenolic headgroup that led to the unusual displacement of water molecules that are generally retained by most other bromodomain inhibitors reported to date. The medicinal chemistry program that led to PFI-3 from an initial fragment screening hit is described in detail, and additional analogues with differing family VIII bromodomain selectivity profiles are also reported. We also describe the full pharmacological characterization of PFI-3 as a chemical probe, along with phenotypic data on adipocyte and myoblast cell differentiation assays.
Collapse
Affiliation(s)
- Brian S Gerstenberger
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - John D Trzupek
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Cynthia Tallant
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Oleg Fedorov
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Panagis Filippakopoulos
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Paul E Brennan
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Vita Fedele
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Sarah Martin
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Sarah Picaud
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Catherine Rogers
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Mihir Parikh
- Pfizer Pharmaceutical Sciences , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Alexandria Taylor
- Pfizer Pharmaceutical Sciences , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brian Samas
- Pfizer Worldwide Medicinal Chemistry , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Alison O'Mahony
- Bioseek Inc., Division of DiscoveRx , 310 Utah Avenue, South San Francisco, California 94080, United States
| | - Ellen Berg
- Bioseek Inc., Division of DiscoveRx , 310 Utah Avenue, South San Francisco, California 94080, United States
| | - Gabriel Pallares
- KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States
| | - Adam D Torrey
- KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States
| | - Daniel K Treiber
- KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States
| | - Ivan J Samardjiev
- Eurofins Lancaster PPS , Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brian T Nasipak
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Teresita Padilla-Benavides
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Qiong Wu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States
| | - Mark E Bunnage
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Susanne Müller
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.,Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe University , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Dafydd R Owen
- Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
5
|
Fedorov O, Castex J, Tallant C, Owen DR, Martin S, Aldeghi M, Monteiro O, Filippakopoulos P, Picaud S, Trzupek JD, Gerstenberger BS, Bountra C, Willmann D, Wells C, Philpott M, Rogers C, Biggin PC, Brennan PE, Bunnage ME, Schüle R, Günther T, Knapp S, Müller S. Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance. Sci Adv 2015; 1:e1500723. [PMID: 26702435 PMCID: PMC4681344 DOI: 10.1126/sciadv.1500723] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/31/2015] [Indexed: 05/13/2023]
Abstract
Mammalian SWI/SNF [also called Brg/Brahma-associated factors (BAFs)] are evolutionarily conserved chromatin-remodeling complexes regulating gene transcription programs during development and stem cell differentiation. BAF complexes contain an ATP (adenosine 5'-triphosphate)-driven remodeling enzyme (either BRG1 or BRM) and multiple protein interaction domains including bromodomains, an evolutionary conserved acetyl lysine-dependent protein interaction motif that recruits transcriptional regulators to acetylated chromatin. We report a potent and cell active protein interaction inhibitor, PFI-3, that selectively binds to essential BAF bromodomains. The high specificity of PFI-3 was achieved on the basis of a novel binding mode of a salicylic acid head group that led to the replacement of water molecules typically maintained in other bromodomain inhibitor complexes. We show that exposure of embryonic stem cells to PFI-3 led to deprivation of stemness and deregulated lineage specification. Furthermore, differentiation of trophoblast stem cells in the presence of PFI-3 was markedly enhanced. The data present a key function of BAF bromodomains in stem cell maintenance and differentiation, introducing a novel versatile chemical probe for studies on acetylation-dependent cellular processes controlled by BAF remodeling complexes.
Collapse
Affiliation(s)
- Oleg Fedorov
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Josefina Castex
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacher Strasse 66, 79106 Freiburg, Germany
| | - Cynthia Tallant
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Dafydd R. Owen
- Pfizer Worldwide Medicinal Chemistry, 610 Main Street, Cambridge, MA 02139, USA
| | - Sarah Martin
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Matteo Aldeghi
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Octovia Monteiro
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX3 7DQ, UK
| | - Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - John D. Trzupek
- Pfizer Worldwide Medicinal Chemistry, 610 Main Street, Cambridge, MA 02139, USA
| | | | - Chas Bountra
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Dominica Willmann
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacher Strasse 66, 79106 Freiburg, Germany
| | - Christopher Wells
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Martin Philpott
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Catherine Rogers
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Paul E. Brennan
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Mark E. Bunnage
- Pfizer Worldwide Medicinal Chemistry, 610 Main Street, Cambridge, MA 02139, USA
| | - Roland Schüle
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacher Strasse 66, 79106 Freiburg, Germany
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, 79106 Freiburg, Germany
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Thomas Günther
- Urologische Klinik und Zentrale Klinische Forschung, Klinikum der Universität Freiburg, Breisacher Strasse 66, 79106 Freiburg, Germany
- Corresponding author. E-mail: (T.G.); (S.M.); (S.K.)
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Corresponding author. E-mail: (T.G.); (S.M.); (S.K.)
| | - Susanne Müller
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
- Corresponding author. E-mail: (T.G.); (S.M.); (S.K.)
| |
Collapse
|
6
|
Wright SW, Choi C, Chung S, Boscoe BP, Drozda SE, Mousseau JJ, Trzupek JD. Reversal of Diastereoselection in the Conjugate Addition of Cuprates to Unsaturated Lactams. Org Lett 2015; 17:5204-7. [DOI: 10.1021/acs.orglett.5b02533] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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)
- Stephen W. Wright
- Worldwide
Medicinal Chemistry, Pfizer Global Research and Development, 445
Eastern Point Road, Groton, Connecticut 06340, United States
| | - Chulho Choi
- Worldwide
Medicinal Chemistry, Pfizer Global Research and Development, 445
Eastern Point Road, Groton, Connecticut 06340, United States
| | - Seungwon Chung
- Worldwide
Medicinal Chemistry, Pfizer Global Research and Development, 445
Eastern Point Road, Groton, Connecticut 06340, United States
| | - Brian P. Boscoe
- Worldwide
Medicinal Chemistry, Pfizer Global Research and Development, 445
Eastern Point Road, Groton, Connecticut 06340, United States
| | - Susan E. Drozda
- Worldwide
Medicinal Chemistry, Pfizer Global Research and Development, 445
Eastern Point Road, Groton, Connecticut 06340, United States
| | - James J. Mousseau
- Worldwide
Medicinal Chemistry, Pfizer Global Research and Development, 445
Eastern Point Road, Groton, Connecticut 06340, United States
| | - John D. Trzupek
- Inflammation & Immunology Research, Pfizer Global Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
7
|
Abstract
While the installation and removal of epigenetic post-translational modifications or ‘marks’ on both DNA and histone proteins are the tangible outcome of enzymatically catalyzed processes, the role of the epigenetic reader proteins looks, at first, less obvious. As they do not catalyze a chemical transformation or process as such, their role is not enzymatic. However, this does not preclude them from being potential targets for drug discovery as their function is clearly correlated to transcriptional activity and as a class of proteins, they appear to have binding sites of sufficient definition and size to be inhibited by small molecules. This suggests that this third class of epigenetic proteins that are involved in the interpretation of post-translational marks (as opposed to the creation or deletion of marks) may represent attractive targets for drug discovery efforts. This review mainly summarizes selected publications, patent literature and company disclosures on these non-enzymatic epigenetic reader proteins from 2009 to the present.
Collapse
Affiliation(s)
- Dafydd R Owen
- Pfizer Worldwide Research and Development, 200 Cambridgepark Drive, Cambridge, MA 02140, USA.
| | - John D Trzupek
- Pfizer Worldwide Research and Development, 200 Cambridgepark Drive, Cambridge, MA 02140, USA
| |
Collapse
|
8
|
Fish PV, Filippakopoulos P, Bish G, Brennan PE, Bunnage ME, Cook AS, Federov O, Gerstenberger BS, Jones H, Knapp S, Marsden B, Nocka K, Owen DR, Philpott M, Picaud S, Primiano MJ, Ralph MJ, Sciammetta N, Trzupek JD. Identification of a chemical probe for bromo and extra C-terminal bromodomain inhibition through optimization of a fragment-derived hit. J Med Chem 2012; 55:9831-7. [PMID: 23095041 PMCID: PMC3506127 DOI: 10.1021/jm3010515] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The posttranslational modification of chromatin through acetylation at selected histone lysine residues is governed by histone acetyltransferases (HATs) and histone deacetylases (HDACs). The significance of this subset of the epigenetic code is interrogated and interpreted by an acetyllysine-specific protein-protein interaction with bromodomain reader modules. Selective inhibition of the bromo and extra C-terminal domain (BET) family of bromodomains with a small molecule is feasible, and this may represent an opportunity for disease intervention through the recently disclosed antiproliferative and anti-inflammatory properties of such inhibitors. Herein, we describe the discovery and structure-activity relationship (SAR) of a novel, small-molecule chemical probe for BET family inhibition that was identified through the application of structure-based fragment assessment and optimization techniques. This has yielded a potent, selective compound with cell-based activity (PFI-1) that may further add to the understanding of BET family function within the bromodomains.
Collapse
Affiliation(s)
- Paul V Fish
- Pfizer Worldwide Medicinal Chemistry, Pfizer Worldwide R&D , Ramsgate Road, Sandwich CT13 9NJ, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Trzupek JD, Lee D, Crowley BM, Marathias VM, Danishefsky SJ. Total synthesis of enantiopure phalarine via a stereospecific Pictet-Spengler reaction: traceless transfer of chirality from L-tryptophan. J Am Chem Soc 2010; 132:8506-12. [PMID: 20509657 DOI: 10.1021/ja1030968] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An appropriately constructed 2-substituted derivative of l-tryptophan undergoes conversion to a prephalarine structure in a single step. The reaction occurs in a diastereoselective fashion, leading shortly thereafter to the naturally occurring version of the alkaloid phalarine.
Collapse
Affiliation(s)
- John D Trzupek
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065, USA
| | | | | | | | | |
Collapse
|
10
|
Shimamura H, Breazzano SP, Garfunkle J, Kimball FS, Trzupek JD, Boger DL. Total synthesis of complestatin: development of a Pd(0)-mediated indole annulation for macrocyclization. J Am Chem Soc 2010; 132:7776-83. [PMID: 20469945 PMCID: PMC2892899 DOI: 10.1021/ja102304p] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Full details of the initial development and continued examination of a powerful intramolecular palladium(0)-mediated indole annulation for macrocyclization closure of the strained 16-membered biaryl ring system found in complestatin (1, chloropeptin II) and the definition of factors impacting its intrinsic atropodiastereoselectivity are described. Its examination and use in an alternative, second-generation total synthesis of complestatin are detailed in which the order of the macrocyclization reactions was reversed from our first-generation total synthesis. In this approach and with the ABCD biaryl ether ring system in place, the key Larock cyclization was conducted with substrate 36 (containing four phenols, five secondary amides, one carbamate, and four labile aryl chlorides) and provided the product 37 (56%) exclusively as a single atropisomer (>20:1, detection limits) possessing the natural (R)-configuration. In this instance, the complexity of the substrate and the reverse macrocyclization order did not diminish the atropodiastereoselectivity; rather, it provided an improvement over the 4:1 selectivity that was observed with the analogous substrate used to provide the isolated DEF ring system in our first-generation approach. Just as significant, the atroposelectivity represents a complete reversal of the diasteroselectivity observed with analogous macrocyclizations conducted using a Suzuki biaryl coupling.
Collapse
Affiliation(s)
- Hiroyuki Shimamura
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Steven P. Breazzano
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Joie Garfunkle
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - F. Scott Kimball
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - John D. Trzupek
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Dale L. Boger
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| |
Collapse
|
11
|
Trzupek JD, Li C, Chan C, Crowley BM, Heimann AC, Danishefsky SJ. Lessons from the Total Synthesis of (±) Phalarine: Insights Into the Mechanism of the Pictet-Spengler Reaction. ACTA ACUST UNITED AC 2010; 82:1735-1748. [PMID: 20711493 DOI: 10.1351/pac-con-09-11-14] [Citation(s) in RCA: 14] [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] [Indexed: 11/16/2022]
Abstract
The furanobisindole alkaloid, phalarine, possesses a unique structural framework within the alkaloid family of natural products. Our laboratory recently disclosed the racemic total synthesis of phalarine, featuring an efficient azaspiroindolenine rearrangement; this achievement is revisited in detail. Upon completion of the first-generation total synthesis, we explored some interesting mechanism-level issues with regard to the key azaspiroindolenine rearrangement. These investigations provided valuable insights into the mechanism of racemization during the azaspiroindolenine rearrangement en route to synthetic phalarine. In addition, in the course of these studies, we demonstrated the Pictet-Spengler capture reaction for C(2)-aryl indoles, and successfully isolated the elusive azaspiroindolenine intermediate of the Pictet-Spengler reaction. Key insights into the remarkably subtle stereoelectronics that govern this rearrangement for C(2)-arylated indoles are discussed.
Collapse
Affiliation(s)
- John D Trzupek
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065
| | | | | | | | | | | |
Collapse
|
12
|
Garfunkle J, Kimball FS, Trzupek JD, Takizawa S, Shimamura H, Tomishima M, Boger DL. Total synthesis of chloropeptin II (complestatin) and chloropeptin I. J Am Chem Soc 2009; 131:16036-8. [PMID: 19839632 PMCID: PMC2783344 DOI: 10.1021/ja907193b] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first total synthesis of chloropeptin II (1, complestatin) is disclosed. Key elements of the approach include the use of an intramolecular Larock indole synthesis for the initial macrocyclization, adopting conditions that permit utilization of a 2-bromoaniline, incorporating a terminal alkyne substituent (-SiEt(3)) that sterically dictates the indole cyclization regioselectivity, and benefiting from an aniline protecting group (-Ac) that enhances the atropdiastereoselectivity and diminishes the strained indole reactivity toward subsequent electrophilic reagents. Not only did this key reaction provide the fully functionalized right-hand ring system of 1 in superb conversion (89%) and good atropdiastereoselectivity (4:1 R:S), but it also represents the first reported example of what will prove to be a useful Larock macrocyclization strategy. Subsequent introduction of the left-hand ring system enlisting an aromatic nucleophilic substitution reaction for macrocyclization with biaryl ether formation completed the assemblage of the core bicyclic structure of 1. Intrinsic in the design of the approach and by virtue of the single-step acid-catalyzed conversion of chloropeptin II (1) to chloropeptin I (2), the route also provides a total synthesis of 2.
Collapse
Affiliation(s)
- Joie Garfunkle
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | | | | | | | | | |
Collapse
|
13
|
Kan C, Trzupek JD, Wu B, Wan Q, Chen G, Tan Z, Yuan Y, Danishefsky SJ. Toward homogeneous erythropoietin: chemical synthesis of the Ala1-Gly28 glycopeptide domain by "alanine" ligation. J Am Chem Soc 2009; 131:5438-43. [PMID: 19334679 PMCID: PMC2765573 DOI: 10.1021/ja808707w] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Ala(1)-Gly(28) glycopeptide fragment (28) of EPO was prepared by chemical synthesis as a single glycoform. Key steps in the synthesis include attachment of a complex dodecasaccharide (7) to a seven amino acid peptide via Lansbury aspartylation, native chemical ligation to join peptide 19 with the glycopeptide domain 18, and a selective desulfurization at the ligation site to reveal the natural Ala(19). This glycopeptide fragment (28) contains both the requisite N-linked dodecasaccharide and a C-terminal (alpha)thioester handle, the latter feature permitting direct coupling with a glycopeptide fragment bearing N-terminal Cys(29) without further functionalization.
Collapse
Affiliation(s)
- Cindy Kan
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065
| | - John D. Trzupek
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065
| | - Bin Wu
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065
| | - Qian Wan
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065
| | - Gong Chen
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065
| | - Zhongping Tan
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065
| | - Yu Yuan
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065
| | - Samuel J. Danishefsky
- Laboratory for Bioorganic Chemistry, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, New York 10065
- Department of Chemistry, Columbia University, Havemeyer Hall, 3000 Broadway, New York, New York 10027
| |
Collapse
|
14
|
Jin W, Trzupek JD, Rayl TJ, Broward MA, Vielhauer GA, Weir SJ, Hwang I, Boger DL. A unique class of duocarmycin and CC-1065 analogues subject to reductive activation. J Am Chem Soc 2007; 129:15391-7. [PMID: 18020335 PMCID: PMC2519901 DOI: 10.1021/ja075398e] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
N-Acyl O-amino phenol derivatives of CBI-TMI and CBI-indole2 are reported as prototypical members of a new class of reductively activated prodrugs of the duocarmycin and CC-1065 class of antitumor agents. The expectation being that hypoxic tumor environments, with their higher reducing capacity, carry an intrinsic higher concentration of "reducing" nucleophiles (e.g., thiols) capable of activating such derivatives (tunable N-O bond cleavage) and increasing their sensitivity to the prodrug treatment. Preliminary studies indicate the prodrugs effectively release the free drug in functional cellular assays for cytotoxic activity approaching or matching the activity of the free drug, yet remain essentially stable and unreactive to in vitro DNA alkylation conditions (<0.1-0.01% free drug release) and pH 7.0 phosphate buffer, and exhibit a robust half-life in human plasma (t1/2 = 3 h). Characterization of a representative O-(acylamino) prodrug in vivo indicates that they approach the potency and exceed the efficacy of the free drug itself (CBI-indole2), indicating that not only is the free drug effectively released from the inactive prodrug but also that they offer additional advantages related to a controlled or targeted release in vivo.
Collapse
Affiliation(s)
- Wei Jin
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, E-mail:
| | - John D. Trzupek
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, E-mail:
| | - Thomas J. Rayl
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, E-mail:
| | - Melinda A. Broward
- Office of Therapeutics, Discovery and Development, University of Kansas Cancer Center, 3901 Rainbow Blvd., Kansas City, Kansas 66160
| | - George A. Vielhauer
- Office of Therapeutics, Discovery and Development, University of Kansas Cancer Center, 3901 Rainbow Blvd., Kansas City, Kansas 66160
| | - Scott J. Weir
- Office of Therapeutics, Discovery and Development, University of Kansas Cancer Center, 3901 Rainbow Blvd., Kansas City, Kansas 66160
| | - Inkyu Hwang
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, E-mail:
| | - Dale L. Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, E-mail:
| |
Collapse
|
15
|
Tichenor MS, MacMillan KS, Trzupek JD, Rayl TJ, Hwang I, Boger DL. Systematic exploration of the structural features of yatakemycin impacting DNA alkylation and biological activity. J Am Chem Soc 2007; 129:10858-69. [PMID: 17691783 PMCID: PMC2519902 DOI: 10.1021/ja072777z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A systematic examination of the impact of the yatakemycin left and right subunits and their substituents is detailed along with a study of its unique three subunit arrangement (sandwiched vs extended and reversed analogues). The examination of the ca. 50 analogues prepared illustrate that within the yatakemycin three subunit structure, the subunit substituents are relatively unimportant and that it is the unique sandwiched arrangement that substantially increases the rate and optimizes the efficiency of its DNA alkylation reaction. This potentiates the cytotoxic activity of yatakemycin and its analogues overcoming limitations typically observed with more traditional compounds in the series (CC-1065, duocarmycins). Moreover, a study of the placement of the alkylation subunit within the three subunit arrangement (sandwiched vs extended and reversed analogues) indicates that it not only has a profound impact on the rate and efficiency of DNA alkylation but also controls and establishes the DNA alkylation selectivity as well, where both enantiomers of such sandwiched agents alkylate the same adenine sites exhibiting the same DNA alkylation selectivity independent of their absolute configuration.
Collapse
|
16
|
Tichenor MS, Trzupek JD, Kastrinsky DB, Shiga F, Hwang I, Boger DL. Asymmetric total synthesis of (+)- and ent-(-)-yatakemycin and duocarmycin SA: evaluation of yatakemycin key partial structures and its unnatural enantiomer. J Am Chem Soc 2006; 128:15683-96. [PMID: 17147378 PMCID: PMC2515590 DOI: 10.1021/ja064228j] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Complementary to studies that provided the first yatakemycin total synthesis resulting in its structure revision and absolute stereochemistry assignment, a second-generation asymmetric total synthesis is disclosed herein. Since the individual yatakemycin subunits are identical to those of duocarmycin SA (alkylation subunit) or CC-1065 (central and right-hand subunits), the studies also provide an improvement in our earlier total synthesis of CC-1065 and, as detailed herein, have been extended to an asymmetric total synthesis of (+)-duocarmycin SA. Further extensions of the studies provided key yatakemycin partial structures and analogues for comparative assessments. This included the definition of the DNA selectivity (adenine central to a five-base-pair AT sequence, e.g., 5'-AAAAA), efficiency, relative rate, and reversibility of ent-(-)-yatakemycin and its comparison with the natural enantiomer (identical selectivity and efficiency), structural characterization of the adenine N3 adduct confirming the nature of the DNA reaction, and comparisons of the cytotoxic activity of the natural product (L1210, IC50 = 5 pM) with those of its unnatural enantiomer (IC50 = 5 pM) and a series of key partial structures including those that probe the role of the C-terminus thiomethyl ester. The only distinguishing features between the enantiomers is that ent-(-)-yatakemycin alkylates DNA at a slower rate (krel = 0.13) and is reversible, whereas (+)-yatakemycin is not. Nonetheless, even ent-(-)-yatakemycin alkylates DNA at a faster rate and with a greater thermodynamic stability than (+)-duocarmycin SA, illustrating the unique characteristics of such "sandwiched" agents.
Collapse
Affiliation(s)
- Mark S. Tichenor
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - John D. Trzupek
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - David B. Kastrinsky
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Futoshi Shiga
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Inkyu Hwang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Dale L. Boger
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| |
Collapse
|
17
|
Toth JL, Trzupek JD, Flores LV, Kiakos K, Hartley JA, Pennington WT, Lee M. A novel achiral seco-amino-cyclopropylindoline (CI) analog of CC-1065 and the duocarmycins: design, synthesis and biological studies. Med Chem 2006; 1:13-9. [PMID: 16789881 DOI: 10.2174/1573406053402523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The design, synthesis and DNA binding properties of a novel achiral and amino-containing seco-cyclopropylindoline analog (seco-amino-CI-TMI, 1) of the duocarmycins are described. Thermal induced DNA cleavage studies on pUC18 DNA revealed compound 1 to preferentially bind in the minor groove and to covalently react with AT-rich sequences, particularly at the underlined adenine-N3 group of 5'-AAAAA(865)-3'. This sequence specificity is similar to adozelesin and CC-1065. Using a 4-day continuous exposure, compound 1 inhibited the growth of K562 human chronic myeloid leukemia cells in culture. Compound 1 has appreciable cytotoxicity (IC50 value of 1.30 microM) relative to compound 2 (0.15 microM), the corresponding racemic and hydroxy-seco-CI-TMI analog. These results indicate that the aminophenethyl chloride group present in compound 1 has similar sequence specific and cytotoxic properties to the hydroxy-containing seco-precursors of CC-1065 and the duocarmycins. Moreover, the results suggest that the chiral center present in the natural products is not absolutely necessary for biological activity. The novel aminophenethyl halide moiety is, therefore, a useful template from which to develop future achiral analogs of CC-1065 and the duocarmycins.
Collapse
Affiliation(s)
- James L Toth
- Department of Chemistry, Furman University, 3300 Poinsett Highway, Greenville, SC 29613, USA
| | | | | | | | | | | | | |
Collapse
|
18
|
Abstract
[reaction: see text] A general method for the photochemical generation of ribose abasic sites within RNA oligonucleotides is reported. Photochemically caged nucleoside phosphoramidite analogues were prepared and incorporated into RNA oligonucleotides by automated RNA synthesis. Irradiation of the modified RNA at 350 nm efficiently produced ribose abasic sites at specific sites within RNA sequences. The current approach offers a chemical route to RNA abasic lesions for RNA biochemical studies.
Collapse
Affiliation(s)
- John D Trzupek
- Department of Chemistry and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
| | | |
Collapse
|
19
|
Trzupek JD, Gottesfeld JM, Boger DL. Alkylation of duplex DNA in nucleosome core particles by duocarmycin SA and yatakemycin. Nat Chem Biol 2006; 2:79-82. [PMID: 16415862 DOI: 10.1038/nchembio761] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 12/08/2005] [Indexed: 11/09/2022]
Abstract
(+)-Yatakemycin (1, Fig. 1) and (+)-duocarmycin SA (2) are exceptionally potent, naturally occurring antitumor agents that derive their biological properties through a characteristic sequence-selective DNA-alkylation reaction. Studies have shown that both the AT-rich binding selectivity (shape-selective recognition) and the alkylation catalysis (shape-dependent catalysis) that contribute to the alkylation selectivity are dependent on the DNA minor groove shape and size characteristics of an AT-rich sequence (ref. 6 and references therein; refs. 7,8). Here we report the alkylation properties of yatakemycin and duocarmycin SA on free DNA (alpha-satellite DNA) and the same sequence bound in a nucleosome core particle (NCP) modeling the state of DNA in eukaryotic cells. Both compounds showed a clear, relatively unaltered ability to alkylate DNA packaged in NCPs in terms of both alkylating efficiency and sequence selectivity, despite the steric and conformational perturbations imposed by NCP packaging. These findings highlight the dynamic nature of NCP-bound DNA and illustrate that cell- and protein-free DNA-alkylation studies of members of this class of antitumor drugs provide valuable insights into their properties.
Collapse
Affiliation(s)
- John D Trzupek
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | |
Collapse
|
20
|
Parrish JP, Trzupek JD, Hughes TV, Hwang I, Boger DL. Synthesis and evaluation of N-aryl and N-alkenyl CBI derivatives. Bioorg Med Chem 2005; 12:5845-56. [PMID: 15498660 DOI: 10.1016/j.bmc.2004.08.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Revised: 08/23/2004] [Accepted: 08/23/2004] [Indexed: 11/29/2022]
Abstract
The preparation of a novel series of N-aryl CBI derivatives in which an aryl substituent could be used to predictably modulate the reactivity of the resulting CC-1065/duocarmycin alkylation subunit analogue is detailed and its extension to a unique series of N-alkenyl derivatives is reported. The N-aryl derivatives were found to be exceptionally stable and to exhibit well-defined relationships between structure (X-ray), reactivity, and cytotoxic potency. When combined with the results of past investigations, the studies define a fundamental parabolic relationship between reactivity and cytotoxic potency. The parabolic relationship establishes that compounds in the series should possess sufficient stability to reach their biological target (DNA), yet maintain sufficient reactivity to effectively alkylate DNA upon reaching the biological target. Just as importantly, it defined this optimal balance of stability and reactivity that may be used for future design of related analogues. Notably, the duocarmycin SA and yatakemycin alkylation subunit lies at this optimal stability/reactivity position, whereas the CC-1065 and duocarmycin A alkylation subunits lie progressively and significantly to the left of this optimal position (too reactive).
Collapse
Affiliation(s)
- Jay P Parrish
- Department of Chemistry and the Skaggs, Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | | | | | | |
Collapse
|