1
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Yang M, Xiang H, Luo G. Targeting focal adhesion kinase (FAK) for cancer therapy: FAK inhibitors, FAK-based dual-target inhibitors and PROTAC degraders. Biochem Pharmacol 2024; 224:116246. [PMID: 38685282 DOI: 10.1016/j.bcp.2024.116246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Focal adhesion kinase (FAK), a non-receptor tyrosine kinase, plays an essential role in regulating cell proliferation, migration and invasion through both kinase-dependent enzymatic function and kinase-independent scaffolding function. The overexpression and activation of FAK is commonly observed in various cancers and some drug-resistant settings. Therefore, targeted disruption of FAK has been identified as an attractive strategy for cancer treatment. To date, numerous structurally diverse inhibitors targeting distinct domains of FAK have been developed, encompassing kinase domain inhibitors, FERM domain inhibitors, and FAT domain inhibitors, with several FAK inhibitors advanced to clinical trials. Moreover, given the critical role of FAK scaffolding function in signal transduction, FAK-targeted PROTACs have also been developed. Although no current FAK-targeted therapeutics have been approved for the market, the combination of FAK inhibitors with other anticancer drugs has shown considerable promise in the clinic. This review provides an overview of current drug discovery strategies targeting FAK, including the development of FAK inhibitors, FAK-based dual-target inhibitors and proteolysis-targeting chimeras (PROTACs) in both literature and patent applications. Accordingly, their design and optimization process, mechanisms of action and biological activities are discussed to offer insights into future directions of FAK-targeting drug discovery in cancer therapy.
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Affiliation(s)
- Ming Yang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Hua Xiang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China.
| | - Guoshun Luo
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China.
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2
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Mslati H, Gentile F, Pandey M, Ban F, Cherkasov A. PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. J Chem Inf Model 2024; 64:3034-3046. [PMID: 38504115 DOI: 10.1021/acs.jcim.3c01878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) that engage two biological targets at once are a promising technology in degrading clinically relevant protein targets. Since factors that influence the biological activities of PROTACs are more complex than those of a small molecule drug, we explored a combination of computational chemistry and deep learning strategies to forecast PROTAC activity and enable automated design. A new method named PROTACable was developed for the de novo design of PROTACs, which includes a robust 3-D modeling workflow to model PROTAC ternary complexes using a library of E3 ligase and linker and an SE(3)-equivariant graph transformer network to predict the activity of newly designed PROTACs. PROTACable is available at https://github.com/giaguaro/PROTACable/.
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Affiliation(s)
- Hazem Mslati
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Francesco Gentile
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1N 6N5, Canada
| | - Mohit Pandey
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
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3
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Hu HH, Wang SQ, Shang HL, Lv HF, Chen BB, Gao SG, Chen XB. Roles and inhibitors of FAK in cancer: current advances and future directions. Front Pharmacol 2024; 15:1274209. [PMID: 38410129 PMCID: PMC10895298 DOI: 10.3389/fphar.2024.1274209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Abstract
Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that exhibits high expression in various tumors and is associated with a poor prognosis. FAK activation promotes tumor growth, invasion, metastasis, and angiogenesis via both kinase-dependent and kinase-independent pathways. Moreover, FAK is crucial for sustaining the tumor microenvironment. The inhibition of FAK impedes tumorigenesis, metastasis, and drug resistance in cancer. Therefore, developing targeted inhibitors against FAK presents a promising therapeutic strategy. To date, numerous FAK inhibitors, including IN10018, defactinib, GSK2256098, conteltinib, and APG-2449, have been developed, which have demonstrated positive anti-tumor effects in preclinical studies and are undergoing clinical trials for several types of tumors. Moreover, many novel FAK inhibitors are currently in preclinical studies to advance targeted therapy for tumors with aberrantly activated FAK. The benefits of FAK degraders, especially in terms of their scaffold function, are increasingly evident, holding promising potential for future clinical exploration and breakthroughs. This review aims to clarify FAK's role in cancer, offering a comprehensive overview of the current status and future prospects of FAK-targeted therapy and combination approaches. The goal is to provide valuable insights for advancing anti-cancer treatment strategies.
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Affiliation(s)
- Hui-Hui Hu
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer and Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
| | - Sai-Qi Wang
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer and Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
| | - Hai-Li Shang
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer and Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
| | - Hui-Fang Lv
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer and Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
| | - Bei-Bei Chen
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer and Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
| | - She-Gan Gao
- Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, China
| | - Xiao-Bing Chen
- Department of Oncology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer and Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, China
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4
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Ichikawa S, Payne NC, Xu W, Chang CF, Vallavoju N, Frome S, Flaxman HA, Mazitschek R, Woo CM. The cyclimids: Degron-inspired cereblon binders for targeted protein degradation. Cell Chem Biol 2024:S2451-9456(24)00039-4. [PMID: 38320555 DOI: 10.1016/j.chembiol.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/02/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024]
Abstract
Cereblon (CRBN) is an E3 ligase substrate adapter widely exploited for targeted protein degradation (TPD) strategies. However, achieving efficient and selective target degradation is a preeminent challenge with ligands that engage CRBN. Here, we report that the cyclimids, ligands derived from the C-terminal cyclic imide degrons of CRBN, exhibit distinct modes of interaction with CRBN and offer a facile approach for developing potent and selective bifunctional degraders. Quantitative TR-FRET-based characterization of 60 cyclimid degraders in binary and ternary complexes across different substrates revealed that ternary complex binding affinities correlated strongly with cellular degradation efficiency. Our studies establish the unique properties of the cyclimids as versatile warheads in TPD and a systematic biochemical approach for quantifying ternary complex formation to predict their cellular degradation activity, which together will accelerate the development of ligands that engage CRBN.
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Affiliation(s)
- Saki Ichikawa
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - N Connor Payne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wenqing Xu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chia-Fu Chang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nandini Vallavoju
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Spencer Frome
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Hope A Flaxman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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5
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Geiger TM, Walz M, Meyners C, Kuehn A, Dreizler JK, Sugiarto WO, Maciel EVS, Zheng M, Lermyte F, Hausch F. Discovery of a Potent Proteolysis Targeting Chimera Enables Targeting the Scaffolding Functions of FK506-Binding Protein 51 (FKBP51). Angew Chem Int Ed Engl 2024; 63:e202309706. [PMID: 37942685 DOI: 10.1002/anie.202309706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
The FK506-binding protein 51 (FKBP51) is a promising target in a variety of disorders including depression, chronic pain, and obesity. Previous FKBP51-targeting strategies were restricted to occupation of the FK506-binding site, which does not affect core functions of FKBP51. Here, we report the discovery of the first FKBP51 proteolysis targeting chimera (PROTAC) that enables degradation of FKBP51 abolishing its scaffolding function. Initial synthesis of 220 FKBP-focused PROTACs yielded a plethora of active PROTACs for FKBP12, six for FKBP51, and none for FKBP52. Structural analysis of a binary FKBP12:PROTAC complex revealed the molecular basis for negative cooperativity. Linker-based optimization of first generation FKBP51 PROTACs led to the PROTAC SelDeg51 with improved cellular activity, selectivity, and high cooperativity. The structure of the ternary FKBP51:SelDeg51:VCB complex revealed how SelDeg51 establishes cooperativity by dimerizing FKBP51 and the von Hippel-Lindau protein (VHL) in a glue-like fashion. SelDeg51 efficiently depletes FKBP51 and reactivates glucocorticoid receptor (GR)-signalling, highlighting the enhanced efficacy of full protein degradation compared to classical FKBP51 binding.
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Affiliation(s)
- Thomas M Geiger
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Michael Walz
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Christian Meyners
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Angela Kuehn
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Johannes K Dreizler
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Wisely O Sugiarto
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Edvaldo V S Maciel
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Min Zheng
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Frederik Lermyte
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Felix Hausch
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64283, Darmstadt, Germany
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6
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Chen S, Zheng Y, Liang B, Yin Y, Yao J, Wang Q, Liu Y, Neamati N. The application of PROTAC in HDAC. Eur J Med Chem 2023; 260:115746. [PMID: 37607440 DOI: 10.1016/j.ejmech.2023.115746] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/29/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023]
Abstract
Inducing protein degradation by proteolysis targeting chimera (PROTAC) has provided great opportunities for scientific research and industrial applications. Histone deacetylase (HDAC)-PROTAC has been widely developed since the first report of its ability to induce the degradation of SIRT2 in 2017. To date, ten of the eighteen HDACs (HDACs 1-8, HDAC10, and SIRT2) have been successfully targeted and degraded by HDAC-PROTACs. HDAC-PROTACs surpass traditional HDAC inhibitors in many aspects, such as higher selectivity, more potent antiproliferative activity, and the ability to disrupt the enzyme-independent functions of a multifunctional protein and overcome drug resistance. Rationally designing HDAC-PROTACs is a main challenge in development because slight variations in chemical structure can lead to drastic effects on the efficiency and selectivity of the degradation. In the future, HDAC-PROTACs can potentially be involved in clinical research with the support of the increased amount of in vivo data, pharmacokinetic evaluation, and pharmacological studies.
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Affiliation(s)
- Shaoting Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yuxiang Zheng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Benji Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yudong Yin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Jian Yao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Quande Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
| | - Yanghan Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, United States.
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7
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Pereira GP, Jiménez-García B, Pellarin R, Launay G, Wu S, Martin J, Souza PCT. Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. J Chem Inf Model 2023; 63:6823-6833. [PMID: 37877240 DOI: 10.1021/acs.jcim.3c01154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose interaction with the ubiquitination machinery leads to target degradation. This technology is emerging as an exciting new avenue for therapeutic development, with several PROTACs currently undergoing clinical trials targeting cancer. Here, we describe a general and computationally efficient methodology combining restraint-based docking, energy-based rescoring, and a filter based on the minimal solvent-accessible surface distance to produce PROTAC-compatible PPIs suitable for when there is no a priori known PROTAC ligand. In a benchmark employing a manually curated data set of 13 ternary complex crystals, we achieved an accuracy of 92% when starting from bound structures and 77% when starting from unbound structures, respectively. Our method only requires that the ligand-bound structures of the monomeric forms of the E3 ligase and target proteins be given to run, making it general, accurate, and highly efficient, with the ability to impact early-stage PROTAC-based drug design campaigns where no structural information about the ternary complex structure is available.
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Affiliation(s)
- Gilberto P Pereira
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | | | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Guillaume Launay
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Sangwook Wu
- PharmCADD, Busan 48792, Republic of Korea
- Department of Physics, Pukyong National University, Busan 48513, Republic of Korea
| | - Juliette Martin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
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8
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Ciulli A, O'Connor S, Chung CW, Hartung IV, Testa A, Daniels DL, Heitman LH. The 17 th EFMC Short Course on Medicinal Chemistry on Small Molecule Protein Degraders. ChemMedChem 2023; 18:e202300464. [PMID: 37817354 DOI: 10.1002/cmdc.202300464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/10/2023] [Indexed: 10/12/2023]
Abstract
The 17th EFMC Short Course on Medicinal Chemistry took place April 23-26, 2023 in Oegstgeest, near Leiden in the Netherlands. It covered for the first time the exciting topic of Targeted Protein Degradation (full title: Small Molecule Protein Degraders: A New Opportunity for Drug Design and Development). The course was oversubscribed, with 35 attendees and 6 instructors mainly from Europe but also from the US and South Africa, and representing both industry and academia. This report summarizes the successful event, key lectures given and topics discussed.
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Affiliation(s)
- Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ Scotland, UK
| | - Suzanne O'Connor
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ Scotland, UK
| | | | - Ingo V Hartung
- Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Andrea Testa
- Amphista Therapeutics Ltd., Cori Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, UK
| | - Danette L Daniels
- Foghorn Therapeutics, 500 Technology Square, Cambridge, MA 02139, USA
| | - Laura H Heitman
- Oncode Institute & Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), P. O. Box 9502, 2300RA, Leiden, The Netherlands
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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10
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Guo C, Li Q, Xiao J, Ma F, Xia X, Shi M. Identification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2023; 41:8654-8670. [PMID: 36281703 DOI: 10.1080/07391102.2022.2135601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/08/2022] [Indexed: 10/31/2022]
Abstract
Focal adhesion kinase (FAK) belongs to the nonreceptor tyrosine kinases, which selectively phosphorylate tyrosine residues on substrate proteins. FAK is associated with bladder, esophageal, gastric, neck, breast, ovarian and lung cancers. Thus, FAK has been considered as a potential target for tumor treatment. Currently, there are six adenosine triphosphate (ATP)-competitive FAK inhibitors tested in clinical trials but no approved inhibitors targeting FAK. Defactinib (VS-6063) is a second-generation FAK inhibitor with an IC50 of 0.6 nM. The binding model of VS-6063 with FAK may provide a reference model for developing new antitumor FAK-targeting drugs. In this study, the VS-6063/FAK binding model was constructed using ensemble docking and molecular dynamics simulations. Furthermore, the molecular mechanics/generalized Born (GB) surface area (MM/GBSA) method was employed to estimate the binding free energy between VS-6063 and FAK. The key residues involved in VS-6063/FAK binding were also determined using per-residue energy decomposition analysis. Based on the binding model, VS-6063 could be separated into seven regions to enhance its binding affinity with FAK. Meanwhile, 60 novel defactinib-based compounds were designed and verified using ensemble docking. Overall, the present study improves our understanding of the binding mechanism of human FAK with VS-6063 and provides new insights into future drug designs targeting FAK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chuan Guo
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Qinxuan Li
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Jiujia Xiao
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Feng Ma
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xun Xia
- Clinical Medical College, Chengdu Medical College, Chengdu, Sichuan, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
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11
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Pan S, Ding A, Li Y, Sun Y, Zhan Y, Ye Z, Song N, Peng B, Li L, Huang W, Shao H. Small-molecule probes from bench to bedside: advancing molecular analysis of drug-target interactions toward precision medicine. Chem Soc Rev 2023; 52:5706-5743. [PMID: 37525607 DOI: 10.1039/d3cs00056g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Over the past decade, remarkable advances have been witnessed in the development of small-molecule probes. These molecular tools have been widely applied for interrogating proteins, pathways and drug-target interactions in preclinical research. While novel structures and designs are commonly explored in probe development, the clinical translation of small-molecule probes remains limited, primarily due to safety and regulatory considerations. Recent synergistic developments - interfacing novel chemical probes with complementary analytical technologies - have introduced and expedited diverse biomedical opportunities to molecularly characterize targeted drug interactions directly in the human body or through accessible clinical specimens (e.g., blood and ascites fluid). These integrated developments thus offer unprecedented opportunities for drug development, disease diagnostics and treatment monitoring. In this review, we discuss recent advances in the structure and design of small-molecule probes with novel functionalities and the integrated development with imaging, proteomics and other emerging technologies. We further highlight recent applications of integrated small-molecule technologies for the molecular analysis of drug-target interactions, including translational applications and emerging opportunities for whole-body imaging, tissue-based measurement and blood-based analysis.
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Affiliation(s)
- Sijun Pan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Aixiang Ding
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yisi Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yaxin Sun
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Yueqin Zhan
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Zhenkun Ye
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Ning Song
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
| | - Wei Huang
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, China.
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an 710072, China
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore 117599, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore 117583, Singapore
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12
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Wurz RP, Rui H, Dellamaggiore K, Ghimire-Rijal S, Choi K, Smither K, Amegadzie A, Chen N, Li X, Banerjee A, Chen Q, Mohl D, Vaish A. Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation. Nat Commun 2023; 14:4177. [PMID: 37443112 PMCID: PMC10344917 DOI: 10.1038/s41467-023-39904-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Targeted protein degradation via "hijacking" of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality. The design of PROTACs is challenging; multiple steps involved in PROTAC-induced degradation make it difficult to establish coherent structure-activity relationships. Herein, we characterize PROTAC-mediated ternary complex formation and degradation by employing von Hippel-Lindau protein (VHL) recruiting PROTACs for two different target proteins, SMARCA2 and BRD4. Ternary-complex attributes and degradation activity parameters are evaluated by varying components of the PROTAC's architecture. Ternary complex binding affinity and cooperativity correlates well with degradation potency and initial rates of degradation. Additionally, we develop a ternary-complex structure modeling workflow to calculate the total buried surface area at the interface, which is in agreement with the measured ternary complex binding affinity. Our findings establish a predictive framework to guide the design of potent degraders.
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Affiliation(s)
- Ryan P Wurz
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Huan Rui
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | | | - Kaylee Choi
- Amgen Research, Amgen Inc., South San Francisco, CA, USA
| | - Kate Smither
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | - Ning Chen
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Xiaofen Li
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | - Qing Chen
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Dane Mohl
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA.
| | - Amit Vaish
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA.
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13
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Ma L, Li Y, Luo R, Wang Y, Cao J, Fu W, Qian B, Zheng L, Tang L, Lv X, Zheng L, Liang G, Chen L. Discovery of a Selective and Orally Bioavailable FGFR2 Degrader for Treating Gastric Cancer. J Med Chem 2023. [PMID: 37220310 DOI: 10.1021/acs.jmedchem.3c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Abnormal activation of fibroblast growth factor receptors (FGFRs) results in the development and progression of human cancers. FGFR2 is frequently amplified or mutated in cancers; therefore, it is an attractive target for tumor therapy. Despite the development of several pan-FGFR inhibitors, their long-term therapeutic efficacy is hindered by acquired mutations and low isoform selectivity. Herein, we report the discovery of an efficient and selective FGFR2 proteolysis-targeting chimeric molecule, LC-MB12, that incorporates an essential rigid linker. LC-MB12 preferentially internalizes and degrades membrane-bound FGFR2 among the four FGFR isoforms; this may promote greater clinical benefits. LC-MB12 exhibits superior potency in FGFR signaling suppression and anti-proliferative activity compared to the parental inhibitor. Furthermore, LC-MB12 is orally bioavailable and shows significant antitumor effects in FGFR2-dependent gastric cancer in vivo. Taken together, LC-MB12 is a candidate FGFR2 degrader for alternative FGFR2-targeting strategies and offers a promising starting point for drug development.
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Affiliation(s)
- Lin Ma
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Yingying Li
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Ruixiang Luo
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Yuhan Wang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Jiaqi Cao
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Weitao Fu
- Department of Computer-Aided Drug Design, Jiangsu Vcare PharmaTech Co. Ltd., Nanjing 211800, China
| | - Bolan Qian
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Lei Zheng
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Longguang Tang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 322000, China
| | - Xinting Lv
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Lulu Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang 310000, China
| | - Guang Liang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Lingfeng Chen
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
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14
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Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. High Accuracy Prediction of PROTAC Complex Structures. J Am Chem Soc 2023; 145:7123-7135. [PMID: 36961978 PMCID: PMC10240388 DOI: 10.1021/jacs.2c09387] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The design of PROteolysis-TArgeting Chimeras (PROTACs) requires bringing an E3 ligase into proximity with a target protein to modulate the concentration of the latter through its ubiquitination and degradation. Here, we present a method for generating high-accuracy structural models of E3 ligase-PROTAC-target protein ternary complexes. The method is dependent on two computational innovations: adding a "silent" convolution term to an efficient protein-protein docking program to eliminate protein poses that do not have acceptable linker conformations and clustering models of multiple PROTACs that use the same E3 ligase and target the same protein. Results show that the largest consensus clusters always have high predictive accuracy and that the ensemble of models can be used to predict the dissociation rate and cooperativity of the ternary complex that relate to the degrading activity of the PROTAC. The method is demonstrated by applications to known PROTAC structures and a blind test involving PROTACs against BRAF mutant V600E. The results confirm that PROTACs function by stabilizing a favorable interaction between the E3 ligase and the target protein but do not necessarily exploit the most energetically favorable geometry for interaction between the proteins.
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Affiliation(s)
- Mikhail Ignatov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Akhil Jindal
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 USA
- Acpharis Inc., Holliston, Massachusetts 01746, USA
| | - Ganna Posternak
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Xiaojing Tang
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
| | - Pierre Maisonneuve
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario L4K-M9W, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Frank Sicheri
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario L4K-M9W, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 USA
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
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15
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Yang YC, Zhao CJ, Jin ZF, Zheng J, Ma LT. Targeted therapy based on ubiquitin-specific proteases, signalling pathways and E3 ligases in non-small-cell lung cancer. Front Oncol 2023; 13:1120828. [PMID: 36969062 PMCID: PMC10036052 DOI: 10.3389/fonc.2023.1120828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/01/2023] [Indexed: 03/11/2023] Open
Abstract
Lung cancer is one of the most common malignant tumours worldwide, with the highest mortality rate. Approximately 1.6 million deaths owing to lung cancer are reported annually; of which, 85% of deaths occur owing to non-small-cell lung cancer (NSCLC). At present, the conventional treatment methods for NSCLC include radiotherapy, chemotherapy, targeted therapy and surgery. However, drug resistance and tumour invasion or metastasis often lead to treatment failure. The ubiquitin–proteasome pathway (UPP) plays an important role in the occurrence and development of tumours. Upregulation or inhibition of proteins or enzymes involved in UPP can promote or inhibit the occurrence and development of tumours, respectively. As regulators of UPP, ubiquitin-specific proteases (USPs) primarily inhibit the degradation of target proteins by proteasomes through deubiquitination and hence play a carcinogenic or anticancer role. This review focuses on the role of USPs in the occurrence and development of NSCLC and the potential of corresponding targeted drugs, PROTACs and small-molecule inhibitors in the treatment of NSCLC.
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Affiliation(s)
- Yu-Chen Yang
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Can-Jun Zhao
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Zhao-Feng Jin
- School of Psychology, Weifang Medical University, Weifang, China
| | - Jin Zheng
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Li-Tian Ma, ; Jin Zheng,
| | - Li-Tian Ma
- Department of Traditional Chinese Medicine, Tangdu Hospital, Air Force Medical University, Xi’an, China
- Department of Gastroenterology, Tangdu Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Li-Tian Ma, ; Jin Zheng,
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16
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Schiemer J, Maxwell A, Horst R, Liu S, Uccello DP, Borzilleri K, Rajamohan N, Brown MF, Calabrese MF. A covalent BTK ternary complex compatible with targeted protein degradation. Nat Commun 2023; 14:1189. [PMID: 36864023 PMCID: PMC9981747 DOI: 10.1038/s41467-023-36738-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 02/15/2023] [Indexed: 03/04/2023] Open
Abstract
Targeted protein degradation using heterobifunctional chimeras holds the potential to expand target space and grow the druggable proteome. Most acutely, this provides an opportunity to target proteins that lack enzymatic activity or have otherwise proven intractable to small molecule inhibition. Limiting this potential, however, is the remaining need to develop a ligand for the target of interest. While a number of challenging proteins have been successfully targeted by covalent ligands, unless this modification affects form or function, it may lack the ability to drive a biological response. Bridging covalent ligand discovery with chimeric degrader design has emerged as a potential mechanism to advance both fields. In this work, we employ a set of biochemical and cellular tools to deconvolute the role of covalent modification in targeted protein degradation using Bruton's tyrosine kinase. Our results reveal that covalent target modification is fundamentally compatible with the protein degrader mechanism of action.
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Affiliation(s)
- James Schiemer
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Andrew Maxwell
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Reto Horst
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Shenping Liu
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Daniel P Uccello
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Kris Borzilleri
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Nisha Rajamohan
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Matthew F Brown
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Matthew F Calabrese
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA.
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17
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Li M, Zhi Y, Liu B, Yao Q. Advancing Strategies for Proteolysis-Targeting Chimera Design. J Med Chem 2023; 66:2308-2329. [PMID: 36788245 DOI: 10.1021/acs.jmedchem.2c01555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) have shown great therapeutic potential by degrading various disease-causing proteins, particularly those related to tumors. Therefore, the introduction of PROTACs has ushered in a new chapter of antitumor drug development, marked by significant advances over recent years. Herein, we describe recent developments in PROTAC technology, focusing on design strategy, development workflow, and future outlooks. We also discuss potential opportunities and challenges for PROTAC research.
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Affiliation(s)
- Minglei Li
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Ying Zhi
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Bo Liu
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Qingqiang Yao
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
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18
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Abstract
X-ray crystal structures of PROTAC-induced ternary complexes provide invaluable insights into the critical species underpinning PROTAC mode of action, explain protein degradation selectivity profiles, and can guide rational degrader design. Nevertheless, crystallization of the ternary complexes formed by PROTACs remains an important bottleneck in employing this method. This is mainly due to the potential flexibility and heterogeneity that is inherent to a non-native protein-protein complex mediated by a small molecule, which together can hamper crystallization of the desired species. To overcome this limitation, selecting PROTAC compounds that enable the formation of stable, high-affinity and preferably cooperative ternary complexes in stoichiometric amount is, in our experience, critical to the success of co-crystallization studies. In this chapter, examples of stable PROTAC-mediated ternary complexes are illustrated. Learnings from biophysical & biochemical data are used as a guideline in achieving the highest "crystallizability" of ternary complexes. A case study of VHL-based SMARCA2 PROTAC degrader ternary complex crystallization is described. The procedure includes over-expression and purification of the E3 ligase and target protein, forming (and sometimes isolating) the ternary complex, and crystallizing it. The protocols can be applied for other combinations of E3 ligase, PROTAC and target protein.
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Affiliation(s)
- Andre J Wijaya
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - William Farnaby
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom.
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19
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Wang YW, Lan L, Wang M, Zhang JY, Gao YH, Shi L, Sun LP. PROTACS: A technology with a gold rush-like atmosphere. Eur J Med Chem 2023; 247:115037. [PMID: 36566716 DOI: 10.1016/j.ejmech.2022.115037] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/03/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
Abnormally expressed or malfunctioning proteins may affect or even damage cells, leading to the onset of diseases. Proteolysis targeting chimera (PROTAC) technology has been proven to be a fresh therapeutic strategy, superior to conventional small molecule inhibitors for the treatment of diseases caused by pathogenic proteins. Unlike conventional small molecule inhibitors that are occupancy-driven, PROTACs are heterobifunctional small molecules with catalytic properties. They combine with E3 ligases and target proteins to form a ternary complex, rendering the target protein ubiquitous and subsequently degraded by the proteasome. This paper focuses first on significant events in the development of PROTAC technology from 2001 to 2022, followed by a brief overview of various PROTACs categorized by target proteins. In addition, the applications of PROTACs in the treatment of diseases and fundamental biology are also under discussion.
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Affiliation(s)
- Yu-Wei Wang
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Li Lan
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Min Wang
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Jin-Yang Zhang
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yu-Hui Gao
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Lei Shi
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Li-Ping Sun
- Jiangsu Key Laboratory of Drug Design & Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing, 210009, PR China.
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20
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Song J, Liu X, Zhang YF, Tian XY, Deng MY, Huang CZ, Zhang SY. The dual FAK-HDAC inhibitor MY-1259 displays potent activities in gastric cancers in vitro and in vivo. Bioorg Chem 2023; 131:106328. [PMID: 36542986 DOI: 10.1016/j.bioorg.2022.106328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Epigenetic regulation and Focal adhesion kinase (FAK) are considered to be two important targets for the development of antitumor drugs. Studies have shown that the combination of FAK and HDAC inhibitors could exhibit synergistic effects in a subset of cancer cells in vitro and in vivo. At present, there are few reports on dual target inhibitors of FAK and HDAC. Here, we first reported a new compound MY-1259 as a dual FAK and HDAC6 inhibitor, which exhibited efficient treatment effects on gastric cancers in vitro and in vivo. MY-1259 exhibited potent inhibitory activities against FAK (IC50 = 132 nM) and HDAC6 (IC50 = 16 nM). Notably, MY-1259 showed selective inhibitory potency on HDAC6 over HDAC1, HDAC2 and HDAC3. In addition, MY-1259 could potently inhibit the proliferative activities of MGC-803 and BGC-823 cells (IC50 = 3.91 and 15.46 nM, respectively, using flow cytometry counting), induce cell apoptosis, and cellular senescence. MY-1259 could effectively down-regulate the levels of Ac-Histone H3 and Ac-α-tubulin, and also inhibit the phosphorylation of FAK at three phosphorylation sites Y397, Y576/577 and Y925, thereby inhibiting the activation of ERK and AKT/mTOR. MY-1259 exhibited more effective antitumor effect in vivo than the HDAC inhibitor SAHA and FAK inhibitor TAE-226 alone or in combination, showing the advantages of FAK/HDAC dual inhibitors in the treatment of gastric cancers. Therefore, the results in this work suggested that inhibition of FAK and HDAC by MY-1259 might represent a promising strategy for the treatment of gastric cancers.
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21
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Chen Q, Liu C, Wang W, Meng X, Cheng X, Li X, Cai L, Luo L, He X, Qu H, Luo J, Wei H, Gao S, Liu G, Wan J, Israel DI, Li J, Dou D. Optimization of PROTAC Ternary Complex Using DNA Encoded Library Approach. ACS Chem Biol 2023; 18:25-33. [PMID: 36606710 PMCID: PMC9872815 DOI: 10.1021/acschembio.2c00797] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023]
Abstract
The proteolysis targeting chimera (PROTAC) strategy results in the down-regulation of unwanted protein(s) for disease treatment. In the PROTAC process, a heterobifunctional degrader forms a ternary complex with a target protein of interest (POI) and an E3 ligase, which results in ubiquitination and proteasomal degradation of the POI. While ternary complex formation is a key attribute of PROTAC degraders, modification of the PROTAC molecule to optimize ternary complex formation and protein degradation can be a labor-intensive and tedious process. In this study, we take advantage of DNA-encoded library (DEL) technology to efficiently synthesize a vast number of possible PROTAC molecules and describe a parallel screening approach that utilizes DNA barcodes as reporters of ternary complex formation and cooperative binding. We use a designed PROTAC DEL against BRD4 and CRBN to describe a dual protein affinity selection method and the direct discovery of novel, potent BRD4 PROTACs that importantly demonstrate clear SAR. Such an approach evaluates all the potential PROTACs simultaneously, avoids the interference of PROTAC solubility and permeability, and uses POI and E3 ligase proteins in an efficient manner.
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Affiliation(s)
- Qiuxia Chen
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Chuan Liu
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Wei Wang
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xiaoyun Meng
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xuemin Cheng
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xianyang Li
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Longying Cai
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Linfu Luo
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Xu He
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Huan Qu
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Jing Luo
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Hong Wei
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Sen Gao
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Guansai Liu
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | - Jinqiao Wan
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
| | | | - Jin Li
- HitGen
Inc., Chengdu, Sichuan 610200, China
| | - Dengfeng Dou
- Lead
Generation Unit and Discovery Chemistry Unit, HitGen Inc., Chengdu, Sichuan 610200, China
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22
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Qin Q, Wang R, Fu Q, Zhang G, Wu T, Liu N, Lv R, Yin W, Sun Y, Sun Y, Zhao D, Cheng M. Design, synthesis, and biological evaluation of potent FAK-degrading PROTACs. J Enzyme Inhib Med Chem 2022; 37:2241-2255. [PMID: 35978496 PMCID: PMC9455338 DOI: 10.1080/14756366.2022.2100886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
FAK mediated tumour cell migration, invasion, survival, proliferation and regulation of tumour stem cells through its kinase-dependent enzymatic functions and kinase-independent scaffolding functions. At present, the development of FAK PROTACs has become one of the hotspots in current pharmaceutical research to solve above problems. Herein, we designed and synthesised a series of FAK-targeting PROTACs consisted of PF-562271 derivative 1 and Pomalidomide. All compounds showed significant in vitro FAK kinase inhibitory activity, the IC50 value of the optimised PROTAC A13 was 26.4 nM. Further, A13 exhibited optimal protein degradation (85% degradation at 10 nM). Meantime, compared with PF-562271, PROTAC A13 exhibited better antiproliferative activity and anti-invasion ability in A549 cells. More, A13 had excellent plasma stability with T1/2 >194.8 min. There are various signs that PROTAC A13 could be useful as expand tool for studying functions of FAK in biological system and as potential therapeutic agents.
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Affiliation(s)
- Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Ruifeng Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China.,Department of Pharmacy, Shanxi Medical University, Taiyuan, PR China
| | - Qinglin Fu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Guoqi Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Nian Liu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Ruicheng Lv
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Yin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, PR China
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23
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Abstract
Proteolysis-targeting chimeras (PROTACs) and targeted covalent inhibitors (TCIs) are currently two exciting strategies in the fields of chemical biology and drug discovery. Extensive research in these two fields has been conducted, and significant progress in these fields has resulted in many clinical candidates, some of which have been approved by FDA. Recently, a novel concept termed covalent PROTACs that combine these two strategies has emerged and gained an increasing interest in the past several years. Herein, we briefly review and highlight the mechanism and advantages of TCIs and PROTACs, respectively, and the recent development of covalent PROTACs using irreversible and reversible covalent chemistry.
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Affiliation(s)
- Dong Lu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston TX 77030, USA.
| | - Xin Yu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston TX 77030, USA.
| | - Hanfeng Lin
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston TX 77030, USA.
| | - Ran Cheng
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston TX 77030, USA.
| | - Erika Y Monroy
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston TX 77030, USA.
| | - Xiaoli Qi
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston TX 77030, USA.
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston TX 77030, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston TX 77030, USA
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston TX 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston TX 77030, USA
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24
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Park D, Izaguirre J, Coffey R, Xu H. Modeling the Effect of Cooperativity in Ternary Complex Formation and Targeted Protein Degradation Mediated by Heterobifunctional Degraders. ACS Bio Med Chem Au 2022; 3:74-86. [PMID: 37101604 PMCID: PMC10125322 DOI: 10.1021/acsbiomedchemau.2c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022]
Abstract
Chemically induced proximity between certain endogenous enzymes and a protein of interest (POI) inside cells may cause post-translational modifications to the POI with biological consequences and potential therapeutic effects. Heterobifunctional (HBF) molecules that bind with one functional part to a target POI and with the other to an E3 ligase induce the formation of a target-HBF-E3 ternary complex, which can lead to ubiquitination and proteasomal degradation of the POI. Targeted protein degradation (TPD) by HBFs offers a promising approach to modulate disease-associated proteins, especially those that are intractable using other therapeutic approaches, such as enzymatic inhibition. The three-way interactions among the HBF, the target POI, and the ligase-including the protein-protein interaction between the POI and the ligase-contribute to the stability of the ternary complex, manifested as positive or negative binding cooperativity in its formation. How such cooperativity affects HBF-mediated degradation is an open question. In this work, we develop a pharmacodynamic model that describes the kinetics of the key reactions in the TPD process, and we use this model to investigate the role of cooperativity in the ternary complex formation and in the target POI degradation. Our model establishes the quantitative connection between the ternary complex stability and the degradation efficiency through the former's effect on the rate of catalytic turnover. We also develop a statistical inference model for determining cooperativity in intracellular ternary complex formation from cellular assay data and demonstrate it by quantifying the change in cooperativity due to site-directed mutagenesis at the POI-ligase interface of the SMARCA2-ACBI1-VHL ternary complex. Our pharmacodynamic model provides a quantitative framework to dissect the complex HBF-mediated TPD process and may inform the rational design of effective HBF degraders.
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Affiliation(s)
- Daniel Park
- Roivant Discovery, New York, New York10036, United States
| | | | - Rory Coffey
- Roivant Discovery, New York, New York10036, United States
| | - Huafeng Xu
- Roivant Discovery, New York, New York10036, United States
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25
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Sun D, Zhang J, Dong G, He S, Sheng C. Blocking Non-enzymatic Functions by PROTAC-Mediated Targeted Protein Degradation. J Med Chem 2022; 65:14276-14288. [DOI: 10.1021/acs.jmedchem.2c01159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donghuan Sun
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Jing Zhang
- Department of Pathology, Changzheng Hospital, Second Military Medical University (Naval Medical University), Shanghai 200003, China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Shipeng He
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University (Naval Medical University), Shanghai 200433, China
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26
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Diehl CJ, Ciulli A. Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders. Chem Soc Rev 2022; 51:8216-8257. [PMID: 35983982 PMCID: PMC9528729 DOI: 10.1039/d2cs00387b] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The von Hippel-Lindau (VHL) Cullin RING E3 ligase is an essential enzyme in the ubiquitin-proteasome system that recruits substrates such as the hypoxia inducible factor for ubiquitination and subsequent proteasomal degradation. The ubiquitin-proteasome pathway can be hijacked toward non-native neo-substrate proteins using proteolysis targeting chimeras (PROTACs), bifunctional molecules designed to simultaneously bind to an E3 ligase and a target protein to induce target ubiquitination and degradation. The availability of high-quality small-molecule ligands with good binding affinity for E3 ligases is fundamental for PROTAC development. Lack of good E3 ligase ligands as starting points to develop PROTAC degraders was initially a stumbling block to the development of the field. Herein, the journey towards the design of small-molecule ligands binding to VHL is presented. We cover the structure-based design of VHL ligands, their application as inhibitors in their own right, and their implementation into rationally designed, potent PROTAC degraders of various target proteins. We highlight the key findings and learnings that have provided strong foundations for the remarkable development of targeted protein degradation, and that offer a blueprint for designing new ligands for E3 ligases beyond VHL.
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Affiliation(s)
- Claudia J Diehl
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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27
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Shi M, Chen T, Wei S, Zhao C, Zhang X, Li X, Tang X, Liu Y, Yang Z, Chen L. Molecular Docking, Molecular Dynamics Simulations, and Free Energy Calculation Insights into the Binding Mechanism between VS-4718 and Focal Adhesion Kinase. ACS Omega 2022; 7:32442-32456. [PMID: 36119979 PMCID: PMC9476166 DOI: 10.1021/acsomega.2c03951] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/24/2022] [Indexed: 05/17/2023]
Abstract
Focal adhesion kinase (FAK) is a 125 kDa nonreceptor tyrosine kinase that plays an important role in many carcinomas. Thus, the targeting of FAK by small molecules is considered to be promising for cancer therapy. Some FAK inhibitors have been reported as potential anticancer drugs and have entered into clinical development; for example, VS-4718 is currently undergoing clinical trials. However, the lack of crystal structural data for the binding of VS-4718 with FAK has hindered the optimization of this anticancer agent. In this work, the VS-4718/FAK interaction model was obtained by molecular docking and molecular dynamics simulations. The binding free energies of VS-4718/FAK were also calculated using the molecular mechanics generalized Born surface area method. It was found that the aminopyrimidine group formed hydrogen bonds with the C502 residue of the hinge loop, while the D564 residue of the T-loop interacted with the amide group. In addition, I428, A452, V484, M499, G505, and L553 residues formed hydrophobic interactions with VS-4718. The obtained results therefore provide an improved understanding of the interaction between human FAK and VS-4718. Based on the obtained binding mechanism, 47 novel compounds were designed to target the adenosine 5'-triphosphate-binding pocket of human FAK, and ensemble docking was performed to assess the effects of these modifications on the inhibitor binding affinity. This work is also expected to provide additional insights into potential future target design strategies based on VS-4718.
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Affiliation(s)
- Mingsong Shi
- State
Key Laboratory of Biotherapy, West China
Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Tao Chen
- State
Key Laboratory of Biotherapy, West China
Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Siping Wei
- Key
Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China
- Department
of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou 646000, China
| | - Chenyu Zhao
- West
China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xinyu Zhang
- West
China School of Pharmacy, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xinghui Li
- West
China School of Pharmacy, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xinyi Tang
- West
China School of Pharmacy, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yan Liu
- State
Key Laboratory of Biotherapy, West China
Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Zhuang Yang
- State
Key Laboratory of Biotherapy, West China
Hospital of Sichuan University, Chengdu 610041, Sichuan, China
- . Phone: +86-28-85164063
| | - Lijuan Chen
- State
Key Laboratory of Biotherapy, West China
Hospital of Sichuan University, Chengdu 610041, Sichuan, China
- . Phone: +86-28-85164063
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28
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Pei Y, Fu J, Shi Y, Zhang M, Luo G, Luo X, Song N, Mi T, Yang Y, Li J, Zhou Y, Zhou B. Discovery of a Potent and Selective Degrader for USP7. Angew Chem Int Ed Engl 2022; 61:e202204395. [PMID: 35691827 DOI: 10.1002/anie.202204395] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Indexed: 01/31/2023]
Abstract
The tumor suppressor p53 is the most frequently mutated gene in human cancer and more than half of cancers contain p53 mutations. The development of novel and effective therapeutic strategies for p53 mutant cancer therapy is a big challenge and highly desirable. Ubiquitin-specific protease 7 (USP7), also known as HAUSP, is a deubiquitinating enzyme and proposed to stabilize the oncogenic E3 ubiquitin ligase MDM2 that promotes the proteosomal degradation of p53. Herein, we report the design and characterization of U7D-1 as the first selective USP7-degrading Proteolysis Targeting Chimera (PROTAC). U7D-1 showed selective and effective USP7 degradation, and maintained potent cell growth inhibition in p53 mutant cancer cells, with USP7 inhibitor showing no activity. These data clearly demonstrated the practicality and importance of PROTAC as a preliminary chemical tool for investigating USP7 protein functions and a promising method for potential p53 mutant cancer therapy.
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Affiliation(s)
- Yuan Pei
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Jingfeng Fu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Yunkai Shi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Mengmeng Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China
| | - Guanghao Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Xiaomin Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ning Song
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Tian Mi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Yaxi Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.,Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong, 528400, P.R. China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yubo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.,Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong, 528400, P.R. China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Bing Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
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29
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Abstract
Targeting proteins’ enzymatic functions with small molecule inhibitors, as well as functions of receptor proteins with small-molecule agonists and antagonists, were the major forms of small-molecule drug development. These small-molecule modulators are based on a conventional occupancy-driven pharmacological approach. For proteome space traditionally considered undruggable by small-molecule modulators, such as enzymes with scaffolding functions, transcription factors, and proteins that lack well-defined binding pockets for small molecules, targeted protein degraders offer the opportunity to drug the proteome with an event-driven pharmacological approach. A degrader molecule, either PROTAC or molecular glue, brings the protein of interest (POI) and E3 ubiquitin ligase in close proximity and engages the ubiquitin-proteasome system (UPS), the cellular waste disposal system for the degradation of the POI. For the development of targeted protein degraders to meet therapeutic needs, several aspects will be considered, namely, the selective degradation of disease-causing proteins, the oral bioavailability of degraders beyond Lipinski’s rule of five (bRo5) scope, demands of new E3 ubiquitin ligases and molecular glue degraders, and drug resistance of the new drug modality. This review will illustrate several under-discussed key considerations in targeted protein degradation drug discovery and development: 1) the contributing factors for the selectivity of PROTAC molecules and the design of PROTACs to selectively degrade synergistic pathological proteins; 2) assay development in combination with a multi-omics approach for the identification of new E3 ligases and their corresponding ligands, as well as molecular glue degraders; 3) a molecular design to improve the oral bioavailability of bRo5 PROTACs, and 4) drug resistance of degraders.
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Affiliation(s)
- Liena Qin
- Insilico Medicine Ltd., Shanghai, China
- *Correspondence: Liena Qin, ; Han Dai, ; Junfeng Wang,
| | - Han Dai
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- *Correspondence: Liena Qin, ; Han Dai, ; Junfeng Wang,
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
- International Magnetobiology Frontier Research Center, Hefei, China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, China
- *Correspondence: Liena Qin, ; Han Dai, ; Junfeng Wang,
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30
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Riching KM, Caine EA, Urh M, Daniels DL. The importance of cellular degradation kinetics for understanding mechanisms in targeted protein degradation. Chem Soc Rev 2022; 51:6210-6221. [PMID: 35792307 DOI: 10.1039/d2cs00339b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeted protein degradation has exploded over the past several years due to preclinical and early clinical therapeutic success of numerous compounds, and the emergence of new degradation modalities, which has broadened the definition of what a degrader is. The most characterized and well-studied small molecule degraders are molecular glues and proteolysis targeting chimeras (PROTACs). These degraders induce a ternary complex between a target protein, degrader, and E3 ligase component, resulting in ubiquitination and subsequent degradation of the target protein via the ubiquitin proteasomal system (UPS). This event-driven process requires success at all steps through a complex cascade of events. As more systems, degraders, and targets are tested, it has become increasingly clear that achieving degradation is only the first critical milestone in a degrader development program. Rather highly efficacious degraders require a combination of multiple optimized parameters: rapid degradation, high potency, high maximal degradation (Dmax), and sustained loss of target without re-dosing. Success to meet these more rigorous goals depends upon the ability to characterize and understand the dynamic cellular degradation profiles and relate them to the underlying mechanism for any given target treated with a specific concentration of degrader. From this starting point, optimization and fine tuning of multiple kinetic parameters such as how fast degradation occurs (the rate), how much of the target is degraded (the extent), and how long the target remains degraded (the duration) can be performed. In this review we explore the diversity of cellular kinetic degradation profiles which can arise after molecular glue and PROTAC treatment and the potential implications of these varying responses. As the overall degradation kinetics are a sum of individual mechanistic steps, each with their own kinetic contributions, we discuss the ways in which changes at any one of these steps could potentially influence the resultant kinetic degradation profiles. Looking forward, we address the importance in characterizing the kinetics of target protein loss in the early stages of degrader design and how this will enable more rapid discovery of therapeutic agents to elicit desired phenotypic outcomes.
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Affiliation(s)
- Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
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31
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Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules consisting of one ligand that binds to a protein of interest (POI) and another that can recruit an E3 ubiquitin ligase. The chemically-induced proximity between the POI and E3 ligase results in ubiquitination and subsequent degradation of the POI by the ubiquitin-proteasome system (UPS). The event-driven mechanism of action (MOA) of PROTACs offers several advantages compared to traditional occupancy-driven small molecule inhibitors, such as a catalytic nature, reduced dosing and dosing frequency, a more potent and longer-lasting effect, an added layer of selectivity to reduce potential toxicity, efficacy in the face of drug-resistance mechanisms, targeting nonenzymatic functions, and expanded target space. Here, we highlight important milestones and briefly discuss lessons learned about targeted protein degradation (TPD) in recent years and conjecture on the efforts still needed to expand the toolbox for PROTAC discovery to ultimately provide promising therapeutics.
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Affiliation(s)
- Ke Li
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA.
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA. .,Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA.,Department of Pharmacology, Yale University, New Haven, Connecticut 06511, USA
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32
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Pei Y, Fu J, Shi Y, Zhang M, Luo G, Luo X, Song N, Mi T, Yang Y, Li J, Zhou Y, Zhou B. Discovery of a Potent and Selective Degrader for USP7. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuan Pei
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Jingfeng Fu
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Yunkai Shi
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Mengmeng Zhang
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Guanghao Luo
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Xiaomin Luo
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Ning Song
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Tian Mi
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Yaxi Yang
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Jia Li
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Yubo Zhou
- Shanghai Institute of Materia Medica Chinese Academy of Sciences Department of Medicinal Chemistry CHINA
| | - Bing Zhou
- Shanghai Institute of Materia Medica Department of Medicinal Chemistry 555 Road Zu Chong Zhi 201203 Shanghai CHINA
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33
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He M, Cao C, Ni Z, Liu Y, Song P, Hao S, He Y, Sun X, Rao Y. PROTACs: great opportunities for academia and industry (an update from 2020 to 2021). Signal Transduct Target Ther 2022; 7:181. [PMID: 35680848 PMCID: PMC9178337 DOI: 10.1038/s41392-022-00999-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
PROteolysis TArgeting Chimeras (PROTACs) technology is a new protein-degradation strategy that has emerged in recent years. It uses bifunctional small molecules to induce the ubiquitination and degradation of target proteins through the ubiquitin–proteasome system. PROTACs can not only be used as potential clinical treatments for diseases such as cancer, immune disorders, viral infections, and neurodegenerative diseases, but also provide unique chemical knockdown tools for biological research in a catalytic, reversible, and rapid manner. In 2019, our group published a review article “PROTACs: great opportunities for academia and industry” in the journal, summarizing the representative compounds of PROTACs reported before the end of 2019. In the past 2 years, the entire field of protein degradation has experienced rapid development, including not only a large increase in the number of research papers on protein-degradation technology but also a rapid increase in the number of small-molecule degraders that have entered the clinical and will enter the clinical stage. In addition to PROTAC and molecular glue technology, other new degradation technologies are also developing rapidly. In this article, we mainly summarize and review the representative PROTACs of related targets published in 2020–2021 to present to researchers the exciting developments in the field of protein degradation. The problems that need to be solved in this field will also be briefly introduced.
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Affiliation(s)
- Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Chaoguo Cao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China.,Tsinghua-Peking Center for Life Sciences, 100084, Beijing, P. R. China
| | - Zhihao Ni
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yongbo Liu
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Peilu Song
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Shuang Hao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yuna He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Xiuyun Sun
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, 100084, Beijing, P. R. China. .,School of Pharmaceutical Sciences, Zhengzhou University, 450001, Zhengzhou, China.
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Spallarossa A, Tasso B, Russo E, Villa C, Brullo C. The Development of FAK Inhibitors: A Five-Year Update. Int J Mol Sci 2022; 23:ijms23126381. [PMID: 35742823 PMCID: PMC9223874 DOI: 10.3390/ijms23126381] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 02/06/2023] Open
Abstract
Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase over-expressed in different solid cancers. In recent years, FAK has been recognized as a new target for the development of antitumor agents, useful to contrast tumor development and metastasis formation. To date, studies on the role of FAK and FAK inhibitors are of great interest for both pharmaceutical companies and academia. This review is focused on compounds able to block FAK with different potencies and with different mechanisms of action, that have appeared in the literature since 2017. Furthermore, new emerging PROTAC molecules have appeared in the literature. This summary could improve knowledge of new FAK inhibitors and provide information for future investigations, in particular, from a medicinal chemistry point of view.
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35
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Goebel GL, Qiu X, Wu P. Kinase-targeting small-molecule inhibitors and emerging bifunctional molecules. Trends Pharmacol Sci 2022; 43:866-881. [PMID: 35589447 DOI: 10.1016/j.tips.2022.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/31/2022] [Accepted: 04/11/2022] [Indexed: 02/07/2023]
Abstract
Kinases are among the most successful drug targets. To date, 72 small-molecule kinase inhibitors (SMKIs) have been approved by the US FDA, together with ~500 SMKIs in clinical trials. Although the topic has been heavily reviewed in recent years, an overview that focused on the currently approved SMKIs in combination with the emerging kinase-targeting bifunctional molecules is absent. Herein, we first provide an updated overview of the approved SMKIs, with an emphasis on their binding modes, classified in groups of type I and II ATP-competitive inhibitors, type III and IV allosteric inhibitors, and covalent inhibitors. We then highlight the novel chemical modalities in kinase targeting by using different types of proximity-inducing bifunctional molecules for kinase degradation and modifications.
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Affiliation(s)
- Georg L Goebel
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Xiaqiu Qiu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund 44227, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen DK-2100, Denmark.
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36
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Aublette MC, Harrison TA, Thorpe EJ, Gadd MS. Selective Wee1 degradation by PROTAC degraders recruiting VHL and CRBN E3 ubiquitin ligases. Bioorg Med Chem Lett 2022; 64:128636. [PMID: 35231578 DOI: 10.1016/j.bmcl.2022.128636] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/14/2022] [Accepted: 02/19/2022] [Indexed: 11/28/2022]
Abstract
The Ser/Thr protein kinase Wee1 plays a regulatory role at the G2/M checkpoint by phosphorylating CDK1 when DNA is damaged to allow time for DNA to repair, disruption of which is a key approach to sensitise cancer cells to DNA-damaging therapies. The main selective inhibitor for Wee1 undergoing development in clinical trials, AZD1775, however, has been shown to have off target effects towards other protein kinases with similar potency. Here we describe the synthesis and assessment of a series of Wee1-degrading PROTACs using AZD1775 linked to either the VHL ligand VH032 or to the CRBN ligand pomalidomide using different types and lengths of linkers. The conversion of AZD1775 into a PROTAC induces selective Wee1 degradation for compounds of both series depending on the nature of the linker.
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Affiliation(s)
- Marine C Aublette
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, United Kingdom
| | - Tom A Harrison
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, United Kingdom
| | - Elizabeth J Thorpe
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, United Kingdom
| | - Morgan S Gadd
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, United Kingdom.
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37
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Sun Y, Wang R, Sun Y, Wang L, Xue Y, Wang J, Wu T, Yin W, Qin Q, Sun Y, Zhao D, Cheng M. Identification of novel and potent PROTACs targeting FAK for non-small cell lung cancer: Design, synthesis, and biological study. Eur J Med Chem 2022; 237:114373. [PMID: 35486993 DOI: 10.1016/j.ejmech.2022.114373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/31/2022] [Accepted: 04/07/2022] [Indexed: 12/22/2022]
Abstract
The intracellular non-receptor tyrosine protein kinase Focal adhesion kinase (FAK) is a key signalling regulator, which mediates tumor survival, invasion, metastasis, and angiogenesis through its kinase catalytic functions and non-kinase scaffolding functions. Previous efforts have clarified that it is crucial to address both FAK kinase and scaffolding functions instead of just inhibiting FAK kinase activity because it may be insufficient to completely block FAK signaling. Proteolysis targeting chimera (PROTAC) technology is a method of targeting a specific protein and inducing its degradation in the cell, which can simultaneously eliminate both kinase-dependent enzymatic functions and scaffolding functions. In current study, we designed and synthesized a series of novel FAK PROTACs and the optimal PROTAC B5 exhibited potent FAK affinity with an IC50 value of 14.9 nM. Furthermore, in A549 cells, PROTAC B5 presented strong FAK degradation activity (86.4% degradation @ 10 nM), powerful antiproliferative activity (IC50 = 0.14 ± 0.01 μM) and inhibited cell migration and invasion in a concentration-dependent manner. Additionally, the in vitro preliminary drug-like properties evaluation of PROTAC B5 showed outstanding plasma stability and moderate membrane permeability. Together, current results provided a promising FAK PROTAC B5 as lead compound for cancer-related drug discovery and FAK-degradation functions exploration in biological systems.
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Affiliation(s)
- Yin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Ruifeng Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China; Department of Pharmacy, Shanxi Medical University, 56 Xinjiannan Road, Yingze District, Taiyuan, 030001, PR China
| | - Yu Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Lin Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Yanli Xue
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Jingkai Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Tianxiao Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Wenbo Yin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
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38
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Abstract
Targeted protein degradation has emerged from the chemical biology toolbox as one of the most exciting areas for novel therapeutic development across the pharmaceutical industry. The ability to induce the degradation, and not just inhibition, of target proteins of interest (POIs) with high potency and selectivity is a particularly attractive property for a protein degrader therapeutic. However, the physicochemical properties and mechanism of action for protein degraders can lead to unique pharmacokinetic (PK) and pharmacodynamic (PD) properties relative to traditional small molecule drugs, requiring a shift in perspective for translational pharmacology. In this review, we provide practical insights for building the PK-PD understanding of protein degraders in the context of translational drug development through the use of quantitative mathematical frameworks and standard experimental assays. Published datasets describing protein degrader pharmacology are used to illustrate the applicability of these insights. The learnings are consolidated into a translational PK-PD roadmap for targeted protein degradation that can enable a systematic, rational design workflow for protein degrader therapeutics.
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Affiliation(s)
- Derek W Bartlett
- Pharmacokinetics, Dynamics, & Metabolism, Pfizer Worldwide Research, Development and Medical, Pfizer Inc, San Diego, CA, USA.
| | - Adam M Gilbert
- Discovery Sciences, Pfizer Worldwide Research, Development and Medical, Pfizer Inc, Groton, CT, USA
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39
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Abstract
Methods to direct the degradation of protein targets with proximity-inducing molecules that coopt the cellular degradation machinery are advancing in leaps and bounds, and diverse modalities are emerging. The most used and well-studied approach is to hijack E3 ligases of the ubiquitin-proteasome system. E3 ligases use specific molecular recognition to determine which proteins in the cell are ubiquitinated and degraded. This review focuses on the structural determinants of E3 ligase recruitment of natural substrates and neo-substrates obtained through monovalent molecular glues and bivalent proteolysis-targeting chimeras. We use structures to illustrate the different types of substrate recognition and assess the basis for neo-protein-protein interactions in ternary complex structures. The emerging structural and mechanistic complexity is reflective of the diverse physiological roles of protein ubiquitination. This molecular insight is also guiding the application of structure-based design approaches to the development of new and existing degraders as chemical tools and therapeutics. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Angus D Cowan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
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40
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Pomella S, Cassandri M, Braghini MR, Marampon F, Alisi A, Rota R. New Insights on the Nuclear Functions and Targeting of FAK in Cancer. Int J Mol Sci 2022; 23:ijms23041998. [PMID: 35216114 PMCID: PMC8874710 DOI: 10.3390/ijms23041998] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 02/01/2023] Open
Abstract
Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase over-expressed and activated in both adult and pediatric cancers, where it plays important roles in the regulation of pathogenesis and progression of the malignant phenotype. FAK exerts its functions in cancer by two different ways: a kinase activity in the cytoplasm, mainly dependent on the integrin signaling, and a scaffolding activity into the nucleus by networking with different gene expression regulators. For this reason, FAK has to be considered a target with high therapeutic values. Indeed, evidence suggests that FAK targeting could be effective, either alone or in combination, with other already available treatments. Here, we propose an overview of the novel insights about FAK’s structure and nuclear functions, with a special focus on the recent findings concerning the roles of this protein in cancer. Additionally, we provide a recent update on FAK inhibitors that are currently in clinical trials for patients with cancer, and discuss the challenge and future directions of drug-based anti-FAK targeted therapies.
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Affiliation(s)
- Silvia Pomella
- Department of Oncohematology, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (S.P.); (M.C.)
| | - Matteo Cassandri
- Department of Oncohematology, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (S.P.); (M.C.)
- Department of Radiotherapy, Policlinico Umberto I, Sapienza University of Rome, 00185 Rome, Italy;
| | - Maria Rita Braghini
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy;
| | - Francesco Marampon
- Department of Radiotherapy, Policlinico Umberto I, Sapienza University of Rome, 00185 Rome, Italy;
| | - Anna Alisi
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy;
- Correspondence: (A.A.); (R.R.); Tel.: +39-06-68592186 (A.A.); +39-06-68592648 (R.R.)
| | - Rossella Rota
- Department of Oncohematology, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (S.P.); (M.C.)
- Correspondence: (A.A.); (R.R.); Tel.: +39-06-68592186 (A.A.); +39-06-68592648 (R.R.)
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41
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Abstract
Protein kinases have been highly fruitful targets for cancer drug discovery in the past two decades, while most of these drugs bind to the "adenosine triphosphate (ATP)-site" and inhibit kinase catalytic activity. Recently, accumulated evidence suggests that kinases possess functions beyond catalysis through their scaffolds, and the scaffolding functions could play critical roles in multiple cellular signaling and cell fate controls. Small molecules modulating the noncatalytic functions of kinases are rarely reported but emerge as new promising therapeutic strategies for various diseases. Herein, we summarize the characterized noncatalytic functions of kinases, and highlight the recent progress on developing small-molecule modulators of the noncatalytic functions of kinases. Mechanisms and characteristics of different kinds of modulators are also discussed. It is also speculated that targeting the noncatalytic functions would represent a new direction for kinase-based drug discovery.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China
| | - Weixue Huang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China
| | - Kaijie Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China
| | - Xiaomei Ren
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, People's Republic of China
| | - Ke Ding
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China.,International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, People's Republic of China.,The First Affiliated Hospital (Huaqiao Hospital), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, People's Republic of China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People's Republic of China
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42
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Shi M, Zhou X, Cai Y, Li P, Qin D, Yan X, Du M, Li S, Xu D. Inhibition mechanism of hydroxyproline-like small inhibitors to disorder HIF-VHL interaction by molecular dynamic simulations and binding free energy calculations. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2110198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Mingsong Shi
- State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xin Zhou
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yao Cai
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Penghui Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Dengxue Qin
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xinrong Yan
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Meng Du
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Shuo Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Dingguo Xu
- College of Chemistry, Sichuan University, Chengdu 610064, China
- Research Center for Material Genome Engineering, Sichuan University, Chengdu 610065, China
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