1
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Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
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Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
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2
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Riege D, Herschel S, Fenkl T, Schade D. Small-Molecule Probes as Pharmacological Tools for the Bone Morphogenetic Protein Signaling Pathway. ACS Pharmacol Transl Sci 2023; 6:1574-1599. [PMID: 37974621 PMCID: PMC10644459 DOI: 10.1021/acsptsci.3c00170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Abstract
The bone morphogenetic protein (BMP) pathway is highly conserved and plays central roles in health and disease. The quality and quantity of its signaling outputs are regulated at multiple levels, offering pharmacological options for targeted modulation. Both target-centric and phenotypic drug discovery (PDD) approaches were applied to identify small-molecule BMP inhibitors and stimulators. In this Review, we accumulated and systematically classified the different reported chemotypes based on their targets as well as modes-of-action, and herein we illustrate the discovery history of selected candidates. A comprehensive summary of available biochemical, cellular, and in vivo activities is provided for the most relevant BMP modulators, along with recommendations on their preferred use as chemical probes to study BMP-related (patho)physiological processes. There are a number of high-quality probes used as BMP inhibitors that potently and selectively interrogate the kinase activities of distinct type I (16 chemotypes available) and type II receptors (3 chemotypes available). In contrast, only a few high-quality BMP stimulator modalities have been introduced to the field due to a lack of profound target knowledge. FK506-derived macrolides such as calcineurin-sparing FKBP12 inhibitors currently represent the best-characterized chemical tools for direct activation of BMP-SMAD signaling at the receptor level. However, several PDD campaigns succeeded in expanding the druggable space of BMP stimulators. Albeit the majority of them do not entirely fulfill the strict chemical probe criteria, many chemotypes exhibit unique and unrecognized mechanisms as pathway potentiators or synergizers, serving as valuable pharmacological tools for BMP perturbation.
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Affiliation(s)
- Daniel Riege
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Sven Herschel
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Teresa Fenkl
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Dennis Schade
- Department
of Pharmaceutical & Medicinal Chemistry, Christian-Albrechts-University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
- Partner
Site Kiel, DZHK, German Center for Cardiovascular
Research, 24105 Kiel, Germany
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3
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Tiek D, Wells CI, Schröder M, Song X, Alamillo-Ferrer C, Goenka A, Iglesia R, Lu M, Hu B, Kwarcinski F, Sintha P, de Silva C, Hossain MA, Picado A, Zuercher W, Zutshi R, Knapp S, Riggins RB, Cheng SY, Drewry DH. SGC-CLK-1: A chemical probe for the Cdc2-like kinases CLK1, CLK2, and CLK4. CURRENT RESEARCH IN CHEMICAL BIOLOGY 2023; 3:100045. [PMID: 38009092 PMCID: PMC10673624 DOI: 10.1016/j.crchbi.2023.100045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Small molecule modulators are important tools to study both basic biology and the complex signaling of protein kinases. The cdc2-like kinases (CLK) are a family of four kinases that have garnered recent interest for their involvement in a diverse set of diseases such as neurodegeneration, autoimmunity, and many cancers. Targeted medicinal chemistry around a CLK inhibitor hit identified through screening of a kinase inhibitor set against a large panel of kinases allowed us to identify a potent and selective inhibitor of CLK1, 2, and 4. Here, we present the synthesis, selectivity, and preliminary biological characterization of this compound - SGC-CLK-1 (CAF-170). We further show CLK2 has the highest binding affinity, and high CLK2 expression correlates with a lower IC50 in a screen of multiple cancer cell lines. Finally, we show that SGC-CLK-1 not only reduces serine arginine-rich (SR) protein phosphorylation but also alters SR protein and CLK2 subcellular localization in a reversible way. Therefore, we anticipate that this compound will be a valuable tool for increasing our understanding of CLKs and their targets, SR proteins, at the level of phosphorylation and subcellular localization.
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Affiliation(s)
- Deanna Tiek
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Martin Schröder
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany
| | - Xiao Song
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Carla Alamillo-Ferrer
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anshika Goenka
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Rebeca Iglesia
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Minghui Lu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Bo Hu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | | | | | | | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alfredo Picado
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - William Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Reena Zutshi
- Luceome Biotechnologies LLC, Tucson, AZ, 85719, USA
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany
| | - Rebecca B. Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, 20057, USA
| | - Shi-Yuan Cheng
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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4
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Green JR, Mahalingaiah PKS, Gopalakrishnan SM, Liguori MJ, Mittelstadt SW, Blomme EAG, Van Vleet TR. Off-target pharmacological activity at various kinases: Potential functional and pathological side effects. J Pharmacol Toxicol Methods 2023; 123:107468. [PMID: 37553032 DOI: 10.1016/j.vascn.2023.107468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/16/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
In drug discovery, during the lead optimization and candidate characterization stages, novel small molecules are frequently evaluated in a battery of in vitro pharmacology assays to identify potential unintended, off-target interactions with various receptors, transporters, ion channels, and enzymes, including kinases. Furthermore, these screening panels may also provide utility at later stages of development to provide a mechanistic understanding of unexpected safety findings. Here, we present a compendium of the most likely functional and pathological outcomes associated with interaction(s) to a panel of 95 kinases based on an extensive curation of the scientific literature. This panel of kinases was designed by AbbVie based on safety-related data extracted from the literature, as well as from over 20 years of institutional knowledge generated from discovery efforts. For each kinase, the scientific literature was reviewed using online databases and the most often reported functional and pathological effects were summarized. This work should serve as a practical guide for small molecule drug discovery scientists and clinical investigators to predict and/or interpret adverse effects related to pharmacological interactions with these kinases.
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Affiliation(s)
- Jonathon R Green
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States.
| | | | - Sujatha M Gopalakrishnan
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Michael J Liguori
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Scott W Mittelstadt
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Eric A G Blomme
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Terry R Van Vleet
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
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5
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Ong HW, Truong A, Kwarcinski F, de Silva C, Avalani K, Havener TM, Chirgwin M, Galal KA, Willis C, Krämer A, Liu S, Knapp S, Derbyshire ER, Zutshi R, Drewry DH. Discovery of potent Plasmodium falciparum protein kinase 6 (PfPK6) inhibitors with a type II inhibitor pharmacophore. Eur J Med Chem 2023; 249:115043. [PMID: 36736152 PMCID: PMC10052868 DOI: 10.1016/j.ejmech.2022.115043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 01/01/2023]
Abstract
Malaria is a devastating disease that causes significant global morbidity and mortality. The rise of drug resistance against artemisinin-based combination therapy demonstrates the necessity to develop alternative antimalarials with novel mechanisms of action. We report the discovery of Ki8751 as an inhibitor of essential kinase PfPK6. 79 derivatives were designed, synthesized and evaluated for PfPK6 inhibition and antiplasmodial activity. Using group efficiency analyses, we established the importance of key groups on the scaffold consistent with a type II inhibitor pharmacophore. We highlight modifications on the tail group that contribute to antiplasmodial activity, cumulating in the discovery of compound 67, a PfPK6 inhibitor (IC50 = 13 nM) active against the P. falciparum blood stage (EC50 = 160 nM), and compound 79, a PfPK6 inhibitor (IC50 < 5 nM) with dual-stage antiplasmodial activity against P. falciparum blood stage (EC50 = 39 nM) and against P. berghei liver stage (EC50 = 220 nM).
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Affiliation(s)
- Han Wee Ong
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anna Truong
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Frank Kwarcinski
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Chandi de Silva
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Krisha Avalani
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Tammy M Havener
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Michael Chirgwin
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA
| | - Kareem A Galal
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Caleb Willis
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA
| | - Andreas Krämer
- Structural Genomics Consortium, Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC, 27599-3420, USA; Department of Chemistry, University of North Carolina, Chapel Hill, NC, 27599-3420, USA
| | - Stefan Knapp
- Structural Genomics Consortium, Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC, 27708, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC, 27710, USA.
| | - Reena Zutshi
- Luceome Biotechnologies, L.L.C, 1665 E. 18th Street, Suite 106, Tucson, AZ, 85719, USA.
| | - David H Drewry
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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6
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Cartwright TN, Meyer SK, Higgins JMG. Robustness of NanoBiT luciferase complementation technology in the presence of widely used kinase inhibitors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:471-475. [PMID: 36162794 DOI: 10.1016/j.slasd.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/08/2022] [Accepted: 09/21/2022] [Indexed: 12/15/2022]
Abstract
Bioluminescence assays using luciferase enzymes are widely used in research to monitor gene expression and an array of other cell properties, and split luciferase enzymes can be used to measure protein interactions in biochemical assays and in living cells. When these methods are employed in chemical library screening efforts, it is vital that the activity of the luciferase enzyme itself is not strongly influenced by library components. Here, we developed a NanoBiT split luciferase assay to measure phosphorylation of Histone H3 peptides and used it to test the robustness of split luciferase to interference from two libraries of commonly used kinase inhibitors, including the Kinase Chemogenomic Set (KCGS). We found that NanoBiT luciferase is not significantly affected by the great majority of kinase inhibitors tested. However, the weak inhibition observed for a small minority of kinase inhibitors encourages the inclusion of suitable controls in NanoBiT (or NanoLuc) assays.
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Affiliation(s)
- Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Stephanie K Meyer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom.
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7
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Zhu Y, Hu X. Molecular Recognition of FDA-Approved Small Molecule Protein Kinase Drugs in Protein Kinases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27207124. [PMID: 36296718 PMCID: PMC9611543 DOI: 10.3390/molecules27207124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022]
Abstract
Protein kinases are key enzymes that catalyze the covalent phosphorylation of substrates via the transfer of the γ-phosphate of ATP, playing a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. Due to their pivotal cellular role, the aberrant function of kinases has been associated with cancers and many other diseases. Consequently, competitive inhibition of the ATP binding site of protein kinases has emerged as an effective means of curing these diseases. Decades of intense development of protein kinase inhibitors (PKIs) resulted in 71 FDA-approved PKI drugs that target dozens of protein kinases for the treatment of various diseases. How do FDA-approved protein kinase inhibitor PKI drugs compete with ATP in their own binding pocket? This is the central question we attempt to address in this work. Based on modes of non-bonded interactions and their calculated interaction strengths by means of the advanced double hybrid DFT method B2PLYP, the molecular recognition of PKI drugs in the ATP-binding pockets was systematically analyzed. It was found that (1) all the FDA-approved PKI drugs studied here form one or more hydrogen bond(s) with the backbone amide N, O atoms in the hinge region of the ATP binding site, mimicking the adenine base; (2) all the FDA-approved PKI drugs feature two or more aromatic rings. The latter reach far and deep into the hydrophobic regions I and II, forming multiple CH-π interactions with aliphatic residues L(3), V(11), A(15), V(36), G(51), L(77) and π-π stacking interactions with aromatic residues F(47) and F(82), but ATP itself does not utilize these regions extensively; (3) all FDA-approved PKI drugs studied here have one thing in common, i.e., they frequently formed non-bonded interactions with a total of 12 residues L(3),V(11), A(15), K(17), E(24),V(36),T(45), F(47), G(51), L(77), D(81) and F(82) in the ATP binding. Many of those 12 commonly involved residues are highly conserved residues with important structural and catalytic functional roles. K(17) and E(24) are the two highly conserved residues crucial for the catalytic function of kinases. D(81) and F(82) belong to the DFG motif; T(45) was dubbed the gate keeper residue. F(47) is located on the hinge region and G(51) sits on the linker that connects the hinge to the αD-helix. It is this targeting of highly conserved residues in protein kinases that led to promiscuous PKI drugs that lack selectivity. Although the formation of hydrogen bond(s) with the backbone of the hinge gives PKI drugs the added binding affinity and the much-needed directionality, selectivity is sacrificed. That is why so many FDA-approved PKI drugs are known to have multiple targets. Moreover, off-target-mediated toxicity caused by a lack of selectivity was one of the major challenges facing the PKI drug discovery community. This work suggests a road map for future PKI drug design, i.e., targeting non-conserved residues in the ATP binding pocket to gain better selectivity so as to avoid off-target-mediated toxicity.
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Affiliation(s)
| | - Xiche Hu
- Correspondence: ; Tel.: +1-4195301513
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8
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Asquith CRM, Temme L, East MP, Laitinen T, Pickett J, Kwarcinski FE, Sinha P, Wells CI, Johnson GL, Zutshi R, Drewry DH. Identification of 4-anilino-quin(az)oline as a cell active Protein Kinase Novel 3 (PKN3) inhibitor chemotype. ChemMedChem 2022; 17:e202200161. [PMID: 35403825 DOI: 10.1002/cmdc.202200161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/08/2022]
Abstract
Deep annotation of a library of 4-anilinoquinolines led to the identification of 7-iodo- N -(3,4,5-trimethoxyphenyl)quinolin-4-amine 16 as a potent inhibitor (IC 50 = 14 nM) of Protein Kinase Novel 3 (PKN3) with micromolar activity in cells. Compound 16 is a potential tool compound to study the cell biology of PKN3 and its role in pancreatic and prostate cancer and T-cell acute lymphoblastic leukemia. These 4-anilinoquinolines may also be useful tools to uncover the therapeutic potential of PKN3 inhibition in a broad range of diseases.
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Affiliation(s)
| | - Louisa Temme
- University of North Carolina at Chapel Hill, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, UNITED STATES
| | - Michael P East
- University of North Carolina at Chapel Hill, Department of Pharmacology, School of Medicine, UNITED STATES
| | - Tuomo Laitinen
- University of Eastern Finland Faculty of Health Sciences: Ita-Suomen yliopisto Terveystieteiden tiedekunta, School of Pharmacy, FINLAND
| | - Julie Pickett
- University of North Carolina at Chapel Hill, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, UNITED STATES
| | - Frank E Kwarcinski
- Luceome Biotechnologies, LLC, Luceome Biotechnologies, LLC, UNITED STATES
| | - Parvathi Sinha
- Luceome Biotechnologies, LLC, Luceome Biotechnologies, LLC, UNITED STATES
| | - Carrow I Wells
- University of North Carolina at Chapel Hill, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, UNITED STATES
| | - Gary L Johnson
- University of North Carolina at Chapel Hill, Department of Pharmacology, School of Medicine,, UNITED STATES
| | - Reena Zutshi
- Luceome Biotechnologies, LLC, Luceome Biotechnologies, LLC,, UNITED STATES
| | - David H Drewry
- University of North Carolina at Chapel Hill, Structural Genomics Consortium, UNC Eshelman School of Pharmacy, UNITED STATES
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9
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Green AC, Lath D, Hudson K, Walkley B, Down JM, Owen R, Evans HR, Paton-Hough J, Reilly GC, Lawson MA, Chantry AD. TGFβ Inhibition Stimulates Collagen Maturation to Enhance Bone Repair and Fracture Resistance in a Murine Myeloma Model. J Bone Miner Res 2019; 34:2311-2326. [PMID: 31442332 DOI: 10.1002/jbmr.3859] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/09/2019] [Accepted: 08/17/2019] [Indexed: 12/12/2022]
Abstract
Multiple myeloma is a plasma cell malignancy that causes debilitating bone disease and fractures, in which TGFβ plays a central role. Current treatments do not repair existing damage and fractures remain a common occurrence. We developed a novel low tumor phase murine model mimicking the plateau phase in patients as we hypothesized this would be an ideal time to treat with a bone anabolic. Using in vivo μCT we show substantial and rapid bone lesion repair (and prevention) driven by SD-208 (TGFβ receptor I kinase inhibitor) and chemotherapy (bortezomib and lenalidomide) in mice with human U266-GFP-luc myeloma. We discovered that lesion repair occurred via an intramembranous fracture repair-like mechanism and that SD-208 enhanced collagen matrix maturation to significantly improve fracture resistance. Lesion healing was associated with VEGFA expression in woven bone, reduced osteocyte-derived PTHrP, increased osteoblasts, decreased osteoclasts, and lower serum tartrate-resistant acid phosphatase 5b (TRACP-5b). SD-208 also completely prevented bone lesion development in mice with aggressive JJN3 tumors, and was more effective than an anti-TGFβ neutralizing antibody (1D11). We also discovered that SD-208 promoted osteoblastic differentiation (and overcame the TGFβ-induced block in osteoblastogenesis) in myeloma patient bone marrow stromal cells in vitro, comparable to normal donors. The improved bone quality and fracture-resistance with SD-208 provides incentive for clinical translation to improve myeloma patient quality of life by reducing fracture risk and fatality. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Alanna C Green
- Sheffield Myeloma Research Team, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.,Mellanby Centre for Bone Research, University of Sheffield Medical School, University of Sheffield, Sheffield, UK
| | - Darren Lath
- Sheffield Myeloma Research Team, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.,Mellanby Centre for Bone Research, University of Sheffield Medical School, University of Sheffield, Sheffield, UK
| | - Katie Hudson
- Sheffield Myeloma Research Team, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.,Mellanby Centre for Bone Research, University of Sheffield Medical School, University of Sheffield, Sheffield, UK
| | - Brant Walkley
- Department of Materials Science and Engineering, The University of Sheffield, Sheffield, UK
| | - Jennifer M Down
- Sheffield Myeloma Research Team, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.,Mellanby Centre for Bone Research, University of Sheffield Medical School, University of Sheffield, Sheffield, UK
| | - Robert Owen
- INSIGNEO Institute of In Silico Medicine, Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK
| | - Holly R Evans
- Sheffield Myeloma Research Team, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.,Mellanby Centre for Bone Research, University of Sheffield Medical School, University of Sheffield, Sheffield, UK
| | - Julia Paton-Hough
- Sheffield Myeloma Research Team, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.,Mellanby Centre for Bone Research, University of Sheffield Medical School, University of Sheffield, Sheffield, UK
| | - Gwendolen C Reilly
- INSIGNEO Institute of In Silico Medicine, Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK
| | - Michelle A Lawson
- Sheffield Myeloma Research Team, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.,Mellanby Centre for Bone Research, University of Sheffield Medical School, University of Sheffield, Sheffield, UK
| | - Andrew D Chantry
- Sheffield Myeloma Research Team, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.,Mellanby Centre for Bone Research, University of Sheffield Medical School, University of Sheffield, Sheffield, UK.,Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust, Royal Hallamshire Hospital, Sheffield, UK
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10
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Cagle P, Niture S, Srivastava A, Ramalinga M, Aqeel R, Rios-Colon L, Chimeh U, Suy S, Collins SP, Dahiya R, Kumar D. MicroRNA-214 targets PTK6 to inhibit tumorigenic potential and increase drug sensitivity of prostate cancer cells. Sci Rep 2019; 9:9776. [PMID: 31278310 PMCID: PMC6611815 DOI: 10.1038/s41598-019-46170-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/14/2019] [Indexed: 01/06/2023] Open
Abstract
Prostate cancer is the most commonly diagnosed cancer in men with African American men disproportionally suffering from the burden of this disease. Biomarkers that could discriminate indolent from aggressive and drug resistance disease are lacking. MicroRNAs are small non-coding RNAs that affect numerous physiological and pathological processes, including cancer development and have been suggested as biomarkers and therapeutic targets. In the present study, we investigated the role of miR-214 on prostate cancer cell survival/migration/invasion, cell cycle regulation, and apoptosis. miR-214 was differentially expressed between Caucasian and African American prostate cancer cells. Importantly, miR-214 overexpression in prostate cancer cells induced apoptosis, inhibiting cell proliferation and colony forming ability. miR-214 expression in prostate cancer cells also inhibited cell migration and 3D spheroid invasion. Mechanistically, miR-214 inhibited prostate cancer cell proliferation by targeting protein tyrosine kinase 6 (PTK6). Restoration of PTK6 expression attenuated the inhibitory effect of miR-214 on cell proliferation. Moreover, simultaneous inhibition of PTK6 by ibrutinib and miR-214 significantly reduced cell proliferation/survival. Our data indicates that miR-214 could act as a tumor suppressor in prostate cancer and could potentially be utilized as a biomarker and therapeutic target.
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Affiliation(s)
- Patrice Cagle
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, 27707, United States
| | - Suryakant Niture
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, 27707, United States
| | - Anvesha Srivastava
- Cancer Research Laboratory, Division of Science and Mathematics, University of the District of Columbia, Washington, DC, 20008, United States
| | - Malathi Ramalinga
- Cancer Research Laboratory, Division of Science and Mathematics, University of the District of Columbia, Washington, DC, 20008, United States
| | - Rasha Aqeel
- Cancer Research Laboratory, Division of Science and Mathematics, University of the District of Columbia, Washington, DC, 20008, United States
| | - Leslimar Rios-Colon
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, 27707, United States
| | - Uchechukwu Chimeh
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, 27707, United States
| | - Simeng Suy
- Department of Radiation Medicine, Georgetown University, Washington, DC, 20057, United States
| | - Sean P Collins
- Department of Radiation Medicine, Georgetown University, Washington, DC, 20057, United States
| | - Rajvir Dahiya
- VA Medical Center and University of California San Francisco, San Francisco, CA, 94121, United States
| | - Deepak Kumar
- Julius L. Chambers Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, NC, 27707, United States. .,Cancer Research Laboratory, Division of Science and Mathematics, University of the District of Columbia, Washington, DC, 20008, United States. .,Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC, 27707, United States.
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11
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Abstract
Phenotypic screens are increasingly utilized in drug discovery for multiple purposes such as lead and/or tool compound finding, and target discovery. Using potent and selective chemical tool compounds against well-defined targets in phenotypic screens can help elucidate biological processes modulating assay phenotypes. Unfortunately the identification of such tools from large heterogeneous bioactivity databases is nontrivial and there is repeated use of published unselective compounds as phenotypic tools. Here we describe a computational model, the compound-target tool score (TS), which is an evidence-based quantitative confidence metric that can be used to systematically rank tool compounds for targets. The identified selective and nonselective tool compounds have applications in phenotypic assays for target hypothesis validation as well as assay development.
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12
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Wu M, White HV, Boehm BA, Meriney CJ, Kerrigan K, Frasso M, Liang M, Gotway EM, Wilcox MR, Johnson JW, Wipf P, Meriney SD. New Cav2 calcium channel gating modifiers with agonist activity and therapeutic potential to treat neuromuscular disease. Neuropharmacology 2017; 131:176-189. [PMID: 29246857 DOI: 10.1016/j.neuropharm.2017.12.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 11/28/2017] [Accepted: 12/10/2017] [Indexed: 12/13/2022]
Abstract
Voltage-gated calcium channels (VGCCs) are critical regulators of many cellular functions, including the activity-dependent release of chemical neurotransmitter from nerve terminals. At nerve terminals, the Cav2 family of VGCCs are closely positioned with neurotransmitter-containing synaptic vesicles. The relationship between calcium ions and transmitter release is such that even subtle changes in calcium flux through VGCCs have a strong influence on the magnitude of transmitter released. Therefore, modulators of the calcium influx at nerve terminals have the potential to strongly affect transmitter release at synapses. We have previously developed novel Cav2-selective VGCC gating modifiers (notably GV-58) that slow the deactivation of VGCC current, increasing total calcium ion flux. Here, we describe ten new gating modifiers based on the GV-58 structure that extend our understanding of the structure-activity relationship for this class of molecules and extend the range of modulation of channel activities. In particular, we show that one of these new compounds (MF-06) was more efficacious than GV-58, another (KK-75) acts more quickly on VGCCs than GV-58, and a third (KK-20) has a mix of increased speed and efficacy. A subset of these new VGCC agonist gating modifiers can increase transmitter release during action potentials at neuromuscular synapses, and as such, show potential as therapeutics for diseases with a presynaptic deficit that results in neuromuscular weakness. Further, several of these new compounds can be useful tool compounds for the study of VGCC gating and function.
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Affiliation(s)
- Man Wu
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Hayley V White
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Blake A Boehm
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Christopher J Meriney
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Kaylan Kerrigan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Michael Frasso
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Mary Liang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Erika M Gotway
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Madeleine R Wilcox
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Jon W Johnson
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Stephen D Meriney
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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13
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Lapek JD, Greninger P, Morris R, Amzallag A, Pruteanu-Malinici I, Benes CH, Haas W. Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities. Nat Biotechnol 2017; 35:983-989. [PMID: 28892078 PMCID: PMC5683351 DOI: 10.1038/nbt.3955] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/08/2017] [Indexed: 12/17/2022]
Abstract
The formation of protein complexes and the co-regulation of the cellular concentrations of proteins are essential mechanisms for cellular signaling and for maintaining homeostasis. Here we use isobaric-labeling multiplexed proteomics to analyze protein co-regulation and show that this allows the identification of protein-protein associations with high accuracy. We apply this 'interactome mapping by high-throughput quantitative proteome analysis' (IMAHP) method to a panel of 41 breast cancer cell lines and show that deviations of the observed protein co-regulations in specific cell lines from the consensus network affects cellular fitness. Furthermore, these aberrant interactions serve as biomarkers that predict the drug sensitivity of cell lines in screens across 195 drugs. We expect that IMAHP can be broadly used to gain insight into how changing landscapes of protein-protein associations affect the phenotype of biological systems.
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Affiliation(s)
- John D Lapek
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Iulian Pruteanu-Malinici
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
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14
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Abstract
We have developed a general methodology to produce bivalent kinase inhibitors for c-Src that interact with the SH2 and ATP binding pockets. Our approach led to a highly selective bivalent inhibitor of c-Src. We demonstrate impressive selectivity for c-Src over homologous kinases. Exploration of the unexpected high level of selectivity yielded insight into the inherent flexibility of homologous kinases. Finally, we demonstrate that our methodology is modular and both the ATP-competitive fragment and conjugation chemistry can be swapped.
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Affiliation(s)
- Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Matthew B. Soellner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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15
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Wang Y, Cornett A, King FJ, Mao Y, Nigsch F, Paris CG, McAllister G, Jenkins JL. Evidence-Based and Quantitative Prioritization of Tool Compounds in Phenotypic Drug Discovery. Cell Chem Biol 2016; 23:862-874. [PMID: 27427232 DOI: 10.1016/j.chembiol.2016.05.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 04/29/2016] [Accepted: 05/13/2016] [Indexed: 01/07/2023]
Abstract
The use of potent and selective chemical tools with well-defined targets can help elucidate biological processes driving phenotypes in phenotypic screens. However, identification of selective compounds en masse to create targeted screening sets is non-trivial. A systematic approach is needed to prioritize probes, which prevents the repeated use of published but unselective compounds. Here we performed a meta-analysis of integrated large-scale, heterogeneous bioactivity data to create an evidence-based, quantitative metric to systematically rank tool compounds for targets. Our tool score (TS) was then tested on hundreds of compounds by assessing their activity profiles in a panel of 41 cell-based pathway assays. We demonstrate that high-TS tools show more reliably selective phenotypic profiles than lower-TS compounds. Additionally we highlight frequently tested compounds that are non-selective tools and distinguish target family polypharmacology from cross-family promiscuity. TS can therefore be used to prioritize compounds from heterogeneous databases for phenotypic screening.
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Affiliation(s)
- Yuan Wang
- Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Allen Cornett
- Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Fred J King
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Yi Mao
- Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, Basel 4056, Switzerland
| | - C Gregory Paris
- Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gregory McAllister
- Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jeremy L Jenkins
- Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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16
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Kwarcinski FE, Brandvold KR, Phadke S, Beleh OM, Johnson TK, Meagher JL, Seeliger MA, Stuckey JA, Soellner MB. Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity. ACS Chem Biol 2016; 11:1296-304. [PMID: 26895387 PMCID: PMC7306399 DOI: 10.1021/acschembio.5b01018] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the kinase field, there are many widely held tenets about conformation-selective inhibitors that have yet to be validated using controlled experiments. We have designed, synthesized, and characterized a series of kinase inhibitor analogues of dasatinib, an FDA-approved kinase inhibitor that binds the active conformation. This inhibitor series includes two Type II inhibitors that bind the DFG-out inactive conformation and two inhibitors that bind the αC-helix-out inactive conformation. Using this series of compounds, we analyze the impact that conformation-selective inhibitors have on target binding and kinome-wide selectivity.
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Affiliation(s)
- Frank E. Kwarcinski
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Sameer Phadke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Omar M. Beleh
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794
| | - Jeanne A. Stuckey
- Center for Structural Biology, University of Michigan, Ann Arbor, MI 48109
| | - Matthew B. Soellner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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17
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Fraser C, Dawson JC, Dowling R, Houston DR, Weiss JT, Munro AF, Muir M, Harrington L, Webster SP, Frame MC, Brunton VG, Patton EE, Carragher NO, Unciti-Broceta A. Rapid Discovery and Structure-Activity Relationships of Pyrazolopyrimidines That Potently Suppress Breast Cancer Cell Growth via SRC Kinase Inhibition with Exceptional Selectivity over ABL Kinase. J Med Chem 2016; 59:4697-710. [PMID: 27115835 PMCID: PMC4885109 DOI: 10.1021/acs.jmedchem.6b00065] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Novel
pyrazolopyrimidines displaying high potency and selectivity
toward SRC family kinases have been developed by combining ligand-based
design and phenotypic screening in an iterative manner. Compounds
were derived from the promiscuous kinase inhibitor PP1 to search for
analogs that could potentially target a broad spectrum of kinases
involved in cancer. Phenotypic screening against MCF7 mammary adenocarcinoma
cells generated target-agnostic structure–activity relationships
that biased subsequent designs toward breast cancer treatment rather
than to a particular target. This strategy led to the discovery of
two potent antiproliferative leads with phenotypically distinct anticancer
mode of actions. Kinase profiling and further optimization resulted
in eCF506, the first small molecule with subnanomolar IC50 for SRC that requires 3 orders of magnitude greater concentration
to inhibit ABL. eCF506 exhibits excellent water solubility, an optimal
DMPK profile and oral bioavailability, halts SRC-associated neuromast
migration in zebrafish embryos without inducing life-threatening heart
defects, and inhibits SRC phosphorylation in tumor xenografts in mice.
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Affiliation(s)
| | | | | | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh , Edinburgh EH9 3BF, United Kingdom
| | | | | | | | - Lea Harrington
- Faculty of Medicine, University of Montreal, Institute for Research in Immunology and Cancer, Chemin de Polytechnique , Montreal, Quebec H3T 1J4, Canada
| | - Scott P Webster
- University/BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh , Edinburgh EH16 4TJ, United Kingdom
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18
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Brandvold KR, Santos SM, Breen ME, Lachacz EJ, Steffey ME, Soellner MB. Exquisitely specific bisubstrate inhibitors of c-Src kinase. ACS Chem Biol 2015; 10:1387-91. [PMID: 25793938 DOI: 10.1021/cb501048b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We have developed a modular approach to bisubstrate inhibition of protein kinases. We apply our methodology to c-Src and identify a highly selective bisubstrate inhibitor for this target. Our approach has yielded the most selective c-Src inhibitor to date, and the methodology to render the bisubstrate inhibitor cell-permeable provides a highly valuable tool for the study of c-Src signaling. In addition, we have applied our bisubstrate inhibitor to develop a novel screening methodology to identify non-ATP-competitive inhibitors of c-Src. Using this methodology, we have discovered the most potent non-ATP-competitive inhibitor reported to date. Our methodology is designed to be general and could be applicable to additional kinases inhibited by the promiscuous ATP-competitive fragment used in our studies.
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Affiliation(s)
- Kristoffer R. Brandvold
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Shana M. Santos
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Meghan E. Breen
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Eric J. Lachacz
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Michael E. Steffey
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Matthew B. Soellner
- Department of Medicinal Chemistry and ‡Department of
Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
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19
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Médard G, Pachl F, Ruprecht B, Klaeger S, Heinzlmeir S, Helm D, Qiao H, Ku X, Wilhelm M, Kuehne T, Wu Z, Dittmann A, Hopf C, Kramer K, Kuster B. Optimized chemical proteomics assay for kinase inhibitor profiling. J Proteome Res 2015; 14:1574-86. [PMID: 25660469 DOI: 10.1021/pr5012608] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Solid supported probes have proven to be an efficient tool for chemical proteomics. The kinobeads technology features kinase inhibitors covalently attached to Sepharose for affinity enrichment of kinomes from cell or tissue lysates. This technology, combined with quantitative mass spectrometry, is of particular interest for the profiling of kinase inhibitors. It often leads to the identification of new targets for medicinal chemistry campaigns where it allows a two-in-one binding and selectivity assay. The assay can also uncover resistance mechanisms and molecular sources of toxicity. Here we report on the optimization of the kinobead assay resulting in the combination of five chemical probes and four cell lines to cover half the human kinome in a single assay (∼ 260 kinases). We show the utility and large-scale applicability of the new version of kinobeads by reprofiling the small molecule kinase inhibitors Alvocidib, Crizotinib, Dasatinib, Fasudil, Hydroxyfasudil, Nilotinib, Ibrutinib, Imatinib, and Sunitinib.
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Affiliation(s)
- Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technische Universität München , Freising, Germany
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20
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Halland N, Schmidt F, Weiss T, Saas J, Li Z, Czech J, Dreyer M, Hofmeister A, Mertsch K, Dietz U, Strübing C, Nazare M. Discovery of N-[4-(1H-Pyrazolo[3,4-b]pyrazin-6-yl)-phenyl]-sulfonamides as Highly Active and Selective SGK1 Inhibitors. ACS Med Chem Lett 2015; 6:73-8. [PMID: 25589934 DOI: 10.1021/ml5003376] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/17/2014] [Indexed: 12/11/2022] Open
Abstract
From a virtual screening starting point, inhibitors of the serum and glucocorticoid regulated kinase 1 were developed through a combination of classical medicinal chemistry and library approaches. This resulted in highly active small molecules with nanomolar activity and a good overall in vitro and ADME profile. Furthermore, the compounds exhibited unusually high kinase and off-target selectivity due to their rigid structure.
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Affiliation(s)
- Nis Halland
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Friedemann Schmidt
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Tilo Weiss
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Joachim Saas
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Ziyu Li
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Jörg Czech
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Matthias Dreyer
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Armin Hofmeister
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Katharina Mertsch
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Uwe Dietz
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Carsten Strübing
- Sanofi R&D, Industriepark Höchst Building G838, D-65926 Frankfurt am Main, Germany
| | - Marc Nazare
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
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21
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Camacho-Soto K, Castillo-Montoya J, Tye B, Ogunleye LO, Ghosh I. Small molecule gated split-tyrosine phosphatases and orthogonal split-tyrosine kinases. J Am Chem Soc 2014; 136:17078-86. [PMID: 25409264 DOI: 10.1021/ja5080745] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinases phosphorylate client proteins, while protein phosphatases catalyze their dephosphorylation and thereby in concert exert reversible control over numerous signal transduction pathways. We have recently reported the design and validation of split-protein kinases that can be conditionally activated by an added small molecule chemical inducer of dimerization (CID), rapamycin. Herein, we provide the rational design and validation of three split-tyrosine phosphatases (PTPs) attached to FKBP and FRB, where catalytic activity can be modulated with rapamycin. We further demonstrate that the orthogonal CIDs, abscisic acid and gibberellic acid, can be used to impart control over the activity of split-tyrosine kinases (PTKs). Finally, we demonstrate that designed split-phosphatases and split-kinases can be activated by orthogonal CIDs in mammalian cells. In sum, we provide a methodology that allows for post-translational orthogonal small molecule control over the activity of user defined split-PTKs and split-PTPs. This methodology has the long-term potential for both interrogating and redesigning phosphorylation dependent signaling pathways.
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Affiliation(s)
- Karla Camacho-Soto
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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22
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Abstract
Drug action can be rationalized as interaction of a molecule with proteins in a regulatory network of targets from a specific biological system. Both drug and side effects are often governed by interaction of the drug molecule with many, often unrelated, targets. Accordingly, arrays of protein–ligand interaction data from numerous in vitro profiling assays today provide growing evidence of polypharmacological drug interactions, even for marketed drugs. In vitro off-target profiling has therefore become an important tool in early drug discovery to learn about potential off-target liabilities, which are sometimes beneficial, but more often safety relevant. The rapidly developing field of in silico profiling approaches is complementing in vitro profiling. These approaches capitalize from large amounts of biochemical data from multiple sources to be exploited for optimizing undesirable side effects in pharmaceutical research. Therefore, current in silico profiling models are nowadays perceived as valuable tools in drug discovery, and promise a platform to support optimally informed decisions.
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23
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Senevirathne C, Pflum MKH. Biotinylated phosphoproteins from kinase-catalyzed biotinylation are stable to phosphatases: implications for phosphoproteomics. Chembiochem 2013; 14:381-7. [PMID: 23335220 PMCID: PMC4524292 DOI: 10.1002/cbic.201200626] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Indexed: 11/11/2022]
Abstract
Kinase-catalyzed protein phosphorylation is involved in a wide variety of cellular events. Development of methods to monitor phosphorylation is critical to understand cell biology. Our lab recently discovered kinase-catalyzed biotinylation, where ATP-biotin is utilized by kinases to label phosphopeptides or phosphoproteins with a biotin tag. To exploit kinase-catalyzed biotinylation for phosphoprotein purification and identification in a cellular context, the susceptibility of the biotin tag to phosphatases was characterized. We found that the phosphorylbiotin group on peptide and protein substrates was relatively insensitive to protein phosphatases. To understand how phosphatase stability would impact phosphoproteomics research applications, kinase-catalyzed biotinylation of cell lysates was performed in the presence of kinase or phosphatase inhibitors. We found that biotinylation with ATP-biotin was sensitive to inhibitors, although with variable effects compared to ATP phosphorylation. The results suggest that kinase-catalyzed biotinylation is well suited for phosphoproteomics studies, with particular utility towards monitoring low-abundance phosphoproteins or characterizing the influence of inhibitor drugs on protein phosphorylation.
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Affiliation(s)
| | - Mary Kay H. Pflum
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, Fax: (+)
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24
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Kwarcinski FE, Fox CC, Steffey ME, Soellner MB. Irreversible inhibitors of c-Src kinase that target a nonconserved cysteine. ACS Chem Biol 2012; 7:1910-7. [PMID: 22928736 DOI: 10.1021/cb300337u] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have developed the first irreversible inhibitors of wild-type c-Src kinase. We demonstrate that our irreversible inhibitors display improved potency and selectivity relative to that of their reversible counterparts. Our strategy involves modifying a promiscuous kinase inhibitor with an electrophile to generate covalent inhibitors of c-Src. We applied this methodology to two inhibitor scaffolds that exhibit increased cellular efficacy when rendered irreversible. In addition, we have demonstrated the utility of irreversible inhibitors in studying the conformation of an important loop in kinases that can control inhibitor selectivity and cause drug resistance. Together, we have developed a general and robust framework for generating selective irreversible inhibitors from reversible, promiscuous inhibitor scaffolds.
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Affiliation(s)
- Frank E. Kwarcinski
- Department
of Medicinal Chemistry and ‡Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann
Arbor, Michigan, 48109, United States
| | - Christel C. Fox
- Department
of Medicinal Chemistry and ‡Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann
Arbor, Michigan, 48109, United States
| | - Michael E. Steffey
- Department
of Medicinal Chemistry and ‡Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann
Arbor, Michigan, 48109, United States
| | - Matthew B. Soellner
- Department
of Medicinal Chemistry and ‡Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann
Arbor, Michigan, 48109, United States
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Lawrence HR, Martin MP, Luo Y, Pireddu R, Yang H, Gevariya H, Ozcan S, Zhu JY, Kendig R, Rodriguez M, Elias R, Cheng JQ, Sebti SM, Schonbrunn E, Lawrence NJ. Development of o-chlorophenyl substituted pyrimidines as exceptionally potent aurora kinase inhibitors. J Med Chem 2012; 55:7392-7416. [PMID: 22803810 DOI: 10.1021/jm300334d] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The o-carboxylic acid substituted bisanilinopyrimidine 1 was identified as a potent hit (Aurora A IC(50) = 6.1 ± 1.0 nM) from in-house screening. Detailed structure-activity relationship (SAR) studies indicated that polar substituents at the para position of the B-ring are critical for potent activity. X-ray crystallography studies revealed that compound 1 is a type I inhibitor that binds the Aurora kinase active site in a DFG-in conformation. Structure-activity guided replacement of the A-ring carboxylic acid with halogens and incorporation of fluorine at the pyrimidine 5-position led to highly potent inhibitors of Aurora A that bind in a DFG-out conformation. B-Ring modifications were undertaken to improve the solubility and cell permeability. Compounds such as 9m with water-solubilizing moieties at the para position of the B-ring inhibited the autophosphorylation of Aurora A in MDA-MB-468 breast cancer cells.
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Affiliation(s)
- Harshani R Lawrence
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Matthew P Martin
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Yunting Luo
- Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Roberta Pireddu
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Hua Yang
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Harsukh Gevariya
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Sevil Ozcan
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Jin-Yi Zhu
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Robert Kendig
- Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Mercedes Rodriguez
- Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Roy Elias
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Jin Q Cheng
- Department of Molecular Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Saïd M Sebti
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA.,Department of Molecular Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Ernst Schonbrunn
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Nicholas J Lawrence
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
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