1
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Zattoni J, Vottero P, Carena G, Uliveto C, Pozzati G, Morabito B, Gitari E, Tuszynski J, Aminpour M. A comprehensive primer and review of PROTACs and their In Silico design. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2025; 264:108687. [PMID: 40058081 DOI: 10.1016/j.cmpb.2025.108687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 01/28/2025] [Accepted: 02/25/2025] [Indexed: 04/05/2025]
Abstract
The cutting-edge technique of Proteolysis Targeting Chimeras, or PROTACs, has gained significant attention as a viable approach for specific protein degradation. This innovative technology has vast potential in fields such as cancer therapy and drug development. The development of effective and specific therapies for a range of diseases is within reach with PROTACs, which can target previously "undruggable" proteins while circumventing the off-target effects of conventional small molecule inhibitors. This manuscript aims to discuss the application of in silico techniques to the design of these groundbreaking molecules and develop PROTAC complexes, in order to identify potential PROTAC candidates with favorable drug-like properties. Additionally, this manuscript reviews the strengths and weaknesses of these methods to demonstrate their utility and highlights the challenges and future prospects of in silico PROTAC design. The present review provides a valuable and beginner-friendly resource for researchers and drug developers interested in using in silico methods for PROTAC design, specifically ternary structure prediction.
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Affiliation(s)
- Jacopo Zattoni
- Department of Biomedical Engineering, University of Alberta, Edmonton, T6G 1Z2, Canada
| | - Paola Vottero
- Department of Biomedical Engineering, University of Alberta, Edmonton, T6G 1Z2, Canada
| | - Gea Carena
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Chiara Uliveto
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Giulia Pozzati
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Benedetta Morabito
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Ebenezea Gitari
- Department of Biochemistry, University of Alberta, Edmonton, T6G 1Z2, Canada
| | - Jack Tuszynski
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, T6G 2M9, Canada
| | - Maral Aminpour
- Department of Biomedical Engineering, University of Alberta, Edmonton, T6G 1Z2, Canada.
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2
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Salerno A, Wieske LHE, Diehl CJ, Ciulli A. Rational Design of PROTAC Linkers Featuring Ferrocene as a Molecular Hinge to Enable Dynamic Conformational Changes. J Am Chem Soc 2025; 147:13328-13344. [PMID: 40208910 DOI: 10.1021/jacs.4c18354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2025]
Abstract
Proteolysis Targeting Chimeras (PROTACs) are bifunctional molecules that induce ubiquitination and degradation of a target protein via recruitment to an E3 ligase. The linker influences many steps of the PROTAC mode of action, from cellular permeability to ternary complex formation and target degradation. Much interest has therefore been devoted to linker design to fine-tune molecular and mechanistic properties of PROTACs. In this study, we present FerroTACs, a novel PROTAC design strategy incorporating ferrocene as the linker chemotype. We exemplify the approach across three different PROTAC systems: VHL-VHL (homo-PROTACs), VHL-CRBN, and VHL-BETs. We find that ferrocene's unique organometallic structure, featuring freely rotating cyclopentadienyl rings around a central Fe(II) ion, acts as a molecular hinge enabling structural adjustment to the environment that results in properties alteration, i.e., chameleonicity. Conformational analyses via NMR spectroscopy support ferrocene's role in fostering intramolecular interactions that result in a more folded state in an apolar environment. This property promotes compact conformations, improving cellular permeability and reducing efflux liabilities. Cellular assays demonstrate that FerroTACs exhibit robust target degradation and cell permeability profiles, en-par or enhanced compared to benchmark PROTACs CM11, 14a, and MZ1. These findings highlight ferrocene's potential as a new linker design strategy, offering a versatile platform to install and control molecular chameleonicity into next-generation PROTACs.
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Affiliation(s)
- Alessandra Salerno
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, U.K
| | - Lianne H E Wieske
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, U.K
| | - Claudia J Diehl
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, U.K
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, U.K
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3
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Mahajan A, Panzade G, Bhuniya T, Das P, Bhattacharjee B, Das S, Chowdhury A, Chakraborty K, Guha S, Samant A, Dey A, Ghosh S. Revolutionizing lung cancer treatment: Introducing PROTAC therapy as a novel paradigm in targeted therapeutics. Curr Probl Cancer 2025; 54:101172. [PMID: 39731828 DOI: 10.1016/j.currproblcancer.2024.101172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 09/23/2024] [Accepted: 12/18/2024] [Indexed: 12/30/2024]
Abstract
This comprehensive review explores the transformative potential of PROTAC (Proteolysis-Targeting Chimeras) therapy as a groundbreaking approach in the landscape of lung cancer treatment. The introduction provides a succinct overview of current challenges in lung cancer treatment, emphasizing the significance of targeted therapies. Focusing on PROTAC therapy, the article elucidates its mechanism of action, comparing it with traditional targeted therapies and highlighting the key components and design principles of PROTAC molecules. In the context of lung cancer, the review meticulously summarizes preclinical evidence, emphasizing efficacy and specificity gleaned from studies evaluating PROTAC therapy. It delves into the implications of this preclinical data, discussing potential advantages over existing targeted therapies. An update on ongoing clinical trials involving PROTAC therapy for lung cancer offers a snapshot of the current progress, with a summary of key outcomes and advancements in early-phase trials. The mechanistic insights into PROTAC therapy's impact on lung cancer cells are explored, alongside a discussion on potential biomarkers for patient stratification and response prediction. The influence of tumor heterogeneity on PROTAC therapy outcomes is also addressed. Safety and tolerability assessments, encompassing preclinical and clinical studies, are comprehensively evaluated, including a comparative analysis with traditional targeted therapies and strategies to mitigate side effects. Looking forward, the article discusses the future perspectives of PROTAC therapy in lung cancer treatment and addresses ongoing challenges, providing a nuanced exploration of potential combination therapies and synergistic approaches. In conclusion, the review summarizes key findings and insights, underscoring the tremendous potential of PROTAC therapy as a promising and innovative avenue in pursuing more effective lung cancer treatments.
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Affiliation(s)
- Atharva Mahajan
- Advance Centre for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai, Mumbai, Maharashtra, India
| | - Gauri Panzade
- Advance Centre for Treatment, Research and Education in Cancer (ACTREC), Navi Mumbai, Mumbai, Maharashtra, India
| | - Tiyasa Bhuniya
- Department of Biotechnology, National Institute of Technology Durgapur, West Bengal, India
| | - Purbasha Das
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | | | - Sagnik Das
- Department of Microbiology, St Xavier's College (autonomous) Kolkata, West Bengal, India
| | - Ankita Chowdhury
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Delhi, India
| | - Kashmira Chakraborty
- Department of Chemistry and Chemical Biology, Indian Institute of Technology Dhanbad, Jharkhand, India
| | - Sudeepta Guha
- Department of Chemistry and Chemical Biology, Indian Institute of Technology Dhanbad, Jharkhand, India
| | - Anushka Samant
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Orissa, India
| | - Anuvab Dey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
| | - Subhrojyoti Ghosh
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India.
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4
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Lin ST, Wang CH, Chen AL, Andrew Wang TS. Utilizing Alkyne-Nitrone Cycloaddition for the Convenient Multi-Component Assembly of Protein Degraders and Biological Probes. Chemistry 2025; 31:e202403184. [PMID: 39642057 DOI: 10.1002/chem.202403184] [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: 08/24/2024] [Revised: 11/28/2024] [Accepted: 12/06/2024] [Indexed: 12/08/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) have become a popular therapeutic strategy, and the development of multi-functional PROTACs has added complexity to their synthetic process. Although click reactions have been widely applied to prepare highly functionalized biomolecules, most of them are limited to two-component reactions, restricting the creation of more complex structures. Here, we developed a convenient multi-component assembly strategy via strain-promoted alkyne-nitrone cycloaddition (SPANC), which can be extended to a 3-component reaction when combined with nitrone formation. Using the 2-component assembly, we demonstrated the targeted protein degradation with both preassembled and in-cell assembled PROTACs. This strategy was also applied to facilitate the screening of E3 ligases in PROTACs and the preparation of various biological probes. Moreover, the 3-component assembly, via sequential nitrone formation and SPANC, enabled the synthesis of trifunctional 3-component PROTACs. The N-substituent, serving as an additional functional moiety, was designed as a photocage for sterically controlling PROTAC activity. The 3-component assembly can be further modified to provide additional control or enhance the cell-targeting ability of PROTACs. In short, our multi-component SPANC assembly strategy offers a modular and versatile synthetic platform for creating multi-functional PROTACs and biological probes.
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Affiliation(s)
- Shiou-Ting Lin
- Department of Chemistry, National Taiwan University, Taipei, 106319, Taiwan, R.O.C
| | - Chien-Hua Wang
- Department of Chemistry, National Taiwan University, Taipei, 106319, Taiwan, R.O.C
| | - Ai-Lin Chen
- Department of Chemistry, National Taiwan University, Taipei, 106319, Taiwan, R.O.C
| | - Tsung-Shing Andrew Wang
- Department of Chemistry, National Taiwan University, Taipei, 106319, Taiwan, R.O.C
- Center for Emerging Material and Advanced Devices, National Taiwan University, Taipei, 106319, Taiwan, R.O.C
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5
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Omar EA, R R, Das PK, Pal R, Purawarga Matada GS, Maji L. Next-generation cancer therapeutics: PROTACs and the role of heterocyclic warheads in targeting resistance. Eur J Med Chem 2025; 281:117034. [PMID: 39527893 DOI: 10.1016/j.ejmech.2024.117034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 10/30/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]
Abstract
One of the major obstacles to sustained cancer treatment effectiveness is the development of medication resistance. Current therapies that block proteins associated with cancer progression often lose their efficacy due to acquired drug resistance, which is frequently driven by mutated or overexpressed protein targets. Proteolysis-targeting chimeras (PROTACs) offer an alternative therapeutic strategy by hijacking the cell's ubiquitin-proteasome system to degrade disease-causing proteins, presenting several potential advantages. Over the past few years, PROTACs have been developed to target various cancer-related proteins, offering new treatment options for patients with previously untreatable malignancies and serving as a foundation for next-generation therapeutics. One of the notable benefits of PROTACs is their ability to overcome certain resistance mechanisms that limit the effectiveness of conventional targeted therapies, as shown in several recent studies. Additionally, research teams are investigating how PROTACs can selectively degrade mutant proteins responsible for resistance to first-line cancer therapies. In the pursuit of novel and effective treatments, this review highlights recent advancements in the development of PROTACs aimed at overcoming cancer resistance. When it comes to drug design, heterocyclic scaffolds often serve as a foundational framework, offering opportunities for modification and optimization of novel molecules. Researchers are similarly exploring various heterocyclic derivatives as "warheads" in the design of PROTACs has been instrumental in pushing the boundaries of targeted protein degradation. As warheads, these heterocyclic compounds are responsible for recognizing and binding to the target protein, which ultimately leads to its degradation via the ubiquitin-proteasome system. This study aims to provide a comprehensive overview of cutting-edge strategies in PROTAC design, offering detailed insights into key concepts and methodologies for creating effective PROTACs. Special emphasis is placed on structure-based rational design, the development of novel warheads, and their critical in influencing biological activity.
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Affiliation(s)
- Ebna Azizal Omar
- Centre for Excellence in Drug Analysis, Department of Pharmaceutical Analysis, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India
| | - Rajesh R
- Centre for Excellence in Drug Analysis, Department of Pharmaceutical Analysis, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India.
| | - Pronoy Kanti Das
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India
| | - Rohit Pal
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India
| | - Gurubasavaraja Swamy Purawarga Matada
- Integrated Drug Discovery Centre, Department of Pharmaceutical Chemistry, Acharya & BM Reddy College of Pharmacy, Bengaluru, 560107, Karnataka, India
| | - Lalmohan Maji
- Tarifa Memorial Institute of Pharmacy, Department of Pharmaceutical Chemistry, Murshidabad, 742166, West Bengal, India
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6
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Bond AG, Muñoz i Ordoño M, Bisbach CM, Craigon C, Makukhin N, Caine EA, Nagala M, Urh M, Winter GE, Riching KM, Ciulli A. Leveraging Dual-Ligase Recruitment to Enhance Protein Degradation via a Heterotrivalent Proteolysis Targeting Chimera. J Am Chem Soc 2024; 146:33675-33711. [PMID: 39606859 PMCID: PMC11638965 DOI: 10.1021/jacs.4c11556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 11/14/2024] [Accepted: 11/14/2024] [Indexed: 11/29/2024]
Abstract
Proteolysis targeting chimera (PROTAC) degraders are typically bifunctional with one E3 ligase ligand connected to one target protein ligand via a linker. While augmented valency has been shown with trivalent PROTACs targeting two binding sites within a given target protein, or used to recruit two different targets, the possibility of recruiting two different E3 ligases within the same compound has not been demonstrated. Here we present dual-ligase recruitment as a strategy to enhance targeted protein degradation. We designed heterotrivalent PROTACs composed of CRBN, VHL and BET targeting ligands, separately tethered via a branched trifunctional linker. Structure-activity relationships of 12 analogues qualifies AB3067 as the most potent and fastest degrader of BET proteins, with minimal E3 ligase cross-degradation. Comparative kinetic analyses in wild-type and ligase single and double knockout cell lines revealed that protein ubiquitination and degradation induced by AB3067 was contributed to by both CRBN and VHL in an additive fashion. We further expand the scope of the dual-ligase approach by developing a heterotrivalent CRBN/VHL-based BromoTag degrader and a tetravalent PROTAC comprising of two BET ligand moieties. In summary, we provide proof-of-concept for dual-E3 ligase recruitment as a strategy to boost degradation fitness by recruiting two E3 ligases with a single degrader molecule. This approach could potentially delay the outset of resistance mechanisms involving loss of E3 ligase functionality.
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Affiliation(s)
- Adam G. Bond
- Centre
for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, U.K.
| | - Miquel Muñoz i Ordoño
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences Vienna 1090, Austria
| | - Celia M. Bisbach
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Conner Craigon
- Centre
for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, U.K.
| | - Nikolai Makukhin
- Centre
for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, U.K.
| | - Elizabeth A. Caine
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Manjula Nagala
- Centre
for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, U.K.
| | - Marjeta Urh
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences Vienna 1090, Austria
| | - Kristin M. Riching
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Alessio Ciulli
- Centre
for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, U.K.
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7
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Li T, Gu C, Zhou C, Mao C, Yang K, Xu J, Lu T, Chen J. Insights into direct KRAS inhibition strategies for cancer treatment. Future Med Chem 2024; 16:2411-2429. [PMID: 39569642 PMCID: PMC11622815 DOI: 10.1080/17568919.2024.2424149] [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: 03/08/2024] [Accepted: 10/23/2024] [Indexed: 11/22/2024] Open
Abstract
KRAS is the most commonly mutated isoform in RAS-driven cancers. In the early stage, KRAS was deemed as an "undruggable" cancer target due to the lack of suitable binding pockets. With the development of KRAS inhibitors in recent years, strategies that directly suppress oncogenic KRAS have achieved significant breakthroughs. In this review, we summarize recent advances in direct small-molecule KRAS inhibitors used for cancer therapy, highlighting their medicinal chemistry optimization processes. Moreover, new PROTACs targeting the KRAS mutation are also presented. Additionally, we put forward the challenges and prospects for the development of future KRAS inhibitors.
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Affiliation(s)
- Tong Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Chenglei Gu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Chen Zhou
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL32610, United States
| | - Chunqin Mao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Kan Yang
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Sciences, Hebei University, Baoding, 071002, China
| | - Jinyi Xu
- State Key Laboratory of Natural Medicines & Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China
| | - Tulin Lu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jichao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
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8
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Thapa R, Bhat AA, Gupta G, Renuka Jyothi S, Kaur I, Kumar S, Sharma N, Prasad GVS, Pramanik A, Ali H. CRBN-PROTACs in Cancer Therapy: From Mechanistic Insights to Clinical Applications. Chem Biol Drug Des 2024; 104:e70009. [PMID: 39496477 DOI: 10.1111/cbdd.70009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 09/28/2024] [Accepted: 10/16/2024] [Indexed: 11/06/2024]
Abstract
Cereblon (CRBN), a member of the E3 ubiquitin ligase complex, has gained significant attention as a therapeutic target in cancer. CRBN regulates the degradation of various proteins in cancer progression, including transcription factors and signaling molecules. PROTACs (proteolysis-targeting chimeras) are a novel approach that uses the cell's degradation system to remove disease-causing proteins selectively. CRBN-dependent PROTACs work by tagging harmful proteins for destruction through the ubiquitin-proteasome system. This strategy offers several advantages over traditional protein inhibition methods, including the potential to overcome drug resistance. Recent progress in developing CRBN-based PROTACs has shown promising preclinical results in both hematologic malignancies and solid tumors. Additionally, CRBN-based PROTACs have enhanced our understanding of CRBN's role in cancer, potentially serving as biomarkers for patient stratification and predicting therapeutic responses. In this review, we delineate the mechanisms of action for CRBN-dependent PROTACs (CRBN-PROTACs), summarize recent advances in preclinical and clinical applications, and provide our perspective on future development.
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Affiliation(s)
- Riya Thapa
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Asif Ahmad Bhat
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Gaurav Gupta
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, India
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, UAE
| | - S Renuka Jyothi
- Department of Biotechnology and Genetics, School of Sciences, JAIN (Deemed to Be University), Bangalore, Karnataka, India
| | - Irwanjot Kaur
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan, India
| | - Sachin Kumar
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | - Naveen Sharma
- Chandigarh Pharmacy College, Chandigarh Group of College, Jhanjeri, Mohali, Punjab, India
| | - G V Siva Prasad
- Department of Chemistry, Raghu Engineering College, Visakhapatnam, Andhra Pradesh, India
| | - Atreyi Pramanik
- School of Applied and Life Sciences, Division of Research and Innovation, Uttaranchal University, Dehradun, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
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9
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Du S, Liu X, Hu X, Zhan P. Viral Protein Dimerization Quality Control: A Design Strategy for a Potential Viral Inhibitor. J Med Chem 2024; 67:16951-16966. [PMID: 39303015 DOI: 10.1021/acs.jmedchem.4c01540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
The global pharmaceutical market has been profoundly impacted by the coronavirus pandemic, leading to an increased demand for specific drugs. Consequently, drug resistance has prompted continuous innovation in drug design strategies to effectively combat resistant pathogens or disease variants. Protein dimers play crucial roles in vivo, including catalytic reactions, signal transduction, and structural stability. The site of action for protein dimerization modulators typically does not reside within the active site of the protein, thereby potentially impeding resistance development. Therefore, harnessing viral protein dimerization modulators could represent a promising avenue for combating viral infections. In this Perspective, we provide a detailed introduction to the design principles and applications of dimerization modulators in antiviral research. Furthermore, we analyze various representative examples to elucidate their modes of action while presenting our perspective on dimerization modulators along with the opportunities and challenges associated with this groundbreaking area of investigation.
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Affiliation(s)
- Shaoqing Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, P. R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, P. R. China
| | - Xueping Hu
- Institute of Frontier Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Qingdao 266237, P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong 250012, P. R. China
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10
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Kamaraj R, Ghosh S, Das S, Sen S, Kumar P, Majumdar M, Dasgupta R, Mukherjee S, Das S, Ghose I, Pavek P, Raja Karuppiah MP, Chuturgoon AA, Anand K. Targeted Protein Degradation (TPD) for Immunotherapy: Understanding Proteolysis Targeting Chimera-Driven Ubiquitin-Proteasome Interactions. Bioconjug Chem 2024; 35:1089-1115. [PMID: 38990186 PMCID: PMC11342303 DOI: 10.1021/acs.bioconjchem.4c00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Targeted protein degradation or TPD, is rapidly emerging as a treatment that utilizes small molecules to degrade proteins that cause diseases. TPD allows for the selective removal of disease-causing proteins, including proteasome-mediated degradation, lysosome-mediated degradation, and autophagy-mediated degradation. This approach has shown great promise in preclinical studies and is now being translated to treat numerous diseases, including neurodegenerative diseases, infectious diseases, and cancer. This review discusses the latest advances in TPD and its potential as a new chemical modality for immunotherapy, with a special focus on the innovative applications and cutting-edge research of PROTACs (Proteolysis TArgeting Chimeras) and their efficient translation from scientific discovery to technological achievements. Our review also addresses the significant obstacles and potential prospects in this domain, while also offering insights into the future of TPD for immunotherapeutic applications.
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Affiliation(s)
- Rajamanikkam Kamaraj
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Subhrojyoti Ghosh
- Department
of Biotechnology, Indian Institute of Technology
Madras, Chennai 600036, India
| | - Souvadra Das
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Shinjini Sen
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Priyanka Kumar
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Madhurima Majumdar
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Renesa Dasgupta
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Sampurna Mukherjee
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Shrimanti Das
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Indrilla Ghose
- Department
of Biotechnology, Heritage Institute of
Technology, Kolkata 700107, India
| | - Petr Pavek
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Muruga Poopathi Raja Karuppiah
- Department
of Chemistry, School of Physical Sciences, Central University of Kerala, Tejaswini Hills, Periye, Kasaragod District, Kerala 671320, India
| | - Anil A. Chuturgoon
- Discipline
of Medical Biochemistry, School of Laboratory Medicine and Medical
Sciences, College of Health Sciences, Howard College Campus, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Krishnan Anand
- Department
of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, Free State 9300, South Africa
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11
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Feng Y, Hu X, Wang X. Targeted protein degradation in hematologic malignancies: clinical progression towards novel therapeutics. Biomark Res 2024; 12:85. [PMID: 39169396 PMCID: PMC11340087 DOI: 10.1186/s40364-024-00638-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024] Open
Abstract
Targeted therapies, such as small molecule kinase inhibitors, have made significant progress in the treatment of hematologic malignancies by directly modulating protein activity. However, issues such as drug toxicity, drug resistance due to target mutations, and the absence of key active sites limit the therapeutic efficacy of these drugs. Targeted protein degradation (TPD) presents an emergent and rapidly evolving therapeutic approach that selectively targets proteins of interest (POI) based on endogenous degradation processes. With an event-driven pharmacology of action, TPD achieves efficacy with catalytic amounts, avoiding drug-related toxicity. Furthermore, TPD has the unique mode of degrading the entire POI, such that resistance derived from mutations in the targeted protein has less impact on its degradation function. Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) are the most maturely developed TPD techniques. In this review, we focus on both preclinical experiments and clinical trials to provide a comprehensive summary of the safety and clinical effectiveness of PROTACs and MGDs in hematologic malignancies over the past two decades. In addition, we also delineate the challenges and opportunities associated with these burgeoning degradation techniques. TPD, as an approach to the precise degradation of specific proteins, provides an important impetus for its future application in the treatment of patients with hematologic malignancies.
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Affiliation(s)
- Yupiao Feng
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China
| | - Xinting Hu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, Shandong, 250021, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, Shandong, 250021, China.
- Taishan Scholars Program of Shandong Province, Jinan, Shandong, 250021, China.
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12
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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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13
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Duan Q, Jia H, Chen W, Qin C, Zhang K, Jia F, Fu T, Wei Y, Fan M, Wu Q, Tan W. Multivalent Aptamer-Based Lysosome-Targeting Chimeras (LYTACs) Platform for Mono- or Dual-Targeted Proteins Degradation on Cell Surface. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308924. [PMID: 38425146 PMCID: PMC11077639 DOI: 10.1002/advs.202308924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/16/2024] [Indexed: 03/02/2024]
Abstract
Selective protein degradation platforms have opened novel avenues in therapeutic development and biological inquiry. Antibody-based lysosome-targeting chimeras (LYTACs) have emerged as a promising technology that extends the scope of targeted protein degradation to extracellular targets. Aptamers offer an advantageous alternative owing to their potential for modification and manipulation toward a multivalent state. In this study, a chemically engineered platform of multivalent aptamer-based LYTACs (AptLYTACs) is established for the targeted degradation of either single or dual protein targets. Leveraging the biotin-streptavidin system as a molecular scaffold, this investigation reveals that trivalently mono-targeted AptLYTACs demonstrate optimum efficiency in degrading membrane proteins. The development of this multivalent AptLYTACs platform provides a principle of concept for mono-/dual-targets degradation, expanding the possibilities of targeted protein degradation.
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Affiliation(s)
- Qiao Duan
- Institute of Molecular Medicine (IMM)Renji HospitalShanghai Jiao Tong University School of MedicineShanghai Jiao Tong UniversityShanghai200120China
| | - Hao‐Ran Jia
- Institute of Molecular Medicine (IMM)Renji HospitalShanghai Jiao Tong University School of MedicineShanghai Jiao Tong UniversityShanghai200120China
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Weichang Chen
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Chunhong Qin
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Kejing Zhang
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
- Department of General SurgeryXiangya HospitalCentral South UniversityChangshaHunan410006China
| | - Fei Jia
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Ting Fu
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Yong Wei
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Mengyang Fan
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Qin Wu
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM)Renji HospitalShanghai Jiao Tong University School of MedicineShanghai Jiao Tong UniversityShanghai200120China
- Hangzhou Institute of Medicine (HIM)Chinese Academy of SciencesHangzhouZhejiang310022China
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14
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Zhu Y, Ye X, Wu Y, Shen H, Cai Z, Xia F, Min W, Hou Y, Wang L, Wang X, Xiao Y, Yang P. Design, Synthesis, and Biological Evaluation of Novel EGFR PROTACs Targeting C797S Mutation. J Med Chem 2024. [PMID: 38676656 DOI: 10.1021/acs.jmedchem.4c00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
The epidermal growth factor receptor (EGFR) tertiary C797S mutation is an important cause of resistance to Osimertinib, which seriously hinders the clinical application of Osimertinib. Developing proteolysis-targeting chimeras (PROTACs) targeting EGFR mutants can offer a promising strategy to overcome drug resistance. In this study, some novel PROTACs targeting C797S mutation were designed and synthesized based on a new EGFR inhibitor and displayed a potent degradation effect in H1975-TM cells harboring EGFRL858R/T790M/C797S. The representative compound C6 exhibited a DC50 of 10.2 nM against EGFRL858R/T790M/C797S and an IC50 of 10.3 nM against H1975-TM. Furthermore, C6 also showed potent degradation activity against various main EGFR mutants, including EGFRDel19/T790M/C797S. Mechanistic studies revealed that the protein degradation was achieved through the ubiquitin-proteasome system. Finally, C6 inhibited tumor growth in the H1975-TM xenograft tumor model effectively and safely. This study identifies a novel and potent EGFR PROTAC to overcome Osimertinib resistance mediated by C797S mutation.
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Affiliation(s)
- Yasheng Zhu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiuquan Ye
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yuxing Wu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Hao Shen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Zeyu Cai
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Fei Xia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Hou
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Liping Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiao Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
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15
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Colarusso E, Chini MG, Bifulco G, Lauro G, Giordano A. Identification and Development of BRD9 Chemical Probes. Pharmaceuticals (Basel) 2024; 17:392. [PMID: 38543178 PMCID: PMC10976250 DOI: 10.3390/ph17030392] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 11/12/2024] Open
Abstract
The development of BRD9 inhibitors involves the design and synthesis of molecules that can specifically bind the BRD9 protein, interfering with the function of the chromatin-remodeling complex ncBAF, with the main advantage of modulating gene expression and controlling cellular processes. Here, we summarize the work conducted over the past 10 years to find new BRD9 binders, with an emphasis on their structure-activity relationships, efficacies, and selectivities in preliminary studies. BRD9 is expressed in a variety of cancer forms, hence, its inhibition holds particular significance in cancer research. However, it is crucial to note that the expanding research in the field, particularly in the development of new degraders, may uncover new therapeutic potentials.
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Affiliation(s)
- Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (E.C.); (G.B.); (G.L.)
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Isernia, Italy;
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (E.C.); (G.B.); (G.L.)
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (E.C.); (G.B.); (G.L.)
| | - Assunta Giordano
- Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale Delle Ricerche (CNR), Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
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16
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Liu Y, Liang J, Zhu R, Yang Y, Wang Y, Wei W, Li H, Chen L. Application of PROTACs in Target Identification and Target Validation. ACTA MATERIA MEDICA 2024; 3:72-87. [PMID: 39373008 PMCID: PMC11452161 DOI: 10.15212/amm-2024-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
PROTAC, as a novel therapeutic drug model, has received widespread attention from the academic and pharmaceutical industries. At the same time, PROTAC technology has led many researchers to focus on developing chemical biology tool properties due to its unique operating mechanism and protein dynamic regulatory properties. In recent years, the rapid development of PROTAC technology has gradually made it an essential tool for target identification and target validation. To further promote the application of PROTAC tools in drug discovery and basic medical sciences research, this review distinguished between target identification and target validation concepts. It summarized the research progress of PROTAC technology in these aspects.
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Affiliation(s)
- Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jing Liang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Rui Zhu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yueying Yang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yali Wang
- Fujian Key Laboratory of Chinese Materia Medica, Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
- Fujian Key Laboratory of Chinese Materia Medica, Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
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17
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Pasieka A, Diamanti E, Uliassi E, Laura Bolognesi M. Click Chemistry and Targeted Degradation: A Winning Combination for Medicinal Chemists? ChemMedChem 2023; 18:e202300422. [PMID: 37706617 DOI: 10.1002/cmdc.202300422] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/01/2023] [Indexed: 09/15/2023]
Abstract
Click chemistry is universally recognized as a powerful strategy for the fast and precise assembly of diverse building blocks. Targeted Protein Degradation (TPD) is a new therapeutic modality based on heterobifunctional small-molecule degraders that provides new opportunities to medicinal chemists dealing with undruggable targets and incurable diseases. Here, we highlight how very recently the TPD field and that of click chemistry have merged, opening up the possibility for fine-tuning the properties of a degrader, chemically assembled through a "click" synthesis. By reviewing concrete examples, we want to provide the reader with the insight that the application of click and bioorthogonal chemistry in the TDP field may be a winning combination.
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Affiliation(s)
- Anna Pasieka
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Eleonora Diamanti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126, Bologna, 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
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18
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Sobhia ME, Kumar H, Kumari S. Bifunctional robots inducing targeted protein degradation. Eur J Med Chem 2023; 255:115384. [PMID: 37119667 DOI: 10.1016/j.ejmech.2023.115384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/01/2023]
Abstract
The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (POI) and E3-ligase, which induce the ubiquitination of POI. These molecules are based on event-driven pharmacology and are applicable in different conditions such as oncology, antiviral, neurodegenerative disease, acne etc., offering tremendous scope to researchers. In this review, primarily, we attempted to compile the recent works available in the literature on PROTACs for various targeted proteins. We summarized the design and development strategies with a focus on molecular information of protein residues and linker design. Rationalization of the ternary complex formation using Artificial Intelligence including machine & deep learning models and traditionally followed computational tools are also included in this study. Moreover, details describing the optimization of PROTACs chemistry and pharmacokinetic properties are added. Advanced PROTAC designs and targeting complex proteins, is summed up to cover the wide spectrum.
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Affiliation(s)
- M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India.
| | - Harish Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India
| | - Sonia Kumari
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector - 67, S. A. S. Nagar, Mohali, Punjab, 160062, India
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19
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Luo G, Wang B, Hou Q, Wu X. Development of Son of Sevenless Homologue 1 (SOS1) Modulators To Treat Cancers by Regulating RAS Signaling. J Med Chem 2023; 66:4324-4341. [PMID: 36987571 DOI: 10.1021/acs.jmedchem.2c01729] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Son of sevenless homologue 1 (SOS1) protein is universally expressed in cells and plays an important role in the RAS signaling pathway. Specifically, this protein interacts with RAS in response to upstream stimuli to promote guanine nucleotide exchange in RAS and activates the downstream signaling pathways. Thus, targeting SOS1 is a new approach for treating RAS-driven cancers. In this Perspective, we briefly summarize the structural and functional aspects of SOS1 and focus on recent advances in the discovery of activators, inhibitors, and PROTACs that target SOS1. This review aims to provide a timely and updated overview on the strategies for targeting SOS1 in cancer therapy.
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Affiliation(s)
- Guangmei Luo
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Bingrui Wang
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Qiangqiang Hou
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy and Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
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20
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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: 17] [Impact Index Per Article: 8.5] [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
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21
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Targeting Breast Cancer: An Overlook on Current Strategies. Int J Mol Sci 2023; 24:ijms24043643. [PMID: 36835056 PMCID: PMC9959993 DOI: 10.3390/ijms24043643] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Breast cancer (BC) is one of the most widely diagnosed cancers and a leading cause of cancer death among women worldwide. Globally, BC is the second most frequent cancer and first most frequent gynecological one, affecting women with a relatively low case-mortality rate. Surgery, radiotherapy, and chemotherapy are the main treatments for BC, even though the latter are often not aways successful because of the common side effects and the damage caused to healthy tissues and organs. Aggressive and metastatic BCs are difficult to treat, thus new studies are needed in order to find new therapies and strategies for managing these diseases. In this review, we intend to give an overview of studies in this field, presenting the data from the literature concerning the classification of BCs and the drugs used in therapy for the treatment of BCs, along with drugs in clinical studies.
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22
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Salama AKAA, Trkulja MV, Casanova E, Uras IZ. Targeted Protein Degradation: Clinical Advances in the Field of Oncology. Int J Mol Sci 2022; 23:15440. [PMID: 36499765 PMCID: PMC9741350 DOI: 10.3390/ijms232315440] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The field of targeted protein degradation (TPD) is a rapidly developing therapeutic modality with the promise to tame disease-relevant proteins in ways that are difficult or impossible to tackle with other strategies. While we move into the third decade of TPD, multiple degrader drugs have entered the stage of the clinic and many more are expected to follow. In this review, we provide an update on the most recent advances in the field of targeted degradation with insights into possible clinical implications for cancer prevention and treatment.
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Affiliation(s)
| | | | | | - Iris Z. Uras
- Department of Pharmacology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria
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23
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Kargbo RB. Potent PROTACs Targeting EGFR Mutants in Drug Discovery. ACS Med Chem Lett 2022; 13:1835-1836. [DOI: 10.1021/acsmedchemlett.2c00459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Indexed: 11/11/2022] Open
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24
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Bhela I, Ranza A, Balestrero FC, Serafini M, Aprile S, Di Martino RMC, Condorelli F, Pirali T. A Versatile and Sustainable Multicomponent Platform for the Synthesis of Protein Degraders: Proof-of-Concept Application to BRD4-Degrading PROTACs. J Med Chem 2022; 65:15282-15299. [PMID: 36323630 PMCID: PMC9706574 DOI: 10.1021/acs.jmedchem.2c01218] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Indexed: 11/06/2022]
Abstract
The use of small molecules to induce targeted protein degradation is increasingly growing in the drug discovery landscape, and protein degraders have progressed rapidly through the pipelines. Despite the advances made so far, their synthesis still represents a significant burden and new approaches are highly demanded. Herein we report an unprecedented platform that leverages the modular nature of both multicomponent reactions and degraders to enable the preparation of highly decorated PROTACs. As a proof of principle, our platform has been applied to the preparation of potential BRD4-degrading PROTACs, resulting in the discovery of a set of degraders endowed with high degradation efficiency. Compared to the existing methods, our approach offers a versatile and cost-effective means to access libraries of protein degraders and increase the chance of identifying successful candidates.
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Affiliation(s)
- Irene
Preet Bhela
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Alice Ranza
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Federica Carolina Balestrero
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | | | - Silvio Aprile
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Rita Maria Concetta Di Martino
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Fabrizio Condorelli
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Tracey Pirali
- Department of Pharmaceutical
Sciences, Università degli Studi
del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
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25
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Nengroo MA, Khan MA, Verma A, Datta D. Demystifying the CXCR4 conundrum in cancer biology: Beyond the surface signaling paradigm. Biochim Biophys Acta Rev Cancer 2022; 1877:188790. [PMID: 36058380 DOI: 10.1016/j.bbcan.2022.188790] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
The oncogenic chemokine duo CXCR4-CXCL12/SDF-1 (C-X-C Receptor 4-C-X-C Ligand 12/ Stromal-derived factor 1) has been the topic of intense scientific disquisitions since Muller et al., in her ground-breaking research, described this axis as a critical determinant of organ-specific metastasis in breast cancer. Elevated CXCR4 levels correlate with distant metastases, poor prognosis, and unfavourable outcomes in most solid tumors. Therapeutic impediment of the axis in clinics with Food and Drug Administration (FDA) approved inhibitors like AMD3100 or Plerixafor yield dubious results, contrary to pre-clinical developments. Clinical trials entailing inhibition of CXCR7 (C-X-C Receptor 7), another convicted chemokine receptor that exhibits affinity for CXCL12, reveal outcomes analogous to that of CXCR4-CXCL12 axis blockade. Of note, the cellular CXCR4 knockout phenotype varies largely from that of inhibitor treatments. These shaky findings pique great curiosity to delve further into the realm of this infamous chemokine receptor to provide a probable explanation. A multitude of recent reports suggests the presence of an increased intracellular CXCR4 pool in various cancers, both cytoplasmic and nuclear. This intracellular CXCR4 protein reserve seems active as it correlates with vital tumor attributes, viz. prognosis, aggressiveness, metastasis, and disease-free survival. Diminishing this entire intracellular CXCR4 load apart from the surface signals looks encouraging from a therapeutic point of view. Transcending beyond the classically accepted concept of ligand-mediated surface signaling, this review sheds new light on plausible associations of intracellularly compartmentalised CXCR4 with various aspects of tumorigenesis. Besides, this review also puts forward a comprehensive account of CXCR4 regulation in different cancers.
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Affiliation(s)
- Mushtaq Ahmad Nengroo
- Division of Cancer Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow-226031, India
| | - Muqtada Ali Khan
- Division of Cancer Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow-226031, India
| | - Ayushi Verma
- Division of Cancer Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow-226031, India
| | - Dipak Datta
- Division of Cancer Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow-226031, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002, India.
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