1
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Abbas A, Ye F. Computational methods and key considerations for in silico design of proteolysis targeting chimera (PROTACs). Int J Biol Macromol 2024; 277:134293. [PMID: 39084437 DOI: 10.1016/j.ijbiomac.2024.134293] [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: 05/29/2024] [Revised: 07/19/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs), as heterobifunctional molecules, have garnered significant attention for their ability to target previously undruggable proteins. Due to the challenges in obtaining crystal structures of PROTAC molecules in the ternary complex, a plethora of computational tools have been developed to aid in PROTAC design. These computational tools can be broadly classified into artificial intelligence (AI)-based or non-AI-based methods. This review aims to provide a comprehensive overview of the latest computational methods for the PROTAC design process, covering both AI and non-AI approaches, from protein selection to ternary complex modeling and prediction. Key considerations for in silico PROTAC design are discussed, along with additional considerations for deploying AI-based models. These considerations are intended to guide subsequent model development in the PROTAC design process. Finally, future directions and recommendations are provided.
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Affiliation(s)
- Amr Abbas
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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2
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Gadiya Y, Shetty S, Hofmann-Apitius M, Gribbon P, Zaliani A. Exploring SureChEMBL from a drug discovery perspective. Sci Data 2024; 11:507. [PMID: 38755219 PMCID: PMC11099139 DOI: 10.1038/s41597-024-03371-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
In the pharmaceutical industry, the patent protection of drugs and medicines is accorded importance because of the high costs involved in the development of novel drugs. Over the years, researchers have analyzed patent documents to identify freedom-to-operate spaces for novel drug candidates. To assist this, several well-established public patent document data repositories have enabled automated methodologies for extracting information on therapeutic agents. In this study, we delve into one such publicly available patent database, SureChEMBL, which catalogues patent documents related to life sciences. Our exploration begins by identifying patent compounds across public chemical data resources, followed by pinpointing sections in patent documents where the chemical annotations were found. Next, we exhibit the potential of compounds to serve as drug candidates by evaluating their conformity to drug-likeness criteria. Lastly, we examine the drug development stage reported for these compounds to understand their clinical success. In summary, our investigation aims at providing a comprehensive overview of the patent compounds catalogued in SureChEMBL, assessing their relevance to pharmaceutical drug discovery.
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Affiliation(s)
- Yojana Gadiya
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525, Hamburg, Germany.
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany.
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53113, Bonn, Germany.
| | - Simran Shetty
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
- Hamburg University of Applied Sciences (HAW), 20099, Hamburg, Germany
| | - Martin Hofmann-Apitius
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53113, Bonn, Germany
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
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3
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Mslati H, Gentile F, Pandey M, Ban F, Cherkasov A. PROTACable Is an Integrative Computational Pipeline of 3-D Modeling and Deep Learning To Automate the De Novo Design of PROTACs. J Chem Inf Model 2024; 64:3034-3046. [PMID: 38504115 DOI: 10.1021/acs.jcim.3c01878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) that engage two biological targets at once are a promising technology in degrading clinically relevant protein targets. Since factors that influence the biological activities of PROTACs are more complex than those of a small molecule drug, we explored a combination of computational chemistry and deep learning strategies to forecast PROTAC activity and enable automated design. A new method named PROTACable was developed for the de novo design of PROTACs, which includes a robust 3-D modeling workflow to model PROTAC ternary complexes using a library of E3 ligase and linker and an SE(3)-equivariant graph transformer network to predict the activity of newly designed PROTACs. PROTACable is available at https://github.com/giaguaro/PROTACable/.
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Affiliation(s)
- Hazem Mslati
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Francesco Gentile
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario K1N 6N5, Canada
| | - Mohit Pandey
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada
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4
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Akash S, Abdelkrim G, Bayil I, Hosen ME, Mukerjee N, Shater AF, Saleh FM, Albadrani GM, Al‐Ghadi MQ, Abdel‐Daim MM, Tok TT. Antimalarial drug discovery against malaria parasites through haplopine modification: An advanced computational approach. J Cell Mol Med 2023; 27:3168-3188. [PMID: 37724615 PMCID: PMC10568677 DOI: 10.1111/jcmm.17940] [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: 06/20/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023] Open
Abstract
The widespread emergence of antimalarial drug resistance has created a major threat to public health. Malaria is a life-threatening infectious disease caused by Plasmodium spp., which includes Apicoplast DNA polymerase and Plasmodium falciparum cysteine protease falcipain-2. These components play a critical role in their life cycle and metabolic pathway, and are involved in the breakdown of erythrocyte hemoglobin in the host, making them promising targets for anti-malarial drug design. Our current study has been designed to explore the potential inhibitors from haplopine derivatives against these two targets using an in silico approach. A total of nine haplopine derivatives were used to perform molecular docking, and the results revealed that Ligands 03 and 05 showed strong binding affinity compared to the control compound atovaquone. Furthermore, these ligand-protein complexes underwent molecular dynamics simulations, and the results demonstrated that the complexes maintained strong stability in terms of RMSD (root mean square deviation), RMSF (root mean square fluctuation), and Rg (radius of gyration) over a 100 ns simulation period. Additionally, PCA (principal component analysis) analysis and the dynamic cross-correlation matrix showed positive outcomes for the protein-ligand complexes. Moreover, the compounds exhibited no violations of the Lipinski rule, and ADMET (absorption, distribution, metabolism, excretion, and toxicity) predictions yielded positive results without indicating any toxicity. Finally, density functional theory (DFT) and molecular electrostatic potential calculations were conducted, revealing that the mentioned derivatives exhibited better stability and outstanding performance. Overall, this computational approach suggests that these haplopine derivatives could serve as a potential source for developing new, effective antimalarial drugs to combat malaria. However, further in vitro or in vivo studies might be conducted to determine their actual effectiveness.
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Affiliation(s)
- Shopnil Akash
- Department of PharmacyFaculty of Allied Health Sciences, Daffodil International, UniversityDhakaBangladesh
| | - Guendouzi Abdelkrim
- Laboratory of Chemistry, Synthesis, Properties and Applications. (LCSPA)University of SaidaSaïdaAlgeria
| | - Imren Bayil
- Department of Bioinformatics and computational biologyGaziantep UniversityGaziantepTurkey
| | - Md. Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Nobendu Mukerjee
- Department of MicrobiologyWest Bengal State UniversityKolkataIndia
- Department of Health SciencesNovel Global Community Educational FoundationHebershamAustralia
| | - Abdullah F. Shater
- Department of Medical Laboratory Technology, Faculty of Applied Medical SciencesUniversity of TabukTabukSaudi Arabia
| | - Fayez M. Saleh
- Department of Medical Microbiology, Faculty of MedicineUniversity of TabukTabukSaudi Arabia
| | - Ghadeer M. Albadrani
- Department of Biology, College of SciencePrincess Nourah bint Abdulrahman UniversityRiyadhSaudi Arabia
| | - Muath Q. Al‐Ghadi
- Department of Zoology, College of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Mohamed M. Abdel‐Daim
- Department of Pharmaceutical Sciences, Pharmacy ProgramBatterjee Medical CollegeJeddahSaudi Arabia
- Pharmacology Department, Faculty of Veterinary MedicineSuez Canal UniversityIsmailiaEgypt
| | - Tuğba Taşkin Tok
- Department of Bioinformatics and computational biologyGaziantep UniversityGaziantepTurkey
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5
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Sakanyan V, Iradyan N, Alves de Sousa R. Targeted Strategies for Degradation of Key Transmembrane Proteins in Cancer. BIOTECH 2023; 12:57. [PMID: 37754201 PMCID: PMC10526213 DOI: 10.3390/biotech12030057] [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: 07/05/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 09/28/2023] Open
Abstract
Targeted protein degradation is an attractive technology for cancer treatment due to its ability to overcome the unpredictability of the small molecule inhibitors that cause resistance mutations. In recent years, various targeted protein degradation strategies have been developed based on the ubiquitin-proteasome system in the cytoplasm or the autophagy-lysosomal system during endocytosis. In this review, we describe and compare technologies for the targeted inhibition and targeted degradation of the epidermal growth factor receptor (EGFR), one of the major proteins responsible for the onset and progression of many types of cancer. In addition, we develop an alternative strategy, called alloAUTO, based on the binding of new heterocyclic compounds to an allosteric site located in close proximity to the EGFR catalytic site. These compounds cause the targeted degradation of the transmembrane receptor, simultaneously activating both systems of protein degradation in cells. Damage to the EGFR signaling pathways promotes the inactivation of Bim sensor protein phosphorylation, which leads to the disintegration of the cytoskeleton, followed by the detachment of cancer cells from the extracellular matrix, and, ultimately, to cancer cell death. This hallmark of targeted cancer cell death suggests an advantage over other targeted protein degradation strategies, namely, the fewer cancer cells that survive mean fewer chemotherapy-resistant mutants appear.
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Affiliation(s)
- Vehary Sakanyan
- Faculté de Pharmacie, Université de Nantes, 44035 Nantes, France
- ProtNeteomix, 29 rue de Provence, 44700 Orvault, France
| | - Nina Iradyan
- Institute of Fine Organic Chemistry after A. Mnjoyan, National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia;
| | - Rodolphe Alves de Sousa
- Faculté des Sciences Fondamentales et Biomédicales, Université Paris Descartes, UMR 8601, CBMIT, 75006 Paris, France;
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6
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Garcia Jimenez D, Vallaro M, Rossi Sebastiano M, Apprato G, D’Agostini G, Rossetti P, Ermondi G, Caron G. Chamelogk: A Chromatographic Chameleonicity Quantifier to Design Orally Bioavailable Beyond-Rule-of-5 Drugs. J Med Chem 2023; 66:10681-10693. [PMID: 37490408 PMCID: PMC10424176 DOI: 10.1021/acs.jmedchem.3c00823] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Indexed: 07/27/2023]
Abstract
New chemical modalities in drug discovery include molecules belonging to the bRo5 chemical space. Because of their complex and flexible structure, bRo5 compounds often suffer from a poor solubility/permeability profile. Chameleonicity describes the capacity of a molecule to adapt to the environment through conformational changes; the design of molecular chameleons is a medicinal chemistry strategy simultaneously optimizing solubility and permeability. A default method to quantify chameleonicity in early drug discovery is still missing. Here we introduce Chamelogk, an automated, fast, and cheap chromatographic descriptor of chameleonicity. Moreover, we report measurements for 55 Ro5 and bRo5 compounds and validate our method with literature data. Then, selected case studies (macrocycles, nonmacrocyclic compounds, and PROTACs) are used to illustrate the application of Chamelogk in combination with lipophilicity (BRlogD) and polarity (Δ log kwIAM) descriptors. Overall, we show how Chamelogk deserves being included in property-based drug discovery strategies to design oral bioavailable bRo5 compounds.
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Affiliation(s)
- Diego Garcia Jimenez
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Apprato
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia D’Agostini
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Paolo Rossetti
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and
Health Sciences Dept., CASSMedChem, University
of Torino, via Quarello 15, 10135 Torino, Italy
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7
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Apprato G, Ermondi G, Caron G. The Quest for Oral PROTAC drugs: Evaluating the Weaknesses of the Screening Pipeline. ACS Med Chem Lett 2023; 14:879-883. [PMID: 37465314 PMCID: PMC10351046 DOI: 10.1021/acsmedchemlett.3c00231] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
A targeted bibliographic search exposed the deficiencies within existing PROTAC preclinical pipelines, including missing, poor-quality data and technical limitations in the experimental assays. Several recommendations are proposed to improve the efficiency of preclinical platforms for PROTACs.
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8
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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: 13] [Impact Index Per Article: 13.0] [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.
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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
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9
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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.
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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
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10
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Abstract
Proteolysis-targeting chimeras (PROTACs) have shown great therapeutic potential by degrading various disease-causing proteins, particularly those related to tumors. Therefore, the introduction of PROTACs has ushered in a new chapter of antitumor drug development, marked by significant advances over recent years. Herein, we describe recent developments in PROTAC technology, focusing on design strategy, development workflow, and future outlooks. We also discuss potential opportunities and challenges for PROTAC research.
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Affiliation(s)
- Minglei Li
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Ying Zhi
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Bo Liu
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
| | - Qingqiang Yao
- School of Pharmacy and Pharmaceutical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117 Shandong, P. R. China
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11
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Apprato G, D’Agostini G, Rossetti P, Ermondi G, Caron G. In Silico Tools to Extract the Drug Design Information Content of Degradation Data: The Case of PROTACs Targeting the Androgen Receptor. Molecules 2023; 28:molecules28031206. [PMID: 36770875 PMCID: PMC9919651 DOI: 10.3390/molecules28031206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Proteolysis-Targeting Chimeras (PROTACs) have recently emerged as a promising technology in the drug discovery landscape. Large interest in the degradation of the androgen receptor (AR) as a new anti-prostatic cancer strategy has resulted in several papers focusing on PROTACs against AR. This study explores the potential of a few in silico tools to extract drug design information from AR degradation data in the format often reported in the literature. After setting up a dataset of 92 PROTACs with consistent AR degradation values, we employed the Bemis-Murcko method for their classification. The resulting clusters were not informative in terms of structure-degradation relationship. Subsequently, we performed Degradation Cliff analysis and identified some key aspects conferring a positive contribution to activity, as well as some methodological limits when applying this approach to PROTACs. Linker structure degradation relationships were also investigated. Then, we built and characterized ternary complexes to validate previous results. Finally, we implemented machine learning classification models and showed that AR degradation for VHL-based but not CRBN-based PROTACs can be predicted from simple permeability-related 2D molecular descriptors.
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12
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Guedeney N, Cornu M, Schwalen F, Kieffer C, Voisin-Chiret AS. PROTAC technology: A new drug design for chemical biology with many challenges in drug discovery. Drug Discov Today 2023; 28:103395. [PMID: 36228895 DOI: 10.1016/j.drudis.2022.103395] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
Target Protein Degradation TPD is a new avenue and revolutionary for therapeutics because redefining the principles of classical drug discovery and guided by event-based target activity rather than the occupancy-driven activity. Since the discovery of the first PROTAC in 2001, TPD represents a rapidly growing technology, with applications in both drug discovery and chemical biology. Over the last decade, many questions have been raised and today the knowledge gained by each team has elucidated a number of them, although there is still a long way to go. The objective of this work is to present the challenges that the PROTAC strategy has very recently addressed in drug design and discovery by presenting extremely recent results from the literature and to provide guidelines in the drug design of new PROTACs as successful therapeutic modality for medicinal chemists.
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Affiliation(s)
| | - Marie Cornu
- Normandie Univ, UNICAEN, CERMN, 14000 Caen, France
| | - Florian Schwalen
- Normandie Univ, UNICAEN, CERMN, 14000 Caen, France; Department of Pharmacy, Caen University Hospital, Caen 14000, France
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13
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Koroleva OA, Dutikova YV, Trubnikov AV, Zenov FA, Manasova EV, Shtil AA, Kurkin AV. PROTAC: targeted drug strategy. Principles and limitations. Russ Chem Bull 2022; 71:2310-2334. [PMID: 36569659 PMCID: PMC9762658 DOI: 10.1007/s11172-022-3659-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 12/23/2022]
Abstract
The PROTAC (PROteolysis TArgeting Chimera) technology is a method of targeting intracellular proteins previously considered undruggable. This technology utilizes the ubiquitin-proteasome system in cells to specifically degrade target proteins, thereby offering significant advantages over conventional small-molecule inhibitors of the enzymatic function. Preclinical and preliminary clinical trials of PROTAC-based compounds (degraders) are presented. The review considers the general principles of the design of degraders. Advances and challenges of the PROTAC technology are discussed.
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Affiliation(s)
- O. A. Koroleva
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
| | - Yu. V. Dutikova
- Patent & Law Firm “A. Zalesov and Partners”, Build. 9, 2 ul. Marshala Rybalko, 123060 Moscow, Russian Federation
| | - A. V. Trubnikov
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
| | - F. A. Zenov
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
| | - E. V. Manasova
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
| | - A. A. Shtil
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Build. 15, 24 Kashirskoe shosse, 115478 Moscow, Russian Federation
| | - A. V. Kurkin
- Department of Chemistry, Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
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14
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Zheng S, Tan Y, Wang Z, Li C, Zhang Z, Sang X, Chen H, Yang Y. Accelerated rational PROTAC design via deep learning and molecular simulations. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00527-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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PROTACs: Current Trends in Protein Degradation by Proteolysis-Targeting Chimeras. BioDrugs 2022; 36:609-623. [PMID: 36098871 DOI: 10.1007/s40259-022-00551-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2022] [Indexed: 11/02/2022]
Abstract
In the recent past, proteolysis-targeting chimera (PROTAC) technology has received enormous attention for its ability to overcome the limitations of protein inhibitors and its capability to target undruggable proteins. The PROTAC molecule consists of three components, a ubiquitin E3 ligase ligand, a linker, and a target protein ligand. The application of this technology is rapidly gaining momentum, especially in cancer therapy. In this review, we first look at the history of degraders, followed by a section on the ubiquitin proteasome system (UPS) and E3 ligases used in PROTAC development. PROTACs are dependent on the UPS for degradation of target proteins. We further discuss the scope and design of degraders and mitigation strategies for overcoming the hook effect seen with degraders. As PROTACs do not follow Lipinski's 'Rule of 5', these molecules face drug metabolism and pharmacokinetic challenges. A detailed section on absorption, distribution, metabolism, and excretion of degraders is provided wherein we discuss methodologies and strategies to surmount the challenges faced by these molecules. For understanding PROTAC-mediated degradation, the characterization and measurement of protein levels in cells is important. Currently used techniques and recent advancements in assessment tools for degraders are discussed. Furthermore, we examine the challenges and emerging technologies that need to be focused on in order to competently develop potent degraders. Many companies are working in this area of emerging new modality and a few PROTACs have already entered clinical trials; the details of the trials are included in this review.
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16
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Rossi Sebastiano M, Garcia Jimenez D, Vallaro M, Caron G, Ermondi G. Refinement of Computational Access to Molecular Physicochemical Properties: From Ro5 to bRo5. J Med Chem 2022; 65:12068-12083. [PMID: 36094896 PMCID: PMC9511483 DOI: 10.1021/acs.jmedchem.2c00774] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
There is a need of computational tools to rank bRo5 drug
candidates
in the very early phases of drug discovery when chemical matter is
unavailable. In this study, we selected three compounds: (a) a Ro5
drug (Pomalidomide), (b) a bRo5 orally available drug (Saquinavir),
and (c) a polar PROTAC (CMP 98) to focus on computational access to
physicochemical properties. To provide a benchmark, the three compounds
were first experimentally characterized for their lipophilicity, polarity,
IMHBs, and chameleonicity. To reproduce the experimental information
content, we generated conformer ensembles with conformational sampling
and molecular dynamics in both water and nonpolar solvents. Then we
calculated Rgyr, 3D PSA, and IMHB number. An innovative pool of strategies
for data analysis was then provided. Overall, we report a contribution
to close the gap between experimental and computational methods for
characterizing bRo5 physicochemical properties.
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Affiliation(s)
- Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Diego Garcia Jimenez
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
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17
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Desantis J, Mammoli A, Eleuteri M, Coletti A, Croci F, Macchiarulo A, Goracci L. PROTACs bearing piperazine-containing linkers: what effect on their protonation state? RSC Adv 2022; 12:21968-21977. [PMID: 36043064 PMCID: PMC9361468 DOI: 10.1039/d2ra03761k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 07/20/2022] [Indexed: 11/21/2022] Open
Abstract
Proteolysis targeting chimeras (PROTACs) represent an emerging class of compounds for innovative therapeutic application. Their bifunctional nature induces the formation of a ternary complex (target protein/PROTAC/E3 ligase) which allows target protein ubiquitination and subsequent proteasomal-dependent degradation. To date, despite great efforts being made to improve their biological efficacy PROTACs rational design still represents a challenging task, above all for the modulation of their physicochemical and pharmacokinetics properties. Considering the pivotal role played by the linker moiety, recently the insertion of a piperazine moiety into the PROTAC linker has been widely used, as this ring can in principle improve rigidity and increase solubility upon protonation. Nevertheless, the pK a of the piperazine ring is significantly affected by the chemical groups located nearby, and slight modifications in the linker could eliminate the desired effect. In the present study, the pK a values of a dataset of synthesized small molecule compounds including PROTACs and their precursors have been evaluated in order to highlight how a fine modulation of piperazine-containing linkers can impact the protonation state of these molecules or similar heterobifunctional ones. Finally, the possibility of predicting the trend through in silico approaches was also evaluated.
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Affiliation(s)
- Jenny Desantis
- Department of Chemistry, Biology, and Biotechnology, University of Perugia Via Elce di Sotto 8 06123 Perugia Italy
| | - Andrea Mammoli
- Department of Pharmaceutical Sciences, University of Perugia Via del Liceo 1 06123 Perugia Italy
| | - Michela Eleuteri
- Department of Chemistry, Biology, and Biotechnology, University of Perugia Via Elce di Sotto 8 06123 Perugia Italy
| | - Alice Coletti
- Department of Pharmaceutical Sciences, University of Perugia Via del Liceo 1 06123 Perugia Italy
| | - Federico Croci
- Department of Chemistry, Biology, and Biotechnology, University of Perugia Via Elce di Sotto 8 06123 Perugia Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia Via del Liceo 1 06123 Perugia Italy
| | - Laura Goracci
- Department of Chemistry, Biology, and Biotechnology, University of Perugia Via Elce di Sotto 8 06123 Perugia Italy
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18
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Trapotsi MA, Mouchet E, Williams G, Monteverde T, Juhani K, Turkki R, Miljković F, Martinsson A, Mervin L, Pryde KR, Müllers E, Barrett I, Engkvist O, Bender A, Moreau K. Cell Morphological Profiling Enables High-Throughput Screening for PROteolysis TArgeting Chimera (PROTAC) Phenotypic Signature. ACS Chem Biol 2022; 17:1733-1744. [PMID: 35793809 PMCID: PMC9295119 DOI: 10.1021/acschembio.2c00076] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) use the ubiquitin-proteasome system to degrade a protein of interest for therapeutic benefit. Advances made in targeted protein degradation technology have been remarkable, with several molecules having moved into clinical studies. However, robust routes to assess and better understand the safety risks of PROTACs need to be identified, which is an essential step toward delivering efficacious and safe compounds to patients. In this work, we used Cell Painting, an unbiased high-content imaging method, to identify phenotypic signatures of PROTACs. Chemical clustering and model prediction allowed the identification of a mitotoxicity signature that could not be expected by screening the individual PROTAC components. The data highlighted the benefit of unbiased phenotypic methods for identifying toxic signatures and the potential to impact drug design.
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Affiliation(s)
- Maria-Anna Trapotsi
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Data Sciences & Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Elizabeth Mouchet
- High Throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Macclesfield SK10 4TF, U.K
| | - Guy Williams
- High Throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Macclesfield SK10 4TF, U.K
| | - Tiziana Monteverde
- High Throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Macclesfield SK10 4TF, U.K
| | - Karolina Juhani
- High Throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Macclesfield SK10 4TF, U.K
| | - Riku Turkki
- Data Sciences & Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg SE-43183, Sweden
| | - Filip Miljković
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences R&D, AstraZeneca, Gothenburg SE-43183, Sweden
| | - Anton Martinsson
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences R&D, AstraZeneca, Gothenburg SE-43183, Sweden
| | - Lewis Mervin
- Molecular AI, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Kenneth R Pryde
- Oncology Safety, Clinical Pharmacology and Safety Sciences R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Erik Müllers
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg SE-43183, Sweden
| | - Ian Barrett
- Data Sciences & Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Ola Engkvist
- Molecular AI, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg SE-43183, Sweden
| | - Andreas Bender
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Kevin Moreau
- Safety Innovation, Clinical Pharmacology and Safety Sciences R&D, AstraZeneca, Cambridge CB2 0AA, U.K
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19
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García Jiménez D, Rossi Sebastiano M, Vallaro M, Mileo V, Pizzirani D, Moretti E, Ermondi G, Caron G. Designing Soluble PROTACs: Strategies and Preliminary Guidelines. J Med Chem 2022; 65:12639-12649. [PMID: 35469399 PMCID: PMC9574862 DOI: 10.1021/acs.jmedchem.2c00201] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Solubility optimization is a crucial step to obtaining oral PROTACs. Here we measured the thermodynamic solubilities (log S) of 21 commercial PROTACs. Next, we measured BRlogD and log kwIAM (lipophilicity), EPSA, and Δ log kwIAM (polarity) and showed that lipophilicity plays a major role in governing log S, but a contribution of polarity cannot be neglected. Two-/three-dimensional descriptors calculated on conformers arising from conformational sampling and steered molecular dynamics failed in modeling solubility. Infographic tools were used to identify a privileged region of soluble PROTACs in a chemical space defined by BRlogD, log kwIAM and topological polar surface area, while machine learning provided a log S classification model. Finally, for three pairs of PROTACs we measured the solubility, lipophilicity, and polarity of the building blocks and identified the limits of estimating PROTAC solubility from the synthetic components. Overall, this paper provides promising guidelines for optimizing PROTAC solubility in early drug discovery programs.
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Affiliation(s)
- Diego García Jiménez
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
| | - Valentina Mileo
- Global Research and Preclinical Development, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy.,Emerging Science & Technology Unit, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy
| | - Daniela Pizzirani
- Global Research and Preclinical Development, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy.,Emerging Science & Technology Unit, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy
| | - Elisa Moretti
- Global Research and Preclinical Development, Research Center, Chiesi Farmaceutici, Largo Belloli 11/a, 43122 Parma, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, CASSMedChem, University of Torino, Via Quarello 15, 10135 Torino, Italy
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20
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Jimenez DG, Sebastiano MR, Caron G, Ermondi G. Are we ready to design oral PROTACs®? ADMET AND DMPK 2022; 9:243-254. [PMID: 35300370 PMCID: PMC8920102 DOI: 10.5599/admet.1037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/22/2021] [Indexed: 12/25/2022] Open
Abstract
PROTACs® are expected to strongly impact the future of drug discovery. Therefore, in this work we firstly performed a statistical study to highlight the distribution of E3 ligases and POIs collected in PROTAC-DB, the main online database focused on degraders. Moreover, since the emerging technology of protein degradation deals with large and complex chemical structures, the second part of the paper focuses on how to set up a property-based design strategy to obtain oral degraders. For this purpose, we calculated a pool of seven previously ad hoc selected 2D descriptors for the 2258 publicly available degraders in PROTAC-DB (average values: MW= 972.9 Da, nC= 49.5, NAR= 4.5, PHI= 17.3, nHDon= 4.5, nHAcc= 17.7 and TPSA= 240 Å2) and compared them to a dataset of 50 bRo5 orally approved drugs. Then, a chemical space based on nC, PHI and TPSA was built and subregions with optimal permeability and bioavailability were identified. Bioavailable degraders (ARV-110 and ARV-471) tend to be closer to the Ro5 region, using mainly semi-rigid linkers. Permeable degraders, on the other hand, are placed in an average central region of the chemical space but chameleonicity could allow them to be located closer to the two Arvinas compounds.
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Affiliation(s)
- Diego Garcia Jimenez
- University of Torino, Molecular Biotechnology and Health Sciences Dept., CASSMedChem, via Quarello 15, 10135 Torino, Italy
| | - Matteo Rossi Sebastiano
- University of Torino, Molecular Biotechnology and Health Sciences Dept., CASSMedChem, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- University of Torino, Molecular Biotechnology and Health Sciences Dept., CASSMedChem, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- University of Torino, Molecular Biotechnology and Health Sciences Dept., CASSMedChem, via Quarello 15, 10135 Torino, Italy
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21
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He S, Dong G, Cheng J, Wu Y, Sheng C. Strategies for designing proteolysis targeting chimaeras (PROTACs). Med Res Rev 2022; 42:1280-1342. [PMID: 35001407 DOI: 10.1002/med.21877] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022]
Abstract
Proteolysis targeting chimaeras (PROTACs) is a cutting edge and rapidly growing technique for new drug discovery and development. Currently, the largest challenge in the molecular design and drug development of PROTACs is efficient identification of potent and drug-like degraders. This review aims to comprehensively summarize and analyse state-of-the-art methods and strategies in the design of PROTACs. We provide a detailed illustration of the general principles and tactics for designing potent PROTACs, highlight representative case studies, and discuss the advantages and limitations of these strategies. Particularly, structure-based rational PROTAC design and emerging new types of PROTACs (e.g., homo-PROTACs, multitargeting PROTACs, photo-control PROTACs and PROTAC-based conjugates) will be focused on.
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Affiliation(s)
- Shipeng He
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Junfei Cheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Ying Wu
- School of Pharmacy, Second Military Medical University, Shanghai, China.,Department of Pharmacy, 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai, China
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22
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Klein VG, Bond AG, Craigon C, Lokey RS, Ciulli A. Amide-to-Ester Substitution as a Strategy for Optimizing PROTAC Permeability and Cellular Activity. J Med Chem 2021; 64:18082-18101. [PMID: 34881891 PMCID: PMC8713283 DOI: 10.1021/acs.jmedchem.1c01496] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Criteria for predicting the druglike properties of "beyond Rule of 5" Proteolysis Targeting Chimeras (PROTAC) degraders are underdeveloped. PROTAC components are often combined via amide couplings due to their reliability. Amides, however, can give rise to poor absorption, distribution, metabolism, and excretion (ADME) properties. We hypothesized that a bioisosteric amide-to-ester substitution could lead to improvements in both physicochemical properties and bioactivity. Using model compounds, bearing either amides or esters, we identify parameters for optimal lipophilicity and permeability. We applied these learnings to design a set of novel amide-to-ester-substituted, VHL-based BET degraders with the goal to increase permeability. Our ester PROTACs retained intracellular stability, were overall more potent degraders than their amide counterparts, and showed an earlier onset of the hook effect. These enhancements were driven by greater cell permeability rather than improvements in ternary complex formation. This largely unexplored amide-to-ester substitution provides a simple strategy to enhance PROTAC permeability and bioactivity and may prove beneficial to other beyond Ro5 molecules.
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Affiliation(s)
- Victoria G Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Adam G Bond
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - Conner Craigon
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, U.K
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23
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Designing small molecules for therapeutic success: A contemporary perspective. Drug Discov Today 2021; 27:538-546. [PMID: 34601124 DOI: 10.1016/j.drudis.2021.09.017] [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: 06/07/2021] [Revised: 08/31/2021] [Accepted: 09/25/2021] [Indexed: 11/23/2022]
Abstract
Successful small-molecule drug design requires a molecular target with inherent therapeutic potential and a molecule with the right properties to unlock its potential. Present-day drug design strategies have evolved to leave little room for improvement in drug-like properties. As a result, inadequate safety or efficacy associated with molecular targets now constitutes the primary cause of attrition in preclinical development through Phase II. This finding has led to a deeper focus on target selection. In this current reality, design tactics that enable rapid identification of risk-balanced clinical candidates, translation of clinical experience into meaningful differentiation strategies, and expansion of the druggable proteome represent significant levers by which drug designers can accelerate the discovery of the next generation of medicines.
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24
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Ermondi G, Garcia Jimenez D, Rossi Sebastiano M, Caron G. Rational Control of Molecular Properties Is Mandatory to Exploit the Potential of PROTACs as Oral Drugs. ACS Med Chem Lett 2021; 12:1056-1060. [PMID: 34262642 PMCID: PMC8274089 DOI: 10.1021/acsmedchemlett.1c00298] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
![]()
To obtain new oral
drugs in the beyond rule of five space, PROTACs
among others, molecular properties should be optimized in early drug
discovery. Degraders call for design strategies which focus on intramolecular
interaction and chameleonicity. In parallel, tailored revalidation
of permeability assessment and prediction methods becomes fundamental
in this innovative chemical space.
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Affiliation(s)
- Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept., CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Diego Garcia Jimenez
- Molecular Biotechnology and Health Sciences Dept., CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology and Health Sciences Dept., CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Dept., CASSMedChem, University of Torino, via Quarello 15, 10135 Torino, Italy
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25
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Cresser-Brown JO, Marsh GP, Maple HJ. Reviewing the toolbox for degrader development in oncology. Curr Opin Pharmacol 2021; 59:43-51. [PMID: 34058637 DOI: 10.1016/j.coph.2021.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022]
Abstract
The field of targeted protein degradation encompasses a growing number of modalities that achieve potent and selective knockdown of target proteins at the post-translational level. Among the most clinically advanced are bifunctional small-molecule degraders, also referred to as PROteolysis Targeting Chimeras, Degronimids, SNIPERs, or uSMITEs. Although applicable to many disease indications, oncology stands to be the first to benefit from this promising therapeutic approach, with the first investigational new drugs (INDs) filed in 2019 and a proliferation of research specifically focused on harnessing degraders for cancer treatment. In this review, we consider the toolbox of guidelines, reagents, and technologies that has evolved alongside the field to support degrader research and development.
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Affiliation(s)
- Joel O Cresser-Brown
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK
| | - Graham P Marsh
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK
| | - Hannah J Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol, UK.
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