1
|
Ortiz G, Longbotham JE, Qin SL, Zhang MY, Lee GM, Neitz RJ, Kelly MJS, Arkin MR, Fujimori DG. Identifying ligands for the PHD1 finger of KDM5A through high-throughput screening. RSC Chem Biol 2024; 5:209-215. [PMID: 38456036 PMCID: PMC10915964 DOI: 10.1039/d3cb00214d] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
PHD fingers are a type of chromatin reader that primarily recognize chromatin as a function of lysine methylation state. Dysregulated PHD fingers are implicated in various human diseases, including acute myeloid leukemia. Targeting PHD fingers with small molecules is considered challenging as their histone tail binding pockets are often shallow and surface-exposed. The KDM5A PHD1 finger regulates the catalytic activity of KDM5A, an epigenetic enzyme often misregulated in cancers. To identify ligands that disrupt the PHD1-histone peptide interaction, we conducted a high-throughput screen and validated hits by orthogonal methods. We further elucidated structure-activity relationships in two classes of compounds to identify features important for binding. Our investigation offers a starting point for further optimization of small molecule PHD1 ligands.
Collapse
Affiliation(s)
- Gloria Ortiz
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Sophia L Qin
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Meng Yao Zhang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Gregory M Lee
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - R Jeffrey Neitz
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Michelle R Arkin
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| |
Collapse
|
2
|
Konstantinidou M, Visser EJ, Vandenboorn E, Chen S, Jaishankar P, Overmans M, Dutta S, Neitz RJ, Renslo AR, Ottmann C, Brunsveld L, Arkin MR. Structure-Based Optimization of Covalent, Small-Molecule Stabilizers of the 14-3-3σ/ERα Protein-Protein Interaction from Nonselective Fragments. J Am Chem Soc 2023; 145:20328-20343. [PMID: 37676236 PMCID: PMC10515640 DOI: 10.1021/jacs.3c05161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 09/08/2023]
Abstract
The stabilization of protein-protein interactions (PPIs) has emerged as a promising strategy in chemical biology and drug discovery. The identification of suitable starting points for stabilizing native PPIs and their subsequent elaboration into selective and potent molecular glues lacks structure-guided optimization strategies. We have previously identified a disulfide fragment that stabilized the hub protein 14-3-3σ bound to several of its clients, including ERα and C-RAF. Here, we show the structure-based optimization of the nonselective fragment toward selective and highly potent small-molecule stabilizers of the 14-3-3σ/ERα complex. The more elaborated molecular glues, for example, show no stabilization of 14-3-3σ/C-RAF up to 150 μM compound. Orthogonal biophysical assays, including mass spectrometry and fluorescence anisotropy, were used to establish structure-activity relationships. The binding modes of 37 compounds were elucidated with X-ray crystallography, which further assisted the concomitant structure-guided optimization. By targeting specific amino acids in the 14-3-3σ/ERα interface and locking the conformation with a spirocycle, the optimized covalent stabilizer 181 achieved potency, cooperativity, and selectivity similar to the natural product Fusicoccin-A. This case study showcases the value of addressing the structure, kinetics, and cooperativity for molecular glue development.
Collapse
Affiliation(s)
- Markella Konstantinidou
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Emira J. Visser
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Edmee Vandenboorn
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Sheng Chen
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Priyadarshini Jaishankar
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Maurits Overmans
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Shubhankar Dutta
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - R. Jeffrey Neitz
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Adam R. Renslo
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| |
Collapse
|
3
|
Visser EJ, Jaishankar P, Sijbesma E, Pennings MAM, Vandenboorn EMF, Guillory X, Neitz RJ, Morrow J, Dutta S, Renslo AR, Brunsveld L, Arkin MR, Ottmann C. From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions through Fragment Linking. Angew Chem Int Ed Engl 2023; 62:e202308004. [PMID: 37455289 DOI: 10.1002/anie.202308004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 06/07/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Small-molecule stabilization of protein-protein interactions (PPIs) is a promising strategy in chemical biology and drug discovery. However, the systematic discovery of PPI stabilizers remains a largely unmet challenge. Herein we report a fragment-linking approach targeting the interface of 14-3-3 and a peptide derived from the estrogen receptor alpha (ERα) protein. Two classes of fragments-a covalent and a noncovalent fragment-were co-crystallized and subsequently linked, resulting in a noncovalent hybrid molecule in which the original fragment interactions were largely conserved. Supported by 20 crystal structures, this initial hybrid molecule was further optimized, resulting in selective, 25-fold stabilization of the 14-3-3/ERα interaction. The high-resolution structures of both the single fragments, their co-crystal structures and those of the linked fragments document a feasible strategy to develop orthosteric PPI stabilizers by linking to an initial tethered fragment.
Collapse
Affiliation(s)
- Emira J Visser
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Marloes A M Pennings
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Edmee M F Vandenboorn
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - R Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - John Morrow
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Shubhankar Dutta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| |
Collapse
|
4
|
Kenanova D, Visser EJ, Virta JM, Sijbesma E, Centorrino F, Vickery HR, Zhong M, Neitz RJ, Brunsveld L, Ottmann C, Arkin MR. A Systematic Approach to the Discovery of Protein-Protein Interaction Stabilizers. ACS Cent Sci 2023; 9:937-946. [PMID: 37252362 PMCID: PMC10214524 DOI: 10.1021/acscentsci.2c01449] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Indexed: 05/31/2023]
Abstract
Dysregulation of protein-protein interactions (PPIs) commonly leads to disease. PPI stabilization has only recently been systematically explored for drug discovery despite being a powerful approach to selectively target intrinsically disordered proteins and hub proteins, like 14-3-3, with multiple interaction partners. Disulfide tethering is a site-directed fragment-based drug discovery (FBDD) methodology for identifying reversibly covalent small molecules. We explored the scope of disulfide tethering for the discovery of selective PPI stabilizers (molecular glues) using the hub protein 14-3-3σ. We screened complexes of 14-3-3 with 5 biologically and structurally diverse phosphopeptides derived from the 14-3-3 client proteins ERα, FOXO1, C-RAF, USP8, and SOS1. Stabilizing fragments were found for 4/5 client complexes. Structural elucidation of these complexes revealed the ability of some peptides to conformationally adapt to make productive interactions with the tethered fragments. We validated eight fragment stabilizers, six of which showed selectivity for one phosphopeptide client, and structurally characterized two nonselective hits and four fragments that selectively stabilized C-RAF or FOXO1. The most efficacious fragment increased 14-3-3σ/C-RAF phosphopeptide affinity by 430-fold. Disulfide tethering to the wildtype C38 in 14-3-3σ provided diverse structures for future optimization of 14-3-3/client stabilizers and highlighted a systematic method to discover molecular glues.
Collapse
Affiliation(s)
- Dyana
N. Kenanova
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - Emira J. Visser
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Johanna M. Virta
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - Eline Sijbesma
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Federica Centorrino
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Holly R. Vickery
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - Mengqi Zhong
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - R. Jeffrey Neitz
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94143, United States
| |
Collapse
|
5
|
Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko DS, Moroz YS, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, Ashworth A, Ahel I, Shoichet BK, Fraser JS. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2212931120. [PMID: 36598939 PMCID: PMC9926234 DOI: 10.1073/pnas.2212931120] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.
Collapse
Affiliation(s)
- Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94158
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, UK
| | - Matteo P. Ferla
- Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, OxfordOX4 2PG, UK
| | - Yagmur Umay Doruk
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Moira Rachman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA94158
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA94158
| | - Morgan Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Siyi Wang
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA94158
| | - R. Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, DidcotOX11 0DE, UK
- Research Complex at Harwell Harwell Science and Innovation Campus, DidcotOX11 0FA, UK
| | - Dmytro S. Radchenko
- Enamine Ltd., Kyiv02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv01601, Ukraine
| | - Yurii S. Moroz
- Taras Shevchenko National University of Kyiv, Kyiv01601, Ukraine
- Chemspace, Kyiv02094, Ukraine
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - Adam R. Renslo
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Jenny C. Taylor
- Wellcome Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, OxfordOX4 2PG, UK
| | - Jason E. Gestwicki
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA94158
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, CA94158
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, DidcotOX11 0DE, UK
- Research Complex at Harwell Harwell Science and Innovation Campus, DidcotOX11 0FA, UK
- Centre for Medicines Discovery, University of Oxford, HeadingtonOX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, HeadingtonOX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park2006, South Africa
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94158
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, UK
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA94158
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94158
| |
Collapse
|
6
|
Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko D, Moroz Y, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, Ashworth A, Ahel I, Shoichet BK, Fraser JS. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2. bioRxiv 2022:2022.06.27.497816. [PMID: 35794891 PMCID: PMC9258288 DOI: 10.1101/2022.06.27.497816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 152 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated protein dynamics within the active site, and key inhibitor motifs that will template future drug development against Mac1.
Collapse
Affiliation(s)
- Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Matteo P. Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - Yagmur Umay Doruk
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Moira Rachman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Morgan Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Siyi Wang
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - R. Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Dmytro Radchenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Yurii Moroz
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
- Chemspace, Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Adam R. Renslo
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, USA
| | - Jenny C. Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, OX4 2PG, UK
| | - Jason E. Gestwicki
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, USA
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
7
|
LaPorte MG, Burnett JC, Colombo R, Bulfer SL, Alverez C, Chou TF, Neitz RJ, Green N, Moore WJ, Yue Z, Li S, Arkin MR, Wipf P, Huryn DM. Optimization of Phenyl Indole Inhibitors of the AAA+ ATPase p97. ACS Med Chem Lett 2018; 9:1075-1081. [PMID: 30429948 PMCID: PMC6231190 DOI: 10.1021/acsmedchemlett.8b00372] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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] [Received: 08/15/2018] [Accepted: 09/18/2018] [Indexed: 12/30/2022] Open
Abstract
![]()
Optimization
of the side-chain of a phenyl indole scaffold identified
from a high-throughput screening campaign for inhibitors of the AAA+
ATPase p97 is reported. The addition of an N-alkyl
piperazine led to high potency of this series in a biochemical assay,
activity in cell-based assays, and excellent pharmaceutical properties.
Molecular modeling based on a subsequently obtained cryo-EM structure
of p97 in complex with a phenyl indole was used to rationalize the
potency of these allosteric inhibitors.
Collapse
Affiliation(s)
- Matthew G. LaPorte
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - James C. Burnett
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Computational Drug Development Group, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Raffaele Colombo
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stacie L. Bulfer
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Celeste Alverez
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Tsui-Fen Chou
- Division of Medical Genetics, Department of Pediatrics, Harbor−UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, California 90502, United States
| | - R. Jeffrey Neitz
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Neal Green
- Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - William J. Moore
- Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Zhizhou Yue
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shan Li
- Division of Medical Genetics, Department of Pediatrics, Harbor−UCLA Medical Center and Los Angeles Biomedical Research Institute, Torrance, California 90502, United States
| | - Michelle R. Arkin
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Peter Wipf
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Donna M. Huryn
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
8
|
Alverez C, Bulfer SL, Chakrasali R, Chimenti MS, Deshaies RJ, Green N, Kelly M, LaPorte MG, Lewis TS, Liang M, Moore WJ, Neitz RJ, Peshkov VA, Walters MA, Zhang F, Arkin MR, Wipf P, Huryn DM. Allosteric Indole Amide Inhibitors of p97: Identification of a Novel Probe of the Ubiquitin Pathway. ACS Med Chem Lett 2016; 7:182-7. [PMID: 26985295 DOI: 10.1021/acsmedchemlett.5b00396] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 10/08/2015] [Accepted: 12/22/2015] [Indexed: 11/28/2022] Open
Abstract
A high-throughput screen to discover inhibitors of p97 ATPase activity identified an indole amide that bound to an allosteric site of the protein. Medicinal chemistry optimization led to improvements in potency and solubility. Indole amide 3 represents a novel uncompetitive inhibitor with excellent physical and pharmaceutical properties that can be used as a starting point for drug discovery efforts.
Collapse
Affiliation(s)
- Celeste Alverez
- Department
of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stacie L. Bulfer
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Ramappa Chakrasali
- Department
of Medicinal Chemistry, and the Institute for Therapeutics Discovery
and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Michael. S. Chimenti
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Raymond J. Deshaies
- Division
of Biology and Biological Engineering, California Institute of Technology and Howard Hughes Medical Institute, Pasadena, California 91007, United States
| | - Neal Green
- Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - Mark Kelly
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Matthew G. LaPorte
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Taber S. Lewis
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Mary Liang
- Department
of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - William J. Moore
- Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - R. Jeffrey Neitz
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Vsevolod A. Peshkov
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael A. Walters
- Department
of Medicinal Chemistry, and the Institute for Therapeutics Discovery
and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Feng Zhang
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Peter Wipf
- Department
of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Donna M. Huryn
- Department
of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- University
of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
9
|
Banerjee S, Bartesaghi A, Merk A, Rao P, Bulfer SL, Yan Y, Green N, Mroczkowski B, Neitz RJ, Wipf P, Falconieri V, Deshaies RJ, Milne JLS, Huryn D, Arkin M, Subramaniam S. 2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Science 2016; 351:871-5. [PMID: 26822609 DOI: 10.1126/science.aad7974] [Citation(s) in RCA: 250] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/14/2016] [Indexed: 12/13/2022]
Abstract
p97 is a hexameric AAA+ adenosine triphosphatase (ATPase) that is an attractive target for cancer drug development. We report cryo-electron microscopy (cryo-EM) structures for adenosine diphosphate (ADP)-bound, full-length, hexameric wild-type p97 in the presence and absence of an allosteric inhibitor at resolutions of 2.3 and 2.4 angstroms, respectively. We also report cryo-EM structures (at resolutions of ~3.3, 3.2, and 3.3 angstroms, respectively) for three distinct, coexisting functional states of p97 with occupancies of zero, one, or two molecules of adenosine 5'-O-(3-thiotriphosphate) (ATPγS) per protomer. A large corkscrew-like change in molecular architecture, coupled with upward displacement of the N-terminal domain, is observed only when ATPγS is bound to both the D1 and D2 domains of the protomer. These cryo-EM structures establish the sequence of nucleotide-driven structural changes in p97 at atomic resolution. They also enable elucidation of the binding mode of an allosteric small-molecule inhibitor to p97 and illustrate how inhibitor binding at the interface between the D1 and D2 domains prevents propagation of the conformational changes necessary for p97 function.
Collapse
Affiliation(s)
- Soojay Banerjee
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alan Merk
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Prashant Rao
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stacie L Bulfer
- Small Molecule Discovery Center, Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Yongzhao Yan
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Neal Green
- Leidos Biomedical Research Inc., Frederick, MD 21702, USA
| | - Barbara Mroczkowski
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - R Jeffrey Neitz
- Small Molecule Discovery Center, Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Peter Wipf
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Veronica Falconieri
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91107, USA
| | | | - Donna Huryn
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michelle Arkin
- Small Molecule Discovery Center, Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD 20892, USA.
| |
Collapse
|
10
|
Long T, Neitz RJ, Beasley R, Kalyanaraman C, Suzuki BM, Jacobson MP, Dissous C, McKerrow JH, Drewry DH, Zuercher WJ, Singh R, Caffrey CR. Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni. PLoS Negl Trop Dis 2016; 10:e0004356. [PMID: 26751972 PMCID: PMC4709140 DOI: 10.1371/journal.pntd.0004356] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [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: 07/22/2015] [Accepted: 12/13/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Schistosoma flatworm parasites cause schistosomiasis, a chronic and debilitating disease of poverty in developing countries. Praziquantel is employed for treatment and disease control. However, its efficacy spectrum is incomplete (less active or inactive against immature stages of the parasite) and there is a concern of drug resistance. Thus, there is a need to identify new drugs and drug targets. METHODOLOGY/PRINCIPAL FINDINGS We show that RNA interference (RNAi) of the Schistosoma mansoni ortholog of human polo-like kinase (huPLK)1 elicits a deleterious phenotypic alteration in post-infective larvae (schistosomula or somules). Phenotypic screening and analysis of schistosomula and adult S. mansoni with small molecule inhibitors of huPLK1 identified a number of potent anti-schistosomals. Among these was a GlaxoSmithKline (GSK) benzimidazole thiophene inhibitor that has completed Phase I clinical trials for treatment of solid tumor malignancies. We then obtained GSKs Published Kinase Inhibitor Sets (PKIS) 1 and 2, and phenotypically screened an expanded series of 38 benzimidazole thiophene PLK1 inhibitors. Computational analysis of controls and PLK1 inhibitor-treated populations of somules demonstrated a distinctive phenotype distribution. Using principal component analysis (PCA), the phenotypes exhibited by these populations were mapped, visualized and analyzed through projection to a low-dimensional space. The phenotype distribution was found to have a distinct shape and topology, which could be elicited using cluster analysis. A structure-activity relationship (SAR) was identified for the benzimidazole thiophenes that held for both somules and adult parasites. The most potent inhibitors produced marked phenotypic alterations at 1-2 μM within 1 h. Among these were compounds previously characterized as potent inhibitors of huPLK1 in cell assays. CONCLUSIONS/SIGNIFICANCE The reverse genetic and chemical SAR data support a continued investigation of SmPLK1 as a possible drug target and/or the prosecution of the benzimidazole thiophene chemotype as a source of novel anti-schistosomals.
Collapse
Affiliation(s)
- Thavy Long
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
| | - R. Jeffrey Neitz
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, California, United States of America
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Rachel Beasley
- Department of Computer Science, San Francisco State University, San Francisco, California, United States of America
| | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Brian M. Suzuki
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Colette Dissous
- Center of Infection and Immunity of Lille, Université Lille Nord de France, Inserm U1019, CNRS-UMR 8204, Institut Pasteur de Lille, Lille, France
| | - James H. McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
| | - David H. Drewry
- Department of Chemical Biology, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - William J. Zuercher
- Department of Chemical Biology, GlaxoSmithKline, Research Triangle Park, North Carolina, United States of America
| | - Rahul Singh
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, California, United States of America
- Department of Computer Science, San Francisco State University, San Francisco, California, United States of America
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
| |
Collapse
|
11
|
Alverez C, Arkin MR, Bulfer SL, Colombo R, Kovaliov M, LaPorte MG, Lim C, Liang M, Moore WJ, Neitz RJ, Yan Y, Yue Z, Huryn DM, Wipf P. Structure-Activity Study of Bioisosteric Trifluoromethyl and Pentafluorosulfanyl Indole Inhibitors of the AAA ATPase p97. ACS Med Chem Lett 2015; 6:1225-30. [PMID: 26713109 DOI: 10.1021/acsmedchemlett.5b00364] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [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: 09/15/2015] [Accepted: 10/19/2015] [Indexed: 11/30/2022] Open
Abstract
Exploratory SAR studies of a new phenyl indole chemotype for p97 inhibition revealed C-5 indole substituent effects in the ADPGlo assay that did not fully correlate with either electronic or steric factors. A focused series of methoxy-, trifluoromethoxy-, methyl-, trifluoromethyl-, pentafluorosulfanyl-, and nitro-analogues was found to exhibit IC50s from low nanomolar to double-digit micromolar. Surprisingly, we found that the trifluoromethoxy-analogue was biochemically a better match of the trifluoromethyl-substituted lead structure than a pentafluorosulfanyl-analogue. Moreover, in spite of their almost equivalent strongly electron-depleting effect on the indole core, pentafluorosulfanyl- and nitro-derivatives were found to exhibit a 430-fold difference in p97 inhibitory activities. Conversely, the electronically divergent C-5 methyl- and nitro-analogues both showed low nanomolar activities.
Collapse
Affiliation(s)
- Celeste Alverez
- Department
of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Stacie L. Bulfer
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Raffaele Colombo
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Marina Kovaliov
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Matthew G. LaPorte
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chaemin Lim
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Mary Liang
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - William J. Moore
- Leidos Biomedical Research, Inc., Frederick, Maryland 21702, United States
| | - R. Jeffrey Neitz
- Department
of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Yongzhao Yan
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Zhizhou Yue
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Donna M. Huryn
- Department
of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Peter Wipf
- Department
of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Chemical
Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
12
|
Khare S, Roach SL, Barnes SW, Hoepfner D, Walker JR, Chatterjee AK, Neitz RJ, Arkin MR, McNamara CW, Ballard J, Lai Y, Fu Y, Molteni V, Yeh V, McKerrow JH, Glynne RJ, Supek F. Utilizing Chemical Genomics to Identify Cytochrome b as a Novel Drug Target for Chagas Disease. PLoS Pathog 2015; 11:e1005058. [PMID: 26186534 PMCID: PMC4506092 DOI: 10.1371/journal.ppat.1005058] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [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: 02/17/2015] [Accepted: 06/30/2015] [Indexed: 11/19/2022] Open
Abstract
Unbiased phenotypic screens enable identification of small molecules that inhibit pathogen growth by unanticipated mechanisms. These small molecules can be used as starting points for drug discovery programs that target such mechanisms. A major challenge of the approach is the identification of the cellular targets. Here we report GNF7686, a small molecule inhibitor of Trypanosoma cruzi, the causative agent of Chagas disease, and identification of cytochrome b as its target. Following discovery of GNF7686 in a parasite growth inhibition high throughput screen, we were able to evolve a GNF7686-resistant culture of T. cruzi epimastigotes. Clones from this culture bore a mutation coding for a substitution of leucine by phenylalanine at amino acid position 197 in cytochrome b. Cytochrome b is a component of complex III (cytochrome bc1) in the mitochondrial electron transport chain and catalyzes the transfer of electrons from ubiquinol to cytochrome c by a mechanism that utilizes two distinct catalytic sites, QN and QP. The L197F mutation is located in the QN site and confers resistance to GNF7686 in both parasite cell growth and biochemical cytochrome b assays. Additionally, the mutant cytochrome b confers resistance to antimycin A, another QN site inhibitor, but not to strobilurin or myxothiazol, which target the QP site. GNF7686 represents a promising starting point for Chagas disease drug discovery as it potently inhibits growth of intracellular T. cruzi amastigotes with a half maximal effective concentration (EC50) of 0.15 µM, and is highly specific for T. cruzi cytochrome b. No effect on the mammalian respiratory chain or mammalian cell proliferation was observed with up to 25 µM of GNF7686. Our approach, which combines T. cruzi chemical genetics with biochemical target validation, can be broadly applied to the discovery of additional novel drug targets and drug leads for Chagas disease. Chagas Disease, or American trypanosomiasis, is caused by the kinetoplastid protozoan Trypanosoma cruzi and is primarily transmitted to a mammalian host via a triatomine insect vector (the “kissing bug”) infected with T. cruzi parasites. Although discovered in 1909 by the physician Dr. Carlos Chagas, the disease gained recognition by the public health community only following a major outbreak in Brazil during the 1960s. Approximately eight million people (primarily in Central and South America) are infected with T. cruzi and cases are becoming more widespread due to migration out of the endemic regions. Current treatment options have severe problems with toxicity, limited efficacy, and long administration. Hence, discovery of new drugs for treatment of Chagas disease has become of prime interest to the biomedical research community. In this study, we report identification of a potent inhibitor of T. cruzi growth and use a chemical genetics-based approach to elucidate the associated mechanism of action. We found that this compound, GNF7686, targets cytochrome b, a component of the mitochondrial electron transport chain crucial for ATP generation. Our study provides new insights into the use of phenotypic screening to identify novel targets for kinetoplastid drug discovery.
Collapse
Affiliation(s)
- Shilpi Khare
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Steven L. Roach
- Department of Medicinal Chemistry, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - S. Whitney Barnes
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - John R. Walker
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Arnab K. Chatterjee
- Department of Medicinal Chemistry, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - R. Jeffrey Neitz
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Michelle R. Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
| | - Case W. McNamara
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Jaime Ballard
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Yin Lai
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Yue Fu
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Valentina Molteni
- Department of Medicinal Chemistry, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Vince Yeh
- Department of Medicinal Chemistry, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Richard J. Glynne
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Frantisek Supek
- Department of Genetics and Neglected Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
- * E-mail:
| |
Collapse
|
13
|
Neitz RJ, Bryant C, Chen S, Gut J, Hugo Caselli E, Ponce S, Chowdhury S, Xu H, Arkin MR, Ellman JA, Renslo AR. Tetrafluorophenoxymethyl ketone cruzain inhibitors with improved pharmacokinetic properties as therapeutic leads for Chagas' disease. Bioorg Med Chem Lett 2015; 25:4834-4837. [PMID: 26144347 DOI: 10.1016/j.bmcl.2015.06.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 06/07/2015] [Accepted: 06/18/2015] [Indexed: 01/26/2023]
Abstract
Inhibition of the cysteine protease cruzain from Trypanosoma cruzi has been studied pre-clinically as a new chemotherapeutic approach to treat Chagas' disease. Efficacious effects of vinylsulfone-based cruzain inhibitors in animal models support this therapeutic hypothesis. More recently, substrate-activity screening was used to identify nonpeptidic tetrafluorophenoxymethyl ketone inhibitors of cruzain that showed promising efficacy in animal models. Herein we report efforts to further optimize the in vitro potency and in vivo pharmacokinetic properties of this new class of cruzain inhibitors. Through modifications of the P1, P2 and/or P3 positions, new analogs have been identified with reduced lipophilicity, enhanced potency, and improved oral exposure and bioavailability.
Collapse
Affiliation(s)
- R Jeffrey Neitz
- Small Molecule Discovery Center, and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Clifford Bryant
- Small Molecule Discovery Center, and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Steven Chen
- Small Molecule Discovery Center, and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Jiri Gut
- Small Molecule Discovery Center, and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Estefania Hugo Caselli
- Small Molecule Discovery Center, and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Servando Ponce
- Small Molecule Discovery Center, and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Somenath Chowdhury
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Haichao Xu
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Michelle R Arkin
- Small Molecule Discovery Center, and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Jonathan A Ellman
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Adam R Renslo
- Small Molecule Discovery Center, and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, United States.
| |
Collapse
|
14
|
Chimenti MS, Bulfer SL, Neitz RJ, Renslo AR, Jacobson MP, James TL, Arkin MR, Kelly MJS. A Fragment-Based Ligand Screen Against Part of a Large Protein Machine: The ND1 Domains of the AAA+ ATPase p97/VCP. ACTA ACUST UNITED AC 2015; 20:788-800. [PMID: 25690569 DOI: 10.1177/1087057115570550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 10/14/2014] [Accepted: 01/02/2015] [Indexed: 01/25/2023]
Abstract
The ubiquitous AAA+ ATPase p97 functions as a dynamic molecular machine driving several cellular processes. It is essential in regulating protein homeostasis, and it represents a potential drug target for cancer, particularly when there is a greater reliance on the endoplasmic reticulum-associated protein degradation pathway and ubiquitin-proteasome pathway to degrade an overabundance of secreted proteins. Here, we report a case study for using fragment-based ligand design approaches against this large and dynamic hexamer, which has multiple potential binding sites for small molecules. A screen of a fragment library was conducted by surface plasmon resonance (SPR) and followed up by nuclear magnetic resonance (NMR), two complementary biophysical techniques. Virtual screening was also carried out to examine possible binding sites for the experimental hits and evaluate the potential utility of fragment docking for this target. Out of this effort, 13 fragments were discovered that showed reversible binding with affinities between 140 µM and 1 mM, binding stoichiometries of 1:1 or 2:1, and good ligand efficiencies. Structural data for fragment-protein interactions were obtained with residue-specific [U-(2)H] (13)CH3-methyl-labeling NMR strategies, and these data were compared to poses from docking. The combination of virtual screening, SPR, and NMR enabled us to find and validate a number of interesting fragment hits and allowed us to gain an understanding of the structural nature of fragment binding.
Collapse
Affiliation(s)
- Michael S Chimenti
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Co-first authors
| | - Stacie L Bulfer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA Co-first authors
| | - R Jeffrey Neitz
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Thomas L James
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA Small Molecule Discovery Center, University of California San Francisco, San Francisco, CA, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
15
|
Neitz RJ, Chen S, Supek F, Yeh V, Kellar D, Gut J, Bryant C, Gallardo-Godoy A, Molteni V, Roach SL, Chatterjee AK, Robertson S, Renslo AR, Arkin M, Glynne R, McKerrow J, Siqueira-Neto JL. Lead Identification to Clinical Candidate Selection. ACTA ACUST UNITED AC 2014; 20:101-11. [DOI: 10.1177/1087057114553103] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Chagas disease affects 8 million people worldwide and remains a main cause of death due to heart failure in Latin America. The number of cases in the United States is now estimated to be 300,000, but there are currently no Food and Drug Administration (FDA)–approved drugs available for patients with Chagas disease. To fill this gap, we have established a public-private partnership between the University of California, San Francisco and the Genomics Institute of the Novartis Research Foundation (GNF) with the goal of delivering clinical candidates to treat Chagas disease. The discovery phase, based on the screening of more than 160,000 compounds from the GNF Academic Collaboration Library, led to the identification of new anti-Chagas scaffolds. Part of the screening campaign used and compared two screening methods, including a colorimetric-based assay using Trypanosoma cruzi expressing β-galactosidase and an image-based, high-content screening (HCS) assay using the CA-I/72 strain of T. cruzi. Comparing molecules tested in both assays, we found that ergosterol biosynthesis inhibitors had greater potency in the colorimetric assay than in the HCS assay. Both assays were used to inform structure-activity relationships for antiparasitic efficacy and pharmacokinetics. A new anti– T. cruzi scaffold derived from xanthine was identified, and we describe its development as lead series.
Collapse
Affiliation(s)
- R. Jeffrey Neitz
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Steven Chen
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Frantisek Supek
- Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA, USA
| | - Vince Yeh
- Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA, USA
| | - Danielle Kellar
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
- Five Prime Therapeutics, San Francisco, CA, USA
| | - Jiri Gut
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Clifford Bryant
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Alejandra Gallardo-Godoy
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Valentina Molteni
- Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA, USA
| | - Steven L. Roach
- Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA, USA
- Dart Neuroscience, San Diego, CA, USA
| | - Arnab K. Chatterjee
- Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA, USA
- California Institute for Biomedical Research (Calibr), San Diego, CA, USA
| | - Stephanie Robertson
- Innovation, Technology, and Alliances, University of California, San Francisco, CA, USA
| | - Adam R. Renslo
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Michelle Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Richard Glynne
- Genomics Institute of the Novartis Research Foundation (GNF), San Diego, CA, USA
| | - James McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, CA, USA
| | - Jair L. Siqueira-Neto
- Center for Discovery and Innovation in Parasitic Diseases, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Science, University of California, San Diego, CA, USA
| |
Collapse
|
16
|
Aubele DL, Hom RK, Adler M, Galemmo RA, Bowers S, Truong AP, Pan H, Beroza P, Neitz RJ, Yao N, Lin M, Tonn G, Zhang H, Bova MP, Ren Z, Tam D, Ruslim L, Baker J, Diep L, Fitzgerald K, Hoffman J, Motter R, Fauss D, Tanaka P, Dappen M, Jagodzinski J, Chan W, Konradi AW, Latimer L, Zhu YL, Sham HL, Anderson JP, Bergeron M, Artis DR. Selective and brain-permeable polo-like kinase-2 (Plk-2) inhibitors that reduce α-synuclein phosphorylation in rat brain. ChemMedChem 2013; 8:1295-313. [PMID: 23794260 DOI: 10.1002/cmdc.201300166] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Indexed: 11/12/2022]
Abstract
Polo-like kinase-2 (Plk-2) has been implicated as the dominant kinase involved in the phosphorylation of α-synuclein in Lewy bodies, which are one of the hallmarks of Parkinson's disease neuropathology. Potent, selective, brain-penetrant inhibitors of Plk-2 were obtained from a structure-guided drug discovery approach driven by the first reported Plk-2-inhibitor complexes. The best of these compounds showed excellent isoform and kinome-wide selectivity, with physicochemical properties sufficient to interrogate the role of Plk-2 inhibition in vivo. One such compound significantly decreased phosphorylation of α-synuclein in rat brain upon oral administration and represents a useful probe for future studies of this therapeutic avenue toward the potential treatment of Parkinson's disease.
Collapse
Affiliation(s)
- Danielle L Aubele
- Molecular Discovery, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Ng RA, Sun M, Bowers S, Hom RK, Probst GD, John V, Fang LY, Maillard M, Gailunas A, Brogley L, Neitz RJ, Tung JS, Pleiss MA, Konradi AW, Sham HL, Dappen MS, Adler M, Yao N, Zmolek W, Nakamura D, Quinn KP, Sauer JM, Bova MP, Ruslim L, Artis DR, Yednock TA. Design and synthesis of hydroxyethylamine (HEA) BACE-1 inhibitors: prime side chromane-containing inhibitors. Bioorg Med Chem Lett 2013; 23:4674-9. [PMID: 23856050 DOI: 10.1016/j.bmcl.2013.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 12/03/2012] [Revised: 05/27/2013] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
Abstract
The structure activity relationship of the prime region of conformationally restricted hydroxyethylamine (HEA) BACE inhibitors is described. Variation of the P1' region provided selectivity over Cat-D with a series of 2,2-dioxo-isothiochromanes and optimization of the P2' substituent of chromane-HEA(s) with polar substituents provided improvements in the compound's in vitro permeability. Significant potency gains were observed with small aliphatic substituents such as methyl, n-propyl, and cyclopropyl when placed at the C-2 position of the chromane.
Collapse
Affiliation(s)
- Raymond A Ng
- Department of Chemical Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Bowers S, Truong AP, Ye M, Aubele DL, Sealy JM, Neitz RJ, Hom RK, Chan W, Dappen MS, Galemmo RA, Konradi AW, Sham HL, Zhu YL, Beroza P, Tonn G, Zhang H, Hoffman J, Motter R, Fauss D, Tanaka P, Bova MP, Ren Z, Tam D, Ruslim L, Baker J, Pandya D, Diep L, Fitzgerald K, Artis DR, Anderson JP, Bergeron M. Design and synthesis of highly selective, orally active Polo-like kinase-2 (Plk-2) inhibitors. Bioorg Med Chem Lett 2013; 23:2743-9. [PMID: 23522834 DOI: 10.1016/j.bmcl.2013.02.065] [Citation(s) in RCA: 21] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/06/2013] [Accepted: 02/13/2013] [Indexed: 12/13/2022]
Abstract
Polo-like kinase-2 (Plk-2) is a potential therapeutic target for Parkinson's disease and this Letter describes the SAR of a series of dihydropteridinone based Plk-2 inhibitors. By optimizing both the N-8 substituent and the biaryl region of the inhibitors we obtained single digit nanomolar compounds such as 37 with excellent selectivity for Plk-2 over Plk-1. When dosed orally in rats, compound 37 demonstrated a 41-45% reduction of pS129-α-synuclein levels in the cerebral cortex.
Collapse
Affiliation(s)
- Simeon Bowers
- Department of Chemical Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Garofalo AW, Adler M, Aubele DL, Bowers S, Franzini M, Goldbach E, Lorentzen C, Neitz RJ, Probst GD, Quinn KP, Santiago P, Sham HL, Tam D, Truong AP, Ye XM, Ren Z. Novel cinnoline-based inhibitors of LRRK2 kinase activity. Bioorg Med Chem Lett 2012; 23:71-4. [PMID: 23219325 DOI: 10.1016/j.bmcl.2012.11.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 10/31/2012] [Accepted: 11/07/2012] [Indexed: 10/27/2022]
Abstract
Leucine rich repeat kinase 2 (LRRK2) has been implicated in the pathogenesis of Parkinson's disease (PD). Inhibition of LRRK2 kinase activity is a therapeutic approach that may lead to new treatments for PD. Herein we report the discovery of a series of cinnoline-3-carboxamides that are potent against both wild-type and mutant LRRK2 kinase activity in biochemical assays. These compounds are also shown to be potent inhibitors in a cellular assay and to have good to excellent CNS penetration.
Collapse
Affiliation(s)
- Albert W Garofalo
- Department of Medicinal Chemistry, Elan Pharmaceuticals, 180 Oyster Point Blvd, South San Francisco, CA 94080, United States.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Bowers S, Truong AP, Jeffrey Neitz R, Hom RK, Sealy JM, Probst GD, Quincy D, Peterson B, Chan W, Galemmo RA, Konradi AW, Sham HL, Tóth G, Pan H, Lin M, Yao N, Artis DR, Zhang H, Chen L, Dryer M, Samant B, Zmolek W, Wong K, Lorentzen C, Goldbach E, Tonn G, Quinn KP, Sauer JM, Wright S, Powell K, Ruslim L, Ren Z, Bard F, Yednock TA, Griswold-Prenner I. Design and synthesis of brain penetrant selective JNK inhibitors with improved pharmacokinetic properties for the prevention of neurodegeneration. Bioorg Med Chem Lett 2011; 21:5521-7. [DOI: 10.1016/j.bmcl.2011.06.100] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 06/20/2011] [Accepted: 06/22/2011] [Indexed: 12/15/2022]
|
21
|
Neitz RJ, Konradi AW, Sham HL, Zmolek W, Wong K, Qin A, Lorentzen C, Nakamura D, Quinn KP, Sauer JM, Powell K, Ruslim L, Chereau D, Ren Z, Anderson J, Bard F, Yednock TA, Griswold-Prenner I. Highly selective c-Jun N-terminal kinase (JNK) 3 inhibitors with in vitro CNS-like pharmacokinetic properties II. Central core replacement. Bioorg Med Chem Lett 2011; 21:3726-9. [DOI: 10.1016/j.bmcl.2011.04.074] [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: 01/12/2011] [Revised: 04/15/2011] [Accepted: 04/19/2011] [Indexed: 01/28/2023]
|
22
|
Bowers S, Truong AP, Neitz RJ, Neitzel M, Probst GD, Hom RK, Peterson B, Galemmo RA, Konradi AW, Sham HL, Tóth G, Pan H, Yao N, Artis DR, Brigham EF, Quinn KP, Sauer JM, Powell K, Ruslim L, Ren Z, Bard F, Yednock TA, Griswold-Prenner I. Design and synthesis of a novel, orally active, brain penetrant, tri-substituted thiophene based JNK inhibitor. Bioorg Med Chem Lett 2011; 21:1838-43. [DOI: 10.1016/j.bmcl.2011.01.046] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 01/17/2023]
|
23
|
Roush WR, Neitz RJ. Studies on the Synthesis of Landomycin A. Synthesis of the Originally Assigned Structure of the Aglycone, Landomycinone, and Revision of Structure. J Org Chem 2004; 69:4906-12. [PMID: 15255715 DOI: 10.1021/jo049426c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The originally proposed structure (2) of landomycinone, the aglycone of landomycin A, has been synthesized and shown to be nonidentical to the naturally derived landomycin A aglycone. The synthesis of 2 features the Dötz benzannulation reaction of chromium carbene 5 and alkyne 6, and the intramolecular Michael-type cyclization reaction of the phenolic naphthoquinone 20. It is proposed that natural landomycinone possesses the alternative structure 3, but attempts to access this structure via the Michael-type cyclization of the isomeric phenolic naphthoquinone 38 have been unsuccessful.
Collapse
Affiliation(s)
- William R Roush
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | | |
Collapse
|
24
|
Shenai BR, Lee BJ, Alvarez-Hernandez A, Chong PY, Emal CD, Neitz RJ, Roush WR, Rosenthal PJ. Structure-activity relationships for inhibition of cysteine protease activity and development of Plasmodium falciparum by peptidyl vinyl sulfones. Antimicrob Agents Chemother 2003; 47:154-60. [PMID: 12499184 PMCID: PMC149004 DOI: 10.1128/aac.47.1.154-160.2003] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [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: 11/20/2022] Open
Abstract
The Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3 appear to be required for hemoglobin hydrolysis by intraerythrocytic malaria parasites. Previous studies showed that peptidyl vinyl sulfone inhibitors of falcipain-2 blocked the development of P. falciparum in culture and exerted antimalarial effects in vivo. We now report the structure-activity relationships for inhibition of falcipain-2, falcipain-3, and parasite development by 39 new vinyl sulfone, vinyl sulfonate ester, and vinyl sulfonamide cysteine protease inhibitors. Levels of inhibition of falcipain-2 and falcipain-3 were generally similar, and many potent compounds were identified. Optimal antimalarial compounds, which inhibited P. falciparum development at low nanomolar concentrations, were phenyl vinyl sulfones, vinyl sulfonate esters, and vinyl sulfonamides with P(2) leucine moieties. Our results identify independent structural correlates of falcipain inhibition and antiparasitic activity and suggest that peptidyl vinyl sulfones have promise as antimalarial agents.
Collapse
Affiliation(s)
- Bhaskar R Shenai
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California 94143, USA.
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Creaser I, Heckel MC, Neitz RJ, Pope MT. Rigid nonlabile polyoxometalate cryptates [ZP5W30O110](15-n)- that exhibit unprecedented selectivity for certain lanthanide and other multivalent cations. Inorg Chem 2002. [DOI: 10.1021/ic00061a010] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|