1
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Ku AF, Sharma KL, Ta HM, Sutton CM, Bohren KM, Wang Y, Chamakuri S, Chen R, Hakenjos JM, Jimmidi R, Kent K, Li F, Li JY, Ma L, Madasu C, Palaniappan M, Palmer SS, Qin X, Robers MB, Sankaran B, Tan Z, Vasquez YM, Wang J, Wilkinson J, Yu Z, Ye Q, Young DW, Teng M, Kim C, Matzuk MM. Reversible male contraception by targeted inhibition of serine/threonine kinase 33. Science 2024; 384:885-890. [PMID: 38781365 DOI: 10.1126/science.adl2688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/03/2024] [Indexed: 05/25/2024]
Abstract
Men or mice with homozygous serine/threonine kinase 33 (STK33) mutations are sterile owing to defective sperm morphology and motility. To chemically evaluate STK33 for male contraception with STK33-specific inhibitors, we screened our multibillion-compound collection of DNA-encoded chemical libraries, uncovered potent STK33-specific inhibitors, determined the STK33 kinase domain structure bound with a truncated hit CDD-2211, and generated an optimized hit CDD-2807 that demonstrates nanomolar cellular potency (half-maximal inhibitory concentration = 9.2 nanomolar) and favorable metabolic stability. In mice, CDD-2807 exhibited no toxicity, efficiently crossed the blood-testis barrier, did not accumulate in brain, and induced a reversible contraceptive effect that phenocopied genetic STK33 perturbations without altering testis size. Thus, STK33 is a chemically validated, nonhormonal contraceptive target, and CDD-2807 is an effective tool compound.
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Affiliation(s)
- Angela F Ku
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kiran L Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hai Minh Ta
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney M Sutton
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yong Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruihong Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - John M Hakenjos
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ravikumar Jimmidi
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Katarzyna Kent
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lang Ma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chandrashekhar Madasu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen S Palmer
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yasmin M Vasquez
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiuji Ye
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Choel Kim
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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2
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Reinecke M, Brear P, Vornholz L, Berger BT, Seefried F, Wilhelm S, Samaras P, Gyenis L, Litchfield DW, Médard G, Müller S, Ruland J, Hyvönen M, Wilhelm M, Kuster B. Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors. Nat Chem Biol 2024; 20:577-585. [PMID: 37904048 PMCID: PMC11062922 DOI: 10.1038/s41589-023-01459-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/22/2023] [Indexed: 11/01/2023]
Abstract
Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover such probes, we profiled 1,183 compounds from drug discovery projects in lysates of cancer cell lines using Kinobeads. The resulting 500,000 compound-target interactions are available in ProteomicsDB and we exemplify how this molecular resource may be used. For instance, the data revealed several hundred reasonably selective compounds for 72 kinases. Cellular assays validated GSK986310C as a candidate SYK (spleen tyrosine kinase) probe and X-ray crystallography uncovered the structural basis for the observed selectivity of the CK2 inhibitor GW869516X. Compounds targeting PKN3 were discovered and phosphoproteomics identified substrates that indicate target engagement in cells. We anticipate that this molecular resource will aid research in drug discovery and chemical biology.
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Affiliation(s)
- Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Larsen Vornholz
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Benedict-Tilmann Berger
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Florian Seefried
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - David William Litchfield
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Guillaume Médard
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Jürgen Ruland
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
- Computational Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
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3
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Schwalm MP, Saxena K, Müller S, Knapp S. Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nat Protoc 2024:10.1038/s41596-024-00979-z. [PMID: 38637703 DOI: 10.1038/s41596-024-00979-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 04/20/2024]
Abstract
The rational development of small-molecule degraders (e.g., proteolysis targeting chimeras) remains a challenge as the rate-limiting steps that determine degrader efficiency are largely unknown. Standard methods in the field of targeted protein degradation mostly rely on classical, low-throughput endpoint assays such as western blots or quantitative proteomics. Here we applied NanoLuciferase- and HaloTag-based screening technologies to determine the kinetics and stability of small-molecule-induced ternary complex formation between a protein of interest and a selected E3 ligase. A collection of live-cell assays were designed to probe the most critical steps of the degradation process while minimizing the number of required expression constructs, making the proposed assay pipeline flexible and adaptable to the requirements of the users. This approach evaluates the underlying mechanism of selective target degraders and reveals the exact characteristics of the developed degrader molecules in living cells. The protocol allows scientists trained in basic cell culture and molecular biology to carry out small-molecule proximity-inducer screening via tracking of the ternary complex formation within 2 weeks of establishment, while degrader screening using the HiBiT system requires a CRISPR-Cas9 engineered cell line whose generation can take up to 3 months. After cell-line generation, degrader screening and validation can be carried out in high-throughput manner within days.
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Affiliation(s)
- Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
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4
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Karim M, Mishra M, Lo CW, Saul S, Cagirici HB, Tran DHN, Agrawal A, Ghita L, Ojha A, East MP, Gammeltoft KA, Sahoo MK, Johnson GL, Das S, Jochmans D, Cohen CA, Gottwein J, Dye J, Neff N, Pinsky BA, Laitinen T, Pantsar T, Poso A, Zanini F, Jonghe SD, Asquith CRM, Einav S. PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589676. [PMID: 38659941 PMCID: PMC11042293 DOI: 10.1101/2024.04.15.589676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
In search for broad-spectrum antivirals, we discovered a small molecule inhibitor, RMC-113, that potently suppresses the replication of multiple RNA viruses including SARS-CoV-2 in human lung organoids. We demonstrated selective dual inhibition of the lipid kinases PIP4K2C and PIKfyve by RMC-113 and target engagement by its clickable analog. Advanced lipidomics revealed alteration of SARS-CoV-2-induced phosphoinositide signature by RMC-113 and linked its antiviral effect with functional PIP4K2C and PIKfyve inhibition. We discovered PIP4K2C's roles in SARS-CoV-2 entry, RNA replication, and assembly/egress, validating it as a druggable antiviral target. Integrating proteomics, single-cell transcriptomics, and functional assays revealed that PIP4K2C binds SARS-CoV-2 nonstructural protein 6 and regulates virus-induced impairment of autophagic flux. Reversing this autophagic flux impairment is a mechanism of antiviral action of RMC-113. These findings reveal virus-induced autophagy regulation via PIP4K2C, an understudied kinase, and propose dual inhibition of PIP4K2C and PIKfyve as a candidate strategy to combat emerging viruses.
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Affiliation(s)
- Marwah Karim
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Manjari Mishra
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Chieh-Wen Lo
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Sirle Saul
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Halise Busra Cagirici
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Do Hoang Nhu Tran
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Aditi Agrawal
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Luca Ghita
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Amrita Ojha
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Michael P East
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karen Anbro Gammeltoft
- Department of Infectious Diseases, University of Copenhagen, Denmark. Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen
- University Hospital-Hvidovre, Hvidovre, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Malaya Kumar Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Gary L Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Soumita Das
- Biomedical & Nutritional Science, Center for Pathogen Research & Training (CPRT), University of Massachusetts-Lowell, USA
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Courtney A Cohen
- US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, Maryland, USA
| | - Judith Gottwein
- Department of Infectious Diseases, University of Copenhagen, Denmark. Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen
- University Hospital-Hvidovre, Hvidovre, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - John Dye
- US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, Maryland, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland
| | - Tatu Pantsar
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland
| | - Fabio Zanini
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, UNSW Sydney, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | | | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
- Department of Microbiology and Immunology, Stanford University, CA, USA
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5
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Rai T, Kaushik N, Malviya R, Sharma PK. A review on marine source as anticancer agents. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:415-451. [PMID: 37675579 DOI: 10.1080/10286020.2023.2249825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/15/2023] [Indexed: 09/08/2023]
Abstract
This review investigates the potential of natural compounds obtained from marine sources for the treatment of cancer. The oceans are believed to contain physiologically active compounds, such as alkaloids, nucleosides, macrolides, and polyketides, which have shown promising effects in slowing human tumor cells both in vivo and in vitro. Various marine species, including algae, mollusks, actinomycetes, fungi, sponges, and soft corals, have been studied for their bioactive metabolites with diverse chemical structures. The review explores the therapeutic potential of various marine-derived substances and discusses their possible applications in cancer treatment.
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Affiliation(s)
- Tamanna Rai
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Gautam Budh Nagar, Greater Noida, Uttar Pradesh 201306, India
| | - Niranjan Kaushik
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Gautam Budh Nagar, Greater Noida, Uttar Pradesh 201306, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Gautam Budh Nagar, Greater Noida, Uttar Pradesh 201306, India
| | - Pramod Kumar Sharma
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Gautam Budh Nagar, Greater Noida, Uttar Pradesh 201306, India
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6
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Sugawara T, Nevedomskaya E, Heller S, Böhme A, Lesche R, von Ahsen O, Grünewald S, Nguyen HM, Corey E, Baumgart SJ, Georgi V, Pütter V, Fernández‐Montalván A, Vasta JD, Robers MB, Politz O, Mumberg D, Haendler B. Dual targeting of the androgen receptor and PI3K/AKT/mTOR pathways in prostate cancer models improves antitumor efficacy and promotes cell apoptosis. Mol Oncol 2024; 18:726-742. [PMID: 38225213 PMCID: PMC10920092 DOI: 10.1002/1878-0261.13577] [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: 08/08/2023] [Revised: 11/27/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024] Open
Abstract
Prostate cancer is a frequent malignancy in older men and has a very high 5-year survival rate if diagnosed early. The prognosis is much less promising if the tumor has already spread outside the prostate gland. Targeted treatments mainly aim at blocking androgen receptor (AR) signaling and initially show good efficacy. However, tumor progression due to AR-dependent and AR-independent mechanisms is often observed after some time, and novel treatment strategies are urgently needed. Dysregulation of the PI3K/AKT/mTOR pathway in advanced prostate cancer and its implication in treatment resistance has been reported. We compared the impact of PI3K/AKT/mTOR pathway inhibitors with different selectivity profiles on in vitro cell proliferation and on caspase 3/7 activation as a marker for apoptosis induction, and observed the strongest effects in the androgen-sensitive prostate cancer cell lines VCaP and LNCaP. Combination treatment with the AR inhibitor darolutamide led to enhanced apoptosis in these cell lines, the effects being most pronounced upon cotreatment with the pan-PI3K inhibitor copanlisib. A subsequent transcriptomic analysis performed in VCaP cells revealed that combining darolutamide with copanlisib impacted gene expression much more than individual treatment. A comprehensive reversal of the androgen response and the mTORC1 transcriptional programs as well as a marked induction of DNA damage was observed. Next, an in vivo efficacy study was performed using the androgen-sensitive patient-derived prostate cancer (PDX) model LuCaP 35 and a superior efficacy was observed after the combined treatment with copanlisib and darolutamide. Importantly, immunohistochemistry analysis of these treated tumors showed increased apoptosis, as revealed by elevated levels of cleaved caspase 3 and Bcl-2-binding component 3 (BBC3). In conclusion, these data demonstrate that concurrent blockade of the PI3K/AKT/mTOR and AR pathways has superior antitumor efficacy and induces apoptosis in androgen-sensitive prostate cancer cell lines and PDX models.
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Affiliation(s)
- Tatsuo Sugawara
- Bayer AG, Pharmaceuticals, Research & Early Development OncologyBerlinGermany
| | | | | | | | | | | | | | | | - Eva Corey
- Department of UrologyUniversity of WashingtonSeattleWAUSA
| | - Simon J. Baumgart
- Bayer AG, Pharmaceuticals, Research & Early Development OncologyBerlinGermany
| | - Victoria Georgi
- Bayer AG, Pharmaceuticals, Research & Early Development OncologyBerlinGermany
| | - Vera Pütter
- Bayer AG, Pharmaceuticals, Research & Early Development OncologyBerlinGermany
| | - Amaury Fernández‐Montalván
- Bayer AG, Pharmaceuticals, Research & Early Development OncologyBerlinGermany
- Present address:
Boehringer Ingelheim Pharma GmbH & Co. KGBiberach an der RißGermany
| | | | | | - Oliver Politz
- Bayer AG, Pharmaceuticals, Research & Early Development OncologyBerlinGermany
| | - Dominik Mumberg
- Bayer AG, Pharmaceuticals, Research & Early Development OncologyBerlinGermany
- Present address:
Adcento ApSCopenhagenDenmark
| | - Bernard Haendler
- Bayer AG, Pharmaceuticals, Research & Early Development OncologyBerlinGermany
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7
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Li Z, Lu W, Beyett TS, Ficarro SB, Jiang J, Tse J, Kim AYJ, Marto JA, Che J, Jänne PA, Eck MJ, Zhang T, Gray NS. ZNL0325, a Pyrazolopyrimidine-Based Covalent Probe, Demonstrates an Alternative Binding Mode for Kinases. J Med Chem 2024; 67:2837-2848. [PMID: 38300264 DOI: 10.1021/acs.jmedchem.3c01891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The pyrazolopyrimidine (PP) heterocycle is a versatile and widely deployed core scaffold for the development of kinase inhibitors. Typically, a 4-amino-substituted pyrazolopyrimidine binds in the ATP-binding pocket in a conformation analogous to the 6-aminopurine of ATP. Here, we report the discovery of ZNL0325 which exhibits a flipped binding mode where the C3 position is oriented toward the ribose binding pocket. ZNL0325 and its analogues feature an acrylamide side chain at the C3 position which is capable of forming a covalent bond with multiple kinases that possess a cysteine at the αD-1 position including BTK, EGFR, BLK, and JAK3. These findings suggest that the ability to form a covalent bond can override the preferred noncovalent binding conformation of the heterocyclic core and provides an opportunity to create structurally distinct covalent kinase inhibitors.
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Affiliation(s)
- Zhengnian Li
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Wenchao Lu
- Lingang Laboratory, Shanghai 200031, China
| | - Tyler S Beyett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais Proteomics Center, Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jie Jiang
- Lowe Center for Thoracic Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jason Tse
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Audrey Yong-Ju Kim
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais Proteomics Center, Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
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8
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Gerninghaus J, Zhubi R, Krämer A, Karim M, Tran DHN, Joerger AC, Schreiber C, Berger LM, Berger BT, Ehret TAL, Elson L, Lenz C, Saxena K, Müller S, Einav S, Knapp S, Hanke T. Back-pocket optimization of 2-aminopyrimidine-based macrocycles leads to potent dual EPHA2/GAK kinase inhibitors with antiviral activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.18.580805. [PMID: 38405908 PMCID: PMC10888910 DOI: 10.1101/2024.02.18.580805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Macrocyclization of acyclic compounds is a powerful strategy for improving inhibitor potency and selectivity. Here, we developed a 2-aminopyrimidine-based macrocyclic dual EPHA2/GAK kinase inhibitor as a chemical tool to study the role of these two kinases in viral entry and assembly. Starting with a promiscuous macrocyclic inhibitor, 6, we performed a structure-guided activity relationship and selectivity study using a panel of over 100 kinases. The crystal structure of EPHA2 in complex with the developed macrocycle 23 provided a basis for further optimization by specifically targeting the back pocket, resulting in compound 55 as a potent dual EPHA2/GAK inhibitor. Subsequent front-pocket derivatization resulted in an interesting in cellulo selectivity profile, favoring EPHA4 over the other ephrin receptor kinase family members. The dual EPHA2/GAK inhibitor 55 prevented dengue virus infection of Huh7 liver cells, mainly via its EPHA2 activity, and is therefore a promising candidate for further optimization of its activity against dengue virus.
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Affiliation(s)
- Joshua Gerninghaus
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Rezart Zhubi
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Marwah Karim
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Do Hoang Nhu Tran
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Christian Schreiber
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Theresa A L Ehret
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Christopher Lenz
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Krishna Saxena
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
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9
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Morozova A, Chan SC, Bayle S, Sun L, Grassie D, Iermolaieva A, Kalaga MN, Frydman S, Sansil S, Schönbrunn E, Duckett D, Monastyrskyi A. Development of potent and selective ULK1/2 inhibitors based on 7-azaindole scaffold with favorable in vivo properties. Eur J Med Chem 2024; 266:116101. [PMID: 38232465 DOI: 10.1016/j.ejmech.2023.116101] [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: 11/18/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024]
Abstract
The UNC-51-like kinase-1 (ULK1) is one of the central upstream regulators of the autophagy pathway, represents a key target for the development of molecular probes to abrogate autophagy and explore potential therapeutic avenues. Here we report the discovery, structure-activity and structure-property relationships of selective, potent, and cell-active ULK1/2 inhibitors based on a 7-azaindole scaffold. Using structure-based drug design, we have developed a series of analogs with excellent binding affinity and biochemical activity against ULK1/2 (IC50 < 25 nM). The validation of cellular target engagement for these compounds was achieved through the employment of the ULK1 NanoBRET intracellular kinase assay. Notably, we have successfully solved the crystal structure of the lead compound, MR-2088, bound to the active site of ULK1. Moreover, the combination treatment of MR-2088 with known KRAS→RAF→MEK→ERK pathway inhibitors, such as trametinib, showed promising synergistic effect in vitro using H2030 (KRASG12C) cell lines. Lastly, our findings underscore MR-2088's potential to inhibit starvation/stimuli-induced autophagic flux, coupled with its suitability for in vivo studies based on its pharmacokinetic properties.
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Affiliation(s)
- Alisa Morozova
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Sean Chin Chan
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Simon Bayle
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Luxin Sun
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Dylan Grassie
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Anna Iermolaieva
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Mahalakshmi N Kalaga
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Sylvia Frydman
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Samer Sansil
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Ernst Schönbrunn
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Derek Duckett
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States
| | - Andrii Monastyrskyi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Dr, Tampa, FL, United States.
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10
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Bathla P, Mujawar A, De A, Sandanaraj BS. Development of Noninvasive Activity-Based Protein Profiling-Bioluminescence Resonance Energy Transfer Platform Technology Enables Target Engagement Studies with Absolute Specificity in Living Systems. ACS Pharmacol Transl Sci 2024; 7:375-383. [PMID: 38357276 PMCID: PMC10863430 DOI: 10.1021/acsptsci.3c00231] [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: 09/09/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 02/16/2024]
Abstract
Noninvasive, real-time, longitudinal imaging of protein functions in living systems with unprecedented specificity is one of the critical challenges of modern biomedical research. Toward that goal, here, we report a platform fusion technology called activity-based protein profiling-bioluminescence resonance energy transfer (ABPP-BRET). This method provides an opportunity to study the post-translational modification of a target protein in real time in living systems in a longitudinal manner. This semisynthetic BRET biosensor method is used for target engagement studies and further for inhibitor profiling in live cells. The simplicity of this method coupled with the critical physical distance-dependent BRET readout turned out to be a powerful method, thus pushing the activity-based protein profiling technology to the next level.
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Affiliation(s)
- Punita Bathla
- Department
of Biology, Department of Chemistry, Indian
Institute of Science Education and Research, Pune 411008, India
| | - Aaiyas Mujawar
- Molecular
Functional Imaging Lab, Advanced Centre
for Treatment Research Education in Cancer (ACTREC), Navi Mumbai 410210, India
- Homi
Bhabha National Institute, Mumbai 400094, India
| | - Abhijit De
- Molecular
Functional Imaging Lab, Advanced Centre
for Treatment Research Education in Cancer (ACTREC), Navi Mumbai 410210, India
- Homi
Bhabha National Institute, Mumbai 400094, India
| | - Britto S. Sandanaraj
- Department
of Biology, Department of Chemistry, Indian
Institute of Science Education and Research, Pune 411008, India
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11
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Takarada JE, Cunha MR, Almeida VM, Vasconcelos SNS, Santiago AS, Godoi PH, Salmazo A, Ramos PZ, Fala AM, de Souza LR, Da Silva IEP, Bengtson MH, Massirer KB, Couñago RM. Discovery of pyrazolo[3,4-d]pyrimidines as novel mitogen-activated protein kinase kinase 3 (MKK3) inhibitors. Bioorg Med Chem 2024; 98:117561. [PMID: 38157838 DOI: 10.1016/j.bmc.2023.117561] [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: 10/14/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
The dual-specificity protein kinase MKK3 has been implicated in tumor cell proliferation and survival, yet its precise role in cancer remains inconclusive. A critical step in elucidating the kinase's involvement in disease biology is the identification of potent, cell-permeable kinase inhibitors. Presently, MKK3 lacks a dedicated tool compound for these purposes, along with validated methods for the facile screening, identification, and optimization of inhibitors. In this study, we have developed a TR-FRET-based enzymatic assay for the detection of MKK3 activity in vitro and a BRET-based assay to assess ligand binding to this enzyme within intact human cells. These assays were instrumental in identifying hit compounds against MKK3 that share a common chemical scaffold, sourced from a library of bioactive kinase inhibitors. Initial hits were subsequently expanded through the synthesis of novel analogs. The resulting structure-activity relationship (SAR) was rationalized using molecular dynamics simulations against a homology model of MKK3. We expect our findings to expedite the development of novel, potent, selective, and bioactive inhibitors, thus facilitating investigations into MKK3's role in various cancers.
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Affiliation(s)
- Jéssica E Takarada
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Micael R Cunha
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Vitor M Almeida
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Stanley N S Vasconcelos
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - André S Santiago
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Paulo H Godoi
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Anita Salmazo
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Priscila Z Ramos
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Angela M Fala
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Lucas R de Souza
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Italo E P Da Silva
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Mario H Bengtson
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Katlin B Massirer
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Rafael M Couñago
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States.
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12
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Yin Y, Zhao SL, Rane D, Lin Z, Wu M, Peterson BR. Quantification of Binding of Small Molecules to Native Proteins Overexpressed in Living Cells. J Am Chem Soc 2024; 146:187-200. [PMID: 38118119 PMCID: PMC10910633 DOI: 10.1021/jacs.3c07488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The affinity and selectivity of small molecules for proteins drive drug discovery and development. We report a fluorescent probe cellular binding assay (FPCBA) for determination of these values for native (untagged) proteins overexpressed in living cells. This method uses fluorophores such as Pacific Blue (PB) linked to cell-permeable protein ligands to generate probes that rapidly and reversibly equilibrate with intracellular targets, as established by kinetic assays of cellular uptake and efflux. To analyze binding to untagged proteins, an internal ribosomal entry site (IRES) vector was employed that allows a single mRNA to encode both the protein target and a separate orthogonal fluorescent protein (mVenus). This enabled cellular uptake of the probe to be correlated with protein expression by flow cytometry, allowing measurement of cellular dissociation constants (Kd) of the probe. This approach was validated by studies of the binding of allosteric activators to eight different Protein Kinase C (PKC) isozymes. Full-length PKCs expressed in transiently transfected HEK293T cells were used to measure cellular Kd values of a probe comprising PB linked to the natural product phorbol via a carbamate. These values were further used to determine competitive binding constants (cellular Ki values) of the nonfluorescent phorbol ester PDBu and the anticancer agent bryostatin 1 for each isozyme. For some PKC-small molecule pairs, these cellular Ki values matched known biochemical Ki values, but for others, altered selectivity was observed in cells. This approach can facilitate quantification of interactions of small molecules with physiologically relevant native proteins.
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Affiliation(s)
- Yuwen Yin
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
| | - Serena Li Zhao
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
| | - Digamber Rane
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
| | - Zhihong Lin
- The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, 460 W. 10 Ave., Columbus, OH 43210, USA
| | - Meng Wu
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, 460 W. 10 Ave., Columbus, OH 43210, USA
| | - Blake R. Peterson
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, 460 W. 10 Ave., Columbus, OH 43210, USA
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13
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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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14
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Galal KA, Krämer A, Strickland BG, Smith JL, Dickmander RJ, Moorman NJ, Willson TM. Identification of 4-(6-((2-methoxyphenyl)amino)pyrazin-2-yl)benzoic acids as CSNK2A inhibitors with antiviral activity and improved selectivity over PIM3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569845. [PMID: 38106118 PMCID: PMC10723276 DOI: 10.1101/2023.12.04.569845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
We report the synthesis of 2,6-disubstituted pyrazines as potent cell active CSNK2A inhibitors. 4'-Carboxyphenyl was found to be the optimal 2-pyrazine substituent for CSNK2A activity, with little tolerance for additional modification. At the 6-position, modifications of the 6-isopropylaminoindazole substituent were explored to improve selectivity over PIM3 while maintaining potent CSNK2A inhibition. The 6-isopropoxyindole analogue 6c was identified as a nanomolar CSNK2A inhibitor with 30-fold selectivity over PIM3 in cells. Replacement of the 6-isopropoxyindole by isosteric ortho-methoxy anilines, such as 7c, generated analogues with selectivity for CSNK2A over PIM3 and improved the kinome-wide selectivity. The optimized 2,6-disubstituted pyrazines showed inhibition of viral replication consistent with their CSNK2A activity.
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Affiliation(s)
- Kareem A. Galal
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, USA
| | - Andreas Krämer
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strabe 15, Frankfurt 60438, Germany
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strabe 9, Frankfurt 60438, Germany
- Frankfurt Cancer Institute, Paul-Ehrlich-Straße 42-44, Frankfurt 60596, Germany
| | - Benjamin G. Strickland
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffery L. Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebekah J. Dickmander
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, USA
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nathaniel J. Moorman
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, USA
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Chapel Hill, NC 27599, USA
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15
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Outhwaite IR, Singh S, Berger BT, Knapp S, Chodera JD, Seeliger MA. Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting. eLife 2023; 12:e86189. [PMID: 38047771 PMCID: PMC10769483 DOI: 10.7554/elife.86189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 12/03/2023] [Indexed: 12/05/2023] Open
Abstract
Kinase inhibitors are successful therapeutics in the treatment of cancers and autoimmune diseases and are useful tools in biomedical research. However, the high sequence and structural conservation of the catalytic kinase domain complicate the development of selective kinase inhibitors. Inhibition of off-target kinases makes it difficult to study the mechanism of inhibitors in biological systems. Current efforts focus on the development of inhibitors with improved selectivity. Here, we present an alternative solution to this problem by combining inhibitors with divergent off-target effects. We develop a multicompound-multitarget scoring (MMS) method that combines inhibitors to maximize target inhibition and to minimize off-target inhibition. Additionally, this framework enables optimization of inhibitor combinations for multiple on-targets. Using MMS with published kinase inhibitor datasets we determine potent inhibitor combinations for target kinases with better selectivity than the most selective single inhibitor and validate the predicted effect and selectivity of inhibitor combinations using in vitro and in cellulo techniques. MMS greatly enhances selectivity in rational multitargeting applications. The MMS framework is generalizable to other non-kinase biological targets where compound selectivity is a challenge and diverse compound libraries are available.
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Affiliation(s)
- Ian R Outhwaite
- Department of Pharmacological Sciences, Stony Brook UniversityStony BrookUnited States
| | - Sukrit Singh
- Department of Pharmacological Sciences, Stony Brook UniversityStony BrookUnited States
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University FrankfurtFrankfurt am MainGermany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University FrankfurtFrankfurt am MainGermany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University FrankfurtFrankfurt am MainGermany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University FrankfurtFrankfurt am MainGermany
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook UniversityStony BrookUnited States
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16
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Vasta JD, Michaud A, Zimprich CA, Beck MT, Swiatnicki MR, Zegzouti H, Thomas MR, Wilkinson J, Crapster JA, Robers MB. Protomer selectivity of type II RAF inhibitors within the RAS/RAF complex. Cell Chem Biol 2023; 30:1354-1365.e6. [PMID: 37643616 DOI: 10.1016/j.chembiol.2023.07.019] [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: 02/08/2023] [Revised: 05/12/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023]
Abstract
RAF dimer inhibitors offer therapeutic potential in RAF- and RAS-driven cancers. The utility of such drugs is predicated on their capacity to occupy both RAF protomers in the RAS-RAF signaling complex. Here we describe a method to conditionally quantify drug-target occupancy at selected RAF protomers within an active RAS-RAF complex in cells. RAF target engagement can be measured in the presence or absence of any mutant KRAS allele, enabling the high-affinity state of RAF dimer inhibitors to be quantified in the cellular milieu. The intracellular protomer selectivity of clinical-stage type II RAF inhibitors revealed that ARAF protomer engagement, but not engagement of BRAF or CRAF, is commensurate with inhibition of MAPK signaling in various mutant RAS cell lines. Our results support a fundamental role for ARAF in mutant RAS signaling and reveal poor ARAF protomer vulnerability for a cohort of RAF inhibitors undergoing clinical evaluation.
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17
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Wichroski M, Benci J, Liu SQ, Chupak L, Fang J, Cao C, Wang C, Onorato J, Qiu H, Shan Y, Banas D, Powles R, Locke G, Witt A, Stromko C, Qi H, Zheng X, Martin S, Ding M, Gentles R, Meanwell N, Velaparthi U, Olson R, Wee S, Tenney D, Parker CG, Cravatt BF, Lawrence M, Borzilleri R, Lees E. DGKα/ζ inhibitors combine with PD-1 checkpoint therapy to promote T cell-mediated antitumor immunity. Sci Transl Med 2023; 15:eadh1892. [PMID: 37878674 DOI: 10.1126/scitranslmed.adh1892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023]
Abstract
Programmed cell death protein 1 (PD-1) immune checkpoint blockade therapy has revolutionized cancer treatment. Although PD-1 blockade is effective in a subset of patients with cancer, many fail to respond because of either primary or acquired resistance. Thus, next-generation strategies are needed to expand the depth and breadth of clinical responses. Toward this end, we designed a human primary T cell phenotypic high-throughput screening strategy to identify small molecules with distinct and complementary mechanisms of action to PD-1 checkpoint blockade. Through these efforts, we selected and optimized a chemical series that showed robust potentiation of T cell activation and combinatorial activity with αPD-1 blockade. Target identification was facilitated by chemical proteomic profiling with a lipid-based photoaffinity probe, which displayed enhanced binding to diacylglycerol kinase α (DGKα) in the presence of the active compound, a phenomenon that correlated with the translocation of DGKα to the plasma membrane. We further found that optimized leads within this chemical series were potent and selective inhibitors of both DGKα and DGKζ, lipid kinases that constitute an intracellular T cell checkpoint that blunts T cell signaling through diacylglycerol metabolism. We show that dual DGKα/ζ inhibition amplified suboptimal T cell receptor signaling mediated by low-affinity antigen presentation and low major histocompatibility complex class I expression on tumor cells, both hallmarks of resistance to PD-1 blockade. In addition, DGKα/ζ inhibitors combined with αPD-1 therapy to elicit robust tumor regression in syngeneic mouse tumor models. Together, these findings support targeting DGKα/ζ as a next-generation T cell immune checkpoint strategy.
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Affiliation(s)
- Michael Wichroski
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Joseph Benci
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Si-Qi Liu
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Louis Chupak
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Jie Fang
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Carolyn Cao
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Cindy Wang
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Joelle Onorato
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Hongchen Qiu
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Yongli Shan
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Dana Banas
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Ryan Powles
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Gregory Locke
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Abigail Witt
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Caitlyn Stromko
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Huilin Qi
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Xiaofan Zheng
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Scott Martin
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Min Ding
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Robert Gentles
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Nicholas Meanwell
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Upender Velaparthi
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Richard Olson
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
| | - Susan Wee
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Daniel Tenney
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | | | - Benjamin F Cravatt
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Lawrence
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Robert Borzilleri
- Research and Development, Bristol Myers Squibb Company, Lawrenceville, NJ 08648, USA
| | - Emma Lees
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA 02142, USA
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18
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Koide E, Mohardt ML, Doctor ZM, Yang A, Hao M, Donovan KA, Kuismi CC, Nelson AJ, Abell K, Aguiar M, Che J, Stokes MP, Zhang T, Aguirre AJ, Fischer ES, Gray NS, Jiang B, Nabet B. Development and Characterization of Selective FAK Inhibitors and PROTACs with In Vivo Activity. Chembiochem 2023; 24:e202300141. [PMID: 37088717 PMCID: PMC10590827 DOI: 10.1002/cbic.202300141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
Focal adhesion kinase (FAK) is an attractive drug target due to its overexpression in cancer. FAK functions as a non-receptor tyrosine kinase and scaffolding protein, coordinating several downstream signaling effectors and cellular processes. While drug discovery efforts have largely focused on targeting FAK kinase activity, FAK inhibitors have failed to show efficacy as single agents in clinical trials. Here, using structure-guided design, we report the development of a selective FAK inhibitor (BSJ-04-175) and degrader (BSJ-04-146) to evaluate the consequences and advantages of abolishing all FAK activity in cancer models. BSJ-04-146 achieves rapid and potent FAK degradation with high proteome-wide specificity in cancer cells and induces durable degradation in mice. Compared to kinase inhibition, targeted degradation of FAK exhibits pronounced improved activity on downstream signaling and cancer cell viability and migration. Together, BSJ-04-175 and BSJ-04-146 are valuable chemical tools to dissect the specific consequences of targeting FAK through small-molecule inhibition or degradation.
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Affiliation(s)
- Eriko Koide
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mikaela L. Mohardt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zainab M. Doctor
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Annan Yang
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingfeng Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Andrew J. Aguirre
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford Medicine, Stanford University, Stanford, CA, USA
| | - Baishan Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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19
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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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20
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Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH. How many kinases are druggable? A review of our current understanding. Biochem J 2023; 480:1331-1363. [PMID: 37642371 PMCID: PMC10586788 DOI: 10.1042/bcj20220217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
There are over 500 human kinases ranging from very well-studied to almost completely ignored. Kinases are tractable and implicated in many diseases, making them ideal targets for medicinal chemistry campaigns, but is it possible to discover a drug for each individual kinase? For every human kinase, we gathered data on their citation count, availability of chemical probes, approved and investigational drugs, PDB structures, and biochemical and cellular assays. Analysis of these factors highlights which kinase groups have a wealth of information available, and which groups still have room for progress. The data suggest a disproportionate focus on the more well characterized kinases while much of the kinome remains comparatively understudied. It is noteworthy that tool compounds for understudied kinases have already been developed, and there is still untapped potential for further development in this chemical space. Finally, this review discusses many of the different strategies employed to generate selectivity between kinases. Given the large volume of information available and the progress made over the past 20 years when it comes to drugging kinases, we believe it is possible to develop a tool compound for every human kinase. We hope this review will prove to be both a useful resource as well as inspire the discovery of a tool for every kinase.
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Affiliation(s)
- Brian Anderson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Peter Rosston
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Zachary W. Davis-Gilbert
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
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21
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Pergu R, Shoba VM, Chaudhary SK, Munkanatta Godage DNP, Deb A, Singha S, Dhawa U, Singh P, Anokhina V, Singh S, Siriwardena SU, Choudhary A. Development and Applications of Chimera Platforms for Tyrosine Phosphorylation. ACS CENTRAL SCIENCE 2023; 9:1558-1566. [PMID: 37637727 PMCID: PMC10450875 DOI: 10.1021/acscentsci.3c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Indexed: 08/29/2023]
Abstract
Chimeric small molecules that induce post-translational modification (PTM) on a target protein by bringing it into proximity to a PTM-inducing enzyme are furnishing novel modalities to perturb protein function. Despite recent advances, such molecules are unavailable for a critical PTM, tyrosine phosphorylation. Furthermore, the contemporary design paradigm of chimeric molecules, formed by joining a noninhibitory binder of the PTM-inducing enzyme with the binder of the target protein, prohibits the recruitment of most PTM-inducing enzymes as their noninhibitory binders are unavailable. Here, we report two platforms to generate phosphorylation-inducing chimeric small molecules (PHICS) for tyrosine phosphorylation. We generate PHICS from both noninhibitory binders (scantily available, platform 1) and kinase inhibitors (abundantly available, platform 2) using cysteine-based group transfer chemistry. PHICS triggered phosphorylation on tyrosine residues in diverse sequence contexts and target proteins (e.g., membrane-associated, cytosolic) and displayed multiple bioactivities, including the initiation of a growth receptor signaling cascade and the death of drug-resistant cancer cells. These studies provide an approach to induce biologically relevant PTM and lay the foundation for pharmacologic PTM editing (i.e., induction or removal) of target proteins using abundantly available inhibitors of PTM-inducing or -erasing enzymes.
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Affiliation(s)
- Rajaiah Pergu
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Veronika M. Shoba
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Santosh K. Chaudhary
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | | | - Arghya Deb
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Santanu Singha
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Uttam Dhawa
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Prashant Singh
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Viktoriya Anokhina
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Sameek Singh
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Sachini U. Siriwardena
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Amit Choudhary
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions
of Renal Medicine and Engineering, Brigham
and Women’s Hospital, Boston, Massachusetts 02115, United States
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22
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Meng X, Qi J. Manipulating Tyrosine Phosphorylation by Heterobifunctional Small Molecules. ACS CENTRAL SCIENCE 2023; 9:1512-1514. [PMID: 37637739 PMCID: PMC10451028 DOI: 10.1021/acscentsci.3c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Affiliation(s)
- Xianke Meng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215-5450, United
States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
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23
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Teske KA, Su W, Corona CR, Wen J, Deng J, Ping Y, Zhang Z, Zhang Q, Wilkinson J, Beck MT, Nealey KR, Vasta JD, Cong M, Meisenheimer PL, Kuai L, Robers MB. DELs enable the development of BRET probes for target engagement studies in cells. Cell Chem Biol 2023; 30:987-998.e24. [PMID: 37490918 DOI: 10.1016/j.chembiol.2023.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 07/27/2023]
Abstract
DNA-encoded libraries (DELs) provide unmatched chemical diversity and starting points for novel drug modalities. Here, we describe a workflow that exploits the bifunctional attributes of DEL ligands as a platform to generate BRET probes for live cell target engagement studies. To establish proof of concept, we performed a DEL screen using aurora kinase A and successfully converted aurora DEL ligands as cell-active BRET probes. Aurora BRET probes enabled the validation and stratification of the chemical series identified from primary selection data. Furthermore, we have evaluated the effective repurposing of pre-existing DEL screen data to find suitable leads for BRET probe development. Our findings support the use of DEL workflows as an engine to create cell-active BRET probes independent of structure or compound SAR. The combination of DEL and BRET technology accelerates hit-to-lead studies in a live cell setting.
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Affiliation(s)
- Kelly A Teske
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Wenji Su
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Cesear R Corona
- Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, CA 93401, USA
| | - Jing Wen
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Jason Deng
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Yan Ping
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Zaihong Zhang
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China
| | | | - Michael T Beck
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Kendra R Nealey
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - James D Vasta
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Mei Cong
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | | | - Letian Kuai
- WuXi AppTec Headquarters, 288 Fute Shong Road Waigaopqiao Free Trade Zone, Pudong District, Shanghai 200131, China.
| | - Matthew B Robers
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA.
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24
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Castano A, Silvestre M, Wells CI, Sanderson JL, Ferrer CA, Ong HW, Lang Y, Richardson W, Silvaroli JA, Bashore FM, Smith JL, Genereux IM, Dempster K, Drewry DH, Pabla NS, Bullock AN, Benke TA, Ultanir SK, Axtman AD. Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin-dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology. eLife 2023; 12:e88206. [PMID: 37490324 PMCID: PMC10406435 DOI: 10.7554/elife.88206] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/24/2023] [Indexed: 07/26/2023] Open
Abstract
Pathological loss-of-function mutations in cyclin-dependent kinase-like 5 (CDKL5) cause CDKL5 deficiency disorder (CDD), a rare and severe neurodevelopmental disorder associated with severe and medically refractory early-life epilepsy, motor, cognitive, visual, and autonomic disturbances in the absence of any structural brain pathology. Analysis of genetic variants in CDD has indicated that CDKL5 kinase function is central to disease pathology. CDKL5 encodes a serine-threonine kinase with significant homology to GSK3β, which has also been linked to synaptic function. Further, Cdkl5 knock-out rodents have increased GSK3β activity and often increased long-term potentiation (LTP). Thus, development of a specific CDKL5 inhibitor must be careful to exclude cross-talk with GSK3β activity. We synthesized and characterized specific, high-affinity inhibitors of CDKL5 that do not have detectable activity for GSK3β. These compounds are very soluble in water but blood-brain barrier penetration is low. In rat hippocampal brain slices, acute inhibition of CDKL5 selectively reduces postsynaptic function of AMPA-type glutamate receptors in a dose-dependent manner. Acute inhibition of CDKL5 reduces hippocampal LTP. These studies provide new tools and insights into the role of CDKL5 as a newly appreciated key kinase necessary for synaptic plasticity. Comparisons to rodent knock-out studies suggest that compensatory changes have limited the understanding of the roles of CDKL5 in synaptic physiology, plasticity, and human neuropathology.
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Affiliation(s)
- Anna Castano
- Department of Pharmacology, University of Colorado School of MedicineAuroraUnited States
| | - Margaux Silvestre
- Kinases and Brain Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Jennifer L Sanderson
- Department of Pharmacology, University of Colorado School of MedicineAuroraUnited States
| | - Carla A Ferrer
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Yi Lang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - William Richardson
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Josie A Silvaroli
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State UniversityColumbusUnited States
| | - Frances M Bashore
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Isabelle M Genereux
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
| | - Kelvin Dempster
- Kinases and Brain Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel HillChapel HillUnited States
| | - Navlot S Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State UniversityColumbusUnited States
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
| | - Tim A Benke
- Departments of Pediatrics, Pharmacology, Neurology and Otolaryngology, University of Colorado School of MedicineAuroraUnited States
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel HillChapel HillUnited States
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25
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González L, Díaz L, Pous J, Baginski B, Duran-Corbera A, Scarpa M, Brun-Heath I, Igea A, Martin-Malpartida P, Ruiz L, Pallara C, Esguerra M, Colizzi F, Mayor-Ruiz C, Biondi RM, Soliva R, Macias MJ, Orozco M, Nebreda AR. Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway. Nat Commun 2023; 14:3318. [PMID: 37308482 DOI: 10.1038/s41467-023-39051-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/26/2023] [Indexed: 06/14/2023] Open
Abstract
p38α is a versatile protein kinase that can control numerous processes and plays important roles in the cellular responses to stress. Dysregulation of p38α signaling has been linked to several diseases including inflammation, immune disorders and cancer, suggesting that targeting p38α could be therapeutically beneficial. Over the last two decades, numerous p38α inhibitors have been developed, which showed promising effects in pre-clinical studies but results from clinical trials have been disappointing, fueling the interest in the generation of alternative mechanisms of p38α modulation. Here, we report the in silico identification of compounds that we refer to as non-canonical p38α inhibitors (NC-p38i). By combining biochemical and structural analyses, we show that NC-p38i efficiently inhibit p38α autophosphorylation but weakly affect the activity of the canonical pathway. Our results demonstrate how the structural plasticity of p38α can be leveraged to develop therapeutic opportunities targeting a subset of the functions regulated by this pathway.
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Affiliation(s)
- Lorena González
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Lucía Díaz
- Nostrum Biodiscovery, 08034, Barcelona, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Blazej Baginski
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Anna Duran-Corbera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Margherita Scarpa
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Ana Igea
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Lidia Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | | | | | - Francesco Colizzi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
- Department of Marine Biology and Oceanography, Institute of Marine Sciences ICM-CSIC, 08003, Barcelona, Spain
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | | | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona, 08028, Barcelona, Spain.
| | - Angel R Nebreda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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26
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Rak M, Tesch R, Berger LM, Shevchenko E, Raab M, Tjaden A, Zhubi R, Balourdas DI, Joerger AC, Poso A, Krämer A, Elson L, Lučić A, Kronenberger T, Hanke T, Strebhardt K, Sanhaji M, Knapp S. Shifting the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one inhibitors towards the salt-inducible kinase (SIK) subfamily. Eur J Med Chem 2023; 254:115347. [PMID: 37094449 DOI: 10.1016/j.ejmech.2023.115347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Salt-inducible kinases 1-3 (SIK1-3) are key regulators of the LKB1-AMPK pathway and play an important role in cellular homeostasis. Dysregulation of any of the three isoforms has been associated with tumorigenesis in liver, breast, and ovarian cancers. We have recently developed the dual pan-SIK/group I p21-activated kinase (PAK) chemical probe MRIA9. However, inhibition of p21-activated kinases has been associated with cardiotoxicity in vivo, which complicates the use of MRIA9 as a tool compound. Here, we present a structure-based approach involving the back-pocket and gatekeeper residues, for narrowing the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one-based inhibitors towards SIK kinases, eliminating PAK activity. Optimization was guided by high-resolution crystal structure analysis and computational methods, resulting in a pan-SIK inhibitor, MR22, which no longer exhibited activity on STE group kinases and displayed excellent selectivity in a representative kinase panel. MR22-dependent SIK inhibition led to centrosome dissociation and subsequent cell-cycle arrest in ovarian cancer cells, as observed with MRIA9, conclusively linking these phenotypic effects to SIK inhibition. Taken together, MR22 represents a valuable tool compound for studying SIK kinase function in cells.
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Affiliation(s)
- Marcel Rak
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Roberta Tesch
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen, 72076, Germany; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Monika Raab
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Rezart Zhubi
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen, 72076, Germany; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany; German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Frankfurt am Main, 60438, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Aleksandar Lučić
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen, 72076, Germany; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Klaus Strebhardt
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Mourad Sanhaji
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany; German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Frankfurt am Main, 60438, Germany.
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27
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Xu Y, Zheng M, Gong L, Liu G, Qian S, Han Y, Kang J. Comprehensive Profiling of Rapamycin Interacting Proteins with Multiple Mass Spectrometry-Based Omics Techniques. Anal Chem 2023. [PMID: 37216191 DOI: 10.1021/acs.analchem.3c00867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Profiling drug-protein interactions is critical for understanding a drug's mechanism of action and predicting the possible adverse side effects. However, to comprehensively profile drug-protein interactions remains a challenge. To address this issue, we proposed a strategy that integrates multiple mass spectrometry-based omics analysis to provided global drug-protein interactions, including physical interactions and functional interactions, with rapamycin (Rap) as a model. Chemoproteomics profiling reveals 47 Rap binding proteins including the known target protein FKBP12 with high confidence. Gen Ontology enrichment analysis suggested that the Rap binding proteins are implicated in several important cellular processes, such as DNA replication, immunity, autophagy, programmed cell death, aging, transcription modulation, vesicle-mediated transport, membrane organization, and carbohydrate and nucleobase metabolic processes. The phosphoproteomics profiling revealed 255 down-regulated and 150 up-regulated phosphoproteins responding to Rap stimulation; they mainly involve the PI3K-Akt-mTORC1 signaling axis. Untargeted metabolomic profiling revealed 22 down-regulated metabolites and 75 up-regulated metabolites responding to Rap stimulation; they are mainly associated with the synthesis processes of pyrimidine and purine. The integrative multiomics data analysis provides deep insight into the drug-protein interactions and reveals Rap's complicated mechanism of action.
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Affiliation(s)
- Yao Xu
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Mengmeng Zheng
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Li Gong
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Guizhen Liu
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| | - Shanshan Qian
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Ying Han
- School of Life Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
| | - Jingwu Kang
- State Key Laboratory of Chemical Biology, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai 200120, China
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28
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Cunha MR, Catta-Preta CMC, Takarada JE, Moreira GA, Massirer KB, Couñago RM. A novel BRET-based assay to investigate binding and residence times of unmodified ligands to the human lysosomal ion channel TRPML1 in intact cells. J Biol Chem 2023:104807. [PMID: 37172730 DOI: 10.1016/j.jbc.2023.104807] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/17/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Here we report a Bioluminescence Resonance Energy Transfer (BRET) assay as a novel way to investigate the binding of unlabeled ligands to the human Transient Receptor Potential Mucolipin 1 (hTRPML1), a lysosomal ion channel involved in several genetic diseases and cancer progression. This novel BRET assay can be used to determine equilibrium and kinetic binding parameters of unlabeled compounds to hTRPML1 using intact human-derived cells, thus complementing the information obtained using functional assays based on ion channel activation. We expect this new BRET assay to expedite the identification and optimization of cell-permeable ligands that interact with hTRPML1 within the physiologically-relevant environment of lysosomes.
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Affiliation(s)
- Micael R Cunha
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil.
| | - Carolina M C Catta-Preta
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Current address: Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jéssica E Takarada
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Gabriela A Moreira
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil
| | - Katlin B Massirer
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil.
| | - Rafael M Couñago
- Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil; Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States.
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29
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Gao Y, Jiang B, Kim H, Berberich MJ, Che J, Donovan KA, Hatcher JM, Huerta F, Kwiatkowski NP, Liu Y, Liuni PP, Metivier RJ, Murali VK, Nowak RP, Zhang T, Fischer ES, Gray NS, Jones LH. Catalytic Degraders Effectively Address Kinase Site Mutations in EML4-ALK Oncogenic Fusions. J Med Chem 2023; 66:5524-5535. [PMID: 37036171 DOI: 10.1021/acs.jmedchem.2c01864] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Heterobifunctional degraders, known as proteolysis targeting chimeras (PROTACs), theoretically possess a catalytic mode-of-action, yet few studies have either confirmed or exploited this potential advantage of event-driven pharmacology. Degraders of oncogenic EML4-ALK fusions were developed by conjugating ALK inhibitors to cereblon ligands. Simultaneous optimization of pharmacology and compound properties using ternary complex modeling and physicochemical considerations yielded multiple catalytic degraders that were more resilient to clinically relevant ATP-binding site mutations than kinase inhibitor drugs. Our strategy culminated in the design of the orally bioavailable derivative CPD-1224 that avoided hemolysis (a feature of detergent-like PROTACs), degraded the otherwise recalcitrant mutant L1196M/G1202R in vivo, and commensurately slowed tumor growth, while the third generation ALK inhibitor drug lorlatinib had no effect. These results validate our original therapeutic hypothesis by exemplifying opportunities for catalytic degraders to proactively address binding site resistant mutations in cancer.
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Affiliation(s)
- Yang Gao
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Baishan Jiang
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Hellen Kim
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Matthew J Berberich
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jianwei Che
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Katherine A Donovan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - John M Hatcher
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Fidel Huerta
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Nicholas P Kwiatkowski
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Yingpeng Liu
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Peter P Liuni
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Rebecca J Metivier
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Vineeth K Murali
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Radosław P Nowak
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Eric S Fischer
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
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30
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Castano A, Silvestre M, Wells CI, Sanderson JL, Ferrer CA, Ong HW, Liang Y, Richardson W, Silvaroli JA, Bashore FM, Smith JL, Genereux IM, Dempster K, Drewry DH, Pabla NS, Bullock AN, Benke TA, Ultanir SK, Axtman AD. Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538049. [PMID: 37162893 PMCID: PMC10168277 DOI: 10.1101/2023.04.24.538049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Pathological loss-of-function mutations in cyclin-dependent kinase-like 5 ( CDKL5 ) cause CDKL5 deficiency disorder (CDD), a rare and severe neurodevelopmental disorder associated with severe and medically refractory early-life epilepsy, motor, cognitive, visual and autonomic disturbances in the absence of any structural brain pathology. Analysis of genetic variants in CDD have indicated that CDKL5 kinase function is central to disease pathology. CDKL5 encodes a serine-threonine kinase with significant homology to GSK3β, which has also been linked to synaptic function. Further, Cdkl5 knock-out rodents have increased GSK3β activity and often increased long-term potentiation (LTP). Thus, development of a specific CDKL5 inhibitor must be careful to exclude cross-talk with GSK3β activity. We synthesized and characterized specific, high-affinity inhibitors of CDKL5 that do not have detectable activity for GSK3β. These compounds are very soluble in water but blood-brain barrier penetration is low. In rat hippocampal brain slices, acute inhibition of CDKL5 selectively reduces post-synaptic function of AMPA-type glutamate receptors in a dose-dependent manner. Acute inhibition of CDKL5 reduces hippocampal LTP. These studies provide new tools and insights into the role of CDKL5 as a newly appreciated, key kinase necessary for synaptic plasticity. Comparisons to rodent knock-out studies suggest that compensatory changes have limited the understanding of the roles of CDKL5 in synaptic physiology, plasticity and human neuropathology.
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31
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Ong HW, Liang Y, Richardson W, Lowry ER, Wells CI, Chen X, Silvestre M, Dempster K, Silvaroli JA, Smith JL, Wichterle H, Pabla NS, Ultanir SK, Bullock AN, Drewry DH, Axtman AD. Discovery of a Potent and Selective CDKL5/GSK3 Chemical Probe That Is Neuroprotective. ACS Chem Neurosci 2023; 14:1672-1685. [PMID: 37084253 PMCID: PMC10161233 DOI: 10.1021/acschemneuro.3c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Despite mediating several essential processes in the brain, including during development, cyclin-dependent kinase-like 5 (CDKL5) remains a poorly characterized human protein kinase. Accordingly, its substrates, functions, and regulatory mechanisms have not been fully described. We realized that availability of a potent and selective small molecule probe targeting CDKL5 could enable illumination of its roles in normal development as well as in diseases where it has become aberrant due to mutation. We prepared analogs of AT-7519, a compound that has advanced to phase II clinical trials and is a known inhibitor of several cyclin-dependent kinases (CDKs) and cyclin-dependent kinase-like kinases (CDKLs). We identified analog 2 as a highly potent and cell-active chemical probe for CDKL5/GSK3 (glycogen synthase kinase 3). Evaluation of its kinome-wide selectivity confirmed that analog 2 demonstrates excellent selectivity and only retains GSK3α/β affinity. We next demonstrated the inhibition of downstream CDKL5 and GSK3α/β signaling and solved a co-crystal structure of analog 2 bound to human CDKL5. A structurally similar analog (4) proved to lack CDKL5 affinity and maintain potent and selective inhibition of GSK3α/β, making it a suitable negative control. Finally, we used our chemical probe pair (2 and 4) to demonstrate that inhibition of CDKL5 and/or GSK3α/β promotes the survival of human motor neurons exposed to endoplasmic reticulum stress. We have demonstrated a neuroprotective phenotype elicited by our chemical probe pair and exemplified the utility of our compounds to characterize the role of CDKL5/GSK3 in neurons and beyond.
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Affiliation(s)
- Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yi Liang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William Richardson
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Emily R Lowry
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- The Project ALS Therapeutics Core, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiangrong Chen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Margaux Silvestre
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Kelvin Dempster
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Josie A Silvaroli
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hynek Wichterle
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- The Project ALS Therapeutics Core, Columbia University Irving Medical Center, New York, New York 10032, United States
- Departments of Neurology, Neuroscience, Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, New York 10032, United States
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Navjot S Pabla
- Division of Pharmaceutics and Pharmacology, College of Pharmacy and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Bashore FM, Marquez AB, Chaikuad A, Howell S, Dunn AS, Beltran AA, Smith JL, Drewry DH, Beltran AS, Axtman AD. Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis. Sci Rep 2023; 13:6118. [PMID: 37059819 PMCID: PMC10104807 DOI: 10.1038/s41598-023-32854-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/03/2023] [Indexed: 04/16/2023] Open
Abstract
Tau tubulin kinase 1 and 2 (TTBK1/2) are highly homologous kinases that are expressed and mediate disease-relevant pathways predominantly in the brain. Distinct roles for TTBK1 and TTBK2 have been delineated. While efforts have been devoted to characterizing the impact of TTBK1 inhibition in diseases like Alzheimer's disease and amyotrophic lateral sclerosis, TTBK2 inhibition has been less explored. TTBK2 serves a critical function during cilia assembly. Given the biological importance of these kinases, we designed a targeted library from which we identified several chemical tools that engage TTBK1 and TTBK2 in cells and inhibit their downstream signaling. Indolyl pyrimidinamine 10 significantly reduced the expression of primary cilia on the surface of human induced pluripotent stem cells (iPSCs). Furthermore, analog 10 phenocopies TTBK2 knockout in iPSCs, confirming a role for TTBK2 in ciliogenesis.
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Affiliation(s)
- Frances M Bashore
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ariana B Marquez
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strabe 15, 60438, Frankfurt, Germany
| | - Stefanie Howell
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrea S Dunn
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alvaro A Beltran
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Adriana S Beltran
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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33
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Yang X, Smith JL, Beck MT, Wilkinson JM, Michaud A, Vasta JD, Robers MB, Willson TM. Development of Cell Permeable NanoBRET Probes for the Measurement of PLK1 Target Engagement in Live Cells. Molecules 2023; 28:molecules28072950. [PMID: 37049713 PMCID: PMC10095950 DOI: 10.3390/molecules28072950] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
PLK1 is a protein kinase that regulates mitosis and is both an important oncology drug target and a potential antitarget of drugs for the DNA damage response pathway or anti-infective host kinases. To expand the range of live cell NanoBRET target engagement assays to include PLK1, we developed an energy transfer probe based on the anilino-tetrahydropteridine chemotype found in several selective PLK inhibitors. Probe 11 was used to configure NanoBRET target engagement assays for PLK1, PLK2, and PLK3 and measure the potency of several known PLK inhibitors. In-cell target engagement for PLK1 was in good agreement with the reported cellular potency for the inhibition of cell proliferation. Probe 11 enabled the investigation of the promiscuity of adavosertib, which had been described as a dual PLK1/WEE1 inhibitor in biochemical assays. Live cell target engagement analysis of adavosertib via NanoBRET demonstrated PLK activity at micromolar concentrations but only selective engagement of WEE1 at clinically relevant doses.
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Affiliation(s)
- Xuan Yang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffery L. Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael T. Beck
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53719, USA (M.B.R.)
| | | | - Ani Michaud
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53719, USA (M.B.R.)
| | - James D. Vasta
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53719, USA (M.B.R.)
| | - Matthew B. Robers
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53719, USA (M.B.R.)
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence:
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34
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Tredup C, Ndreshkjana B, Schneider NS, Tjaden A, Kemas AM, Youhanna S, Lauschke VM, Berger BT, Krämer A, Berger LM, Röhm S, Knapp S, Farin HF, Müller S. Deep Annotation of Donated Chemical Probes (DCP) in Organotypic Human Liver Cultures and Patient-Derived Organoids from Tumor and Normal Colorectum. ACS Chem Biol 2023; 18:822-836. [PMID: 36944371 PMCID: PMC10127199 DOI: 10.1021/acschembio.2c00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Well-characterized small molecules are essential tools for studying the biology and therapeutic relevance of a target protein. However, many compounds reported in the literature and routinely studied in biomedical research lack the potency and selectivity required for mechanistic cellular studies on the function of a given protein. Furthermore, commercially available compounds often do not include useful tools developed by industry as part of their research and development efforts, as they frequently remain proprietary. The freely available donated chemical probe (DCP) library, fueled by generous donations of compounds from industry and academia, enables easy access to a steadily growing collection of these valuable and well-characterized tools. Here, we provide a systematic description of the current DCP library collection and their associated comprehensive characterization data, including a variety of in vitro and cellular assays. Of note, we characterized the set in relevant human primary models by employing hepatotoxicity screening in primary human liver spheroids and viability screening in patient-derived colorectal cancer organoids and matched normal-adjacent epithelium. Taken together, the DCP library represents a well-annotated, openly available collection of tool compounds for studying a wide range of targets, including kinases, G-protein-coupled receptors, and ion channels. As such, it represents a unique resource for the biomedical research community.
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Affiliation(s)
- Claudia Tredup
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Benardina Ndreshkjana
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596Frankfurt am Main, Germany
| | - Natalie S Schneider
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Aurino M Kemas
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65Stockholm, Sweden
| | - Sonia Youhanna
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65Stockholm, Sweden
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376Stuttgart, Germany
- University of Tübingen, 72074Tübingen, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main60596, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Sandra Röhm
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main60596, Germany
| | - Henner F Farin
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main60596, Germany
- German Cancer Consortium (DKTK), Heidelberg69120, Germany
- German Cancer Research Center (DKFZ), 69120Heidelberg, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438Frankfurt am Main, Germany
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Lu W, Liu Y, Gao Y, Geng Q, Gurbani D, Li L, Ficarro SB, Meyer CJ, Sinha D, You I, Tse J, He Z, Ji W, Che J, Kim AY, Yu T, Wen K, Anderson KC, Marto JA, Westover KD, Zhang T, Gray NS. Development of a Covalent Inhibitor of c-Jun N-Terminal Protein Kinase (JNK) 2/3 with Selectivity over JNK1. J Med Chem 2023; 66:3356-3371. [PMID: 36826833 DOI: 10.1021/acs.jmedchem.2c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family, which includes JNK1-JNK3. Interestingly, JNK1 and JNK2 show opposing functions, with JNK2 activity favoring cell survival and JNK1 stimulating apoptosis. Isoform-selective small molecule inhibitors of JNK1 or JNK2 would be useful as pharmacological probes but have been difficult to develop due to the similarity of their ATP binding pockets. Here, we describe the discovery of a covalent inhibitor YL5084, the first such inhibitor that displays selectivity for JNK2 over JNK1. We demonstrated that YL5084 forms a covalent bond with Cys116 of JNK2, exhibits a 20-fold higher Kinact/KI compared to that of JNK1, and engages JNK2 in cells. However, YL5084 exhibited JNK2-independent antiproliferative effects in multiple myeloma cells, suggesting the existence of additional targets relevant in this context. Thus, although not fully optimized, YL5084 represents a useful chemical starting point for the future development of JNK2-selective chemical probes.
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Affiliation(s)
- Wenchao Lu
- Department of Chemical and Systems Biology, Chem-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
- Lingang Laboratory, Shanghai 200031, China
| | - Yao Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yang Gao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Qixiang Geng
- Department of Chemical and Systems Biology, Chem-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Deepak Gurbani
- Department of Radiation Oncology, Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Lianbo Li
- Department of Radiation Oncology, Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Scott B Ficarro
- Department of Cancer Biology, Blais Proteomics Center, Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Cynthia J Meyer
- Department of Radiation Oncology, Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Dhiraj Sinha
- Department of Radiation Oncology, Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Jason Tse
- Department of Chemical and Systems Biology, Chem-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Zhixiang He
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Wenzhi Ji
- Department of Chemical and Systems Biology, Chem-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Audrey Y Kim
- Department of Chemical and Systems Biology, Chem-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Tengteng Yu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Kenneth Wen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jarrod A Marto
- Department of Cancer Biology, Blais Proteomics Center, Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Kenneth D Westover
- Department of Radiation Oncology, Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, Chem-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
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Yang X, Smith JL, Beck MT, Wilkinson JM, Michaud A, Vasta JD, Robers MB, Willson TM. Development of Cell Permeable NanoBRET Probes for the Measurement of PLK1 Target Engagement in Live Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.529946. [PMID: 36865333 PMCID: PMC9980182 DOI: 10.1101/2023.02.25.529946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
PLK1 is a protein kinase that regulates mitosis and is both an important oncology drug target and a potential anti target of drugs for the DNA damage response pathway or anti-infective host kinases. To expand the range of live cell NanoBRET target engagement assays to include PLK1 we developed an energy transfer probe based on the anilino-tetrahydropteridine chemotype found in several selective PLK inhibitors. Probe 11 was used to configure NanoBRET target engagement assays for PLK1, PLK2, and PLK3 and measure the potency of several known PLK inhibitors. In cell target engagement for PLK1 was in good agreement with the reported cellular potency for inhibition of cell proliferation. Probe 11 enabled investigation of the promiscuity of adavosertib, which had been described as a dual PLK1/WEE1 inhibitor in biochemical assays. Live cell target engagement analysis of adavosertib by NanoBRET demonstrated PLK activity at micromolar concentrations but only selective engagement of WEE1 at clinically relevant doses.
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Affiliation(s)
- Xuan Yang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeffery L. Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael T. Beck
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | | | - Ani Michaud
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - James D. Vasta
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Matthew B. Robers
- Promega Corporation, 2800 Woods Hollow Road, Fitchburg, WI 53711, USA
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence:
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37
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Targeting Human Proteins for Antiviral Drug Discovery and Repurposing Efforts: A Focus on Protein Kinases. Viruses 2023; 15:v15020568. [PMID: 36851782 PMCID: PMC9966946 DOI: 10.3390/v15020568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Despite the great technological and medical advances in fighting viral diseases, new therapies for most of them are still lacking, and existing antivirals suffer from major limitations regarding drug resistance and a limited spectrum of activity. In fact, most approved antivirals are directly acting antiviral (DAA) drugs, which interfere with viral proteins and confer great selectivity towards their viral targets but suffer from resistance and limited spectrum. Nowadays, host-targeted antivirals (HTAs) are on the rise, in the drug discovery and development pipelines, in academia and in the pharmaceutical industry. These drugs target host proteins involved in the virus life cycle and are considered promising alternatives to DAAs due to their broader spectrum and lower potential for resistance. Herein, we discuss an important class of HTAs that modulate signal transduction pathways by targeting host kinases. Kinases are considered key enzymes that control virus-host interactions. We also provide a synopsis of the antiviral drug discovery and development pipeline detailing antiviral kinase targets, drug types, therapeutic classes for repurposed drugs, and top developing organizations. Furthermore, we detail the drug design and repurposing considerations, as well as the limitations and challenges, for kinase-targeted antivirals, including the choice of the binding sites, physicochemical properties, and drug combinations.
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38
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Small-molecule inhibition of the archetypal UbiB protein COQ8. Nat Chem Biol 2023; 19:230-238. [PMID: 36302899 PMCID: PMC9898131 DOI: 10.1038/s41589-022-01168-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/08/2022] [Indexed: 02/06/2023]
Abstract
Small-molecule tools have enabled mechanistic investigations and therapeutic targeting of the protein kinase-like (PKL) superfamily. However, such tools are still lacking for many PKL members, including the highly conserved and disease-related UbiB family. Here, we sought to develop and characterize an inhibitor for the archetypal UbiB member COQ8, whose function is essential for coenzyme Q (CoQ) biosynthesis. Guided by crystallography, activity assays and cellular CoQ measurements, we repurposed the 4-anilinoquinoline scaffold to selectively inhibit human COQ8A in cells. Our chemical tool promises to lend mechanistic insights into the activities of these widespread and understudied proteins and to offer potential therapeutic strategies for human diseases connected to their dysfunction.
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39
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Outhwaite IR, Singh S, Berger BT, Knapp S, Chodera JD, Seeliger MA. Death by a Thousand Cuts â€" Combining Kinase Inhibitors for Selective Target Inhibition and Rational Polypharmacology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523972. [PMID: 36711619 PMCID: PMC9882273 DOI: 10.1101/2023.01.13.523972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Kinase inhibitors are successful therapeutics in the treatment of cancers and autoimmune diseases and are useful tools in biomedical research. The high sequence and structural conservation of the catalytic kinase domain complicates the development of specific kinase inhibitors. As a consequence, most kinase inhibitors also inhibit off-target kinases which complicates the interpretation of phenotypic responses. Additionally, inhibition of off-targets may cause toxicity in patients. Therefore, highly selective kinase inhibition is a major goal in both biomedical research and clinical practice. Currently, efforts to improve selective kinase inhibition are dominated by the development of new kinase inhibitors. Here, we present an alternative solution to this problem by combining inhibitors with divergent off-target activities. We have developed a multicompound-multitarget scoring (MMS) method framework that combines inhibitors to maximize target inhibition and to minimize off-target inhibition. Additionally, this framework enables rational polypharmacology by allowing optimization of inhibitor combinations against multiple selected on-targets and off-targets. Using MMS with previously published chemogenomic kinase inhibitor datasets we determine inhibitor combinations that achieve potent activity against a target kinase and that are more selective than the most selective single inhibitor against that target. We validate the calculated effect and selectivity of a combination of inhibitors using the in cellulo NanoBRET assay. The MMS framework is generalizable to other pharmacological targets where compound specificity is a challenge and diverse compound libraries are available.
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40
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Schröder M, Leiendecker M, Grädler U, Braun J, Blum A, Wanior M, Berger BT, Krämer A, Müller S, Esdar C, Knapp S, Heinrich T. MSC-1186, a Highly Selective Pan-SRPK Inhibitor Based on an Exceptionally Decorated Benzimidazole-Pyrimidine Core. J Med Chem 2023; 66:837-854. [PMID: 36516476 DOI: 10.1021/acs.jmedchem.2c01705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The highly conserved catalytic sites in protein kinases make it difficult to identify ATP competitive inhibitors with kinome-wide selectivity. Serendipitously, during a dedicated fragment campaign for the focal adhesion kinase (FAK), a scaffold that had lost its initial FAK affinity showed remarkable potency and selectivity for serine-arginine-protein kinases 1-3 (SRPK1-3). Non-conserved interactions with the uniquely structured hinge region of the SRPK family were the key drivers of the exclusive selectivity of the discovered fragment hit. Structure-guided medicinal chemistry efforts led to the SRPK inhibitor MSC-1186, which fulfills all hallmarks of a reversible chemical probe, including nanomolar cellular potency and excellent kinome-wide selectivity. The combination of MSC-1186 with CDC2-like kinase (CLK) inhibitors showed additive attenuation of SR-protein phosphorylation compared to the single agents. MSC-1186 and negative control (MSC-5360) are chemical probes available via the Structural Genomics Consortium chemical probe program (https://www.sgc-ffm.uni-frankfurt.de/).
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Affiliation(s)
- Martin Schröder
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | | | - Ulrich Grädler
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Juliane Braun
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Andreas Blum
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Marek Wanior
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Christina Esdar
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Stefan Knapp
- SGC Frankfurt, Goethe University Frankfurt, Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Timo Heinrich
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
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Wells C, Liang Y, Pulliam TL, Lin C, Awad D, Eduful B, O’Byrne S, Hossain MA, Catta-Preta CMC, Ramos PZ, Gileadi O, Gileadi C, Couñago RM, Stork B, Langendorf CG, Nay K, Oakhill JS, Mukherjee D, Racioppi L, Means AR, York B, McDonnell DP, Scott JW, Frigo DE, Drewry DH. SGC-CAMKK2-1: A Chemical Probe for CAMKK2. Cells 2023; 12:287. [PMID: 36672221 PMCID: PMC9856672 DOI: 10.3390/cells12020287] [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: 11/04/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
The serine/threonine protein kinase calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) plays critical roles in a range of biological processes. Despite its importance, only a handful of inhibitors of CAMKK2 have been disclosed. Having a selective small molecule tool to interrogate this kinase will help demonstrate that CAMKK2 inhibition can be therapeutically beneficial. Herein, we disclose SGC-CAMKK2-1, a selective chemical probe that targets CAMKK2.
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Affiliation(s)
- Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yi Liang
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas L. Pulliam
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chenchu Lin
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dominik Awad
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Benjamin Eduful
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sean O’Byrne
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolina Moura Costa Catta-Preta
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Opher Gileadi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Carina Gileadi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Brittany Stork
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Kevin Nay
- St Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia
| | | | - Debarati Mukherjee
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - Luigi Racioppi
- Department of Medicine, Division of Hematological Malignancies and Cellular Therapy, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Anthony R. Means
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donald P. McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - John W. Scott
- St Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC 3052, Australia
| | - Daniel E. Frigo
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX 77204, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC 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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42
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Baljinnyam B, Ronzetti M, Simeonov A. Advances in luminescence-based technologies for drug discovery. Expert Opin Drug Discov 2023; 18:25-35. [PMID: 36562206 PMCID: PMC9892298 DOI: 10.1080/17460441.2023.2160441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Luminescence-based technologies, specifically bioluminescence and chemiluminescence, are powerful tools with extensive use in drug discovery. Production of light during chemiluminescence and bioluminescence, unlike fluorescence, doesn't require an excitation light source, resulting in high signal-to-noise ratio, less background interference, and no issues from phototoxicity and photobleaching. These characteristics of luminescence technologies offer unique advantages for experimental designs, allowing for greater flexibility to target a wide range of proteins and biological processes for drug discovery at different stages. AREAS COVERED This review provides a basic overview of luciferase-based technologies and details recent advances and use cases of luciferase and luciferin variations and their applicability in the drug discovery toolset. The authors expand upon specific applications of luciferase technologies, including chemiluminescent and bioluminescent-based microscopy. Finally, the authors lay out forward-looking statements on the field of luminescence and how it may shape the translational scientists' work moving forward. EXPERT OPINION The demand for improved luciferase and luciferin pairs correlates strongly with efforts to improve the sensitivity and robustness of high-throughput assays. As luminescent reporter systems improve, so will the expansion of use cases for luminescence-based technologies in early-stage drug discovery. With the synthesis of novel, non-enzymatic chemiluminescence-based probes, which previously were restrained to only basic research applications, they may now be readily implemented in drug discovery campaigns.
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Affiliation(s)
- Bolormaa Baljinnyam
- Staff Scientist, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Michael Ronzetti
- Predoctoral IRTA Fellow, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Anton Simeonov
- Group Leader, Scientific Director, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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43
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Nieman AN, Dunn Hoffman KK, Dominguez ER, Wilkinson J, Vasta JD, Robers MB, Lam N. NanoBRET™ Live-Cell Kinase Selectivity Profiling Adapted for High-Throughput Screening. Methods Mol Biol 2023; 2706:97-124. [PMID: 37558944 DOI: 10.1007/978-1-0716-3397-7_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Kinases represent one of the most therapeutically tractable targets for drug discovery in the twenty-first century. However, confirming engagement and achieving intracellular kinase selectivity for small-molecule kinase inhibitors can represent noteworthy challenges. The NanoBRETTM platform enables broad-spectrum live-cell kinase selectivity profiling in most laboratory settings, without advanced instrumentation or expertise. However, the prototype workflow for this selectivity profiling is currently limited to manual liquid handling and 96-well plates. Herein, we describe a scalable workflow with automation and acoustic dispensing, thus dramatically improving the throughput. Such adaptations enable profiling of larger compound sets against 192 full-length protein kinases in live cells, with statistical robustness supporting quantitative analysis.
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Affiliation(s)
| | | | | | | | | | | | - Ngan Lam
- Promega Corporation, Madison, WI, USA.
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44
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Wells CI, Drewry DH. Developing a Kinase Chemogenomic Set: Facilitating Investigation into Kinase Biology by Linking Phenotypes to Targets. Methods Mol Biol 2023; 2706:11-24. [PMID: 37558938 DOI: 10.1007/978-1-0716-3397-7_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Advances in increasingly complex phenotypic screening with lower throughput have necessitated the screening of smaller more highly annotated sets. One such collection of compounds which has been recently assembled is the kinase chemogenomic set. This is a set of curated kinase inhibitors built upon previous iterations, PKIS and PKIS2, and donations from our partners. Each compound in the set has been carefully selected based on selectivity, potency, and kinome coverage. These compounds as a set have been made available to the scientific community, enabling phenotypic screens to identify kinases that drive novel biology. Additionally, the associated data deposited in the public domain have also been used to inform new inhibitor design. Further expansion of this set to complete kinome coverage will allow for a greater understanding of kinase biology and its role in disease.
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Affiliation(s)
- Carrow I Wells
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC, USA.
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC, USA.
| | - David H Drewry
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC, USA
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC, USA
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45
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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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46
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Amrhein JA, Berger LM, Tjaden A, Krämer A, Elson L, Tolvanen T, Martinez-Molina D, Kaiser A, Schubert-Zsilavecz M, Müller S, Knapp S, Hanke T. Discovery of 3-Amino-1 H-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family. Int J Mol Sci 2022; 23:ijms232314834. [PMID: 36499165 PMCID: PMC9736855 DOI: 10.3390/ijms232314834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
The PCTAIRE subfamily belongs to the CDK (cyclin-dependent kinase) family and represents an understudied class of kinases of the dark kinome. They exhibit a highly conserved binding pocket and are activated by cyclin Y binding. CDK16 is targeted to the plasma membrane after binding to N-myristoylated cyclin Y and is highly expressed in post-mitotic tissues, such as the brain and testis. Dysregulation is associated with several diseases, including breast, prostate, and cervical cancer. Here, we used the N-(1H-pyrazol-3-yl)pyrimidin-4-amine moiety from the promiscuous inhibitor 1 to target CDK16, by varying different residues. Further optimization steps led to 43d, which exhibited high cellular potency for CDK16 (EC50 = 33 nM) and the other members of the PCTAIRE and PFTAIRE family with 20-120 nM and 50-180 nM, respectively. A DSF screen against a representative panel of approximately 100 kinases exhibited a selective inhibition over the other kinases. In a viability assessment, 43d decreased the cell count in a dose-dependent manner. A FUCCI cell cycle assay revealed a G2/M phase cell cycle arrest at all tested concentrations for 43d, caused by inhibition of CDK16.
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Affiliation(s)
- Jennifer Alisa Amrhein
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lena Marie Berger
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Tuomas Tolvanen
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institute, Solnavägen 1, 17177 Solna, Sweden
| | | | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Manfred Schubert-Zsilavecz
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
- Correspondence: (S.K.); (T.H.)
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- Correspondence: (S.K.); (T.H.)
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47
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Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Reply to Correspondence on "Synergy and Antagonism between Allosteric and Active-Site Inhibitors of Abl Tyrosine Kinase". Angew Chem Int Ed Engl 2022; 61:e202209518. [PMID: 36283971 DOI: 10.1002/anie.202209518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Indexed: 10/22/2023]
Abstract
Manley and co-workers provide data demonstrating that, at super-pharmacological concentrations (300 μM), a ternary complex between Abl, asciminib, and ATP-competitive inhibitors is possible. The work in our manuscript concerns the interplay of asciminib (and GNF-2) with ATP-competitive inhibitors at pharmacologically relevant concentrations (Cmax =1.6-3.7 μM for asciminib). Manley and co-workers do not question any of the studies that we reported, nor do they provide explanations for how our work fits into their preferred model. Herein, we consider the data presented by Manley and co-workers. In addition, we provide new data supporting the findings in our Communication. Asciminib and ATP-competitive inhibitors do not simultaneously bind Abl at pharmacologically relevant concentrations unless the conformation selectivity for both ligands is matched.
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Affiliation(s)
- Taylor K Johnson
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Daniel A Bochar
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Nathalie M Vandecan
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Jessica Furtado
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Michael P Agius
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Sameer Phadke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA
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48
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Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Reply to Correspondence on “Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase”. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Taylor K. Johnson
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Daniel A. Bochar
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Nathalie M. Vandecan
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Jessica Furtado
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Michael P. Agius
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Sameer Phadke
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Matthew B. Soellner
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
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49
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Poller B, Werner S, Domange N, Mettler L, Stein RR, Loretan J, Wartmann M, Faller B, Huth F. Time Matters - In vitro Cellular Disposition Kinetics Help Rationalizing Cellular Potency Disconnects. Xenobiotica 2022; 52:878-889. [PMID: 36189672 DOI: 10.1080/00498254.2022.2130837] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
Loss in potency is commonly observed in early drug discovery when moving from biochemical to more complex cellular systems. Among other factors, low permeability is often considered to cause such potency disconnects.We developed a novel cellular disposition assay in MDCK cells to determine passive uptake clearance (PSinf), cell-to-medium ratios at steady-state (Kp) and the time to reach 90% steady-state (TTSS90) from a single experiment in a high-throughput format.The assay was validated using 40 marketed drugs, showing a wide distribution of PSinf and Kp values. The parameters generally correlated with transcellular permeability and lipophilicity, while PSinf data revealed better resolution in the high and low permeability ranges compared to traditional permeability data. A linear relationship between the Kp/PSinf ratio and TTSS90 was mathematically derived and experimentally validated, demonstrating the dependency of TTSS90 on the rate and extent of cellular accumulation.Cellular disposition parameters could explain potency (IC50) disconnects noted for seven Bruton's tyrosine kinase degrader compounds in a cellular potency assay. In contrast to transcellular permeability, PSinf data enabled identification of the compounds with IC50 disconnects based on their time to reach equilibrium. Overall, the novel assay offers the possibility to address potency disconnects in early drug discovery.
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Affiliation(s)
- Birk Poller
- Pharmacokinetic Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sophie Werner
- Pharmacokinetic Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Norbert Domange
- Pharmacokinetic Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Lina Mettler
- Pharmacokinetic Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Richard R Stein
- Pharmacokinetic Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jacqueline Loretan
- Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Markus Wartmann
- Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Bernard Faller
- Pharmacokinetic Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Felix Huth
- Pharmacokinetic Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
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50
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Al-Amin RA, Johansson L, Abdurakhmanov E, Landegren N, Löf L, Arngården L, Blokzijl A, Svensson R, Hammond M, Lönn P, Haybaeck J, Kamali-Moghaddam M, Jensen A, Danielson U, Artursson P, Lundbäck T, Landegren U. Monitoring drug-target interactions through target engagement-mediated amplification on arrays and in situ. Nucleic Acids Res 2022; 50:e129. [PMID: 36189884 PMCID: PMC9825164 DOI: 10.1093/nar/gkac842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 01/29/2023] Open
Abstract
Drugs are designed to bind their target proteins in physiologically relevant tissues and organs to modulate biological functions and elicit desirable clinical outcomes. Information about target engagement at cellular and subcellular resolution is therefore critical for guiding compound optimization in drug discovery, and for probing resistance mechanisms to targeted therapies in clinical samples. We describe a target engagement-mediated amplification (TEMA) technology, where oligonucleotide-conjugated drugs are used to visualize and measure target engagement in situ, amplified via rolling-circle replication of circularized oligonucleotide probes. We illustrate the TEMA technique using dasatinib and gefitinib, two kinase inhibitors with distinct selectivity profiles. In vitro binding by the dasatinib probe to arrays of displayed proteins accurately reproduced known selectivity profiles, while their differential binding to fixed adherent cells agreed with expectations from expression profiles of the cells. We also introduce a proximity ligation variant of TEMA to selectively investigate binding to specific target proteins of interest. This form of the assay serves to improve resolution of binding to on- and off-target proteins. In conclusion, TEMA has the potential to aid in drug development and clinical routine by conferring valuable insights in drug-target interactions at spatial resolution in protein arrays, cells and in tissues.
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Affiliation(s)
- Rasel A Al-Amin
- To whom correspondence should be addressed. Tel: +46 70 0535324;
| | - Lars Johansson
- Department of Medical Biochemistry and Biophysics, Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Eldar Abdurakhmanov
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nils Landegren
- Center for Molecular Medicine, Department of Medicine (Solna), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Liza Löf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Linda Arngården
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andries Blokzijl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Svensson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling (UDOPP), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Hammond
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Peter Lönn
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johannes Haybaeck
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Annika Jenmalm Jensen
- Department of Medical Biochemistry and Biophysics, Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - U Helena Danielson
- Department of Chemistry-BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling (UDOPP), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thomas Lundbäck
- Department of Medical Biochemistry and Biophysics, Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Ulf Landegren
- Correspondence may also be addressed to Ulf Landegren. Tel: +46 18 4714910; Fax: +46 18 4714808;
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