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Koldenhof P, Bemelmans MP, Ghosh B, Damm-Ganamet KL, van Vlijmen HWT, Pande V. Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases. Proteins 2024; 92:819-829. [PMID: 38337153 DOI: 10.1002/prot.26675] [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: 10/13/2023] [Revised: 01/12/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
Proteolysis Targeting Chimeras (PROTACs) are an emerging therapeutic modality and chemical biology tools for Targeted Protein Degradation (TPD). PROTACs contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. There are over 600 E3 ligases known so far, but only a handful have been exploited for TPD applications. A key reason for this is the scarcity of ligands binding various E3 ligases and the paucity of structural data available, which complicates ligand design across the family. In this study, we aim to progress PROTAC discovery by proposing a shortlist of E3 ligases that can be prioritized for covalent targeting by performing systematic structural ligandability analysis on a chemoproteomic dataset of potentially reactive cysteines across hundreds of E3 ligases. One of the goals of this study is to apply AlphaFold (AF) models for ligandability evaluations, as for a vast majority of these ligases an experimental structure is not available in the protein data bank (PDB). Using a combination of pocket features, AF model quality and additional aspects, we propose a shortlist of E3 ligases and corresponding cysteines that can be prioritized to potentially discover covalent ligands and expand the PROTAC toolbox.
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Affiliation(s)
- Patrick Koldenhof
- Computer-Aided Drug Design, Janssen Pharmaceuticals, Beerse, Belgium
| | | | - Brahma Ghosh
- Discovery Chemistry, Janssen Pharmaceuticals, Spring House, Pennsylvania, USA
| | | | | | - Vineet Pande
- Computer-Aided Drug Design, Janssen Pharmaceuticals, Beerse, Belgium
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2
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Zhou Y, Zhang Q, Zhao Z, Hu X, You Q, Jiang Z. Targeting kelch-like (KLHL) proteins: achievements, challenges and perspectives. Eur J Med Chem 2024; 269:116270. [PMID: 38490062 DOI: 10.1016/j.ejmech.2024.116270] [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: 01/02/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
Kelch-like proteins (KLHLs) are a large family of BTB-containing proteins. KLHLs function as the substrate adaptor of Cullin 3-RING ligases (CRL3) to recognize substrates. KLHLs play pivotal roles in regulating various physiological and pathological processes by modulating the ubiquitination of their respective substrates. Mounting evidence indicates that mutations or abnormal expression of KLHLs are associated with various human diseases. Targeting KLHLs is a viable strategy for deciphering the KLHLs-related pathways and devising therapies for associated diseases. Here, we comprehensively review the known KLHLs inhibitors to date and the brilliant ideas underlying their development.
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Affiliation(s)
- Yangguo Zhou
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qiong Zhang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ziquan Zhao
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiuqi Hu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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3
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Sahu S, Rao AR, Sahu TK, Pandey J, Varshney S, Kumar A, Gaikwad K. Predictive Role of Cluster Bean ( Cyamopsis tetragonoloba) Derived miRNAs in Human and Cattle Health. Genes (Basel) 2024; 15:448. [PMID: 38674383 PMCID: PMC11049822 DOI: 10.3390/genes15040448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 04/28/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding conserved molecules with lengths varying between 18-25nt. Plants miRNAs are very stable, and probably they might have been transferred across kingdoms via food intake. Such miRNAs are also called exogenous miRNAs, which regulate the gene expression in host organisms. The miRNAs present in the cluster bean, a drought tolerant legume crop having high commercial value, might have also played a regulatory role for the genes involved in nutrients synthesis or disease pathways in animals including humans due to dietary intake of plant parts of cluster beans. However, the predictive role of miRNAs of cluster beans for gene-disease association across kingdoms such as cattle and humans are not yet fully explored. Thus, the aim of the present study is to (i) find out the cluster bean miRNAs (cb-miRs) functionally similar to miRNAs of cattle and humans and predict their target genes' involvement in the occurrence of complex diseases, and (ii) identify the role of cb-miRs that are functionally non-similar to the miRNAs of cattle and humans and predict their targeted genes' association with complex diseases in host systems. Here, we predicted a total of 33 and 15 functionally similar cb-miRs (fs-cb-miRs) to human and cattle miRNAs, respectively. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the participation of targeted genes of fs-cb-miRs in 24 and 12 different pathways in humans and cattle, respectively. Few targeted genes in humans like LCP2, GABRA6, and MYH14 were predicted to be associated with disease pathways of Yesinia infection (hsa05135), neuroactive ligand-receptor interaction (hsa04080), and pathogenic Escherichia coli infection (hsa05130), respectively. However, targeted genes of fs-cb-miRs in humans like KLHL20, TNS1, and PAPD4 are associated with Alzheimer's, malignant tumor of the breast, and hepatitis C virus infection disease, respectively. Similarly, in cattle, targeted genes like ATG2B and DHRS11 of fs-cb-miRs participate in the pathways of Huntington disease and steroid biosynthesis, respectively. Additionally, the targeted genes like SURF4 and EDME2 of fs-cb-miRs are associated with mastitis and bovine osteoporosis, respectively. We also found a few cb-miRs that do not have functional similarity with human and cattle miRNAs but are found to target the genes in the host organisms and as well being associated with human and cattle diseases. Interestingly, a few genes such as NRM, PTPRE and SUZ12 were observed to be associated with Rheumatoid Arthritis, Asthma and Endometrial Stromal Sarcoma diseases, respectively, in humans and genes like SCNN1B associated with renal disease in cattle.
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Affiliation(s)
- Sarika Sahu
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Atmakuri Ramakrishna Rao
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
- Indian Council of Agricultural Research, New Delhi 110001, India
| | - Tanmaya Kumar Sahu
- Indian Grassland and Fodder Research Institute, ICAR, Jhansi 284003, India;
| | - Jaya Pandey
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Shivangi Varshney
- Indian Agricultural Statistics Research Institute, ICAR, New Delhi 110012, India; (S.S.); (J.P.); (S.V.)
| | - Archna Kumar
- Amity Institute of Biotechnology, Amity University, Noida 201303, India;
| | - Kishor Gaikwad
- National Institute for Plant Biotechnology, ICAR, New Delhi 110012, India;
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4
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Kuroda Y, Ikeda A, Naruto T, Kurosawa K. Early-onset West syndrome with developmental delay associated with a novel KLHL20 variant. Am J Med Genet A 2024:e63600. [PMID: 38513146 DOI: 10.1002/ajmg.a.63600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Affiliation(s)
- Yukiko Kuroda
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Azusa Ikeda
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takuya Naruto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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Teng F, Wang Y, Liu M, Tian S, Stjepanovic G, Su MY. Cryo-EM structure of the KLHL22 E3 ligase bound to an oligomeric metabolic enzyme. Structure 2023; 31:1431-1440.e5. [PMID: 37788672 DOI: 10.1016/j.str.2023.09.002] [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: 04/13/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 10/05/2023]
Abstract
CULLIN-RING ligases constitute the largest group of E3 ubiquitin ligases. While some CULLIN family members recruit adapters before engaging further with different substrate receptors, homo-dimeric BTB-Kelch family proteins combine adapter and substrate receptor into a single polypeptide for the CULLIN3 family. However, the entire structural assembly and molecular details have not been elucidated to date. Here, we present a cryo-EM structure of the CULLIN3RBX1 in complex with Kelch-like protein 22 (KLHL22) and a mitochondrial glutamate dehydrogenase complex I (GDH1) at 3.06 Å resolution. The structure adopts a W-shaped architecture formed by E3 ligase dimers. Three CULLIN3KLHL22-RBX1 dimers were found to be dynamically associated with a single GDH1 hexamer. CULLIN3KLHL22-RBX1 ligase mediated the polyubiquitination of GDH1 in vitro. Together, these results enabled the establishment of a structural model for understanding the complete assembly of BTB-Kelch proteins with CULLIN3 and how together they recognize oligomeric substrates and target them for ubiquitination.
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Affiliation(s)
- Fei Teng
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
| | - Yang Wang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
| | - Ming Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
| | - Shuyun Tian
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Goran Stjepanovic
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China.
| | - Ming-Yuan Su
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China.
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Chang H, Hou J, Shao Y, Xu M, Weng X, Du Y, Shi J, Zhang L, Cui H. Sanggenon C inhibits cell proliferation and induces apoptosis by regulating the MIB1/DAPK1 axis in glioblastoma. MedComm (Beijing) 2023; 4:e281. [PMID: 37346933 PMCID: PMC10279945 DOI: 10.1002/mco2.281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 06/23/2023] Open
Abstract
Sanggenon C (SC), a herbal flavonoid extracted from Cortex Mori, has been mentioned to possess more than one treasured organic properties. However, the molecular mechanism of its anti-tumor impact in glioblastoma (GBM) remains unclear. In this study, we reported that SC displayed a GBM-suppressing impact in vitro and in vivo with no apparent organ toxicity. SC dramatically suppressed cell proliferation-induced cell apoptosis in GBM cells. Mechanistically, we unveiled that SC modulated the protein expression of death associated protain kinase 1 (DAPK1) by controlling the ubiquitination and degradation of DAPK1. Quantitative proteomic and Western blot analyses showed that SC improved DAPK1 protein degradation via decreasing the expression of E3 ubiquitin ligase Mindbomb 1 (MIB1). More importantly, the effects of SC on cell proliferation and apoptosis of GBM cells have been in part reversed through DAPK1 downregulation or MIB1 overexpression, respectively. These results indicated that SC might suppress cell proliferation and induce cell apoptosis by decreasing MIB1-mediated DAPK1 degradation. Furthermore, we found that SC acted synergistically with temozolomide (TMZ), an anti-cancer drug used in GBM, resulting in elevated chemotherapeutic sensitivity of GBM to TMZ. Collectively, our data suggest that SC might be a promising anti-cancer agent for GBM therapy.
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Affiliation(s)
- Hongbo Chang
- State Key Laboratory of Resource InsectsMedical Research InstituteSouthwest UniversityChongqingChina
| | - Jianbing Hou
- State Key Laboratory of Resource InsectsMedical Research InstituteSouthwest UniversityChongqingChina
| | - Yaqian Shao
- State Key Laboratory of Resource InsectsMedical Research InstituteSouthwest UniversityChongqingChina
| | - Minghao Xu
- State Key Laboratory of Resource InsectsMedical Research InstituteSouthwest UniversityChongqingChina
| | - Xuelian Weng
- State Key Laboratory of Resource InsectsMedical Research InstituteSouthwest UniversityChongqingChina
| | - Yi Du
- State Key Laboratory of Resource InsectsMedical Research InstituteSouthwest UniversityChongqingChina
| | - Junbo Shi
- State Key Laboratory of Resource InsectsMedical Research InstituteSouthwest UniversityChongqingChina
| | - Li Zhang
- Department of Radiology and Nuclear MedicineThe First Hospital of HeBei Medical UniversityHebeiChina
| | - Hongjuan Cui
- State Key Laboratory of Resource InsectsMedical Research InstituteSouthwest UniversityChongqingChina
- Jinfeng LaboratoryChongqingChina
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7
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Schiemer J, Maxwell A, Horst R, Liu S, Uccello DP, Borzilleri K, Rajamohan N, Brown MF, Calabrese MF. A covalent BTK ternary complex compatible with targeted protein degradation. Nat Commun 2023; 14:1189. [PMID: 36864023 PMCID: PMC9981747 DOI: 10.1038/s41467-023-36738-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 02/15/2023] [Indexed: 03/04/2023] Open
Abstract
Targeted protein degradation using heterobifunctional chimeras holds the potential to expand target space and grow the druggable proteome. Most acutely, this provides an opportunity to target proteins that lack enzymatic activity or have otherwise proven intractable to small molecule inhibition. Limiting this potential, however, is the remaining need to develop a ligand for the target of interest. While a number of challenging proteins have been successfully targeted by covalent ligands, unless this modification affects form or function, it may lack the ability to drive a biological response. Bridging covalent ligand discovery with chimeric degrader design has emerged as a potential mechanism to advance both fields. In this work, we employ a set of biochemical and cellular tools to deconvolute the role of covalent modification in targeted protein degradation using Bruton's tyrosine kinase. Our results reveal that covalent target modification is fundamentally compatible with the protein degrader mechanism of action.
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Affiliation(s)
- James Schiemer
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Andrew Maxwell
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Reto Horst
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Shenping Liu
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Daniel P Uccello
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Kris Borzilleri
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Nisha Rajamohan
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Matthew F Brown
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - Matthew F Calabrese
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, CT, USA.
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8
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Sleyp Y, Valenzuela I, Accogli A, Ballon K, Ben-Zeev B, Berkovic SF, Broly M, Callaerts P, Caylor RC, Charles P, Chatron N, Cohen L, Coppola A, Cordeiro D, Cuccurullo C, Cuscó I, Janette diMonda, Duran-Romaña R, Ekhilevitch N, Fernández-Alvarez P, Gordon CT, Isidor B, Keren B, Lesca G, Maljaars J, Mercimek-Andrews S, Morrow MM, Muir AM, Rousseau F, Salpietro V, Scheffer IE, Schnur RE, Schymkowitz J, Souche E, Steyaert J, Stolerman ES, Vengoechea J, Ville D, Washington C, Weiss K, Zaid R, Sadleir LG, Mefford HC, Peeters H. De novo missense variants in the E3 ubiquitin ligase adaptor KLHL20 cause a developmental disorder with intellectual disability, epilepsy, and autism spectrum disorder. Genet Med 2022; 24:2464-2474. [PMID: 36214804 DOI: 10.1016/j.gim.2022.08.020] [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: 03/07/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
PURPOSE KLHL20 is part of a CUL3-RING E3 ubiquitin ligase involved in protein ubiquitination. KLHL20 functions as the substrate adaptor that recognizes substrates and mediates the transfer of ubiquitin to the substrates. Although KLHL20 regulates neurite outgrowth and synaptic development in animal models, a role in human neurodevelopment has not yet been described. We report on a neurodevelopmental disorder caused by de novo missense variants in KLHL20. METHODS Patients were ascertained by the investigators through Matchmaker Exchange. Phenotyping of patients with de novo missense variants in KLHL20 was performed. RESULTS We studied 14 patients with de novo missense variants in KLHL20, delineating a genetic syndrome with patients having mild to severe intellectual disability, febrile seizures or epilepsy, autism spectrum disorder, hyperactivity, and subtle dysmorphic facial features. We observed a recurrent de novo missense variant in 11 patients (NM_014458.4:c.1069G>A p.[Gly357Arg]). The recurrent missense and the 3 other missense variants all clustered in the Kelch-type β-propeller domain of the KLHL20 protein, which shapes the substrate binding surface. CONCLUSION Our findings implicate KLHL20 in a neurodevelopmental disorder characterized by intellectual disability, febrile seizures or epilepsy, autism spectrum disorder, and hyperactivity.
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Affiliation(s)
- Yoeri Sleyp
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Andrea Accogli
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Katleen Ballon
- Centre for Developmental Disabilities, University Hospitals Leuven, Leuven, Belgium
| | - Bruria Ben-Zeev
- Pediatric Neurology Institute, The Edmond & Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Tel-Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Martin Broly
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France; Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | | | | | - Perrine Charles
- Salpêtrière Hospital Genetic Department and Reference Center for Rare Intellectual Disabilities, APHP, Paris, France
| | - Nicolas Chatron
- Department of Medical Genetics, Hospices Civils de Lyon and NeuroMyogene Institute, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Lior Cohen
- Genetic Institute, Barzilai University Medical Center, Ashkelon, Israel; Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheba, Israel
| | - Antonietta Coppola
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | - Dawn Cordeiro
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudia Cuccurullo
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy
| | - Ivon Cuscó
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Janette diMonda
- Department of Human Genetics, Emory Clinic, Emory Healthcare, Atlanta, GA
| | - Ramon Duran-Romaña
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Paula Fernández-Alvarez
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Imagine, Université de Paris, Paris, France
| | - Bertrand Isidor
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | - Boris Keren
- Département de Génétique, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - Gaetan Lesca
- Department of Medical Genetics, Hospices Civils de Lyon and NeuroMyogene Institute, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Jarymke Maljaars
- Parenting and Special Education Research Unit, KU Leuven, Leuven, Belgium
| | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Medical Genetics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Alison M Muir
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA
| | | | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Vincenzo Salpietro
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Victoria, Australia; Florey and Murdoch Children's Research Institutes, Melbourne, Victoria, Australia
| | | | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Erika Souche
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Jean Steyaert
- Center for Developmental Psychiatry, KU Leuven, Leuven, Belgium
| | | | - Jaime Vengoechea
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA
| | - Dorothée Ville
- Pediatric Neurology Department, Lyon University Hospital, Lyon, France
| | | | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Haifa, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Rinat Zaid
- Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA; Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium.
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Venkatesan J, Murugan D, Rangasamy L. A Perspective on Newly Emerging Proteolysis-Targeting Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel) 2022; 11:1717. [PMID: 36551374 PMCID: PMC9774230 DOI: 10.3390/antibiotics11121717] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Targeted protein degradation is a new aspect in the field of drug discovery. Traditionally, developing an antibiotic includes tedious and expensive processes, such as drug screening, lead optimization, and formulation. Proteolysis-targeting chimeras (PROTACs) are new-generation drugs that use the proteolytic mechanism to selectively degrade and eliminate proteins involved in human diseases. The application of PROTACs is explored immensely in the field of cancer, and various PROTACs are in clinical trials. Thus, researchers have a profound interest in pursuing PROTAC technology as a new weapon to fight pathogenic viruses and bacteria. This review highlights the importance of antimicrobial PROTACs and other similar "PROTAC-like" techniques to degrade pathogenic target proteins (i.e., viral/bacterial proteins). These techniques can perform specific protein degradation of the pathogenic protein to avoid resistance caused by mutations or abnormal expression of the pathogenic protein. PROTAC-based antimicrobial therapeutics have the advantage of high specificity and the ability to degrade "undruggable" proteins, such as nonenzymatic and structural proteins.
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Affiliation(s)
- Janarthanan Venkatesan
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular, and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Dhanashree Murugan
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular, and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
- School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
| | - Loganathan Rangasamy
- Drug Discovery Unit (DDU), Centre for Biomaterials, Cellular, and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, Tamil Nadu, India
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10
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Chen Z, Ioris RM, Richardson S, Van Ess AN, Vendrell I, Kessler BM, Buffa FM, Busino L, Clifford SC, Bullock AN, D'Angiolella V. Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST degradation. Cell Death Differ 2022; 29:1955-1969. [PMID: 35379950 PMCID: PMC9525703 DOI: 10.1038/s41418-022-00983-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/30/2022] Open
Abstract
Medulloblastoma is the most common malignant brain tumour in children. Genomic studies have identified distinct disease subgroups: wnt/wingless (WNT), sonic hedgehog (SHH), and non-WNT/non-SHH, comprising group 3 and group 4. Alterations in WNT and SHH signalling form the pathogenetic basis for their subgroups, whereas those for non-WNT/non-SHH tumours remain largely elusive. Recent analyses have revealed recurrent in-frame insertions in the E3 ubiquitin ligase adaptor Kelch Repeat and BTB Domain Containing 4 (KBTBD4) in cases of group 3/4 medulloblastoma. Critically, group 3/4 tumours with KBTBD4 mutations typically lack other gene-specific alterations, such as MYC amplification, indicating KBTBD4 insertion mutations as the primary genetic driver. Delineating the role of KBTBD4 mutations thus offers significant opportunities to understand tumour pathogenesis and to exploit the underpinning mechanisms therapeutically. Here, we show a novel mechanism in cancer pathogenesis whereby indel mutations in KBTBD4 drive its recognition of neo-substrates for degradation. We observe that KBTBD4 mutants promote the recruitment and ubiquitylation of the REST Corepressor (CoREST), which forms a complex to modulate chromatin accessibility and transcriptional programmes. The degradation of CoREST promoted by KBTBD4 mutation diverts epigenetic programmes inducing significant alterations in transcription to promote increased stemness of cancer cells. Transcriptional analysis of >200 human group 3 and 4 medulloblastomas by RNA-seq, highlights the presence of CoREST and stem-like signatures in tumours with KBTBD4 mutations, which extend to a further sub-set of non-mutant tumours, suggesting CoREST alterations as a novel pathogenetic mechanism of wide relevance in groups 3 and 4. Our findings uncover KBTBD4 mutation as a novel driver of epigenetic reprogramming in non-WNT/non-SHH medulloblastoma, establish a novel mode of tumorigenesis through gain-of-function mutations in ubiquitin ligases (neo-substrate recruitment) and identify both mutant KBTBD4 and CoREST complexes as new druggable targets for improved tumour-specific therapies.
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Affiliation(s)
- Zhuoyao Chen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Rafael M Ioris
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Stacey Richardson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, NE1 7RU, UK
| | - Ava N Van Ess
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Iolanda Vendrell
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Francesca M Buffa
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Luca Busino
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, NE1 7RU, UK
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Vincenzo D'Angiolella
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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11
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Farrell BM, Gerth F, Yang CHR, Yeh JTH. A synthetic KLHL20 ligand to validate CUL3 KLHL20 as a potent E3 ligase for targeted protein degradation. Genes Dev 2022; 36:1031-1042. [PMID: 36328355 PMCID: PMC9732910 DOI: 10.1101/gad.349717.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/31/2022] [Indexed: 11/06/2022]
Abstract
Targeted protein degradation (TPD) has risen as a promising therapeutic modality. Leveraging the catalytic nature of the ubiquitin-proteasome enzymatic machinery, TPD exhibits higher potency to eliminate disease-causing target proteins such as oncogenic transcription factors that may otherwise be difficult to abrogate by conventional inhibitors. However, there are challenges that remain. Currently, nearly all degraders engage CUL4CRBN or CUL2VHL as the E3 ligase for target ubiquitination. While their immediate efficacies are evident, the narrowed E3 ligase options make TPD vulnerable to potential drug resistance. In addition, E3 ligases show differential tissue expression and have intrinsic limitations in accessing varying types of disease-relevant targets. As the success of TPD is closely associated with the ability of E3 ligases to efficiently polyubiquitinate the target of interest, the long-term outlook of TPD drug development will depend on whether E3 ligases such as CUL4CRBN and CUL2VHL are accessible to the targets of interest. To overcome these potential caveats, a broad collection of actionable E3 ligases is required. Here, we designed a macrocyclic degrader engaging CUL3KLHL20 for targeting BET proteins and validated CUL3KLHL20 as an E3 ligase system suitable for TPD. This work thus contributes to the expansion of usable E3 ligases for potential drug development.
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Affiliation(s)
- Brian M Farrell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Fabian Gerth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Cheng-Hao R Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Johannes T-H Yeh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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12
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Cowan AD, Ciulli A. Driving E3 Ligase Substrate Specificity for Targeted Protein Degradation: Lessons from Nature and the Laboratory. Annu Rev Biochem 2022; 91:295-319. [PMID: 35320687 DOI: 10.1146/annurev-biochem-032620-104421] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methods to direct the degradation of protein targets with proximity-inducing molecules that coopt the cellular degradation machinery are advancing in leaps and bounds, and diverse modalities are emerging. The most used and well-studied approach is to hijack E3 ligases of the ubiquitin-proteasome system. E3 ligases use specific molecular recognition to determine which proteins in the cell are ubiquitinated and degraded. This review focuses on the structural determinants of E3 ligase recruitment of natural substrates and neo-substrates obtained through monovalent molecular glues and bivalent proteolysis-targeting chimeras. We use structures to illustrate the different types of substrate recognition and assess the basis for neo-protein-protein interactions in ternary complex structures. The emerging structural and mechanistic complexity is reflective of the diverse physiological roles of protein ubiquitination. This molecular insight is also guiding the application of structure-based design approaches to the development of new and existing degraders as chemical tools and therapeutics. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Angus D Cowan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
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13
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Hushpulian DM, Ammal Kaidery N, Ahuja M, Poloznikov AA, Sharma SM, Gazaryan IG, Thomas B. Challenges and Limitations of Targeting the Keap1-Nrf2 Pathway for Neurotherapeutics: Bach1 De-Repression to the Rescue. Front Aging Neurosci 2021; 13:673205. [PMID: 33897412 PMCID: PMC8060438 DOI: 10.3389/fnagi.2021.673205] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
The Keap1-Nrf2 signaling axis is a validated and promising target for cellular defense and survival pathways. This minireview discusses the potential off-target effects and their impact on future drug development originating from Keap1-targeting small molecules that function as displacement activators of the redox-sensitive transcription factor Nrf2. We argue that small-molecule displacement activators, similarly to electrophiles, will release both Nrf2 and other Keap1 client proteins from the ubiquitin ligase complex. This non-specificity is likely unavoidable and may result in off-target effects during Nrf2 activation by targeting Keap1. The small molecule displacement activators may also target Kelch domains in proteins other than Keap1, causing additional off-target effects unless designed to ensure specificity for the Kelch domain only in Keap1. A potentially promising and alternative therapeutic approach to overcome this non-specificity emerging from targeting Keap1 is to inhibit the Nrf2 repressor Bach1 for constitutive activation of the Nrf2 pathway and bypass the Keap1-Nrf2 complex.
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Affiliation(s)
- Dmitry M. Hushpulian
- P. A. Hertsen Moscow Oncology Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia
| | - Navneet Ammal Kaidery
- Darby Children’s Research Institute, Medical University of South Carolina, Charleston, SC, United States
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, United States
| | - Manuj Ahuja
- Darby Children’s Research Institute, Medical University of South Carolina, Charleston, SC, United States
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, United States
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Andrey A. Poloznikov
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia
| | - Sudarshana M. Sharma
- Hollings Cancer Center, Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Irina G. Gazaryan
- P. A. Hertsen Moscow Oncology Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia
- Department of Chemical Enzymology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Department of Chemistry and Physical Sciences, Dyson College of Arts and Sciences, Pace University, Pleasantville, NY, United States
| | - Bobby Thomas
- Darby Children’s Research Institute, Medical University of South Carolina, Charleston, SC, United States
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC, United States
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, United States
- Department of Drug Discovery, Medical University of South Carolina, Charleston, SC, United States
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14
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Paladino A, D'Angelo F, Noviello TMR, Iavarone A, Ceccarelli M. Structural Model for Recruitment of RIT1 to the LZTR1 E3 Ligase: Evidences from an Integrated Computational Approach. J Chem Inf Model 2021; 61:1875-1888. [PMID: 33792302 PMCID: PMC8154269 DOI: 10.1021/acs.jcim.1c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leucine-zipper transcription regulator 1 (LZTR1) is a highly mutated tumor suppressor gene, involved in the pathogenesis of several cancer types and developmental disorders. In proteasomal degradation, it acts as an adaptor protein responsible for the recognition and recruitment of substrates to be ubiquitinated in Cullin3-RING ligase E3 (CRL3) machinery. LZTR1 belongs to the BTB-Kelch family, a multi-domain protein where the Kelch propeller plays as the substrate recognition region and for which no experimental structure has been solved. Recently, large effort mutational analyses pointed to the role of disease-associated LZTR1 mutations in the RAS/MAPK signaling pathway and RIT1, a small Ras-related GTPase protein, has been identified by mass spectroscopy to interact with LZTR1. Hence, a better understanding of native structure, molecular mechanism, and substrate specificity would help clarifying the role of LZTR1 in pathological diseases, thus promoting advancement in the development of novel therapeutic strategies. Here, we address the interaction model between adaptor LZTR1 and substrate RIT1 by applying an integrated computational approach, including molecular modeling and docking techniques. We observe that the interaction model LZTR1-RIT1 is stabilized by an electrostatic bond network established between the two protein surfaces, which is reminiscent of homologous ubiquitin ligases complexes. Then, running MD simulations, we characterize differential conformational dynamics of the multi-domain LZTR1, offering interesting implications on the mechanistic role of specific point mutations. We identify G248R and R283Q as damaging mutations involved in the recognition process of the substrate RIT1 and R412C as a possible allosteric mutation from the Kelch to the C-term BTB-domain. Our findings provide important structural insights on targeting CRL3s for drug discovery.
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Affiliation(s)
- Antonella Paladino
- BIOGEM Istituto di Ricerche Genetiche "G. Salvatore", via Camporeale, Ariano Irpino 83031, Italy
| | - Fulvio D'Angelo
- BIOGEM Istituto di Ricerche Genetiche "G. Salvatore", via Camporeale, Ariano Irpino 83031, Italy.,Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, New York 10032, United States
| | - Teresa Maria Rosaria Noviello
- BIOGEM Istituto di Ricerche Genetiche "G. Salvatore", via Camporeale, Ariano Irpino 83031, Italy.,Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", Via Claudio 21, Naples 80128, Italy
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, New York 10032, United States.,Department of Pathology and Cell Biology, Columbia University Medical Center, 1130 St Nicholas Ave, New York , New York 10032 United States.,Department of Neurology, Columbia University Medical Center, 1130 St Nicholas Ave, New York, New York 10032, United States
| | - Michele Ceccarelli
- BIOGEM Istituto di Ricerche Genetiche "G. Salvatore", via Camporeale, Ariano Irpino 83031, Italy.,Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", Via Claudio 21, Naples 80128, Italy
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15
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Ishida T, Ciulli A. E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:484-502. [PMID: 33143537 PMCID: PMC8013866 DOI: 10.1177/2472555220965528] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Bifunctional degrader molecules, also called proteolysis-targeting chimeras (PROTACs), are a new modality of chemical tools and potential therapeutics to understand and treat human disease. A required PROTAC component is a ligand binding to an E3 ubiquitin ligase, which is then joined to another ligand binding to a protein to be degraded via the ubiquitin-proteasome system. The advent of nonpeptidic small-molecule E3 ligase ligands, notably for von Hippel-Lindau (VHL) and cereblon (CRBN), revolutionized the field and ushered in the design of drug-like PROTACs with potent and selective degradation activity. A first wave of PROTAC drugs are now undergoing clinical development in cancer, and the field is seeking to extend the repertoire of chemistries that allow hijacking new E3 ligases to improve the scope of targeted protein degradation.Here, we briefly review how traditional E3 ligase ligands were discovered, and then outline approaches and ligands that have been recently used to discover new E3 ligases for PROTACs. We will then take an outlook at current and future strategies undertaken that invoke either target-based screening or phenotypic-based approaches, including the use of DNA-encoded libraries (DELs), display technologies and cyclic peptides, smaller molecular glue degraders, and covalent warhead ligands. These approaches are ripe for expanding the chemical space of PROTACs and usher in the advent of other emerging bifunctional modalities of proximity-based pharmacology.
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Affiliation(s)
- Tasuku Ishida
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
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16
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Building ubiquitination machineries: E3 ligase multi-subunit assembly and substrate targeting by PROTACs and molecular glues. Curr Opin Struct Biol 2020; 67:110-119. [PMID: 33271439 DOI: 10.1016/j.sbi.2020.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 12/22/2022]
Abstract
E3 ubiquitin ligase machineries are emerging as attractive therapeutic targets because they confer specificity to substrate ubiquitination and can be hijacked for targeted protein degradation. In this review, we bring to focus our current structural understanding of E3 ligase complexes, in particular the multi-subunit cullin RING ligases, and modulation thereof by small-molecule glues and PROTAC degraders. We highlight recent advances in elucidating the modular assembly of E3 ligase machineries, their diverse substrate and degron recognition mechanisms, and how these structural features impact on ligase function. We then outline the emergence of structures of E3 ligases bound to neo-substrates and degrader molecules, and highlight the importance of studying such ternary complexes for structure-based degrader design.
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17
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Chen Y, Jin J. The application of ubiquitin ligases in the PROTAC drug design. Acta Biochim Biophys Sin (Shanghai) 2020; 52:776-790. [PMID: 32506133 DOI: 10.1093/abbs/gmaa053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022] Open
Abstract
Protein ubiquitylation plays important roles in many biological activities. Protein ubiquitylation is a unique process that is mainly controlled by ubiquitin ligases. The ubiquitin-proteasome system (UPS) is the main process to degrade short-lived and unwanted proteins in eukaryotes. Many components in the UPS are attractive drug targets. Recent studies indicated that ubiquitin ligases can be employed as tools in proteolysis-targeting chimeras (PROTACs) for drug discovery. In this review article, we will discuss the recent progress of the application of ubiquitin ligases in the PROTAC drug design. We will also discuss advantages and existing problems of PROTACs. Moreover, we will propose a few principles for selecting ubiquitin ligases in PROTAC applications.
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Affiliation(s)
- Yilin Chen
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
| | - Jianping Jin
- Life Science Institute, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
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18
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Chen Z, Wasney GA, Picaud S, Filippakopoulos P, Vedadi M, D'Angiolella V, Bullock AN. Identification of a PGXPP degron motif in dishevelled and structural basis for its binding to the E3 ligase KLHL12. Open Biol 2020; 10:200041. [PMID: 32574548 PMCID: PMC7333892 DOI: 10.1098/rsob.200041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Wnt signalling is dependent on dishevelled proteins (DVL1-3), which assemble an intracellular Wnt signalosome at the plasma membrane. The levels of DVL1-3 are regulated by multiple Cullin-RING E3 ligases that mediate their ubiquitination and degradation. The BTB-Kelch protein KLHL12 was the first E3 ubiquitin ligase to be identified for DVL1-3, but the molecular mechanisms determining its substrate interactions have remained unknown. Here, we mapped the interaction of DVL1-3 to a ‘PGXPP' motif that is conserved in other known partners and substrates of KLHL12, including PLEKHA4, PEF1, SEC31 and DRD4. To determine the binding mechanism, we solved a 2.4 Å crystal structure of the Kelch domain of KLHL12 in complex with a DVL1 peptide that bound with low micromolar affinity. The DVL1 substrate adopted a U-shaped turn conformation that enabled hydrophobic interactions with all six blades of the Kelch domain β-propeller. In cells, the mutation or deletion of this motif reduced the binding and ubiquitination of DVL1 and increased its stability confirming this sequence as a degron motif for KLHL12 recruitment. These results define the molecular mechanisms determining DVL regulation by KLHL12 and establish the KLHL12 Kelch domain as a new protein interaction module for a novel proline-rich motif.
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Affiliation(s)
- Zhuoyao Chen
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Gregory A Wasney
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7, Canada
| | - Sarah Picaud
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College Street, Toronto, M5G 1L7, Canada
| | - Vincenzo D'Angiolella
- Department of Oncology, Cancer Research UK and Medical Research Council Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Alex N Bullock
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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19
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Zhao B, Payne WG, Sai J, Lu Z, Olejniczak ET, Fesik SW. Structural Elucidation of Peptide Binding to KLHL-12, a Substrate Specific Adapter Protein in a Cul3-Ring E3 Ligase Complex. Biochemistry 2020; 59:964-969. [DOI: 10.1021/acs.biochem.9b01073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - William G. Payne
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - Edward T. Olejniczak
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States
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20
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Targeted protein degradation: expanding the toolbox. Nat Rev Drug Discov 2019; 18:949-963. [PMID: 31666732 DOI: 10.1038/s41573-019-0047-y] [Citation(s) in RCA: 471] [Impact Index Per Article: 94.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/19/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) and related molecules that induce targeted protein degradation by the ubiquitin-proteasome system represent a new therapeutic modality and are the focus of great interest, owing to potential advantages over traditional occupancy-based inhibitors with respect to dosing, side effects, drug resistance and modulating 'undruggable' targets. However, the technology is still maturing, and the design elements for successful PROTAC-based drugs are currently being elucidated. Importantly, fewer than 10 of the more than 600 E3 ubiquitin ligases have so far been exploited for targeted protein degradation, and expansion of knowledge in this area is a key opportunity. Here, we briefly discuss lessons learned about targeted protein degradation in chemical biology and drug discovery and systematically review the expression profile, domain architecture and chemical tractability of human E3 ligases that could expand the toolbox for PROTAC discovery.
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21
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Konstantinidou M, Li J, Zhang B, Wang Z, Shaabani S, Ter Brake F, Essa K, Dömling A. PROTACs- a game-changing technology. Expert Opin Drug Discov 2019; 14:1255-1268. [PMID: 31538491 PMCID: PMC7008130 DOI: 10.1080/17460441.2019.1659242] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Introduction: Proteolysis – targeting chimeras (PROTACs) have emerged as a new modality with the potential to revolutionize drug discovery. PROTACs are heterobifunctional molecules comprising of a ligand targeting a protein of interest, a ligand targeting an E3 ligase and a connecting linker. The aim is instead of inhibiting the target to induce its proteasomal degradation. Areas covered: PROTACs, due to their bifunctional design, possess properties that differentiate them from classical inhibitors. A structural analysis, based on published crystal aspects, kinetic features and aspects of selectivity are discussed. Specific types such as homoPROTACs, PROTACs targeting Tau protein and the first PROTACs recently entering clinical trials are examined. Expert opinion: PROTACs have shown remarkable biological responses in challenging targets, including an unprecedented selectivity over protein family members and even efficacy starting from weak or unspecific binders. Moreover, PROTACs are standing out from classical pharmacology by inducing the degradation of the target protein and not merely its inhibition. However, there are also challenges in the field, such as the rational structure optimization, the evolution of computational tools, limited structural data and the greatly anticipated clinical data. Despite the remaining hurdles, PROTACs are expected to soon become a new therapeutic category of drugs.
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Affiliation(s)
| | - Jingyao Li
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Bidong Zhang
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Zefeng Wang
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Shabnam Shaabani
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Frans Ter Brake
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Khaled Essa
- Drug Design, University of Groningen , Groningen , The Netherlands
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