1
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Venturi A, Di Bona S, Desantis J, Eleuteri M, Bartalucci M, Baroni M, Benedetti P, Goracci L, Cruciani G. Between Theory and Practice: Computational/Experimental Integrated Approaches to Understand the Solubility and Lipophilicity of PROTACs. J Med Chem 2024; 67:16355-16380. [PMID: 39271471 DOI: 10.1021/acs.jmedchem.4c01235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
Emerging drug candidates more often fall in the beyond-rule-of-five chemical space. Among them, proteolysis targeting chimeras (PROTACs) have gained great attention in the past decade. Although physicochemical properties of small molecules accomplishing Lipinski's rule-of-five can now be easily predicted through models generated by large data collections, for PROTACs the knowledge is still limited and heterogeneous, hampering their prediction. Here, the kinetic solubility and the coefficient of distribution at pH 7.4 (LogD7.4) of 44 PROTACs, designed and synthesized to cover a wide chemical space, were measured. Their generally low solubility and high lipophilicity required an optimization of the experimental methods. Concerning the LogD7.4, several in silico prediction tools were tested, which were quite accurate for classical small molecules but provided dissimilar outcomes for PROTACs. Finally, in silico models for the prediction of PROTACs' kinetic solubility and LogD7.4 were proposed by combining in-house generated experimental data with 3D description of PROTACs' structures.
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Affiliation(s)
- Andrea Venturi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Stefano Di Bona
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Jenny Desantis
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Michela Eleuteri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Matteo Bartalucci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Massimo Baroni
- Kinetic Business Centre, Molecular Discovery Ltd., Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Paolo Benedetti
- Kinetic Business Centre, Molecular Discovery Ltd., Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, Perugia 06123, Italy
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2
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Pirie R, Stanway-Gordon HA, Stewart HL, Wilson KL, Patton S, Tyerman J, Cole DJ, Fowler K, Waring MJ. An analysis of the physicochemical properties of oral drugs from 2000 to 2022. RSC Med Chem 2024; 15:3125-3132. [PMID: 39309358 PMCID: PMC11411612 DOI: 10.1039/d4md00160e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/20/2024] [Indexed: 09/25/2024] Open
Abstract
Calculable physicochemical descriptors are a useful guide to assist compound design in medicinal chemistry. It is well established that controlling size, lipophilicity, hydrogen bonding, flexibility and shape, guided by descriptors that approximate to these properties, can greatly increase the chances of successful drug discovery. Many therapeutic targets and new modalities are incompatible with the optimal ranges of these properties and thus there is much interest in approaches to find oral drug candidates outside of this space. These considerations have been a focus for a while and hence we analysed the physicochemical properties of oral drugs approved by the FDA from 2000 to 2022 to assess if such concepts had influenced the output of the drug-discovery community. Our findings show that it is possible to find drug molecules that lie outside of the optimal descriptor ranges and that large molecules in particular (molecular weight >500 Da) can be oral drugs. The analysis suggests that this is more likely if lipophilicity, hydrogen bonding and flexibility are controlled. Crude physicochemical descriptors are useful in that regard but more accurate and robust means of understanding substructural classes, shape and conformation are likely to be required to improve the chances of success in this space.
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Affiliation(s)
- Rachael Pirie
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Harriet A Stanway-Gordon
- Cancer Research Horizons Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Hannah L Stewart
- Cancer Research Horizons Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Kirsty L Wilson
- Cancer Research Horizons Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Summer Patton
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Jack Tyerman
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Daniel J Cole
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Katherine Fowler
- Cancer Research Horizons Therapeutic Innovation, Jonas Webb Building Babraham Research Campus Cambridge CB22 3AT UK
| | - Michael J Waring
- Cancer Research Horizons Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
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3
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Choi HI, Choi J, Kim JW, Lee YH, Cho KH, Koo TS. Stability Evaluation and Pharmacokinetic Profiling of Vepdegestrant in Rodents Using Liquid Chromatography-Tandem Mass Spectrometry. Molecules 2024; 29:4048. [PMID: 39274896 PMCID: PMC11396746 DOI: 10.3390/molecules29174048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/16/2024] Open
Abstract
Vepdegestrant (formerly ARV-471), a novel proteolysis-targeting chimera (PROTAC), targets estrogen receptor alpha (ERα) for degradation, offering a promising option to treat advanced ER-positive breast cancer. We developed and validated a sensitive and rapid liquid chromatography-tandem mass spectrometry method to quantify vepdegestrant in rodent plasma using bavdegalutamide (formerly ARV-110) as an internal standard. Plasma samples were prepared with protein precipitation using acetonitrile and analyzed using reverse-phase C18 columns and a mobile phase of 10 mM ammonium formate in distilled water and acetonitrile. The method demonstrated linearity from 1 to 1000 ng/mL in mouse and rat plasma, meeting all validation criteria, and successfully applied to in vivo and in vitro studies. Pharmacokinetic analysis revealed low-to-moderate clearance (313.3, 1053 mL/h/kg) and oral bioavailability (17.91, 24.12%) of vepdegestrant in mice and rats, respectively. It was unstable in buffer solutions across pH 2-10 and in phosphate-buffered saline (pH 7.4), likely due to adsorption, but remained stable in mouse and rat plasma at varying temperatures. In liver microsomes, vepdegestrant exhibited moderate stability in rats but was stable in mice, dogs, and humans. These findings enhance the understanding of pharmacokinetic properties of vepdegestrant supporting further development of PROTAC drugs.
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Affiliation(s)
- Hae-In Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jinyoung Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jin Woo Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Yoon Ha Lee
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kwan Hyung Cho
- College of Pharmacy and Inje Institute of Pharmaceutical Sciences and Research, Inje University, Gimhae 50834, Republic of Korea
| | - Tae-Sung Koo
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
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4
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He Y, Zheng Y, Zhu C, Lei P, Yu J, Tang C, Chen H, Diao X. Radioactive ADME Demonstrates ARV-110's High Druggability Despite Low Oral Bioavailability. J Med Chem 2024; 67:14277-14291. [PMID: 39072617 DOI: 10.1021/acs.jmedchem.4c01104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) have emerged as potentially effective therapeutic medicines, but their high molecular weight and poor solubility directly impact their oral bioavailability. This work synthesized 14C-labeled bavdegalutamide (ARV-110) as a model compound of PROTACs to evaluate its ADME features. Compared with targeted antitumor drugs, the use of food increased oral bioavailability of ARV-110 in rats from 10.75% to 20.97%, which is still undesirable. However, the therapeutic effect of ARV-110 at a low dose was much better than that of enzalutamide, demonstrating the specific catalytic medicinal properties of PROTACs. Moreover, the specific distribution of ARV-110 in subcutaneous prostate tumors was determined by quantitative whole-body autoradiography (QWBA). Notably, the specificity and activity of PROTACs take precedence over their oral absorption, and high oral bioavailability is not necessary to produce excellent therapeutic effects. This work presents a roadmap for developing future PROTAC medications from a radioactive drug metabolism and pharmacokinetics (DMPK) perspective.
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Affiliation(s)
- Yifei He
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuandong Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chenggu Zhu
- Wuxi Beita Pharmatech Co., Ltd., Wuxi 214437, China
| | - Peng Lei
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jinghua Yu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | - Hao Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xingxing Diao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- XenoFinder Co., Ltd., Suzhou 215123, China
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5
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Kamaraj R, Ghosh S, Das S, Sen S, Kumar P, Majumdar M, Dasgupta R, Mukherjee S, Das S, Ghose I, Pavek P, Raja Karuppiah MP, Chuturgoon AA, Anand K. Targeted Protein Degradation (TPD) for Immunotherapy: Understanding Proteolysis Targeting Chimera-Driven Ubiquitin-Proteasome Interactions. Bioconjug Chem 2024; 35:1089-1115. [PMID: 38990186 PMCID: PMC11342303 DOI: 10.1021/acs.bioconjchem.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Targeted protein degradation or TPD, is rapidly emerging as a treatment that utilizes small molecules to degrade proteins that cause diseases. TPD allows for the selective removal of disease-causing proteins, including proteasome-mediated degradation, lysosome-mediated degradation, and autophagy-mediated degradation. This approach has shown great promise in preclinical studies and is now being translated to treat numerous diseases, including neurodegenerative diseases, infectious diseases, and cancer. This review discusses the latest advances in TPD and its potential as a new chemical modality for immunotherapy, with a special focus on the innovative applications and cutting-edge research of PROTACs (Proteolysis TArgeting Chimeras) and their efficient translation from scientific discovery to technological achievements. Our review also addresses the significant obstacles and potential prospects in this domain, while also offering insights into the future of TPD for immunotherapeutic applications.
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Affiliation(s)
- Rajamanikkam Kamaraj
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Subhrojyoti Ghosh
- Department
of Biotechnology, Indian Institute of Technology
Madras, Chennai 600036, India
| | - Souvadra Das
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Shinjini Sen
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Priyanka Kumar
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Madhurima Majumdar
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Renesa Dasgupta
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Sampurna Mukherjee
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Shrimanti Das
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Indrilla Ghose
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Petr Pavek
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Muruga Poopathi Raja Karuppiah
- Department
of Chemistry, School of Physical Sciences, Central University of Kerala, Tejaswini Hills, Periye, Kasaragod District, Kerala 671320, India
| | - Anil A. Chuturgoon
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Krishnan Anand
- Department
of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, Free State 9300, South Africa
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6
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Jones LH. Synthetic modification of protein surfaces to mediate induced-proximity pharmacology. RSC Med Chem 2024:d4md00388h. [PMID: 39185450 PMCID: PMC11342125 DOI: 10.1039/d4md00388h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024] Open
Abstract
Molecular glues and bifunctional small molecules, such as targeted protein degraders, induce protein proximity to mediate gain-of-function pharmacology. Emerging technologies that synthetically manipulate protein surfaces to create neoproteins, and the development of covalent chemical probes for intra- and inter-protein surface labeling are described. Ligand-directed protein surface modification strategies have the potential to enhance the induced-proximity pharmacology toolkit and expand the druggable proteome, and this Opinion considers the opportunities and challenges that lie ahead.
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Affiliation(s)
- Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute 360 Longwood Avenue Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston MA USA
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7
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Wang X, Su L, Niu C, Li X, Wang R, Li B, Liu S, Xu Y. Targeted degradation of KRAS protein in non-small cell lung cancer: Therapeutic strategies using liposomal PROTACs with enhanced cellular uptake and pharmacokinetic profiles. Drug Dev Res 2024; 85:e22241. [PMID: 39104176 DOI: 10.1002/ddr.22241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/28/2024] [Accepted: 07/14/2024] [Indexed: 08/07/2024]
Abstract
The role of KRAS mutation in non-small cell lung cancer (NSCLC) initiation and progression is well-established. However, "undruggable" KRAS protein poses the research of small molecule inhibitors a significant challenge. Addressing this, proteolysis-targeting chimeras (PROTACs) have become a cutting-edge treatment method, emphasizing protein degradation. A modified ethanol injection method was employed in this study to formulate liposomes encapsulating PROTAC drug LC-2 (LC-2 LPs). Precise surface modifications using cell-penetrating peptide R8 yielded R8-LC-2 liposomes (R8-LC-2 LPs). Comprehensive cellular uptake and cytotoxicity studies unveiled that R8-LC-2 LPs depended on concentration and time, showcasing the superior performance of R8-LC-2 LPs compared to normal liposomes. In vivo pharmacokinetic profiles demonstrated the capacity of DSPE-PEG2000 to prolong the circulation time of LC-2, leading to higher plasma concentrations compared to free LC-2. In vivo antitumor efficacy research underscored the remarkable ability of R8-LC-2 LPs to effectively suppress tumor growth. This study contributed to the exploration of enhanced therapeutic strategies for NSCLC, specifically focusing on the development of liposomal PROTACs targeting the "undruggable" KRAS protein. The findings provide valuable insights into the potential of this innovative approach, offering prospects for improved drug delivery and heightened antitumor efficacy.
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Affiliation(s)
- Xiaowen Wang
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs, School of Pharmacy, Yantai University, Yantai, Shandong, China
| | - Linyu Su
- MabPlex International, Yantai, Shandong, China
| | - Chong Niu
- Shandong Institute for Food and Drug Control, Jinan, Shandong, China
| | - Xiao Li
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs, School of Pharmacy, Yantai University, Yantai, Shandong, China
| | - Ruijie Wang
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs, School of Pharmacy, Yantai University, Yantai, Shandong, China
| | - Bo Li
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs, School of Pharmacy, Yantai University, Yantai, Shandong, China
| | - Sha Liu
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs, School of Pharmacy, Yantai University, Yantai, Shandong, China
| | - Yuwen Xu
- Shandong Institute for Food and Drug Control, Jinan, Shandong, China
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8
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Agarwal P, Reid DL, Amiji M. CNS delivery of targeted protein degraders. J Control Release 2024; 372:661-673. [PMID: 38936742 DOI: 10.1016/j.jconrel.2024.06.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
Heterobifunctional small molecule degraders are a subset of targeted protein degraders (TPDs), consisting of two ligands joined by a linker to induce proteasomal degradation of a target protein. As compared to traditional small molecules these compounds generally demonstrate inflated physicochemical properties, which may require innovative formulation strategies to enable their delivery and exert pharmacodynamic effect. The blood brain barrier (BBB) serves an essential function in human physiology, but its presence requires advanced approaches for treating central nervous system (CNS) diseases. By integrating emerging modalities like TPDs with conventional concepts of drug delivery, novel strategies to overcome the BBB can be developed. Amongst the available routes, lipid and polymer-based long-acting delivery seems to be the most amenable to TPDs, due to their ability to encapsulate lipophilic cargo and potential to be functionalized for targeted delivery. Another key consideration will be understanding E3 ligase expression in the different regions of the brain. Discovery of new brain or CNS disease specific E3 ligases could help overcome some of the barriers currently associated with CNS delivery of TPDs. This review discusses the current strategies that exist to overcome and improve therapeutic delivery of TPDs to the CNS.
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Affiliation(s)
- Prashant Agarwal
- Drug Product Technologies, Process Development, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, United States of America; Department of Chemical Engineering, College of Engineering, Northeastern University, 360 Huntington Ave, Boston, MA 02115, United States of America
| | - Darren L Reid
- Drug Product Technologies, Process Development, Amgen, Inc., 360 Binney St, Cambridge, MA 02142, United States of America
| | - Mansoor Amiji
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, 360 Huntington Ave, Boston, MA 02115, United States of America; Department of Chemical Engineering, College of Engineering, Northeastern University, 360 Huntington Ave, Boston, MA 02115, United States of America.
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9
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Schade M, Scott JS, Hayhow TG, Pike A, Terstiege I, Ahlqvist M, Johansson JR, Diene CR, Fallan C, Balazs AYS, Chiarparin E, Wilson D. Structural and Physicochemical Features of Oral PROTACs. J Med Chem 2024. [PMID: 39078401 DOI: 10.1021/acs.jmedchem.4c01017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Achieving oral bioavailability with Proteolysis Targeting Chimeras (PROTACs) is a key challenge. Here, we report the in vivo pharmacokinetic properties in mouse, rat, and dog of four clinical oral PROTACs and compare with an internally derived data set. We use NMR to determine 3D molecular conformations and structural preorganization free in solution, and we introduce the new experimental descriptors, solvent-exposed H-bond donors (eHBD), and acceptors (eHBA). We derive an upper limit of eHBD ≤ 2 for oral PROTACs in apolar environments and show a greater tolerance for other properties (eHBA, polarity, lipophilicity, and molecular weight) than for Rule-of-5 compliant oral drugs. Within a set of structurally related PROTACs, we show that examples with eHBD > 2 have much lower oral bioavailability than those that have eHBD ≤ 2. We summarize our findings as an experimental "Rule-of-oral-PROTACs" in order to assist medicinal chemists to achieve oral bioavailability in this challenging space.
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Affiliation(s)
- Markus Schade
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - James S Scott
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Thomas G Hayhow
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Andy Pike
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Ina Terstiege
- Chemistry and DMPK, Research and Early Development, Respiratory and Immunology, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 43183, Sweden
| | - Marie Ahlqvist
- Chemistry and DMPK, Research and Early Development, Respiratory and Immunology, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 43183, Sweden
| | - Johan R Johansson
- Chemistry and DMPK, Research and Early Development, Respiratory and Immunology, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 43183, Sweden
| | - Coura R Diene
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Charlene Fallan
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Amber Y S Balazs
- Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Elisabetta Chiarparin
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - David Wilson
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
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10
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Yadav J, Maldonato BJ, Roesner JM, Vergara AG, Paragas EM, Aliwarga T, Humphreys S. Enzyme-mediated drug-drug interactions: a review of in vivo and in vitro methodologies, regulatory guidance, and translation to the clinic. Drug Metab Rev 2024:1-33. [PMID: 39057923 DOI: 10.1080/03602532.2024.2381021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
Enzyme-mediated pharmacokinetic drug-drug interactions can be caused by altered activity of drug metabolizing enzymes in the presence of a perpetrator drug, mostly via inhibition or induction. We identified a gap in the literature for a state-of-the art detailed overview assessing this type of DDI risk in the context of drug development. This manuscript discusses in vitro and in vivo methodologies employed during the drug discovery and development process to predict clinical enzyme-mediated DDIs, including the determination of clearance pathways, metabolic enzyme contribution, and the mechanisms and kinetics of enzyme inhibition and induction. We discuss regulatory guidance and highlight the utility of in silico physiologically-based pharmacokinetic modeling, an approach that continues to gain application and traction in support of regulatory filings. Looking to the future, we consider DDI risk assessment for targeted protein degraders, an emerging small molecule modality, which does not have recommended guidelines for DDI evaluation. Our goal in writing this report was to provide early-career researchers with a comprehensive view of the enzyme-mediated pharmacokinetic DDI landscape to aid their drug development efforts.
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Affiliation(s)
- Jaydeep Yadav
- Department of Pharmacokinetics, Dynamics, Metabolism & Bioanalytics (PDMB), Merck & Co., Inc., Boston, MA, USA
| | - Benjamin J Maldonato
- Department of Nonclinical Development and Clinical Pharmacology, Revolution Medicines, Inc., Redwood City, CA, USA
| | - Joseph M Roesner
- Department of Pharmacokinetics, Dynamics, Metabolism & Bioanalytics (PDMB), Merck & Co., Inc., Boston, MA, USA
| | - Ana G Vergara
- Department of Pharmacokinetics, Dynamics, Metabolism & Bioanalytics (PDMB), Merck & Co., Inc., Rahway, NJ, USA
| | - Erickson M Paragas
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, South San Francisco, CA, USA
| | - Theresa Aliwarga
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, South San Francisco, CA, USA
| | - Sara Humphreys
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, South San Francisco, CA, USA
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11
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Jarusiewicz JA, Yoshimura S, Actis M, Li Y, Fu X, Yang L, Narina S, Pruett-Miller SM, Zhou S, Wang X, High AA, Nishiguchi G, Yang JJ, Rankovic Z. Development of an Orally Bioavailable LCK PROTAC Degrader as a Potential Therapeutic Approach to T-Cell Acute Lymphoblastic Leukemia. J Med Chem 2024; 67:11868-11884. [PMID: 38973320 DOI: 10.1021/acs.jmedchem.4c00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Despite significant advances over recent years, the treatment of T cell acute lymphoblastic leukemia (T-ALL) remains challenging. We have recently shown that a subset of T-ALL cases exhibited constitutive activation of the lymphocyte-specific protein tyrosine kinase (LCK) and were consequently responsive to treatments with LCK inhibitors and degraders such as dasatinib and dasatinib-based PROTACs. Here we report the design, synthesis and in vitro/vivo evaluation of SJ45566, a potent and orally bioavailable LCK PROTAC.
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Affiliation(s)
- Jamie A Jarusiewicz
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Satoshi Yoshimura
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Marisa Actis
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yong Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xiang Fu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Shilpa Narina
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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12
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Xu M, Fu J, Pei Y, Li M, Kan W, Yan R, Xia C, Ma J, Wang P, Zhang Y, Gao Y, Yang Y, Zhou Y, Li J, Zhou B. Discovery of a Highly Potent, Selective and Efficacious USP7 Degrader for the Treatment of Acute Lymphoblastic Leukemia. J Med Chem 2024. [PMID: 39028938 DOI: 10.1021/acs.jmedchem.4c01134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
USP7 is an attractive therapeutic target for cancers, especially for acute lymphoblastic leukemia (ALL) with wild-type p53. Herein, we report the discovery of XM-U-14 as a highly potent, selective and efficacious USP7 proteolysis-targeting chimera degrader. XM-U-14 achieves DC50 values of 0.74 nM and Dmax of 93% in inducing USP7 degradation in RS4;11 cell lines, and also significantly inhibits ALL cell growth. XM-U-14 even at 5 mg/kg dosed daily effectively inhibits RS4;11 tumor growth with 64.7% tumor regressions and causes no signs of toxicity in mice. XM-U-14 is a promising USP7 degrader for further optimization for ALL treatment.
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Affiliation(s)
- Miaomiao Xu
- 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
| | - 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
| | - Mengna Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Weijuan Kan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Ruyu Yan
- 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
| | - Chaoyue Xia
- 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
| | - Jingkun Ma
- 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
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Tsuihang New District, Zhongshan, Guangdong 528400, China
| | - Peipei Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yan Zhang
- 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
| | - Yue Gao
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, 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
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, 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
| | - 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
- 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, Tsuihang New District, Zhongshan, Guangdong 528400, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, 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
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, 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, Tsuihang New District, Zhongshan, Guangdong 528400, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, 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
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, 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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13
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Rynn C, Duevel HM. Meeting report: DMPK optimisation strategies and quantitative translational PKPD frameworks to predict human PK and efficacious dose of targeted protein degraders. Xenobiotica 2024:1-5. [PMID: 38934475 DOI: 10.1080/00498254.2024.2369787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024]
Affiliation(s)
- Caroline Rynn
- Department of Pharmaceutical Sciences, Roche Products Ltd, Welwyn, UK
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14
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Ma X, Wang X, Chen F, Zou W, Ren J, Xin L, He P, Liang J, Xu Z, Dong C, Lan K, Wu S, Zhou HB. Novel Acyl Thiourea-Based Hydrophobic Tagging Degraders Exert Potent Anti-Influenza Activity through Two Distinct Endonuclease Polymerase Acidic-Targeted Degradation Pathways. J Med Chem 2024; 67:8791-8816. [PMID: 38775356 DOI: 10.1021/acs.jmedchem.4c00131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
The spread of the influenza virus has caused devastating pandemics and huge economic losses worldwide. Antiviral drugs with diverse action modes are urgently required to overcome the challenges of viral mutation and drug resistance, and targeted protein degradation strategies constitute excellent candidates for this purpose. Herein, the first degradation of the influenza virus polymerase acidic (PA) protein using small-molecule degraders developed by hydrophobic tagging (HyT) technology to effectively combat the influenza virus was reported. The SAR results revealed that compound 19b with Boc2-(L)-Lys demonstrated excellent inhibitory activity against A/WSN/33/H1N1 (EC50 = 0.015 μM) and amantadine-resistant strain (A/PR/8/H1N1), low cytotoxicity, high selectivity, substantial degradation ability, and good drug-like properties. Mechanistic studies demonstrated that the proteasome system and autophagic lysosome pathway were the potential drivers of these HyT degraders. Thus, this study provides a powerful tool for investigating the targeted degradation of influenza virus proteins and for antiviral drug development.
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Affiliation(s)
- Xiaoyu Ma
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xueyun Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Feifei Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenting Zou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Junrui Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lilan Xin
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Pei He
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jinsen Liang
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhichao Xu
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Chune Dong
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hai-Bing Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Provincial Key Laboratory of Developmentally Originated Disease, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Wuhan University, Wuhan 430071, China
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15
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Wu H, Murray J, Ishisoko N, Frommlet A, Deshmukh G, DiPasquale A, Mulvihill MM, Zhang D, Quinn JG, Blake RA, Fairbrother WJ, Fuhrmann J. Potency-Enhanced Peptidomimetic VHL Ligands with Improved Oral Bioavailability. J Med Chem 2024; 67:8585-8608. [PMID: 38809766 DOI: 10.1021/acs.jmedchem.3c02203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The von Hippel-Lindau (VHL) protein plays a pivotal role in regulating the hypoxic stress response and has been extensively studied and utilized in the targeted protein degradation field, particularly in the context of bivalent degraders. In this study, we present a comprehensive peptidomimetic structure-activity relationship (SAR) approach, combined with cellular NanoBRET target engagement assays to enhance the existing VHL ligands. Through systematic modifications of the molecule, we identified the 1,2,3-triazole group as an optimal substitute of the left-hand side amide bond that yields 10-fold higher binding activity. Moreover, incorporating conformationally constrained alterations on the methylthiazole benzylamine moiety led to the development of highly potent VHL ligands with picomolar binding affinity and significantly improved oral bioavailability. We anticipate that our optimized VHL ligand, GNE7599, will serve as a valuable tool compound for investigating the VHL pathway and advancing the field of targeted protein degradation.
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Affiliation(s)
- Hao Wu
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jeremy Murray
- Department of Structural Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Noriko Ishisoko
- Department of Biochemical & Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Alexandra Frommlet
- Department of Biochemical & Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Gauri Deshmukh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Antonio DiPasquale
- Department of Small Molecule Pharmaceutical Sciences, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Melinda M Mulvihill
- Department of Biochemical & Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Donglu Zhang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - John G Quinn
- Department of Biochemical & Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert A Blake
- Department of Biochemical & Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Wayne J Fairbrother
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jakob Fuhrmann
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
- Department of Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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16
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Thompson PE, Shortt J. Defeating MYC with drug combinations or dual-targeting drugs. Trends Pharmacol Sci 2024; 45:490-502. [PMID: 38782688 DOI: 10.1016/j.tips.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
Members of the MYC family of proteins are a major target for cancer drug discovery, but the development of drugs that block MYC-driven cancers has not yet been successful. Approaches to achieve success may include the development of combination therapies or dual-acting drugs that target MYC at multiple nodes. Such treatments hold the possibility of additive or synergistic activity, potentially reducing side effect profiles and the emergence of resistance. In this review, we examine the prominent MYC-related targets and highlight those that have been targeted in combination and/or dual-target approaches. Finally, we explore the challenges of combination and dual-target approaches from a drug development perspective.
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Affiliation(s)
- Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.
| | - Jake Shortt
- Blood Cancer Therapeutics Laboratory, School of Clinical Sciences at Monash Health, Faculty of Medicine Nursing and Health Sciences, Monash University, Melbourne, Victoria 3168, Australia; Monash Hematology, Monash Health, Melbourne, Victoria 3168, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria 3000, Australia
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17
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Leon ASC, Waterman KC, Wang G, Wang L, Cai T, Zhang X. Accelerated stability modeling of recrystallization from amorphous solid Dispersions: A Griseofulvin/HPMC-AS case study. Int J Pharm 2024; 657:124189. [PMID: 38701906 DOI: 10.1016/j.ijpharm.2024.124189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/14/2024] [Accepted: 04/30/2024] [Indexed: 05/05/2024]
Abstract
Amorphous solid dispersions (ASDs) represent an important approach for enhancing oral bioavailability for poorly water soluble compounds; however, assuring that these ASDs do not recrystallize to a significant extent during storage can be time-consuming. Therefore, various efforts have been undertaken to predict ASD crystallization levels with kinetic models. However, only limited success has been achieved due to limits on crystal content quantification methods and the complexity of crystallization kinetics. To increase the prediction accuracy, the accelerated stability assessment program (ASAP), employing isoconversion (time to hit a specification limit) and a modified Arrhenius approach, are employed here for predictive shelf-life modeling. In the current study, a model ASD was prepared by spray drying griseofulvin and HPMC-AS-LF. This ASD was stressed under a designed combinations of temperature, relative humidity and time with the conditions set to ensure stressing was carried out below the glass transition temperature (Tg) of the ASD. Crystal content quantification method by X-ray powder diffraction (XRPD) with sufficient sensitivity was developed and employed for stressed ASD. Crystallization modeling of the griseofulvin ASD using ASAPprime® demonstrated good agreement with long-term (40 °C/75 %RH) crystallinity levels and support the use of this type of accelerated stability studies for further improving ASD shelf-life prediction accuracy.
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Affiliation(s)
| | | | - Guanhua Wang
- Level 2, Block C3, Maple Science Park, Qixia District, Nanjing 210048 China
| | - Likun Wang
- Level 2, Block C3, Maple Science Park, Qixia District, Nanjing 210048 China.
| | - Ting Cai
- China Pharmaceutical University, 24 Tongjiaxiang Road, Nanjing 210009 China
| | - Xiaohua Zhang
- 99 HengGuang Road, Nanjing Development Zone, Nanjing 210038 China
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18
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Wang C, Zhang Y, Chen W, Wu Y, Xing D. New-generation advanced PROTACs as potential therapeutic agents in cancer therapy. Mol Cancer 2024; 23:110. [PMID: 38773495 PMCID: PMC11107062 DOI: 10.1186/s12943-024-02024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) technology has garnered significant attention over the last 10 years, representing a burgeoning therapeutic approach with the potential to address pathogenic proteins that have historically posed challenges for traditional small-molecule inhibitors. PROTACs exploit the endogenous E3 ubiquitin ligases to facilitate degradation of the proteins of interest (POIs) through the ubiquitin-proteasome system (UPS) in a cyclic catalytic manner. Despite recent endeavors to advance the utilization of PROTACs in clinical settings, the majority of PROTACs fail to progress beyond the preclinical phase of drug development. There are multiple factors impeding the market entry of PROTACs, with the insufficiently precise degradation of favorable POIs standing out as one of the most formidable obstacles. Recently, there has been exploration of new-generation advanced PROTACs, including small-molecule PROTAC prodrugs, biomacromolecule-PROTAC conjugates, and nano-PROTACs, to improve the in vivo efficacy of PROTACs. These improved PROTACs possess the capability to mitigate undesirable physicochemical characteristics inherent in traditional PROTACs, thereby enhancing their targetability and reducing off-target side effects. The new-generation of advanced PROTACs will mark a pivotal turning point in the realm of targeted protein degradation. In this comprehensive review, we have meticulously summarized the state-of-the-art advancements achieved by these cutting-edge PROTACs, elucidated their underlying design principles, deliberated upon the prevailing challenges encountered, and provided an insightful outlook on future prospects within this burgeoning field.
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Affiliation(s)
- Chao Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Wujun Chen
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China
| | - Yudong Wu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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19
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Zhang D, Ma B, Dragovich PS, Ma L, Chen S, Chen EC, Ye X, Liu J, Pizzano J, Bortolon E, Chan E, Zhang X, Chen YC, Levy ES, Yauch RL, Khojasteh SC, Hop CECA. Tissue distribution and retention drives efficacy of rapidly clearing VHL-based PROTACs. COMMUNICATIONS MEDICINE 2024; 4:87. [PMID: 38755248 PMCID: PMC11099041 DOI: 10.1038/s43856-024-00505-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Proteolysis-targeting chimeras (PROTACs) are being developed for therapeutic use. However, they have poor pharmacokinetic profiles and their tissue distribution kinetics are not known. METHODS A typical von Hippel-Lindau tumor suppressor (VHL)-PROTAC 14C-A947 (BRM degrader)-was synthesized and its tissue distribution kinetics was studied by quantitative whole-body autoradiography (QWBA) and tissue excision in rats following IV dosing. Bile duct-cannulated (BDC) rats allowed the elucidation of in vivo clearance pathways. Distribution kinetics was evaluated in the tissues and tumors of mice to support PK-PD correlation. In vitro studies enabled the evaluation of cell uptake mechanisms and cell retention properties. RESULTS Here, we show that A947 quickly distributes into rat tissues after IV dosing, where it accumulates and is retained in tissues such as the lung and liver although it undergoes fast clearance from circulation. Similar uptake/retention kinetics enable tumor growth inhibition over 2-3 weeks in a lung cancer model. A947 quickly excretes in the bile of rats. Solute carrier (SLC) transporters are involved in hepatocyte uptake of PROTACs. Sustained BRM protein degradation is seen after extensive washout that supports prolonged cell retention of A947 in NCI-H1944 cells. A947 tissue exposure and pharmacodynamics are inversely correlated in tumors. CONCLUSIONS Plasma sampling for VHL-PROTAC does not represent the tissue concentrations necessary for efficacy. Understanding of tissue uptake and retention could enable less frequent IV administration to be used for therapeutic dosing.
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Affiliation(s)
- Donglu Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Bin Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Li Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Shu Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Eugene C Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xiaofen Ye
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Joyce Liu
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jennifer Pizzano
- Arvinas; 5 Science Park, 395 Winchester Ave, New Haven, CT, 06511, USA
| | | | - Emily Chan
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xing Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yi-Chen Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Robert L Yauch
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
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20
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Hayhow TG, Williamson B, Lawson M, Cureton N, Braybrooke EL, Campbell A, Carbajo RJ, Cheraghchi-Bashi A, Chiarparin E, Diène CR, Fallan C, Fisher DI, Goldberg FW, Hopcroft L, Hopcroft P, Jackson A, Kettle JG, Klinowska T, Künzel U, Lamont G, Lewis HJ, Maglennon G, Martin S, Gutierrez PM, Morrow CJ, Nikolaou M, Nissink JWM, O'Shea P, Polanski R, Schade M, Scott JS, Smith A, Weber J, Wilson J, Yang B, Crafter C. Metabolism-driven in vitro/in vivo disconnect of an oral ERɑ VHL-PROTAC. Commun Biol 2024; 7:563. [PMID: 38740899 DOI: 10.1038/s42003-024-06238-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Targeting the estrogen receptor alpha (ERα) pathway is validated in the clinic as an effective means to treat ER+ breast cancers. Here we present the development of a VHL-targeting and orally bioavailable proteolysis-targeting chimera (PROTAC) degrader of ERα. In vitro studies with this PROTAC demonstrate excellent ERα degradation and ER antagonism in ER+ breast cancer cell lines. However, upon dosing the compound in vivo we observe an in vitro-in vivo disconnect. ERα degradation is lower in vivo than expected based on the in vitro data. Investigation into potential causes for the reduced maximal degradation reveals that metabolic instability of the PROTAC linker generates metabolites that compete for binding to ERα with the full PROTAC, limiting degradation. This observation highlights the requirement for metabolically stable PROTACs to ensure maximal efficacy and thus optimisation of the linker should be a key consideration when designing PROTACs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Anne Jackson
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bin Yang
- Oncology R&D, AstraZeneca, Waltham, MA, USA
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21
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Lei YH, Tang Q, Ni Y, Li CH, Luo P, Huang K, Chen X, Zhu YX, Wang NY. Design, synthesis and biological evaluation of new RNF126-based p300/CBP degraders. Bioorg Chem 2024; 148:107427. [PMID: 38728911 DOI: 10.1016/j.bioorg.2024.107427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/22/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
Histone acetyltransferase CREB-binding protein (CBP) and its homologous protein p300 are key transcriptional activators that can activate oncogene transcription, which present promising targets for cancer therapy. Here, we designed and synthesized a series of p300/CBP targeted low molecular weight PROTACs by assembling the covalent ligand of RNF126 E3 ubiquitin ligase and the bromodomain ligand of the p300/CBP. The optimal molecule A8 could effectively degrade p300 and CBP through the ubiquitin-proteasome system in time- and concentration-dependent manners, with half-maximal degradation (DC50) concentrations of 208.35/454.35 nM and 82.24/79.45 nM for p300/CBP in MV4-11 and Molm13 cell lines after 72 h of treatment. And the degradation of p300/CBP by A8 is dependent on the ubiquitin-proteasome pathway and its simultaneous interactions with the target proteins and RNF126. A8 exhibits good antiproliferative activity in a series of p300/CBP-dependent cancer cells. It could transcriptionally inhibit the expression of c-Myc, induce cell cycle arrest in the G0/G1 phase and apoptosis in MV4-11 cells. This study thus provided us a new chemotype for the development of drug-like PROTACs targeting p300/CBP, which is expected to be applied in cancer therapy.
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Affiliation(s)
- Yan-Hua Lei
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Qing Tang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Yang Ni
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Cai-Hua Li
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Peng Luo
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Kun Huang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Xin Chen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Yong-Xia Zhu
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology, Chengdu, China.
| | - Ning-Yu Wang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China.
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22
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Ito T. Protein degraders - from thalidomide to new PROTACs. J Biochem 2024; 175:507-519. [PMID: 38140952 DOI: 10.1093/jb/mvad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Recently, the development of protein degraders (protein-degrading compounds) has prominently progressed. There are two remarkable classes of protein degraders: proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs). Almost 70 years have passed since thalidomide was initially developed as a sedative-hypnotic drug, which is currently recognized as one of the most well-known MGDs. During the last two decades, a myriad of PROTACs and MGDs have been developed, and the molecular mechanism of action (MOA) of thalidomide was basically elucidated, including identifying its molecular target cereblon (CRBN). CRBN forms a Cullin Ring Ligase 4 with Cul4 and DDB1, whose substrate specificity is controlled by its binding ligands. Thalidomide, lenalidomide and pomalidomide, three CRBN-binding MGDs, were clinically approved to treat several intractable diseases (including multiple myeloma). Several other MGDs and CRBN-based PROTACs (ARV-110 and AVR-471) are undergoing clinical trials. In addition, several new related technologies regarding PROTACs and MGDs have also been developed, and achievements of protein degraders impact not only therapeutic fields but also basic biological science. In this article, I introduce the history of protein degraders, from the development of thalidomide to the latest PROTACs and related technologies.
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Affiliation(s)
- Takumi Ito
- Institute of Medical Science, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
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23
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Kuemper S, Cairns AG, Birchall K, Yao Z, Large JM. Targeted protein degradation in CNS disorders: a promising route to novel therapeutics? Front Mol Neurosci 2024; 17:1370509. [PMID: 38685916 PMCID: PMC11057381 DOI: 10.3389/fnmol.2024.1370509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Targeted protein degradation (TPD) is a rapidly expanding field, with various PROTACs (proteolysis-targeting chimeras) in clinical trials and molecular glues such as immunomodulatory imide drugs (IMiDs) already well established in the treatment of certain blood cancers. Many current approaches are focused on oncology targets, leaving numerous potential applications underexplored. Targeting proteins for degradation offers a novel therapeutic route for targets whose inhibition remains challenging, such as protein aggregates in neurodegenerative diseases. This mini review focuses on the prospect of utilizing TPD for neurodegenerative disease targets, particularly PROTAC and molecular glue formats and opportunities for novel CNS E3 ligases. Some key challenges of utilizing such modalities including molecular design of degrader molecules, drug delivery and blood brain barrier penetrance will be discussed.
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Affiliation(s)
- Sandra Kuemper
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, United Kingdom
| | - Andrew G. Cairns
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, United Kingdom
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24
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Rej RK, Allu SR, Roy J, Acharyya RK, Kiran INC, Addepalli Y, Dhamodharan V. Orally Bioavailable Proteolysis-Targeting Chimeras: An Innovative Approach in the Golden Era of Discovering Small-Molecule Cancer Drugs. Pharmaceuticals (Basel) 2024; 17:494. [PMID: 38675453 PMCID: PMC11054475 DOI: 10.3390/ph17040494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) are an emerging therapeutic modality that show promise to open a target space not accessible to conventional small molecules via a degradation-based mechanism. PROTAC degraders, due to their bifunctional nature, which is categorized as 'beyond the Rule of Five', have gained attention as a distinctive therapeutic approach for oral administration in clinical settings. However, the development of PROTACs with adequate oral bioavailability remains a significant hurdle, largely due to their large size and less than ideal physical and chemical properties. This review encapsulates the latest advancements in orally delivered PROTACs that have entered clinical evaluation as well as developments highlighted in recent scholarly articles. The insights and methodologies elaborated upon in this review could be instrumental in supporting the discovery and refinement of novel PROTAC degraders aimed at the treatment of various human cancers.
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Affiliation(s)
- Rohan Kalyan Rej
- Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (S.R.A.); (R.K.A.)
| | - Srinivasa Rao Allu
- Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (S.R.A.); (R.K.A.)
| | - Joyeeta Roy
- Rogel Cancer Center, Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Ranjan Kumar Acharyya
- Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (S.R.A.); (R.K.A.)
| | - I. N. Chaithanya Kiran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA;
| | - Yesu Addepalli
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - V. Dhamodharan
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Wuerzburg, Am Hubland, 97074 Würzburg, Germany;
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25
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Wang X, Zhao Y, Li X, Zhang Q, He J, Liu Y, Li M, Luo Z. Liposomal STAT3-Degrading PROTAC Prodrugs Promote Anti-Hepatocellular Carcinoma Immunity via Chemically Reprogramming Cancer Stem Cells. NANO LETTERS 2024. [PMID: 38598369 DOI: 10.1021/acs.nanolett.4c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Cancer stem cells (CSCs) with hyperactivated signal transducer and activator of transcription 3 (STAT3) are a major driver of hepatocellular carcinoma (HCC). Herein, we report a nanointegrative proteolysis-targeting chimera (PROTAC)-based STAT3 degradation strategy that enables efficient chemical reprogramming of HCC-associated CSCs, which potently inhibits CSC growth while evoking anti-HCC immune responses. The PROTAC prodrug was synthesized by conjugating the STAT3 binding domain (inS3) with a thioketal-caged E3 ligase ligand (VL-TK) via an oligo(ethylene glycol) linker (OEG) with tuned length and flexibility and encapsulating it in cRGD-modified cationic liposomes for CSC-targeted delivery while facilitating their lysosomal escape. The PROTAC prodrugs were activated by the upregulated ROS levels in CSCs and efficiently degraded STAT3 for chemical reprogramming, which would not only impair their stemness features but also remodel the immunosuppressive TME into an immunosupportive state to boost anti-HCC immunity. This strategy provides an approach for improving HCC treatment in clinics.
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Affiliation(s)
- Xuan Wang
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Youbo Zhao
- Center for Tissue Engineering and Stem Cell Research, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, China
| | - Xin Li
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
| | - Qiqi Zhang
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Jinming He
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Yingqi Liu
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Menghuan Li
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Zhong Luo
- School of Life Science, Chongqing University, Chongqing 400044, China
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26
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Hernández-Morán BA, Taylor G, Lorente-Macías Á, Wood AJ. Degron tagging for rapid protein degradation in mice. Dis Model Mech 2024; 17:dmm050613. [PMID: 38666498 PMCID: PMC11073515 DOI: 10.1242/dmm.050613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
Degron tagging allows proteins of interest to be rapidly degraded, in a reversible and tuneable manner, in response to a chemical stimulus. This provides numerous opportunities for understanding disease mechanisms, modelling therapeutic interventions and constructing synthetic gene networks. In recent years, many laboratories have applied degron tagging successfully in cultured mammalian cells, spurred by rapid advances in the fields of genome editing and targeted protein degradation. In this At a Glance article, we focus on recent efforts to apply degron tagging in mouse models, discussing the distinct set of challenges and opportunities posed by the in vivo environment.
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Affiliation(s)
- Brianda A. Hernández-Morán
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Gillian Taylor
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Álvaro Lorente-Macías
- Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XR, UK
| | - Andrew J. Wood
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
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27
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Apprato G, Poongavanam V, Garcia Jimenez D, Atilaw Y, Erdelyi M, Ermondi G, Caron G, Kihlberg J. Exploring the chemical space of orally bioavailable PROTACs. Drug Discov Today 2024; 29:103917. [PMID: 38360147 DOI: 10.1016/j.drudis.2024.103917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
A principal challenge in the discovery of proteolysis targeting chimeras (PROTACs) as oral medications is their bioavailability. To facilitate drug design, it is therefore essential to identify the chemical space where orally bioavailable PROTACs are more likely to be situated. To this aim, we extracted structure-bioavailability insights from published data using traditional 2D descriptors, thereby shedding light on their potential and limitations as drug design tools. Subsequently, we describe cutting-edge experimental, computational and hybrid design strategies based on 3D descriptors, which show promise for enhancing the probability of discovering PROTACs with high oral bioavailability.
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Affiliation(s)
- Giulia Apprato
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | | | - Diego Garcia Jimenez
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy.
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden.
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28
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Guo Y, Li X, Xie Y, Wang Y. What influences the activity of Degrader-Antibody conjugates (DACs). Eur J Med Chem 2024; 268:116216. [PMID: 38387330 DOI: 10.1016/j.ejmech.2024.116216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
The targeted protein degradation (TPD) technology employing proteolysis-targeting chimeras (PROTACs) has been widely applied in drug chemistry and chemical biology for the treatment of cancer and other diseases. PROTACs have demonstrated significant advantages in targeting undruggable targets and overcoming drug resistance. However, despite the efficient degradation of targeted proteins achieved by PROTACs, they still face challenges related to selectivity between normal and cancer cells, as well as issues with poor membrane permeability due to their substantial molecular weight. Additionally, the noteworthy toxicity resulting from off-target effects also needs to be addressed. To solve these issues, Degrader-Antibody Conjugates (DACs) have been developed, leveraging the targeting and internalization capabilities of antibodies. In this review, we elucidates the characteristics and distinctions between DACs, and traditional Antibody-drug conjugates (ADCs). Meanwhile, we emphasizes the significance of DACs in facilitating the delivery of PROTACs and delves into the impact of various components on DAC activity. These components include antibody targets, drug-antibody ratio (DAR), linker types, PROTACs targets, PROTACs connections, and E3 ligase ligands. The review also explores the suitability of different targets (antibody targets or PROTACs targets) for DACs, providing insights to guide the design of PROTACs better suited for antibody conjugation.
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Affiliation(s)
- Yaolin Guo
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China
| | - Xiaoxue Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yang Xie
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China
| | - Yuxi Wang
- Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, Sichuan, China.
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29
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Cuyckens F, Hvenegaard MG, Cassidy KC, Spracklin DK, James AD, Pedersen ML, Scarfe G, Wagner DS, Georgi K, Schulz SI, Schieferstein H, Bjornsdottir I, Romeo AA, Da Violante G, Blech S, Moliner P, Young GC. Recommendations on the Use of Multiple Labels in Human Mass Balance Studies. Drug Metab Dispos 2024; 52:153-158. [PMID: 38216306 DOI: 10.1124/dmd.123.001429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024] Open
Abstract
The administration of radiolabeled drug candidates is considered the gold standard in absorption, distribution, metabolism, and excretion studies for small-molecule drugs since it allows facile and accurate quantification of parent drug, metabolites, and total drug-related material independent of the compound structure. The choice of the position of the radiolabel, typically 14C or 3H, is critical to obtain relevant information. Sometimes, a biotransformation reaction may lead to cleavage of a part of the molecule. As a result, only the radiolabeled portion can be followed, and information on the fate of the nonlabeled metabolite may be lost. Synthesis and administration of two or more radiolabeled versions of the parent drug as a mixture or in separate studies may resolve this issue but comes with additional challenges. In this paper, we address the questions that may be considered to help make the right choice whether to use a single or multiple radiolabel approach and discuss the pros and cons of different multiple-labeling strategies that can be taken as well as alternative methods that allow the nonlabeled part of the molecule to be followed. SIGNIFICANCE STATEMENT: Radiolabeled studies are the gold standard in drug metabolism research, but molecules can undergo cleavage with loss of the label. This often results in discussions around potential use of multiple labels, which seem to be occurring with increased frequency since an increasing proportion of the small-molecule drugs are tending towards larger molecular weights. This review provides insight and decision criteria in considering a multiple-label approach as well as pros and cons of different strategies that can be followed.
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Affiliation(s)
- Filip Cuyckens
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Mette G Hvenegaard
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Kenneth C Cassidy
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Douglas K Spracklin
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Alexander D James
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Mette L Pedersen
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Graeme Scarfe
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - David S Wagner
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Katrin Georgi
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Simone I Schulz
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Hanno Schieferstein
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Inga Bjornsdottir
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Andrea A Romeo
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Georges Da Violante
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Stefan Blech
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Patricia Moliner
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
| | - Graeme C Young
- Janssen R&D, Beerse, Belgium (F.C.); H. Lundbeck A/S, Copenhagen, Denmark (M.G.H.); Eli Lilly and Company, Indianapolis, Indiana (K.C.C.); Pfizer Inc., Groton, Connecticut (D.K.S.); Novartis, Basel, Switzerland (A.D.J.); Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden (M.L.P.); Sosei Heptares, Cambridge, United Kingdom (G.S.); AbbVie, North Chicago, Illinois (D.S.W.); Bayer AG, Wuppertal, Germany (K.G., S.I.S.); The Healthcare Business of Merck KGaA, Darmstadt, Germany (H.S.); Novo Nordisk, Maaloev, Denmark (I.B.); Roche Pharma Research and Early Development, Basel, Switzerland (A.A.R.); Servier, Gif-sur-Yvette, France (G.Da.V.); Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany (S.B.); Sanofi, Montpellier, France (P.M.); and GSK Research & Development Ltd., Stevenage (G.C.Y.)
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30
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Yang W, Saboo S, Zhou L, Askin S, Bak A. Early evaluation of opportunities in oral delivery of PROTACs to overcome their molecular challenges. Drug Discov Today 2024; 29:103865. [PMID: 38154757 DOI: 10.1016/j.drudis.2023.103865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) offer new opportunities in modern medicine by targeting proteins that are intractable to classic inhibitors. Heterobifunctional in nature, PROTACs are small molecules that offer a unique mechanism of protein degradation by hijacking the ubiquitin-mediated protein degradation pathway, known as the ubiquitin-proteasome system. Herein, we present an analysis on the structural characteristics of this novel chemical modality. Furthermore, we review and discuss the formulation opportunities to overcome the oral delivery challenges of PROTACs in drug discovery.
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Affiliation(s)
- Wenzhan Yang
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, USA.
| | - Sugandha Saboo
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, USA
| | - Liping Zhou
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, USA
| | - Sean Askin
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Annette Bak
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, USA
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31
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Peng X, Hu Z, Zeng L, Zhang M, Xu C, Lu B, Tao C, Chen W, Hou W, Cheng K, Bi H, Pan W, Chen J. Overview of epigenetic degraders based on PROTAC, molecular glue, and hydrophobic tagging technologies. Acta Pharm Sin B 2024; 14:533-578. [PMID: 38322348 PMCID: PMC10840439 DOI: 10.1016/j.apsb.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 02/08/2024] Open
Abstract
Epigenetic pathways play a critical role in the initiation, progression, and metastasis of cancer. Over the past few decades, significant progress has been made in the development of targeted epigenetic modulators (e.g., inhibitors). However, epigenetic inhibitors have faced multiple challenges, including limited clinical efficacy, toxicities, lack of subtype selectivity, and drug resistance. As a result, the design of new epigenetic modulators (e.g., degraders) such as PROTACs, molecular glue, and hydrophobic tagging (HyT) degraders has garnered significant attention from both academia and pharmaceutical industry, and numerous epigenetic degraders have been discovered in the past decade. In this review, we aim to provide an in-depth illustration of new degrading strategies (2017-2023) targeting epigenetic proteins for cancer therapy, focusing on the rational design, pharmacodynamics, pharmacokinetics, clinical status, and crystal structure information of these degraders. Importantly, we also provide deep insights into the potential challenges and corresponding remedies of this approach to drug design and development. Overall, we hope this review will offer a better mechanistic understanding and serve as a useful guide for the development of emerging epigenetic-targeting degraders.
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Affiliation(s)
- Xiaopeng Peng
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Zhihao Hu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Limei Zeng
- College of Basic Medicine, Gannan Medical University, Ganzhou 314000, China
| | - Meizhu Zhang
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Congcong Xu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Benyan Lu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Chengpeng Tao
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Weiming Chen
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Wen Hou
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huichang Bi
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wanyi Pan
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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32
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Hofmann N, Harms M, Mäder K. ASDs of PROTACs: Spray-dried solid dispersions as enabling formulations. Int J Pharm 2024; 650:123725. [PMID: 38113976 DOI: 10.1016/j.ijpharm.2023.123725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are a promising class of pharmaceutical agents with a unique mode of action. PROTACs enable the targeting of a broad variety of structures including transcription factors and other "undruggable" targets. The poor solubility and slow dissolution of PROTACs currently limit the extensive use of their potential. Up to date, only very limited drug delivery options have been examined to address this challenge. Therefore, we explored the potential of amorphous solid dispersions (ASDs) by spray drying a model PROTAC with different polymers. The resulting formulations were assessed in terms of purity, solid state, dissolution performance, and stability. A strong increase in supersaturation compared to the physical mixture was provided, although in both systems the PROTAC molecule itself was already in the amorphous state. Evaluation of the reasons for the superiority of the ASD formulations revealed that the major factor was the homogeneous, molecular distribution of the active pharmaceutical ingredient (API) in the polymer matrix, as well as improved wettability of the formulation containing Soluplus compared to the physical mixture. The manufactured formulations were stable over a minimum of 8 weeks when protected from light and humidity.
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Affiliation(s)
- Nicole Hofmann
- Global Drug Product Development, Orals Development, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany; Institute of Pharmacy, Faculty I of Natural Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Meike Harms
- Global Drug Product Development, Orals Development, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Karsten Mäder
- Institute of Pharmacy, Faculty I of Natural Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany.
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Tian L, Qiang T, Yang X, Gao Y, Zhai X, Kang K, Du C, Lu Q, Gao H, Zhang D, Xie X, Liang C. Development of de-novo coronavirus 3-chymotrypsin-like protease (3CL pro) inhibitors since COVID-19 outbreak: A strategy to tackle challenges of persistent virus infection. Eur J Med Chem 2024; 264:115979. [PMID: 38048696 DOI: 10.1016/j.ejmech.2023.115979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/30/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023]
Abstract
Although no longer a public health emergency of international concern, COVID-19 remains a persistent and critical health concern. The development of effective antiviral drugs could serve as the ultimate piece of the puzzle to curbing this global crisis. 3-chymotrypsin-like protease (3CLpro), with its substrate specificity mirroring that of the main picornavirus 3C protease and conserved across various coronaviruses, emerges as an ideal candidate for broad-spectrum antiviral drug development. Moreover, it holds the potential as a reliable contingency option to combat emerging SARS-CoV-2 variants. In this light, the approved drugs, promising candidates, and de-novo small molecule therapeutics targeting 3CLpro since the COVID-19 outbreak in 2020 are discussed. Emphasizing the significance of diverse structural characteristics in inhibitors, be they peptidomimetic or nonpeptidic, with a shared mission to minimize the risk of cross-resistance. Moreover, the authors propose an innovative optimization strategy for 3CLpro reversible covalent PROTACs, optimizing pharmacodynamics and pharmacokinetics to better prepare for potential future viral outbreaks.
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Affiliation(s)
- Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Xiuding Yang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Yue Gao
- College of Pharmacy, Jinan University, Guangzhou, 511436, PR China
| | - Xiaopei Zhai
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Xi'an, 710032, PR China
| | - Kairui Kang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Cong Du
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Qi Lu
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Hong Gao
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Pioneer Biotech Co., Ltd., Xi'an, 710021, PR China
| | - Dezhu Zhang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Xiaolin Xie
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Chengyuan Liang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
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Asano D, Takakusa H, Nakai D. Oral Absorption of Middle-to-Large Molecules and Its Improvement, with a Focus on New Modality Drugs. Pharmaceutics 2023; 16:47. [PMID: 38258058 PMCID: PMC10820198 DOI: 10.3390/pharmaceutics16010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
To meet unmet medical needs, middle-to-large molecules, including peptides and oligonucleotides, have emerged as new therapeutic modalities. Owing to their middle-to-large molecular sizes, middle-to-large molecules are not suitable for oral absorption, but there are high expectations around orally bioavailable macromolecular drugs, since oral administration is the most convenient dosing route. Therefore, extensive efforts have been made to create bioavailable middle-to-large molecules or develop absorption enhancement technology, from which some successes have recently been reported. For example, Rybelsus® tablets and Mycapssa® capsules, both of which contain absorption enhancers, were approved as oral medications for type 2 diabetes and acromegaly, respectively. The oral administration of Rybelsus and Mycapssa exposes their pharmacologically active peptides with molecular weights greater than 1000, namely, semaglutide and octreotide, respectively, into systemic circulation. Although these two medications represent major achievements in the development of orally absorbable peptide formulations, the oral bioavailability of peptides after taking Rybelsus and Mycapssa is still only around 1%. In this article, we review the approaches and recent advances of orally bioavailable middle-to-large molecules and discuss challenges for improving their oral absorption.
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Affiliation(s)
- Daigo Asano
- Drug Metabolism and Pharmacokinetics Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan; (H.T.); (D.N.)
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35
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Yang N, Fan Z, Sun S, Hu X, Mao Y, Jia C, Cai X, Xu T, Li B, Li Y, Han L, Wei T, Qian X, Qin W, Li P, Zheng Z, Li S. Discovery of highly potent and selective KRAS G12C degraders by VHL-recruiting PROTACs for the treatment of tumors with KRAS G12C-Mutation. Eur J Med Chem 2023; 261:115857. [PMID: 37852032 DOI: 10.1016/j.ejmech.2023.115857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Although several covalent KRASG12C inhibitors have made great progress in the treatment of KRASG12C-mutant cancer, their clinical applications are limited by adaptive resistance, motivating novel therapeutic strategies. Through drug design and structure optimization, a series of highly potent and selective KRASG12C Proteolysis Targeting Chimeras (PROTACs) were developed by incorporating AMG510 and VHL ligand VH032. Among them, degrader YN14 significantly inhibited KRASG12C-dependent cancer cells growth with nanomolar IC50 and DC50 values, and > 95 % maximum degradation (Dmax). Molecular dynamics (MD) simulation showed that YN14 induced a stable KRASG12C: YN14: VHL ternary complex with low binding free energy (ΔG). Notably, YN14 led to tumor regression with tumor growth inhibition (TGI%) rates more than 100 % in the MIA PaCa-2 xenograft model with well-tolerated dose-schedules. We also found that KRASG12C degradation exhibited advantages in overcoming adaptive KRASG12C feedback resistance over KRASG12C inhibition. Furthermore, combination of RTKs, SHP2, or CDK9 inhibitors with YN14 exhibited synergetic efficacy in KRASG12C-mutant cancer cells. Overall, these results demonstrated that YN14 holds exciting prospects for the treatment of tumors with KRASG12C-mutation and boosted efficacy could be achieved for greater clinical applications via drug combination.
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Affiliation(s)
- Ning Yang
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Zhiya Fan
- National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206, China
| | - Shiyang Sun
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Xiaotong Hu
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Yaqiu Mao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Changkai Jia
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Xu Cai
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Tingting Xu
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Bingkun Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Yi Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Luobing Han
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Ting Wei
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
| | - Xiaohong Qian
- National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206, China
| | - Weijie Qin
- National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206, China.
| | - Pengyun Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China.
| | - Zhibing Zheng
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China.
| | - Song Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology Institution, Beijing, 100850, China
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36
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Song J, Hu M, Zhou J, Xie S, Li T, Li Y. Targeted protein degradation in drug development: Recent advances and future challenges. Eur J Med Chem 2023; 261:115839. [PMID: 37778240 DOI: 10.1016/j.ejmech.2023.115839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/12/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
Targeted protein degradation (TPD) has emerged as a promising therapeutic approach with potential advantages over traditional occupancy-based inhibitors in terms of dosing, side effects and targeting "undruggable" proteins. Targeted degraders can theoretically bind any nook or cranny of targeted proteins to drive degradation. This offers convenience versus the small-molecule inhibitors that must function in a well-defined pocket. The degradation process depends mainly on two cell self-destruction mechanisms, namely the ubiquitin-proteasome system and the lysosomal degradation pathway. Various TPD strategies (e.g., proteolytic-targeting chimeras, molecular glues, lysosome-targeting chimeras, and autophagy-targeting chimeras) have been developed. These approaches hold great potential for targeting dysregulated proteins, potentially offering therapeutic benefits. In this article, we systematically review the mechanisms of various TPD strategies, potential applications to drug discovery, and recent advances. We also discuss the benefits and challenges associated with these TPD strategies, aiming to provide insight into the targeting of dysregulated proteins and facilitate their clinical applications.
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Affiliation(s)
- Jian Song
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Mingzheng Hu
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China; College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Songbo Xie
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China; School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
| | - Tianliang Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China.
| | - Yan Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China.
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Amirian R, Azadi Badrbani M, Izadi Z, Samadian H, Bahrami G, Sarvari S, Abdolmaleki S, Nabavi SM, Derakhshankhah H, Jaymand M. Targeted protein modification as a paradigm shift in drug discovery. Eur J Med Chem 2023; 260:115765. [PMID: 37659194 DOI: 10.1016/j.ejmech.2023.115765] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Targeted Protein Modification (TPM) is an umbrella term encompassing numerous tools and approaches that use bifunctional agents to induce a desired modification over the POI. The most well-known TPM mechanism is PROTAC-directed protein ubiquitination. PROTAC-based targeted degradation offers several advantages over conventional small-molecule inhibitors, has shifted the drug discovery paradigm, and is acquiring increasing interest as over ten PROTACs have entered clinical trials in the past few years. Targeting the protein of interest for proteasomal degradation by PROTACS was the pioneer of various toolboxes for selective protein degradation. Nowadays, the ever-increasing number of tools and strategies for modulating and modifying the POI has expanded far beyond protein degradation, which phosphorylation and de-phosphorylation of the protein of interest, targeted acetylation, and selective modification of protein O-GlcNAcylation are among them. These novel strategies have opened new avenues for achieving more precise outcomes while remaining feasible and minimizing side effects. This field, however, is still in its infancy and has a long way to precede widespread use and translation into clinical practice. Herein, we investigate the pros and cons of these novel strategies by exploring the latest advancements in this field. Ultimately, we briefly discuss the emerging potential applications of these innovations in cancer therapy, neurodegeneration, viral infections, and autoimmune and inflammatory diseases.
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Affiliation(s)
- Roshanak Amirian
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Azadi Badrbani
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Zhila Izadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Hadi Samadian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Gholamreza Bahrami
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Sajad Sarvari
- Department of Pharmaceutical Science, School of Pharmacy, West Virginia University, Morgantown, WV, USA.
| | - Sara Abdolmaleki
- Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran.
| | - Seyed Mohammad Nabavi
- Department of Science and Technology, University of Sannio, 82100, Benevento, Italy.
| | - Hossein Derakhshankhah
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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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] [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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Castellani B, Eleuteri M, Di Bona S, Cruciani G, Desantis J, Goracci L. VHL-Modified PROteolysis TArgeting Chimeras (PROTACs) as a Strategy to Evade Metabolic Degradation in In Vitro Applications. J Med Chem 2023; 66:13148-13171. [PMID: 37699425 DOI: 10.1021/acs.jmedchem.3c01144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are tripartite molecules consisting of a linker connecting a ligand for a protein of interest to an E3 ligase recruiter, whose rationale relies on proteasome-based protein degradation. PROTACs have expanded as a therapeutic strategy to open new avenues for unmet medical needs. Leveraging our expertise, we undertook a series of in vitro experiments aimed at elucidating PROTAC metabolism. In particular, we focused on PROTACs recruiting the von Hippel-Lindau (VHL) E3 ligase. After high-resolution mass spectrometry measurements, a characteristic metabolite with mass reduction of 200 units was detected and successively confirmed as a product deriving from the cleavage of the VHL ligand moiety. Subsequently, we identified hepatic and extrahepatic prolyl endopeptidases as the main putative metabolic enzymes involved. Finally, we designed and synthesized analogs of the VHL ligands that we further exploited for the synthesis of novel VHL-directed PROTACs with an improved metabolic stability in in vitro applications.
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Affiliation(s)
| | - Michela Eleuteri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | | | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | - Jenny Desantis
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia 06123, Italy
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Li B, Ran T, Chen H. 3D based generative PROTAC linker design with reinforcement learning. Brief Bioinform 2023; 24:bbad323. [PMID: 37670499 DOI: 10.1093/bib/bbad323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/06/2023] [Accepted: 08/20/2023] [Indexed: 09/07/2023] Open
Abstract
Proteolysis targeting chimera (PROTAC), has emerged as an effective modality to selectively degrade disease-related proteins by harnessing the ubiquitin-proteasome system. Due to PROTACs' hetero-bifunctional characteristics, in which a linker joins a warhead binding to a protein of interest (POI), conferring specificity and a E3-ligand binding to an E3 ubiquitin ligase, this could trigger the ubiquitination and transportation of POI to the proteasome, followed by degradation. The rational PROTAC linker design is challenging due to its relatively large molecular weight and the complexity of maintaining the binding mode of warhead and E3-ligand in the binding pockets of counterpart. Conventional linker generation method can only generate linkers in either 1D SMILES or 2D graph, without taking into account the information of ternary structures. Here we propose a novel 3D linker generative model PROTAC-INVENT which can not only generate SMILES of PROTAC but also its 3D putative binding conformation coupled with the target protein and the E3 ligase. The model is trained jointly with the RL approach to bias the generation of PROTAC structures toward pre-defined 2D and 3D based properties. Examples were provided to demonstrate the utility of the model for generating reasonable 3D conformation of PROTACs. On the other hand, our results show that the associated workflow for 3D PROTAC conformation generation can also be used as an efficient docking protocol for PROTACs.
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Affiliation(s)
- Baiqing Li
- Guangzhou Laboratory, Guangzhou 510005, Guangdong Province, China
| | - Ting Ran
- Guangzhou Laboratory, Guangzhou 510005, Guangdong Province, China
| | - Hongming Chen
- Guangzhou Laboratory, Guangzhou 510005, Guangdong Province, China
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Mostofian B, Martin HJ, Razavi A, Patel S, Allen B, Sherman W, Izaguirre JA. Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods. J Chem Inf Model 2023; 63:5408-5432. [PMID: 37602861 PMCID: PMC10498452 DOI: 10.1021/acs.jcim.3c00603] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Indexed: 08/22/2023]
Abstract
The therapeutic approach of targeted protein degradation (TPD) is gaining momentum due to its potentially superior effects compared with protein inhibition. Recent advancements in the biotech and pharmaceutical sectors have led to the development of compounds that are currently in human trials, with some showing promising clinical results. However, the use of computational tools in TPD is still limited, as it has distinct characteristics compared with traditional computational drug design methods. TPD involves creating a ternary structure (protein-degrader-ligase) responsible for the biological function, such as ubiquitination and subsequent proteasomal degradation, which depends on the spatial orientation of the protein of interest (POI) relative to E2-loaded ubiquitin. Modeling this structure necessitates a unique blend of tools initially developed for small molecules (e.g., docking) and biologics (e.g., protein-protein interaction modeling). Additionally, degrader molecules, particularly heterobifunctional degraders, are generally larger than conventional small molecule drugs, leading to challenges in determining drug-like properties like solubility and permeability. Furthermore, the catalytic nature of TPD makes occupancy-based modeling insufficient. TPD consists of multiple interconnected yet distinct steps, such as POI binding, E3 ligase binding, ternary structure interactions, ubiquitination, and degradation, along with traditional small molecule properties. A comprehensive set of tools is needed to address the dynamic nature of the induced proximity ternary complex and its implications for ubiquitination. In this Perspective, we discuss the current state of computational tools for TPD. We start by describing the series of steps involved in the degradation process and the experimental methods used to characterize them. Then, we delve into a detailed analysis of the computational tools employed in TPD. We also present an integrative approach that has proven successful for degrader design and its impact on project decisions. Finally, we examine the future prospects of computational methods in TPD and the areas with the greatest potential for impact.
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Affiliation(s)
- Barmak Mostofian
- OpenEye, Cadence Molecular Sciences, Boston, Massachusetts 02114 United States
| | - Holli-Joi Martin
- Laboratory
for Molecular Modeling, Division of Chemical Biology and Medicinal
Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599 United States
| | - Asghar Razavi
- ENKO
Chem, Inc, Mystic, Connecticut 06355 United States
| | - Shivam Patel
- Psivant
Therapeutics, Boston, Massachusetts 02210 United States
| | - Bryce Allen
- Differentiated
Therapeutics, San Diego, California 92056 United States
| | - Woody Sherman
- Psivant
Therapeutics, Boston, Massachusetts 02210 United States
| | - Jesus A Izaguirre
- Differentiated
Therapeutics, San Diego, California 92056 United States
- Atommap
Corporation, New York, New York 10013 United States
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42
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Kong NR, Jones LH. Clinical Translation of Targeted Protein Degraders. Clin Pharmacol Ther 2023; 114:558-568. [PMID: 37399310 DOI: 10.1002/cpt.2985] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
Targeted protein degradation (TPD) has emerged as a potentially transformational therapeutic modality with considerable promise. Molecular glue degraders remodel the surface of E3 ligases inducing interactions with neosubstrates resulting in their polyubiquitination and proteasomal degradation. Molecular glues are clinically precedented and have demonstrated the ability to degrade proteins-of-interest (POIs) previously deemed undruggable due to the absence of a traditional small molecule binding pocket. Heterobifunctional proteolysis targeting chimeras (PROTACs) possess ligands for an E3 complex and the POIs, which are chemically linked together, and similarly hijack the ubiquitin machinery to deplete the target. There has been a recent surge in the number of degraders entering clinical trials, particularly directed toward cancer. Nearly all utilize CRL4CRBN as the E3 ligase, and a relatively limited diversity of POIs are currently targeted. In this review, we provide an overview of the degraders in clinical trials and provide a perspective on the lessons learned from their development and emerging human data that will be broadly useful to those working in the TPD field.
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Affiliation(s)
- Nikki R Kong
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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Riley CM, Elwood JML, Henry MC, Hunter I, Daniel Lopez-Fernandez J, McEwan IJ, Jamieson C. Current and emerging approaches to noncompetitive AR inhibition. Med Res Rev 2023; 43:1701-1747. [PMID: 37062876 DOI: 10.1002/med.21961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 04/18/2023]
Abstract
The androgen receptor (AR) has been shown to be a key determinant in the pathogenesis of castration-resistant prostate cancer (CRPC). The current standard of care therapies targets the ligand-binding domain of the receptor and can afford improvements to life expectancy often only in the order of months before resistance occurs. Emerging preclinical and clinical compounds that inhibit receptor activity via differentiated mechanisms of action which are orthogonal to current antiandrogens show promise for overcoming treatment resistance. In this review, we present an authoritative summary of molecules that noncompetitively target the AR. Emerging small molecule strategies for targeting alternative domains of the AR represent a promising area of research that shows significant potential for future therapies. The overall quality of lead candidates in the area of noncompetitive AR inhibition is discussed, and it identifies the key chemotypes and associated properties which are likely to be, or are currently, positioned to be first in human applications.
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Affiliation(s)
- Christopher M Riley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Jessica M L Elwood
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Martyn C Henry
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Irene Hunter
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Iain J McEwan
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Craig Jamieson
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
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Xie S, Zhu J, Li J, Zhan F, Yao H, Xu J, Xu S. Small-Molecule Hydrophobic Tagging: A Promising Strategy of Druglike Technology for Targeted Protein Degradation. J Med Chem 2023; 66:10917-10933. [PMID: 37535706 DOI: 10.1021/acs.jmedchem.3c00736] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Targeted protein degradation (TPD) technologies have catalyzed a paradigm shift in therapeutic strategies and offer innovative avenues for drug design. Hydrophobic tags (HyTs) are bifunctional TPD molecules consisting of a ″lipophilic small-molecule tags″ group and a small-molecule ligand for the target protein. Despite the vast potential of HyTs, they have received relatively limited attention as a promising frontier. Leveraging their lower molecular weight and reduced numbers of hydrogen bond donors/acceptors (HBDs/HBAs) in comparison with proteolysis-targeting chimeras (PROTACs), HyTs present a compelling approach for enhancing druglike properties. In this Perspective, we explore the diverse range of HyT structures and their corresponding degradation mechanisms, thereby illuminating their broad applicability in targeting a diverse array of proteins, including previously elusive targets. Moreover, we scrutinize the challenges and opportunities entailed in developing this technology as a viable and fruitful strategy for drug discovery.
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Affiliation(s)
- Shaowen Xie
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Jingjie Zhu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Junda Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Feiyan Zhan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Hong Yao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Jinyi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Shengtao Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
- Department of Hepatobiliary Surgery, The First People's Hospital of Kunshan, Suzhou 215300, China
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Teng M, Gray NS. The rise of degrader drugs. Cell Chem Biol 2023; 30:864-878. [PMID: 37494935 DOI: 10.1016/j.chembiol.2023.06.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
The cancer genomics revolution has served up a plethora of promising and challenging targets for the drug discovery community. The field of targeted protein degradation (TPD) uses small molecules to reprogram the protein homeostasis system to destroy desired target proteins. In the last decade, remarkable progress has enabled the rational development of degraders for a large number of target proteins, with over 20 molecules targeting more than 12 proteins entering clinical development. While TPD has been fully credentialed by the prior development of immunomodulatory drug (IMiD) class for the treatment of multiple myeloma, the field is poised for a "Gleevec moment" in which robust clinical efficacy of a rationally developed novel degrader against a preselected target is firmly established. Here, we endeavor to provide a high-level evaluation of exciting developments in the field and comment on steps that may realize the full potential of this new therapeutic modality.
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Affiliation(s)
- Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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Zhao C, Wang H, Zhan W, Lv X, Ma X. Exploitation of Proximity-Mediated Effects in Drug Discovery: An Update of Recent Research Highlights in Perturbing Pathogenic Proteins and Correlated Issues. J Med Chem 2023; 66:10122-10149. [PMID: 37489834 DOI: 10.1021/acs.jmedchem.3c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The utilization of proximity-mediated effects to perturb pathogenic proteins of interest (POIs) has emerged as a powerful strategic alternative to conventional drug design approaches based on target occupancy. Over the past three years, the burgeoning field of targeted protein degradation (TPD) has witnessed the expansion of degradable POIs to membrane-associated, extracellular, proteasome-resistant, and even microbial proteins. Beyond TPD, researchers have achieved the proximity-mediated targeted protein stabilization, the recruitment of intracellular immunophilins to disturb undruggable targets, and the nonphysiological post-translational modifications of POIs. All of these strides provide new avenues for innovative drug discovery aimed at battling human malignancies and other major diseases. This perspective presents recent research highlights and discusses correlated issues in developing therapeutic modalities that exploit proximity-mediated effects to modulate pathogenic proteins, thereby guiding future academic and industrial efforts in this field.
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Affiliation(s)
- Can Zhao
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Henian Wang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Wenhu Zhan
- iCarbonX (Shenzhen) Co., Ltd., Shenzhen, 518000, China
| | - Xiaoqing Lv
- College of Medicine, Jiaxing University, Jiaxing 314001, China
| | - Xiaodong Ma
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
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Liu X, Ciulli A. Proximity-Based Modalities for Biology and Medicine. ACS CENTRAL SCIENCE 2023; 9:1269-1284. [PMID: 37521793 PMCID: PMC10375889 DOI: 10.1021/acscentsci.3c00395] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Indexed: 08/01/2023]
Abstract
Molecular proximity orchestrates biological function, and blocking existing proximities is an established therapeutic strategy. By contrast, strengthening or creating neoproximity with chemistry enables modulation of biological processes with high selectivity and has the potential to substantially expand the target space. A plethora of proximity-based modalities to target proteins via diverse approaches have recently emerged, opening opportunities for biopharmaceutical innovation. This Outlook outlines the diverse mechanisms and molecules based on induced proximity, including protein degraders, blockers, and stabilizers, inducers of protein post-translational modifications, and agents for cell therapy, and discusses opportunities and challenges that the field must address to mature and unlock translation in biology and medicine.
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Li P, Li B, Yang N, Xu T, Zheng Z. The next generation of EGFR inhibitors: a patenting perspective of PROTACs based EGFR degraders. Expert Opin Ther Pat 2023; 33:477-492. [PMID: 37873645 DOI: 10.1080/13543776.2023.2262176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
INTRODUCTION Abnormal expression of epidermal growth factor receptor (EGFR) contributes to tumor development, especially in non-small cell lung cancer (NSCLC). Although multiple inhibitors have been developed to target diverse EGFR mutations and several have been approved, the inevitable drug resistance and side effect remain a challenge, which motivates novel strategies. Proteolysis-targeting chimeras (PROTACs) have been gaining momentum for their potential as novel therapeutics for human diseases by triggering protein degradation. To date, various potent and specific EGFR PROTACs have been discovered and some of them have entered clinical trials. AREAS COVERED This review provides an overview of EGFR degraders in patents from 2016 to 2022. It provides an update of the discovery strategies, chemical structures, and molecular profiling of all available EGFR PROTACs. SciFinder, PubMed, Web of Science, EPO, and CNIPA databases were used for searching the literature and patents for EGFR PROTACs. EXPERT OPINION By employing the PROTAC technology, highly potent and selective EGFR degraders based on four generation EGFR inhibitors have been developed, which offer a new strategy to target EGFR mutations and overcome the drug resistance. Despite the satisfactory result in vitro and in vivo studies, their therapeutic value awaits more rigorous preclinical testing and clinical investigation.
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Affiliation(s)
- Pengyun Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Bingkun Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Ning Yang
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Tingting Xu
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Zhibing Zheng
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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Park SY, Gurung R, Hwang JH, Kang JH, Jung HJ, Zeb A, Hwang JI, Park SJ, Maeng HJ, Shin D, Oh SH. Development of KEAP1-targeting PROTAC and its antioxidant properties: In vitro and in vivo. Redox Biol 2023; 64:102783. [PMID: 37348157 DOI: 10.1016/j.redox.2023.102783] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023] Open
Abstract
Oxidative stress due to abnormal accumulation of reactive oxygen species (ROS) is an initiator of a large number of human diseases, and thus, the elimination and prevention of excessive ROS are important aspects of preventing the development of such diseases. Nuclear factor erythroid 2-related factor 2 (NRF2) is an essential transcription factor that defends against oxidative stress, and its function is negatively controlled by Kelch-like ECH-associated protein 1 (KEAP1). Therefore, activating NRF2 by inhibiting KEAP1 is viewed as a strategy for combating oxidative stress-related diseases. Here, we generated a cereblon (CRBN)-based proteolysis-targeting chimera (PROTAC), which we named SD2267, that induces the proteasomal degradation of KEAP1 and leads to NRF2 activation. As was intended, SD2267 bound to KEAP1, recruited CRBN, and induced the degradation of KEAP1. Furthermore, the KEAP1 degradation efficacy of SD2267 was diminished by MG132 (a proteasomal degradation inhibitor) but not by chloroquine (an autophagy inhibitor), which suggested that KEAP1 degradation by SD2267 was proteasomal degradation-dependent and autophagy-independent. Following KEAP1 degradation, SD2267 induced the nuclear translocation of NRF2, which led to the expression of NRF2 target genes and attenuated ROS accumulation induced by acetaminophen (APAP) in hepatocytes. Based on in vivo pharmacokinetic study, SD2267 was injected intraperitoneally at 1 or 3 mg/kg in APAP-induced liver injury mouse model. We observed that SD2267 degraded hepatic KEAP1 and attenuated APAP-induced liver damage. Summarizing, we described the synthesis of a KEAP1-targeting PROTAC (SD2267) and its efficacy and mode of action in vitro and in vivo. The results obtained suggest that SD2267 could be used to treat hepatic diseases related to oxidative stress.
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Affiliation(s)
- Se Yong Park
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Raju Gurung
- College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - Jung Ho Hwang
- College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - Ju-Hee Kang
- College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - Hyun Jin Jung
- College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - Alam Zeb
- College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - Jong-Ik Hwang
- Graduate School of Medicine, Korea University, Seoul, Republic of Korea
| | - Sung Jean Park
- College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - Han-Joo Maeng
- College of Pharmacy, Gachon University, Incheon, Republic of Korea
| | - Dongyun Shin
- College of Pharmacy, Gachon University, Incheon, Republic of Korea.
| | - Seung Hyun Oh
- College of Pharmacy, Gachon University, Incheon, Republic of Korea.
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Whitehurst BC, Bauer MR, Edfeldt F, Gunnarsson A, Margreitter C, Rawlins PB, Storer RI. Design and Evaluation of a Low Hydrogen Bond Donor Count Fragment Screening Set to Aid Hit Generation of PROTACs Intended for Oral Delivery. J Med Chem 2023. [PMID: 37224440 DOI: 10.1021/acs.jmedchem.3c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The development of orally bioavailable PROTACs presents a significant challenge due to the inflated physicochemical properties of such heterobifunctional molecules. Molecules occupying this "beyond rule of five" space often demonstrate limited oral bioavailability due to the compounding effects of elevated molecular weight and hydrogen bond donor count (among other properties), but it is possible to achieve sufficient oral bioavailability through physicochemical optimization. Herein, we disclose the design and evaluation of a low hydrogen bond donor count (≤1 HBD) fragment screening set to aid hit generation of PROTACs intended for an oral route of delivery. We demonstrate that application of this library can enhance fragment screens against PROTAC proteins of interest and ubiquitin ligases, yielding fragment hits containing ≤1 HBD suitable for optimizing toward orally bioavailable PROTACs.
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Affiliation(s)
- Benjamin C Whitehurst
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Matthias R Bauer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Fredrik Edfeldt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Mölndal, Gothenburg 431 50, Sweden
| | - Anders Gunnarsson
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Mölndal, Gothenburg 431 50, Sweden
| | - Christian Margreitter
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Mölndal, Gothenburg 431 50, Sweden
| | - Philip B Rawlins
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
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