1
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Wang C, Zhang Y, Chen W, Wu Y, Xing D. New-generation advanced PROTACs as potential therapeutic agents in cancer therapy. Mol Cancer 2024; 23:110. [PMID: 38773495 PMCID: PMC11107062 DOI: 10.1186/s12943-024-02024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) technology has garnered significant attention over the last 10 years, representing a burgeoning therapeutic approach with the potential to address pathogenic proteins that have historically posed challenges for traditional small-molecule inhibitors. PROTACs exploit the endogenous E3 ubiquitin ligases to facilitate degradation of the proteins of interest (POIs) through the ubiquitin-proteasome system (UPS) in a cyclic catalytic manner. Despite recent endeavors to advance the utilization of PROTACs in clinical settings, the majority of PROTACs fail to progress beyond the preclinical phase of drug development. There are multiple factors impeding the market entry of PROTACs, with the insufficiently precise degradation of favorable POIs standing out as one of the most formidable obstacles. Recently, there has been exploration of new-generation advanced PROTACs, including small-molecule PROTAC prodrugs, biomacromolecule-PROTAC conjugates, and nano-PROTACs, to improve the in vivo efficacy of PROTACs. These improved PROTACs possess the capability to mitigate undesirable physicochemical characteristics inherent in traditional PROTACs, thereby enhancing their targetability and reducing off-target side effects. The new-generation of advanced PROTACs will mark a pivotal turning point in the realm of targeted protein degradation. In this comprehensive review, we have meticulously summarized the state-of-the-art advancements achieved by these cutting-edge PROTACs, elucidated their underlying design principles, deliberated upon the prevailing challenges encountered, and provided an insightful outlook on future prospects within this burgeoning field.
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Affiliation(s)
- Chao Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Wujun Chen
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China
| | - Yudong Wu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China.
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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2
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Grifagni D, Lenci E, De Santis A, Orsetti A, Barracchia CG, Tedesco F, Bellini Puglielli R, Lucarelli F, Lauriola A, Assfalg M, Cantini F, Calderone V, Guardavaccaro D, Trabocchi A, D’Onofrio M, Ciofi-Baffoni S. Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2. ACS Med Chem Lett 2024; 15:250-257. [PMID: 38352832 PMCID: PMC10860180 DOI: 10.1021/acsmedchemlett.3c00498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 02/16/2024] Open
Abstract
We have applied a proteolysis targeting chimera (PROTAC) technology to obtain a peptidomimetic molecule able to trigger the degradation of SARS-CoV-2 3-chymotrypsin-like protease (3CLPro). The PROTAC molecule was designed by conjugating a GC-376 based dipeptidyl 3CLPro ligand to a pomalidomide moiety through a piperazine-piperidine linker. NMR and crystallographic data complemented with enzymatic and cellular studies showed that (i) the dipeptidyl moiety of PROTAC binds to the active site of the dimeric state of SARS-CoV-2 3CLPro forming a reversible covalent bond with the sulfur atom of catalytic Cys145, (ii) the linker and the pomalidomide cereblon-ligand of PROTAC protrude from the protein, displaying a high degree of flexibility and no interactions with other regions of the protein, and (iii) PROTAC reduces the protein levels of SARS-CoV-2 3CLPro in cultured cells. This study paves the way for the future applicability of peptidomimetic PROTACs to tackle 3CLPro-dependent viral infections.
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Affiliation(s)
- Deborah Grifagni
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Elena Lenci
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Alessia De Santis
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Andrea Orsetti
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | | | - Filomena Tedesco
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Raffaele Bellini Puglielli
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Francesca Lucarelli
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Angela Lauriola
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Michael Assfalg
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Francesca Cantini
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Vito Calderone
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Daniele Guardavaccaro
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Andrea Trabocchi
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
| | - Mariapina D’Onofrio
- Department
of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Simone Ciofi-Baffoni
- Magnetic
Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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3
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Stein RR, Fouché M, Kearns JD, Roth HJ. A model-informed method to retrieve intrinsic from apparent cooperativity and project cellular target occupancy for ternary complex-forming compounds. RSC Chem Biol 2023; 4:512-523. [PMID: 37415863 PMCID: PMC10320841 DOI: 10.1039/d2cb00216g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/19/2023] [Indexed: 07/08/2023] Open
Abstract
There is an increasing interest to develop therapeutics that modulate challenging or undruggable target proteins via a mechanism that involves ternary complexes. In general, such compounds can be characterized by their direct affinities to a chaperone and a target protein and by their degree of cooperativity in the formation of the ternary complex. As a trend, smaller compounds have a greater dependency on intrinsic cooperativity to their thermodynamic stability relative to direct target (or chaperone) binding. This highlights the need to consider intrinsic cooperativity of ternary complex-forming compounds early in lead optimization, especially as they provide more control over target selectivity (especially for isoforms) and more insight into the relationship between target occupancy and target response via estimation of ternary complex concentrations. This motivates the need to quantify the natural constant of intrinsic cooperativity (α) which is generally defined as the gain (or loss) in affinity of a compound to its target in pre-bound vs. unbound state. Intrinsic cooperativities can be retrieved via a mathematical binding model from EC50 shifts of binary binding curves of the ternary complex-forming compound with either a target or chaperone relative to the same experiment but in the presence of the counter protein. In this manuscript, we present a mathematical modeling methodology that estimates the intrinsic cooperativity value from experimentally observed apparent cooperativities. This method requires only the two binary binding affinities and the protein concentrations of target and chaperone and is therefore suitable for use in early discovery therapeutic programs. This approach is then extended from biochemical assays to cellular assays (i.e., from a closed system to an open system) by accounting for differences in total ligand vs. free ligand concentrations in the calculations of ternary complex concentrations. Finally, this model is used to translate biochemical potency of ternary complex-forming compounds into expected cellular target occupancy, which could ultimately serve as a way for validation or de-validation of hypothesized biological mechanisms of action.
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Affiliation(s)
- Richard R Stein
- Novartis Institutes for BioMedical Research Basel Switzerland
| | - Marianne Fouché
- Novartis Institutes for BioMedical Research Basel Switzerland
| | | | - Hans-Joerg Roth
- Novartis Institutes for BioMedical Research Basel Switzerland
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4
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Zhu L, Hu S, Yan X, Zeng Q, Zhang B, Jiang L, Yao SQ, Ge J. Ugi reaction-assisted assembly of covalent PROTACs against glutathione peroxidase 4. Bioorg Chem 2023; 134:106461. [PMID: 36924654 DOI: 10.1016/j.bioorg.2023.106461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/06/2022] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Inducing cell ferroptosis by inactivating glutathione peroxidase 4 (GPX4) is a popular cancer treatment strategy. However, only few GPX4 inhibitors have been developed to date. PROteolysis Targeting Chimera (PROTAC) is a promising approach to provide new opportunities to overcome limitations of traditional therapeutics. Herein, a PROTAC-like activity-based probe PD-Q2 was first assembled using Ugi reaction, consisting of a known GPX4 inhibitor ML-162 homolog to the E3 ligase cereblon ligand-pomalidomide. Pull-down and immunoblotting analysis revealed that GPX4 was a covalent target of PD-Q2, but the degradation efficiency was weak. Therefore, a series of degraders was further synthesized by varying the linkers of heterofunctional PROTACs. Among these degraders, PD-4 and PD-P2 were found to promote effective GPX4 degradation via the ubiquitin-proteasome system and cause lipid ROS accumulation. PD-4 and PD-P2 showed potent inhibitory of colony formation and cell growth. Furthermore, we found that with pomalidomide, the degraders exhibit a high fluorescent signal that is mostly localized in the lysosome, which may affect the effectiveness of anti-cell proliferation. Overall, we provide GPX4 degraders for further exploring therapeutic potential of regulating ferroptosis.
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Affiliation(s)
- Liquan Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Shiqi Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xiaoqiao Yan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Qian Zeng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Bei Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Linye Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore.
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China.
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5
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Espinoza-Chávez R, Salerno A, Liuzzi A, Ilari A, Milelli A, Uliassi E, Bolognesi ML. Targeted Protein Degradation for Infectious Diseases: from Basic Biology to Drug Discovery. ACS BIO & MED CHEM AU 2023; 3:32-45. [PMID: 37101607 PMCID: PMC10125329 DOI: 10.1021/acsbiomedchemau.2c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/04/2022] [Accepted: 11/23/2022] [Indexed: 04/28/2023]
Abstract
Targeted protein degradation (TPD) is emerging as one of the most innovative strategies to tackle infectious diseases. Particularly, proteolysis-targeting chimera (PROTAC)-mediated protein degradation may offer several benefits over classical anti-infective small-molecule drugs. Because of their peculiar and catalytic mechanism of action, anti-infective PROTACs might be advantageous in terms of efficacy, toxicity, and selectivity. Importantly, PROTACs may also overcome the emergence of antimicrobial resistance. Furthermore, anti-infective PROTACs might have the potential to (i) modulate "undruggable" targets, (ii) "recycle" inhibitors from classical drug discovery approaches, and (iii) open new scenarios for combination therapies. Here, we try to address these points by discussing selected case studies of antiviral PROTACs and the first-in-class antibacterial PROTACs. Finally, we discuss how the field of PROTAC-mediated TPD might be exploited in parasitic diseases. Since no antiparasitic PROTAC has been reported yet, we also describe the parasite proteasome system. While in its infancy and with many challenges ahead, we hope that PROTAC-mediated protein degradation for infectious diseases may lead to the development of next-generation anti-infective drugs.
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Affiliation(s)
- Rocío
Marisol Espinoza-Chávez
- Department
of Pharmacy and Biotechnology, Alma Mater
Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Alessandra Salerno
- Department
of Pharmacy and Biotechnology, Alma Mater
Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Anastasia Liuzzi
- Institute
of Molecular Biology and Pathology of the Italian National Research
Council (IBPM-CNR) - Department of Biochemical Sciences, Sapienza University, P.le A. Moro 5, 00185 Roma, Italy
| | - Andrea Ilari
- Institute
of Molecular Biology and Pathology of the Italian National Research
Council (IBPM-CNR) - Department of Biochemical Sciences, Sapienza University, P.le A. Moro 5, 00185 Roma, Italy
| | - Andrea Milelli
- Department
for Life Quality Studies, Alma Mater Studiorum
- University of Bologna, Corso d’Augusto 237, 47921 Rimini, Italy
| | - Elisa Uliassi
- Department
of Pharmacy and Biotechnology, Alma Mater
Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Maria Laura Bolognesi
- Department
of Pharmacy and Biotechnology, Alma Mater
Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- E-mail:
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6
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Zhang C, Xu M, He S, Huang J, Xu C, Pu K. Checkpoint Nano-PROTACs for Activatable Cancer Photo-Immunotherapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208553. [PMID: 36427459 DOI: 10.1002/adma.202208553] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Checkpoint immunotherapy holds great potential to treat malignancies via blocking the immunosuppressive signaling pathways, which however suffers from inefficiency and off-target adverse effects. Herein, checkpoint nano-proteolysis targeting chimeras (nano-PROTACs) in combination with photodynamic tumor regression and immunosuppressive protein degradation to block checkpoint signaling pathways for activatable cancer photo-immunotherapy are reported. These nano-PROTACs are composed of a photosensitizer (protoporphyrin IX, PpIX) and an Src homology 2 domain-containing phosphatase 2 (SHP2)-targeting PROTAC peptide (aPRO) via a caspase 3-cleavable segment. aPRO is activated by the increased expression of caspase 3 in tumor cells after phototherapeutic treatment and induces targeted degradation of SHP2 via the ubiquitin-proteasome system. The persistent depletion of SHP2 blocks the immunosuppressive checkpoint signaling pathways (CD47/SIRPα and PD-1/PD-L1), thus reinvigorating antitumor macrophages and T cells. Such a checkpoint PROTAC strategy synergizes immunogenic phototherapy to boost antitumor immune response. Thus, this study represents a generalized PROTAC platform to modulate immune-related signaling pathways for improved anticancer therapy.
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Affiliation(s)
- Chi Zhang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Mengke Xu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Shasha He
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Jingsheng Huang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Cheng Xu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Kanyi Pu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
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7
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Wang C, Zhang Y, Yang S, Chen W, Xing D. PROTACs for BRDs proteins in cancer therapy: a review. J Enzyme Inhib Med Chem 2022; 37:1694-1703. [PMID: 35702740 PMCID: PMC9225710 DOI: 10.1080/14756366.2022.2081164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
BRDs proteins that recognise chromatin acetylation regulate gene expression, are epigenetic readers and master transcription coactivators. BRDs proteins are now emerging as targets for new therapeutic development. Blocking the function of any of BRDs proteins can be a control agent for diseases, such as cancer. Traditional drugs like enzyme inhibitors and protein–protein inhibitors have many limitations. The therapeutic efficacy of them remains to be proven. Recently, Proteolysis-Targeting Chimaeras (PROTACs) have become an advanced tool in therapeutic intervention as they remove disease-causing proteins. Extremely potent and efficacious small-molecule PROTACs of the BRDs proteins, based on available, potent, and selective BRDs inhibitors, have been reported. This review presents a comprehensive overview of the development of PROTACs for BRDs proteins regulation in cancer, and the chances and challenges associated with this area are also highlighted.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao University, Qingdao, PR China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, PR China.,School of Pharmacy, Qingdao University, Qingdao, PR China
| | - Shanbo Yang
- The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao University, Qingdao, PR China
| | - Wujun Chen
- The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao University, Qingdao, PR China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao University, Qingdao, PR China.,School of Life Sciences, Tsinghua University, Beijing, PR China
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8
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Ma L, Li G, Yang T, Zhang L, Wang X, Xu X, Ni H. An inhibitor of BRD4, GNE987, inhibits the growth of glioblastoma cells by targeting C-Myc and S100A16. Cancer Chemother Pharmacol 2022; 90:431-444. [PMID: 36224471 PMCID: PMC9637061 DOI: 10.1007/s00280-022-04483-7] [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: 07/27/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022]
Abstract
PURPOSE Among children, glioblastomas (GBMs) are a relatively common type of brain tumor. BRD4 expression was elevated in GBM and negatively correlated with the prognosis of glioma. We investigated the anti-GBM effects of a novel BRD4 inhibitor GNE987. METHODS We evaluated the anti-tumor effect of GNE987 in vitro and in vivo by Western blot, CCK8, flow cytometry detection, clone formation, the size of xenografts, and Ki67 immunohistochemical staining, and combined ChIP-seq with RNA-seq techniques to find its anti-tumor mechanism. RESULTS In vitro experiments showed that GNE987 significantly degraded BRD4, inhibited the proliferation of GBM cells, blocked the cell cycle, and induced apoptosis. Similarly, in vivo experiments, GNE987 also inhibited GBM growth as seen from the size of xenografts and Ki67 immunohistochemical staining. Based on Western blotting, GNE987 can significantly reduce the protein level of C-Myc; meanwhile, we combined ChIP-seq with RNA-seq techniques to confirm that GNE987 downregulated the transcription of S100A16 by disturbing H3K27Ac. Furthermore, we validated that S100A16 is indispensable in GBM growth. CONCLUSION GNE987 may be effective against GBM that targets C-Myc expression and influences S100A16 transcription through downregulation of BRD4.
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Affiliation(s)
- Liya Ma
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, People's Republic of China
| | - Gen Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, People's Republic of China
- Medical College of Soochow University, Suzhou, 215123, Jiangsu, People's Republic of China
| | - Tianquan Yang
- Department of Neurosurgery, Children's Hospital of Soochow University, Suzhou, 215003, People's Republic of China
| | - Li Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, People's Republic of China
| | - Xinxin Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, People's Republic of China
| | - Xiaowen Xu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, People's Republic of China
| | - Hong Ni
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, People's Republic of China.
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9
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Wang C, Zhang Y, Zhang T, Shi L, Geng Z, Xing D. Proteolysis-targeting chimaeras (PROTACs) as pharmacological tools and therapeutic agents: advances and future challenges. J Enzyme Inhib Med Chem 2022; 37:1667-1693. [PMID: 35702041 PMCID: PMC9225776 DOI: 10.1080/14756366.2022.2076675] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Proteolysis-targeting chimaeras (PROTACs) have been developed to be an emerging technology for targeted protein degradation and attracted the favour of academic institutions, large pharmaceutical enterprises, and biotechnology companies. The mechanism is based on the inhibition of protein function by hijacking a ubiquitin E3 ligase for protein degradation. The heterobifunctional PROTACs contain a ligand for recruiting an E3 ligase, a linker, and another ligand to bind with the protein targeted for degradation. To date, PROTACs targeting ∼70 proteins, many of which are clinically validated drug targets, have been successfully developed with several in clinical trials for diseases therapy. In this review, the recent advances in PROTACs against clinically validated drug targets are summarised and the chemical structure, cellular and in vivo activity, pharmacokinetics, and pharmacodynamics of these PROTACs are highlighted. In addition, the potential advantages, challenges, and prospects of PROTACs technology in disease treatment are discussed.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China.,School of Pharmacy, Qingdao University, Qingdao, China
| | - Tingting Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Lingyu Shi
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Zhongmin Geng
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, China.,School of Life Sciences, Tsinghua University, Beijing, China
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10
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Fang Y, Wang J, Zhao M, Zheng Q, Ren C, Wang Y, Zhang J. Progress and Challenges in Targeted Protein Degradation for Neurodegenerative Disease Therapy. J Med Chem 2022; 65:11454-11477. [PMID: 36006861 DOI: 10.1021/acs.jmedchem.2c00844] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Neurodegenerative diseases (NDs) are currently incurable diseases that cause progressive degeneration of nerve cells. Many of the disease-causing proteins of NDs are "undruggable" for traditional small-molecule inhibitors (SMIs). None of the compounds that attenuated the amyloid-β (Aβ) accumulation process have entered clinical practice, and many phase III clinical trials of SMIs for Alzheimer's disease (AD) have failed. In recent years, emerging targeted protein degradation (TPD) technologies such as proteolysis-targeting chimeras (PROTACs), lysosome-targeting chimaeras (LYTACs), and autophagy-targeting chimeras (AUTACs) with TPD-assistive technologies such as click-formed proteolysis-targeting chimeras (CLIPTACs) and deubiquitinase-targeting chimera (DUBTAC) have developed rapidly. In vitro and in vivo experiments have also confirmed that TPD technology can target the degradation of ND pathogenic proteins, bringing hope for the treatment of NDs. Herein, we review the latest TPD technologies, introduce their targets and technical characteristics, and discuss the emerging TPD technologies with potential in ND research, with the hope of providing a new perspective for the development of TPD technology in the NDs field.
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Affiliation(s)
- Yingxu Fang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Min Zhao
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Tianfu Jincheng Laboratory, Chengdu 610041, Sichuan, China
| | - Qinwen Zheng
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu 611130, Sichuan, China
| | - Yuxi Wang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Tianfu Jincheng Laboratory, Chengdu 610041, Sichuan, China
| | - Jifa Zhang
- Joint Research Institution of Altitude Health, Department of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Tianfu Jincheng Laboratory, Chengdu 610041, Sichuan, China
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11
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Liu Z, Zhang Y, Xiang Y, Kang X. Small-Molecule PROTACs for Cancer Immunotherapy. Molecules 2022; 27:molecules27175439. [PMID: 36080223 PMCID: PMC9458232 DOI: 10.3390/molecules27175439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Abstract
Unsatisfactory physicochemical properties of macromolecular drugs seriously hinder their application in tumor immunotherapy. However, these problems can be effectively solved by small-molecule compounds. In the promising field of small-molecule drug development, proteolysis targeting chimera (PROTAC) offers a novel mode of action in the interactions between small molecules and therapeutic targets (mainly proteins). This revolutionary technology has shown considerable impact on several proteins related to tumor survival but is rarely exploited in proteins associated with immuno-oncology up until now. This review attempts to comprehensively summarize the well-studied and less-developed immunological targets available for PROTAC technology, as well as some targets to be explored, aiming to provide more options and opportunities for the development of small-molecule-based tumor immunotherapy. In addition, some novel directions that can magnify and broaden the protein degradation efficiency are mentioned to improve PROTAC design in the future.
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Affiliation(s)
| | | | | | - Xin Kang
- Correspondence: ; Tel.: +86-19138939183
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12
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Chen Y, Tandon I, Heelan W, Wang Y, Tang W, Hu Q. Proteolysis-targeting chimera (PROTAC) delivery system: advancing protein degraders towards clinical translation. Chem Soc Rev 2022; 51:5330-5350. [PMID: 35713468 PMCID: PMC9382890 DOI: 10.1039/d1cs00762a] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteolysis Targeting Chimeras (PROTACs), an emerging therapeutic entity designed to degrade target proteins by hijacking the ubiquitin-proteasome system, have the potential to revolutionize the healthcare industry. The broad applicability of this protein degradation strategy has been verified with a few E3 ligases and a variety of distinct targets through the construction of modular chimeric structures. Despite recent efforts to promote the use of PROTACs for clinical applications, most PROTACs do not make it beyond the preclinical stage of drug development. There are several reasons that prevent PROTACs from reaching the market, and the inadequate delivery to the target site is one of the most challenging hurdles. With the increasing need for accelerating the translational process, combining the concepts of PROTACs and delivery systems has been explored to enhance the in vivo performance of PROTACs. These improved delivery strategies can eliminate unfavorable physicochemical properties of PROTACs, improve their targetability, and decrease their off-target side effects. The integration of powerful PROTACs and versatile delivery systems will inaugurate a burgeoning orientation for the field of targeted protein degradation. In this review, we will survey the latest progress in improving the in vivo degradation efficacy of PROTACs through delivery strategies, outline design principles for PROTAC-based delivery systems, discuss the current challenges with PROTACs, and outlook future opportunities in this field.
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Affiliation(s)
- Yu Chen
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ira Tandon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - William Heelan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Yixin Wang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Weiping Tang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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13
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Wang F, Cao XY, Lin GQ, Tian P, Gao D. Novel inhibitors of the STAT3 signaling pathway: an updated patent review (2014-present). Expert Opin Ther Pat 2022; 32:667-688. [PMID: 35313119 DOI: 10.1080/13543776.2022.2056013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION STAT3 is a critical transcription factor that transmits signals from the cell surface to the nucleus, thus influencing the transcriptional regulation of some oncogenes. The inhibition of the activation of STAT3 is considered a promising strategy for cancer therapy. Numerous STAT3 inhibitors bearing different scaffolds have been reported to date, with a few of them having been considered in clinical trials. AREAS COVERED This review summarizes the advances on STAT3 inhibitors with different structural skeletons, focusing on the structure-activity relationships in the related patent literature published from 2014 to date. EXPERT OPINION Since the X-ray crystal structure of STAT3β homo dimer bound to DNA was solved in 1998, the development of STAT3 inhibitors has gone through a boom in recent years. However, none of them have been approved for marketing, probably due to the complex biological functions of the STAT3 signaling pathway, including its character and the poor drug-like physicochemical properties of its inhibitors. Nonetheless, targeting STAT3 continues to be an exciting field for the development of anti-tumor agents along with the emergence of new STAT3 inhibitors with unique mechanisms of action.
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Affiliation(s)
- Feng Wang
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Xin-Yu Cao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Guo-Qiang Lin
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Ping Tian
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Dingding Gao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
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14
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Carroll EC, Marqusee S. Site-specific ubiquitination: Deconstructing the degradation tag. Curr Opin Struct Biol 2022; 73:102345. [PMID: 35247748 DOI: 10.1016/j.sbi.2022.102345] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/28/2021] [Accepted: 01/17/2022] [Indexed: 02/04/2023]
Abstract
Ubiquitin is a small eukaryotic protein so named for its cellular abundance and originally recognized for its role as the posttranslational modification (PTM) "tag" condemning substrates to degradation by the 26S proteasome. Since its discovery in the 1970s, protein ubiquitination has also been identified as a key regulatory feature in dozens of non-degradative cellular processes. This myriad of roles illustrates the versatility of ubiquitin as a PTM; however, understanding the cellular and molecular factors that enable discrimination between degradative versus non-degradative ubiquitination events has been a persistent challenge. Here, we discuss recent advances in uncovering how site-specificity - the exact residue that gets modified - modulates distinct protein fates and cellular outcomes with an emphasis on how ubiquitination site specificity regulates proteasomal degradation. We explore recent advances in structural biology, biophysics, and cell biology that have enabled a broader understanding of the role of ubiquitination in altering the dynamics of the target protein, including implications for the design of targeted protein degradation therapeutics.
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Affiliation(s)
- Emma C Carroll
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, 94038, USA.
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA; QB3 Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, 94720, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA.
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15
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Zhong Y, Chi F, Wu H, Liu Y, Xie Z, Huang W, Shi W, Qian H. Emerging targeted protein degradation tools for innovative drug discovery: From classical PROTACs to the novel and beyond. Eur J Med Chem 2022; 231:114142. [DOI: 10.1016/j.ejmech.2022.114142] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/22/2022]
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16
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Wang C, Zhang Y, Wang J, Xing D. VHL-based PROTACs as potential therapeutic agents: Recent progress and perspectives. Eur J Med Chem 2022; 227:113906. [PMID: 34656901 DOI: 10.1016/j.ejmech.2021.113906] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023]
Abstract
Proteolysis targeting chimeras (PROTACs), which hijack proteins of interest (POIs) and recruit E3 ligases for target degradation via the ubiquitin-proteasome pathway, are a novel drug discovery paradigm that has been widely used as biological tools and medicinal molecules with the potential of clinical application value. To date, a wide variety of small molecule PROTACs have been developed. Importantly, VHL-based PROTACs have emerged to be a promising approach for proteins, including those non-druggable ones, such as transcriptional factors and scaffold proteins. VHL-based PRTOACs have been developed for the treatment of diseases that are difficult to be dealt with by conventional methods, such as radiotherapy, chemotherapy, and small molecule inhibitors. In this review, the recent advances of VHL-based PRTOACs were summarized, and the chances and challenges associated with this area were also highlighted.
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Affiliation(s)
- Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, 266071, Shandong, China; School of Pharmacy, Qingdao University, Qingdao, 266021, Shandong, China.
| | - Jie Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, 266071, Shandong, China.
| | - Dongming Xing
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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17
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Zhong J, Yan W, Wang C, Liu W, Lin X, Zou Z, Sun W, Chen Y. BRAF Inhibitor Resistance in Melanoma: Mechanisms and Alternative Therapeutic Strategies. Curr Treat Options Oncol 2022; 23:1503-1521. [PMID: 36181568 PMCID: PMC9596525 DOI: 10.1007/s11864-022-01006-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 01/30/2023]
Abstract
OPINION STATEMENT Melanoma is caused by a variety of somatic mutations, and among these mutations, BRAF mutation occurs most frequently and has routinely been evaluated as a critical diagnostic biomarker in clinical practice. The introduction of targeted agents for BRAF-mutant melanoma has significantly improved overall survival in a large proportion of patients. However, there is BRAF inhibitor resistance in most patients, and its mechanisms are complicated and need further clarification. Additionally, treatment approaches to overcome resistance have evolved rapidly, shifting from monotherapy to multimodality treatment, which has dramatically improved patient outcomes in clinical trials and practice. This review highlights the mechanisms of BRAF inhibitor resistance in melanoma and discusses the current state of its therapeutic approaches that can be further explored in clinical practice.
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Affiliation(s)
- Jingqin Zhong
- grid.452404.30000 0004 1808 0942Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Xuhui, Shanghai, China
| | - Wangjun Yan
- grid.452404.30000 0004 1808 0942Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Xuhui, Shanghai, China
| | - Chunmeng Wang
- grid.452404.30000 0004 1808 0942Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Xuhui, Shanghai, China
| | - Wanlin Liu
- grid.452404.30000 0004 1808 0942Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Xuhui, Shanghai, China
| | - Xinyi Lin
- grid.452404.30000 0004 1808 0942Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Xuhui, Shanghai, China
| | - Zijian Zou
- grid.452404.30000 0004 1808 0942Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Xuhui, Shanghai, China
| | - Wei Sun
- grid.452404.30000 0004 1808 0942Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Xuhui, Shanghai, China
| | - Yong Chen
- grid.452404.30000 0004 1808 0942Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, 270 Dongan Road, Xuhui, Shanghai, China
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