1
|
Mslati H, Gentile F, Pandey M, Ban F, Cherkasov A. PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. J Chem Inf Model 2024; 64:3034-3046. [PMID: 38504115 DOI: 10.1021/acs.jcim.3c01878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) that engage two biological targets at once are a promising technology in degrading clinically relevant protein targets. Since factors that influence the biological activities of PROTACs are more complex than those of a small molecule drug, we explored a combination of computational chemistry and deep learning strategies to forecast PROTAC activity and enable automated design. A new method named PROTACable was developed for the de novo design of PROTACs, which includes a robust 3-D modeling workflow to model PROTAC ternary complexes using a library of E3 ligase and linker and an SE(3)-equivariant graph transformer network to predict the activity of newly designed PROTACs. PROTACable is available at https://github.com/giaguaro/PROTACable/.
Collapse
Affiliation(s)
- Hazem Mslati
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Francesco Gentile
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1N 6N5, Canada
| | - Mohit Pandey
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| |
Collapse
|
2
|
Bouvier C, Lawrence R, Cavallo F, Xolalpa W, Jordan A, Hjerpe R, Rodriguez MS. Breaking Bad Proteins-Discovery Approaches and the Road to Clinic for Degraders. Cells 2024; 13:578. [PMID: 38607017 PMCID: PMC11011670 DOI: 10.3390/cells13070578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) describe compounds that bind to and induce degradation of a target by simultaneously binding to a ubiquitin ligase. More generally referred to as bifunctional degraders, PROTACs have led the way in the field of targeted protein degradation (TPD), with several compounds currently undergoing clinical testing. Alongside bifunctional degraders, single-moiety compounds, or molecular glue degraders (MGDs), are increasingly being considered as a viable approach for development of therapeutics, driven by advances in rational discovery approaches. This review focuses on drug discovery with respect to bifunctional and molecular glue degraders within the ubiquitin proteasome system, including analysis of mechanistic concepts and discovery approaches, with an overview of current clinical and pre-clinical degrader status in oncology, neurodegenerative and inflammatory disease.
Collapse
Affiliation(s)
- Corentin Bouvier
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
| | - Rachel Lawrence
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Francesca Cavallo
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Wendy Xolalpa
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62209, Morelos, Mexico;
| | - Allan Jordan
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Roland Hjerpe
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Manuel S. Rodriguez
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
- Pharmadev, UMR 152, Université de Toulouse, IRD, UT3, 31400 Toulouse, France
- B Molecular, Centre Pierre Potier, Canceropôle, 31106 Toulouse, France
| |
Collapse
|
3
|
A S BG, Agrawal D, Kulkarni NM, Vetrivel R, Gurram K. PROTAC-Design-Evaluator (PRODE): An Advanced Method for In-Silico PROTAC Design. ACS OMEGA 2024; 9:12611-12621. [PMID: 38524483 PMCID: PMC10955709 DOI: 10.1021/acsomega.3c07318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 03/26/2024]
Abstract
PROTAC (proteolysis-targeting chimeras) is a rapidly evolving technology to target undruggable targets. The mechanism by which this happens is when a bifunctional molecule binds to a target protein and also brings an E3 ubiquitin ligase in proximity to trigger ubiquitination and degradation of the target protein. Yet, in-silico-driven approaches to design these heterobifunctional molecules that have the desired functional properties to induce proximity between the target protein and E3 ligase remain to be established. In this paper, we present a novel in-silico method for PROTAC design and to demonstrate the validity of our approach, we show that for a BRD4-VHL-PROTAC-mediated ternary complex known in the literature, we are able to reproduce the PROTAC binding mode, the structure of the ternary complex formed therein, and the free energy (ΔG) thermodynamics favoring ternary complexation through theoretical/computational methodologies. Further, we demonstrate the use of thermal titration molecule dynamics (TTMD) to differentiate the stability of PROTAC-mediated ternary complexes. We employ the proposed methodology to design a PROTAC for a new system of FGFR1-MDM2 to degrade the FGFR1 (fibroblast growth factor receptor 1) that is overexpressed in cancer. Our work presented here and named as PROTAC-Designer-Evaluator (PRODE) contributes to the growing literature of in-silico approaches to PROTAC design and evaluation by incorporating the latest in-silico methods and demonstrates advancement over previously published PROTAC in-silico literature.
Collapse
Affiliation(s)
- Ben Geoffrey A S
- Sravathi AI Technology Pvt.
Ltd., 63-B, Bommasandra
Industrial Area, Bengaluru, Karnataka 560099, India
| | - Deepak Agrawal
- Sravathi AI Technology Pvt.
Ltd., 63-B, Bommasandra
Industrial Area, Bengaluru, Karnataka 560099, India
| | - Nagaraj M. Kulkarni
- Sravathi AI Technology Pvt.
Ltd., 63-B, Bommasandra
Industrial Area, Bengaluru, Karnataka 560099, India
| | - Rajappan Vetrivel
- Sravathi AI Technology Pvt.
Ltd., 63-B, Bommasandra
Industrial Area, Bengaluru, Karnataka 560099, India
| | - Kishan Gurram
- Sravathi AI Technology Pvt.
Ltd., 63-B, Bommasandra
Industrial Area, Bengaluru, Karnataka 560099, India
| |
Collapse
|
4
|
Bouguenina H, Scarpino A, O'Hanlon JA, Warne J, Wang HZ, Wah Hak LC, Sadok A, McAndrew PC, Stubbs M, Pierrat OA, Hahner T, Cabry MP, Le Bihan YV, Mitsopoulos C, Sialana FJ, Roumeliotis TI, Burke R, van Montfort RLM, Choudhari J, Chopra R, Caldwell JJ, Collins I. A Degron Blocking Strategy Towards Improved CRL4 CRBN Recruiting PROTAC Selectivity. Chembiochem 2023; 24:e202300351. [PMID: 37418539 DOI: 10.1002/cbic.202300351] [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: 05/10/2023] [Revised: 06/16/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
Small molecules inducing protein degradation are important pharmacological tools to interrogate complex biology and are rapidly translating into clinical agents. However, to fully realise the potential of these molecules, selectivity remains a limiting challenge. Herein, we addressed the issue of selectivity in the design of CRL4CRBN recruiting PROteolysis TArgeting Chimeras (PROTACs). Thalidomide derivatives used to generate CRL4CRBN recruiting PROTACs have well described intrinsic monovalent degradation profiles by inducing the recruitment of neo-substrates, such as GSPT1, Ikaros and Aiolos. We leveraged structural insights from known CRL4CRBN neo-substrates to attenuate and indeed remove this monovalent degradation function in well-known CRL4CRBN molecular glues degraders, namely CC-885 and Pomalidomide. We then applied these design principles on a previously published BRD9 PROTAC (dBRD9-A) and generated an analogue with improved selectivity profile. Finally, we implemented a computational modelling pipeline to show that our degron blocking design does not impact PROTAC-induced ternary complex formation. We believe that the tools and principles presented in this work will be valuable to support the development of targeted protein degradation.
Collapse
Affiliation(s)
- Habib Bouguenina
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Andrea Scarpino
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Jack A O'Hanlon
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Justin Warne
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Hannah Z Wang
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Laura Chan Wah Hak
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Amine Sadok
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Monte Rosa Therapeutics AG, Aeschenvorstadt 36, 4051, Basel, Switzerland
| | - P Craig McAndrew
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Mark Stubbs
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Olivier A Pierrat
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Tamas Hahner
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Marc P Cabry
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Yann-Vaï Le Bihan
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Costas Mitsopoulos
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Fernando J Sialana
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
| | - Theodoros I Roumeliotis
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
| | - Rosemary Burke
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Rob L M van Montfort
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Jyoti Choudhari
- Functional Proteomics Group, The Institute of Cancer Research, Chester Beatty Laboratories, London, SW3 6JB, UK
| | - Rajesh Chopra
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
- Apple Tree Partners, The Gridiron Building, Suite 6.05, 1 St Pancras Square, London, N1 C 4AG, UK
| | - John J Caldwell
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Ian Collins
- Centre for Cancer Drug Discovery, Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| |
Collapse
|
5
|
Danishuddin, Jamal MS, Song KS, Lee KW, Kim JJ, Park YM. Revolutionizing Drug Targeting Strategies: Integrating Artificial Intelligence and Structure-Based Methods in PROTAC Development. Pharmaceuticals (Basel) 2023; 16:1649. [PMID: 38139776 PMCID: PMC10747325 DOI: 10.3390/ph16121649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
PROteolysis TArgeting Chimera (PROTAC) is an emerging technology in chemical biology and drug discovery. This technique facilitates the complete removal of the target proteins that are "undruggable" or challenging to target through chemical molecules via the Ubiquitin-Proteasome System (UPS). PROTACs have been widely explored and outperformed not only in cancer but also in other diseases. During the past few decades, several academic institutes and pharma companies have poured more efforts into PROTAC-related technologies, setting the stage for several major degrader trial readouts in clinical phases. Despite their promising results, the formation of robust ternary orientation, off-target activity, poor permeability, and binding affinity are some of the limitations that hinder their development. Recent advancements in computational technologies have facilitated progress in the development of PROTACs. Researchers have been able to utilize these technologies to explore a wider range of E3 ligases and optimize linkers, thereby gaining a better understanding of the effectiveness and safety of PROTACs in clinical settings. In this review, we briefly explore the computational strategies reported to date for the formation of PROTAC components and discuss the key challenges and opportunities for further research in this area.
Collapse
Affiliation(s)
- Danishuddin
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | | | - Kyoung-Seob Song
- Department of Medical Science, Kosin University College of Medicine, 194 Wachi-ro, Yeongdo-gu, Busan 49104, Republic of Korea;
| | - Keun-Woo Lee
- Division of Life Science, Department of Bio & Medical Big-Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
- Angel i-Drug Design (AiDD), 33-3 Jinyangho-ro 44, Jinju 52650, Republic of Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Yeong-Min Park
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neugdong-ro, Gwangjin-gu, Seoul 05006, Republic of Korea
| |
Collapse
|
6
|
Hu L, Li H, Qin J, Yang D, Liu J, Luo X, Ma J, Luo C, Ye F, Zhou Y, Li J, Wang M. Discovery of PVD-06 as a Subtype-Selective and Efficient PTPN2 Degrader. J Med Chem 2023; 66:15269-15287. [PMID: 37966047 DOI: 10.1021/acs.jmedchem.3c01348] [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: 11/16/2023]
Abstract
Protein tyrosine phosphatase nonreceptor Type 2 (PTPN2) is an attractive target for cancer immunotherapy. PTPN2 and another subtype of PTP1B are highly similar in structure, but their biological functions are distinct. Therefore, subtype-selective targeting of PTPN2 remains a challenge for researchers. Herein, the development of small molecular PTPN2 degraders based on a thiadiazolidinone dioxide-naphthalene scaffold and a VHL E3 ligase ligand is described, and the PTPN2/PTP1B subtype-selective degradation is achieved for the first time. The linker structure modifications led to the discovery of the subtype-selective PTPN2 degrader PVD-06 (PTPN2/PTP1B selective index > 60-fold), which also exhibits excellent proteome-wide degradation selectivity. PVD-06 induces PTPN2 degradation in a ubiquitination- and proteasome-dependent manner. It efficiently promotes T cell activation and amplifies IFN-γ-mediated B16F10 cell growth inhibition. This study provides a convenient chemical knockdown tool for PTPN2-related research and a paradigm for subtype-selective PTP degradation through nonspecific substrate-mimicking ligands, demonstrating the therapeutic potential of PTPN2 subtype-selective degradation.
Collapse
Affiliation(s)
- Linghao Hu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | - Huiyun Li
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmacy, Zunyi Medical University, Zunyi 563000, Guizhou China
| | - Junlin Qin
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Dan Yang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmaceutical Sciences, Southern Medical University, No.1023, South Shatai Road, Baiyun District, Guangzhou 510515, Guangdong, China
| | - Jieming Liu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | - Xiaomin Luo
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | | | - Cheng Luo
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yubo Zhou
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
| | - Jia Li
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmacy, Zunyi Medical University, Zunyi 563000, Guizhou China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Mingliang Wang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District, Guangdong 528400, China
- School of Pharmaceutical Sciences, Southern Medical University, No.1023, South Shatai Road, Baiyun District, Guangzhou 510515, Guangdong, China
| |
Collapse
|
7
|
Pereira GP, Jiménez-García B, Pellarin R, Launay G, Wu S, Martin J, Souza PCT. Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. J Chem Inf Model 2023; 63:6823-6833. [PMID: 37877240 DOI: 10.1021/acs.jcim.3c01154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose interaction with the ubiquitination machinery leads to target degradation. This technology is emerging as an exciting new avenue for therapeutic development, with several PROTACs currently undergoing clinical trials targeting cancer. Here, we describe a general and computationally efficient methodology combining restraint-based docking, energy-based rescoring, and a filter based on the minimal solvent-accessible surface distance to produce PROTAC-compatible PPIs suitable for when there is no a priori known PROTAC ligand. In a benchmark employing a manually curated data set of 13 ternary complex crystals, we achieved an accuracy of 92% when starting from bound structures and 77% when starting from unbound structures, respectively. Our method only requires that the ligand-bound structures of the monomeric forms of the E3 ligase and target proteins be given to run, making it general, accurate, and highly efficient, with the ability to impact early-stage PROTAC-based drug design campaigns where no structural information about the ternary complex structure is available.
Collapse
Affiliation(s)
- Gilberto P Pereira
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | | | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Guillaume Launay
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Sangwook Wu
- PharmCADD, Busan 48792, Republic of Korea
- Department of Physics, Pukyong National University, Busan 48513, Republic of Korea
| | - Juliette Martin
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086 and Université Claude Bernard Lyon 1, 7 Passage du Vercors, 69007 Lyon, France
- Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239 and Inserm U1293, 46 Allée d'Italie, 69007 Lyon, France
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
10
|
Croft D, Lodhia P, Lourenco S, MacKay C. Effectively utilizing publicly available databases for cancer target evaluation. NAR Cancer 2023; 5:zcad035. [PMID: 37457379 PMCID: PMC10346432 DOI: 10.1093/narcan/zcad035] [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: 01/19/2023] [Revised: 05/12/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
The majority of compounds designed against cancer drug targets do not progress to become approved drugs, mainly due to lack of efficacy and/or unmanageable toxicity. Robust target evaluation is therefore required before progressing through the drug discovery process to reduce the high attrition rate. There are a wealth of publicly available databases that can be mined to generate data as part of a target evaluation. It can, however, be challenging to learn what databases are available, how and when they should be used, and to understand the associated limitations. Here, we have compiled and present key, freely accessible and easy-to-use databases that house informative datasets from in vitro, in vivo and clinical studies. We also highlight comprehensive target review databases that aim to bring together information from multiple sources into one-stop portals. In the post-genomics era, a key objective is to exploit the extensive cell, animal and patient characterization datasets in order to deliver precision medicine on a patient-specific basis. Effective utilization of the highlighted databases will go some way towards supporting the cancer research community achieve these aims.
Collapse
Affiliation(s)
- Daniel Croft
- Cancer Research Horizons, The Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Puja Lodhia
- Cancer Research Horizons, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sofia Lourenco
- Cancer Research Horizons, The Francis Crick Institute, London, NW1 1AT, UK
| | - Craig MacKay
- Cancer Research Horizons, The Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| |
Collapse
|
11
|
Wurz RP, Rui H, Dellamaggiore K, Ghimire-Rijal S, Choi K, Smither K, Amegadzie A, Chen N, Li X, Banerjee A, Chen Q, Mohl D, Vaish A. Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation. Nat Commun 2023; 14:4177. [PMID: 37443112 PMCID: PMC10344917 DOI: 10.1038/s41467-023-39904-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Targeted protein degradation via "hijacking" of the ubiquitin-proteasome system using proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality. The design of PROTACs is challenging; multiple steps involved in PROTAC-induced degradation make it difficult to establish coherent structure-activity relationships. Herein, we characterize PROTAC-mediated ternary complex formation and degradation by employing von Hippel-Lindau protein (VHL) recruiting PROTACs for two different target proteins, SMARCA2 and BRD4. Ternary-complex attributes and degradation activity parameters are evaluated by varying components of the PROTAC's architecture. Ternary complex binding affinity and cooperativity correlates well with degradation potency and initial rates of degradation. Additionally, we develop a ternary-complex structure modeling workflow to calculate the total buried surface area at the interface, which is in agreement with the measured ternary complex binding affinity. Our findings establish a predictive framework to guide the design of potent degraders.
Collapse
Affiliation(s)
- Ryan P Wurz
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Huan Rui
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | | | - Kaylee Choi
- Amgen Research, Amgen Inc., South San Francisco, CA, USA
| | - Kate Smither
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | - Ning Chen
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Xiaofen Li
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | | | - Qing Chen
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Dane Mohl
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA.
| | - Amit Vaish
- Amgen Research, Amgen Inc., Thousand Oaks, CA, USA.
| |
Collapse
|
12
|
Liang J, Wu Y, Lan K, Dong C, Wu S, Li S, Zhou HB. Antiviral PROTACs: Opportunity borne with challenge. CELL INSIGHT 2023; 2:100092. [PMID: 37398636 PMCID: PMC10308200 DOI: 10.1016/j.cellin.2023.100092] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 07/04/2023]
Abstract
Proteolysis targeting chimera (PROTAC) degradation of pathogenic proteins by hijacking of the ubiquitin-proteasome-system has become a promising strategy in drug design. The overwhelming advantages of PROTAC technology have ensured a rapid and wide usage, and multiple PROTACs have entered clinical trials. Several antiviral PROTACs have been developed with promising bioactivities against various pathogenic viruses. However, the number of reported antiviral PROTACs is far less than that of other diseases, e.g., cancers, immune disorders, and neurodegenerative diseases, possibly because of the common deficiencies of PROTAC technology (e.g., limited available ligands and poor membrane permeability) plus the complex mechanism involved and the high tendency of viral mutation during transmission and replication, which may challenge the successful development of effective antiviral PROTACs. This review highlights the important advances in this rapidly growing field and critical limitations encountered in developing antiviral PROTACs by analyzing the current status and representative examples of antiviral PROTACs and other PROTAC-like antiviral agents. We also summarize and analyze the general principles and strategies for antiviral PROTAC design and optimization with the intent of indicating the potential strategic directions for future progress.
Collapse
Affiliation(s)
- Jinsen Liang
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Yihe Wu
- 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, 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
| | - Chune Dong
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shu Li
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Hai-Bing Zhou
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
- 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, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| |
Collapse
|
13
|
Ma L, Li Y, Luo R, Wang Y, Cao J, Fu W, Qian B, Zheng L, Tang L, Lv X, Zheng L, Liang G, Chen L. Discovery of a Selective and Orally Bioavailable FGFR2 Degrader for Treating Gastric Cancer. J Med Chem 2023. [PMID: 37220310 DOI: 10.1021/acs.jmedchem.3c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Abnormal activation of fibroblast growth factor receptors (FGFRs) results in the development and progression of human cancers. FGFR2 is frequently amplified or mutated in cancers; therefore, it is an attractive target for tumor therapy. Despite the development of several pan-FGFR inhibitors, their long-term therapeutic efficacy is hindered by acquired mutations and low isoform selectivity. Herein, we report the discovery of an efficient and selective FGFR2 proteolysis-targeting chimeric molecule, LC-MB12, that incorporates an essential rigid linker. LC-MB12 preferentially internalizes and degrades membrane-bound FGFR2 among the four FGFR isoforms; this may promote greater clinical benefits. LC-MB12 exhibits superior potency in FGFR signaling suppression and anti-proliferative activity compared to the parental inhibitor. Furthermore, LC-MB12 is orally bioavailable and shows significant antitumor effects in FGFR2-dependent gastric cancer in vivo. Taken together, LC-MB12 is a candidate FGFR2 degrader for alternative FGFR2-targeting strategies and offers a promising starting point for drug development.
Collapse
Affiliation(s)
- Lin Ma
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Yingying Li
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Ruixiang Luo
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Yuhan Wang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Jiaqi Cao
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Weitao Fu
- Department of Computer-Aided Drug Design, Jiangsu Vcare PharmaTech Co. Ltd., Nanjing 211800, China
| | - Bolan Qian
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Lei Zheng
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Longguang Tang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang 322000, China
| | - Xinting Lv
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Lulu Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang 310000, China
| | - Guang Liang
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| | - Lingfeng Chen
- Affiliated Yongkang First People's Hospital and School of Pharmacy, Hangzhou Medical College, Hangzhou 310012 Zhejiang, China
| |
Collapse
|
14
|
Li Q, Zhou L, Qin S, Huang Z, Li B, Liu R, Yang M, Nice EC, Zhu H, Huang C. Proteolysis-targeting chimeras in biotherapeutics: Current trends and future applications. Eur J Med Chem 2023; 257:115447. [PMID: 37229829 DOI: 10.1016/j.ejmech.2023.115447] [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: 03/12/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023]
Abstract
The success of inhibitor-based therapeutics is largely constrained by the acquisition of therapeutic resistance, which is partially driven by the undruggable proteome. The emergence of proteolysis targeting chimera (PROTAC) technology, designed for degrading proteins involved in specific biological processes, might provide a novel framework for solving the above constraint. A heterobifunctional PROTAC molecule could structurally connect an E3 ubiquitin ligase ligand with a protein of interest (POI)-binding ligand by chemical linkers. Such technology would result in the degradation of the targeted protein via the ubiquitin-proteasome system (UPS), opening up a novel way of selectively inhibiting undruggable proteins. Herein, we will highlight the advantages of PROTAC technology and summarize the current understanding of the potential mechanisms involved in biotherapeutics, with a particular focus on its application and development where therapeutic benefits over classical small-molecule inhibitors have been achieved. Finally, we discuss how this technology can contribute to developing biotherapeutic drugs, such as antivirals against infectious diseases, for use in clinical practices.
Collapse
Affiliation(s)
- Qiong Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Li Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, PR China
| | - Siyuan Qin
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Zhao Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Bowen Li
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Ruolan Liu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China
| | - Mei Yang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Huili Zhu
- Department of Reproductive Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, 610041, PR China.
| | - Canhua Huang
- West China School of Basic Medical Sciences and Forensic Medicine, State Key Laboratory of Biotherapy and Cancer Center, and West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.
| |
Collapse
|
15
|
Sobhia ME, Kumar H, Kumari S. Bifunctional robots inducing targeted protein degradation. Eur J Med Chem 2023; 255:115384. [PMID: 37119667 DOI: 10.1016/j.ejmech.2023.115384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/01/2023]
Abstract
The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (POI) and E3-ligase, which induce the ubiquitination of POI. These molecules are based on event-driven pharmacology and are applicable in different conditions such as oncology, antiviral, neurodegenerative disease, acne etc., offering tremendous scope to researchers. In this review, primarily, we attempted to compile the recent works available in the literature on PROTACs for various targeted proteins. We summarized the design and development strategies with a focus on molecular information of protein residues and linker design. Rationalization of the ternary complex formation using Artificial Intelligence including machine & deep learning models and traditionally followed computational tools are also included in this study. Moreover, details describing the optimization of PROTACs chemistry and pharmacokinetic properties are added. Advanced PROTAC designs and targeting complex proteins, is summed up to cover the wide spectrum.
Collapse
Affiliation(s)
- M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India.
| | - Harish Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India
| | - Sonia Kumari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India
| |
Collapse
|
16
|
Chirnomas D, Hornberger KR, Crews CM. Protein degraders enter the clinic - a new approach to cancer therapy. Nat Rev Clin Oncol 2023; 20:265-278. [PMID: 36781982 DOI: 10.1038/s41571-023-00736-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2023] [Indexed: 02/15/2023]
Abstract
Heterobifunctional protein degraders, such as PROteolysis TArgeting Chimera (PROTAC) protein degraders, constitute a novel therapeutic modality that harnesses the cell's natural protein-degradation machinery - that is, the ubiquitin-proteasome system - to selectively target proteins involved in disease pathogenesis for elimination. Protein degraders have several potential advantages over small-molecule inhibitors that have traditionally been used for cancer treatment, including their event-driven (rather than occupancy-driven) pharmacology, which permits sub-stoichiometric drug concentrations for activity, their capacity to act iteratively and target multiple copies of a protein of interest, and their potential to target nonenzymatic proteins that were previously considered 'undruggable'. Following numerous innovations in protein degrader design and rigorous evaluation in preclinical models, protein degraders entered clinical testing in 2019. Currently, 18 protein degraders are in phase I or phase I/II clinical trials that involve patients with various tumour types, with a phase III trial of one initiated in 2022. The first safety, efficacy and pharmacokinetic data from these studies are now materializing and, although considerably more evidence is needed, protein degraders are showing promising activity as cancer therapies. Herein, we review advances in protein degrader development, the preclinical research that supported their entry into clinical studies, the available data for protein degraders in patients and future directions for this new class of drugs.
Collapse
Affiliation(s)
| | | | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA.
- Department of Pharmacology, Yale University, New Haven, CT, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
| |
Collapse
|
17
|
Li M, Zhi Y, Liu B, Yao Q. Advancing Strategies for Proteolysis-Targeting Chimera Design. J Med Chem 2023; 66:2308-2329. [PMID: 36788245 DOI: 10.1021/acs.jmedchem.2c01555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) have shown great therapeutic potential by degrading various disease-causing proteins, particularly those related to tumors. Therefore, the introduction of PROTACs has ushered in a new chapter of antitumor drug development, marked by significant advances over recent years. Herein, we describe recent developments in PROTAC technology, focusing on design strategy, development workflow, and future outlooks. We also discuss potential opportunities and challenges for PROTAC research.
Collapse
Affiliation(s)
- Minglei Li
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Ying Zhi
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Bo Liu
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Qingqiang Yao
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| |
Collapse
|
18
|
Mai H, Zimmer MH, Miller TF. Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods. J Phys Chem B 2023; 127:446-455. [PMID: 36607139 PMCID: PMC9869335 DOI: 10.1021/acs.jpcb.2c05795] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/18/2022] [Indexed: 01/07/2023]
Abstract
Proteolysis targeting chimera (PROTAC) is a novel drug modality that facilitates the degradation of a target protein by inducing proximity with an E3 ligase. In this work, we present a new computational framework to model the cooperativity between PROTAC-E3 binding and PROTAC-target binding principally through protein-protein interactions (PPIs) induced by the PROTAC. Due to the scarcity and low resolution of experimental measurements, the physical and chemical drivers of these non-native PPIs remain to be elucidated. We develop a coarse-grained (CG) approach to model interactions in the target-PROTAC-E3 complexes, which enables converged thermodynamic estimations using alchemical free energy calculation methods despite an unconventional scale of perturbations. With minimal parametrization, we successfully capture fundamental principles of cooperativity, including the optimality of intermediate PROTAC linker lengths that originates from configurational entropy. We qualitatively characterize the dependency of cooperativity on PROTAC linker lengths and protein charges and shapes. Minimal inclusion of sequence- and conformation-specific features in our current force field, however, limits quantitative modeling to reproduce experimental measurements, but further development of the CG model may allow for efficient computational screening to optimize PROTAC cooperativity.
Collapse
Affiliation(s)
- Huanghao Mai
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Matthew H. Zimmer
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California91125, United States
| | - Thomas F. Miller
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California91125, United States
| |
Collapse
|
19
|
Tunjic TM, Weber N, Brunsteiner M. Computer aided drug design in the development of proteolysis targeting chimeras. Comput Struct Biotechnol J 2023; 21:2058-2067. [PMID: 36968015 PMCID: PMC10030821 DOI: 10.1016/j.csbj.2023.02.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
Proteolysis targeting chimeras represent a class of drug molecules with a number of attractive properties, most notably a potential to work for targets that, so far, have been in-accessible for conventional small molecule inhibitors. Due to their different mechanism of action, and physico-chemical properties, many of the methods that have been designed and applied for computer aided design of traditional small molecule drugs are not applicable for proteolysis targeting chimeras. Here we review recent developments in this field focusing on three aspects: de-novo linker-design, estimation of absorption for beyond-rule-of-5 compounds, and the generation and ranking of ternary complex structures. In spite of this field still being young, we find that a good number of models and algorithms are available, with the potential to assist the design of such compounds in-silico, and accelerate applied pharmaceutical research.
Collapse
|
20
|
Hill-Payne B, Dilones S, Burslem G. The importance of controls in targeted protein degradation: Determining mechanism. Methods Enzymol 2022; 681:215-240. [PMID: 36764758 DOI: 10.1016/bs.mie.2022.10.006] [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: 12/13/2022]
Abstract
Targeted protein degradation has emerged as a useful approach for both basic biological investigations and therapeutic development. However, it can provide confounding results if not properly controlled. In this manuscript, we discuss the importance of proper controls and provide a detailed protocol for their application to proteolysis targeting chimera mediated degradation.
Collapse
Affiliation(s)
- Brianna Hill-Payne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sebastian Dilones
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - George Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| |
Collapse
|
21
|
Weng G, Cai X, Cao D, Du H, Shen C, Deng Y, He Q, Yang B, Li D, Hou T. PROTAC-DB 2.0: an updated database of PROTACs. Nucleic Acids Res 2022; 51:D1367-D1372. [PMID: 36300631 PMCID: PMC9825472 DOI: 10.1093/nar/gkac946] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/23/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023] Open
Abstract
Proteolysis targeting chimeras (PROTACs), which harness the ubiquitin-proteasome system to selectively induce targeted protein degradation, represent an emerging therapeutic technology with the potential to modulate traditional undruggable targets. Over the past few years, this technology has moved from academia to industry and more than 10 PROTACs have been advanced into clinical trials. However, designing potent PROTACs with desirable drug-like properties still remains a great challenge. Here, we report an updated online database, PROTAC-DB 2.0, which is a repository of structural and experimental data about PROTACs. In this 2nd release, we expanded the number of PROTACs to 3270, which corresponds to a 96% expansion over the first version. Meanwhile, the numbers of warheads (small molecules targeting the proteins of interest), linkers, and E3 ligands (small molecules recruiting E3 ligases) have increased to over 360, 1500 and 80, respectively. In addition, given the importance and the limited number of the crystal target-PROTAC-E3 ternary complex structures, we provide the predicted ternary complex structures for PROTACs with good degradation capability using our PROTAC-Model method. To further facilitate the analysis of PROTAC data, a new filtering strategy based on the E3 ligases is also added. PROTAC-DB 2.0 is available online at http://cadd.zju.edu.cn/protacdb/.
Collapse
Affiliation(s)
| | | | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410004, Hunan, China
| | - Hongyan Du
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yafeng Deng
- CarbonSilicon AI Technology Co., Ltd, Hangzhou 310018, Zhejiang, China
| | - Qiaojun He
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China,Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Bo Yang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Dan Li
- Correspondence may also be addressed to Dan Li.
| | - Tingjun Hou
- To whom correspondence should be addressed. Tel: +86 517 8820 8412;
| |
Collapse
|
22
|
Advances in AR-targeting chimeras: a case study of proteolysis-targeting chimeras from bench to bedside. Future Med Chem 2022; 14:1471-1489. [PMID: 36214138 DOI: 10.4155/fmc-2022-0147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Proteolysis-targeting chimera (PROTAC) is an emerging revolutionary technology that promotes degradation of target proteins by proteolysis. AR-targeting PROTACs marked many milestones in the history of PROTAC development. In this review, the author discusses the development of AR-targeting PROTACs over the last two decades. Also included in this focused review are medicinal chemistry strategies, pharmacokinetic profiles and clinical development. Taking AR targeting PROTACs for case study, this review provides a target specific overview of how PROTAC technology has advanced from a revolutionary concept and achieved proof of concept leading to drug candidates that benefit patients.
Collapse
|
23
|
Zhang W, Roy Burman SS, Chen J, Donovan KA, Cao Y, Shu C, Zhang B, Zeng Z, Gu S, Zhang Y, Li D, Fischer ES, Tokheim C, Shirley Liu X. Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:882-898. [PMID: 36494034 PMCID: PMC10025769 DOI: 10.1016/j.gpb.2022.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022]
Abstract
Targeted protein degradation (TPD) has rapidly emerged as a therapeutic modality to eliminate previously undruggable proteins by repurposing the cell's endogenous protein degradation machinery. However, the susceptibility of proteins for targeting by TPD approaches, termed "degradability", is largely unknown. Here, we developed a machine learning model, model-free analysis of protein degradability (MAPD), to predict degradability from features intrinsic to protein targets. MAPD shows accurate performance in predicting kinases that are degradable by TPD compounds [with an area under the precision-recall curve (AUPRC) of 0.759 and an area under the receiver operating characteristic curve (AUROC) of 0.775] and is likely generalizable to independent non-kinase proteins. We found five features with statistical significance to achieve optimal prediction, with ubiquitination potential being the most predictive. By structural modeling, we found that E2-accessible ubiquitination sites, but not lysine residues in general, are particularly associated with kinase degradability. Finally, we extended MAPD predictions to the entire proteome to find 964 disease-causing proteins (including proteins encoded by 278 cancer genes) that may be tractable to TPD drug development.
Collapse
Affiliation(s)
- Wubing Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shourya S Roy Burman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jiaye Chen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yang Cao
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Chelsea Shu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Research Scholar Initiative, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Boning Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shengqing Gu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Dian Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| |
Collapse
|
24
|
Cao C, He M, Wang L, He Y, Rao Y. Chemistries of bifunctional PROTAC degraders. Chem Soc Rev 2022; 51:7066-7114. [PMID: 35916511 DOI: 10.1039/d2cs00220e] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) technology is a novel and promising therapeutic strategy using small molecules to induce ubiquitin-dependent degradation of proteins. It has received extensive attention from both academia and industry as it can potentially access previously inaccessible targets. However, the design and optimization of PROTACs present big challenges for researchers, and the general strategy for its development and optimization is a lot of trial and error based on experience. This review highlights the important advances in this rapidly growing field and critical limitations of the traditional trial-and-error approach to developing PROTACs by analyzing numerous representative examples of PROTACs development. We summarize and analyze the general principles and strategies for PROTACs design and optimization from the perspective of chemical structure design, and propose potential future pathways to facilitate the development of PROTACs.
Collapse
Affiliation(s)
- Chaoguo Cao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China. .,Tsinghua-Peking Center for Life Sciences, Beijing 100084, P. R. China
| | - Ming He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | - Liguo Wang
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | - Yuna He
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| | - Yu Rao
- Ministry of Education (MOE) Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, P. R. China.
| |
Collapse
|
25
|
Zhu CL, Luo X, Tian T, Rao Z, Wang H, Zhou Z, Mi T, Chen D, Xu Y, Wu Y, Che J, Zhou Y, Li J, Dong X. Structure-based rational design enables efficient discovery of a new selective and potent AKT PROTAC degrader. Eur J Med Chem 2022; 238:114459. [DOI: 10.1016/j.ejmech.2022.114459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/13/2022]
|
26
|
Riching KM, Caine EA, Urh M, Daniels DL. The importance of cellular degradation kinetics for understanding mechanisms in targeted protein degradation. Chem Soc Rev 2022; 51:6210-6221. [PMID: 35792307 DOI: 10.1039/d2cs00339b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeted protein degradation has exploded over the past several years due to preclinical and early clinical therapeutic success of numerous compounds, and the emergence of new degradation modalities, which has broadened the definition of what a degrader is. The most characterized and well-studied small molecule degraders are molecular glues and proteolysis targeting chimeras (PROTACs). These degraders induce a ternary complex between a target protein, degrader, and E3 ligase component, resulting in ubiquitination and subsequent degradation of the target protein via the ubiquitin proteasomal system (UPS). This event-driven process requires success at all steps through a complex cascade of events. As more systems, degraders, and targets are tested, it has become increasingly clear that achieving degradation is only the first critical milestone in a degrader development program. Rather highly efficacious degraders require a combination of multiple optimized parameters: rapid degradation, high potency, high maximal degradation (Dmax), and sustained loss of target without re-dosing. Success to meet these more rigorous goals depends upon the ability to characterize and understand the dynamic cellular degradation profiles and relate them to the underlying mechanism for any given target treated with a specific concentration of degrader. From this starting point, optimization and fine tuning of multiple kinetic parameters such as how fast degradation occurs (the rate), how much of the target is degraded (the extent), and how long the target remains degraded (the duration) can be performed. In this review we explore the diversity of cellular kinetic degradation profiles which can arise after molecular glue and PROTAC treatment and the potential implications of these varying responses. As the overall degradation kinetics are a sum of individual mechanistic steps, each with their own kinetic contributions, we discuss the ways in which changes at any one of these steps could potentially influence the resultant kinetic degradation profiles. Looking forward, we address the importance in characterizing the kinetics of target protein loss in the early stages of degrader design and how this will enable more rapid discovery of therapeutic agents to elicit desired phenotypic outcomes.
Collapse
Affiliation(s)
- Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| |
Collapse
|
27
|
Protein–Protein Interaction Prediction for Targeted Protein Degradation. Int J Mol Sci 2022; 23:ijms23137033. [PMID: 35806036 PMCID: PMC9266413 DOI: 10.3390/ijms23137033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 02/04/2023] Open
Abstract
Protein–protein interactions (PPIs) play a fundamental role in various biological functions; thus, detecting PPI sites is essential for understanding diseases and developing new drugs. PPI prediction is of particular relevance for the development of drugs employing targeted protein degradation, as their efficacy relies on the formation of a stable ternary complex involving two proteins. However, experimental methods to detect PPI sites are both costly and time-intensive. In recent years, machine learning-based methods have been developed as screening tools. While they are computationally more efficient than traditional docking methods and thus allow rapid execution, these tools have so far primarily been based on sequence information, and they are therefore limited in their ability to address spatial requirements. In addition, they have to date not been applied to targeted protein degradation. Here, we present a new deep learning architecture based on the concept of graph representation learning that can predict interaction sites and interactions of proteins based on their surface representations. We demonstrate that our model reaches state-of-the-art performance using AUROC scores on the established MaSIF dataset. We furthermore introduce a new dataset with more diverse protein interactions and show that our model generalizes well to this new data. These generalization capabilities allow our model to predict the PPIs relevant for targeted protein degradation, which we show by demonstrating the high accuracy of our model for PPI prediction on the available ternary complex data. Our results suggest that PPI prediction models can be a valuable tool for screening protein pairs while developing new drugs for targeted protein degradation.
Collapse
|
28
|
Domostegui A, Nieto-Barrado L, Perez-Lopez C, Mayor-Ruiz C. Chasing molecular glue degraders: screening approaches. Chem Soc Rev 2022; 51:5498-5517. [PMID: 35723413 DOI: 10.1039/d2cs00197g] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein-protein interactions (PPIs) govern all biological processes. Some small molecules modulate PPIs through induced protein proximity. In particular, molecular glue degraders are monovalent compounds that orchestrate interactions between a target protein and an E3 ubiquitin ligase, prompting the proteasomal degradation of the former. This and other pharmacological strategies of targeted protein degradation (e.g. proteolysis-targeting chimeras - PROTACs) overcome some limitations of traditional occupancy-based therapeutics. Here, we provide an overview of the "molecular glue" concept, with a special focus on natural and synthetic inducers of proximity to E3s. We then briefly highlight the serendipitous discoveries of some clinical and preclinical molecular glue degraders, and discuss the first examples of intentional discoveries. Specifically, we outline the different screening strategies reported in this rapidly evolving arena and our thoughts on future perspectives. By mastering the ability to influence PPIs, molecular glue degraders can induce the degradation of unligandable proteins, thus providing an exciting path forward to broaden the targetable proteome.
Collapse
Affiliation(s)
- Ana Domostegui
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Luis Nieto-Barrado
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Carles Perez-Lopez
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Cristina Mayor-Ruiz
- IRB Barcelona - Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
| |
Collapse
|
29
|
Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules consisting of one ligand that binds to a protein of interest (POI) and another that can recruit an E3 ubiquitin ligase. The chemically-induced proximity between the POI and E3 ligase results in ubiquitination and subsequent degradation of the POI by the ubiquitin-proteasome system (UPS). The event-driven mechanism of action (MOA) of PROTACs offers several advantages compared to traditional occupancy-driven small molecule inhibitors, such as a catalytic nature, reduced dosing and dosing frequency, a more potent and longer-lasting effect, an added layer of selectivity to reduce potential toxicity, efficacy in the face of drug-resistance mechanisms, targeting nonenzymatic functions, and expanded target space. Here, we highlight important milestones and briefly discuss lessons learned about targeted protein degradation (TPD) in recent years and conjecture on the efforts still needed to expand the toolbox for PROTAC discovery to ultimately provide promising therapeutics.
Collapse
Affiliation(s)
- Ke Li
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA.
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA. .,Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA.,Department of Pharmacology, Yale University, New Haven, Connecticut 06511, USA
| |
Collapse
|
30
|
Liao J, Nie X, Unarta IC, Ericksen SS, Tang W. In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses. J Med Chem 2022; 65:6116-6132. [PMID: 35412837 DOI: 10.1021/acs.jmedchem.1c02155] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteolysis targeting chimeras (PROTACs) are molecules that induce protein degradation via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The rational design of PROTACs requires accurate knowledge of the native configuration of the PROTAC-induced ternary complex. This study demonstrates that native and non-native ternary complex poses can be distinguished based on the pose occupancy time in MD, where native poses exhibit longer occupancy times at both room and higher temperatures. Candidate poses are generated by MD sampling and pre-ranked by classic MM/GBSA. A specific heating scheme is then applied to accelerate ternary pose departure, with the pose occupancy time and fraction being measured. This scoring identifies the native pose in all systems tested. Its success is partially attributed to the dynamic nature of pose departure analyses, which accounts for entropic effects typically neglected in the faster static scoring methods, while entropy plays a greater role in protein-protein than in protein-ligand systems.
Collapse
Affiliation(s)
- Junzhuo Liao
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xueqing Nie
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ilona Christy Unarta
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Spencer S Ericksen
- Drug Development Core, UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weiping Tang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Drug Development Core, UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| |
Collapse
|
31
|
Ma S, Ji J, Tong Y, Zhu Y, Dou J, Zhang X, Xu S, Zhu T, Xu X, You Q, Jiang Z. Non-small molecule PROTACs (NSM-PROTACs): Protein degradation kaleidoscope. Acta Pharm Sin B 2022; 12:2990-3005. [PMID: 35865099 PMCID: PMC9293674 DOI: 10.1016/j.apsb.2022.02.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/29/2022] [Accepted: 02/14/2022] [Indexed: 12/29/2022] Open
Abstract
The proteolysis targeting chimeras (PROTACs) technology has been rapidly developed since its birth in 2001, attracting rapidly growing attention of scientific institutes and pharmaceutical companies. At present, a variety of small molecule PROTACs have entered the clinical trial. However, as small molecule PROTACs flourish, non-small molecule PROTACs (NSM-PROTACs) such as peptide PROTACs, nucleic acid PROTACs and antibody PROTACs have also advanced considerably over recent years, exhibiting the unique characters beyond the small molecule PROTACs. Here, we briefly introduce the types of NSM-PROTACs, describe the advantages of NSM-PROTACs, and summarize the development of NSM-PROTACs so far in detail. We hope this article could not only provide useful insights into NSM-PROTACs, but also expand the research interest of NSM-PROTACs.
Collapse
Affiliation(s)
- Sinan Ma
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Jianai Ji
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Yuanyuan Tong
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Zhu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Junwei Dou
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Xian Zhang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Shicheng Xu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Tianbao Zhu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaoli Xu
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Corresponding authors. Tel./fax: +86 25 83271351.
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Corresponding authors. Tel./fax: +86 25 83271351.
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Corresponding authors. Tel./fax: +86 25 83271351.
| |
Collapse
|
32
|
Li W, Zhang J, Guo L, Wang Q. Importance of Three-Body Problems and Protein-Protein Interactions in Proteolysis-Targeting Chimera Modeling: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:523-532. [PMID: 35084845 DOI: 10.1021/acs.jcim.1c01150] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) are a class of bifunctional molecules that can induce the ubiquitin degradation of its target protein by hijacking the E3 ligase to form a target protein-PROTAC-E3 ligase ternary complex. Its underlying principle has inspired the development of a wide range of protein degraders that are similar to or beyond PROTACs in recent years. The formation of the ternary complexes is the key to the success of PROTAC-induced protein degradation. Nevertheless, the lack of effective ternary complex modeling techniques has limited the application of computer-aided drug discovery tools to this emerging and fast developing new land in drug industry. Thus, in this study, we explored the application of the more physically sound molecular dynamics simulation and the molecular mechanics combined with the generalized Born and surface area continuum solvation (MM/GBSA) method to solve the underlying three-body problem in PROTAC modeling. We first verified the accuracy of our approach using a series of known Brd4 BD2 degraders. The calculated binding energy showed a good correlation with the experimental Kd values. The modeling of a unique property, namely, the α value, for PROTACs was also first and accurately performed to our best knowledge. The results also demonstrated the importance of PROTAC-induced protein-protein interactions in its modeling, either qualitatively or quantitatively. Finally, by standing on the success of earlier docking-based approaches, our protocol was also applied as a rescoring function in pose prediction. The results showed a notable improvement in reranking the initial poses generated from a modified Rosetta method, which was reportedly one of the best among a handful of PROTAC modeling approaches available in this field. We hope this work could provide a practical protocol and more insights to study the binding and the design of PROTACs and other protein degraders.
Collapse
Affiliation(s)
- Wenqing Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Jiabin Zhang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Li Guo
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| |
Collapse
|