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Ma B, Liu D, Wang Z, Zhang D, Jian Y, Zhang K, Zhou T, Gao Y, Fan Y, Ma J, Gao Y, Chen Y, Chen S, Liu J, Li X, Li L. A Top-Down Design Approach for Generating a Peptide PROTAC Drug Targeting Androgen Receptor for Androgenetic Alopecia Therapy. J Med Chem 2024. [PMID: 38836467 DOI: 10.1021/acs.jmedchem.4c00828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
While large-scale artificial intelligence (AI) models for protein structure prediction and design are advancing rapidly, the translation of deep learning models for practical macromolecular drug development remains limited. This investigation aims to bridge this gap by combining cutting-edge methodologies to create a novel peptide-based PROTAC drug development paradigm. Using ProteinMPNN and RFdiffusion, we identified binding peptides for androgen receptor (AR) and Von Hippel-Lindau (VHL), followed by computational modeling with Alphafold2-multimer and ZDOCK to predict spatial interrelationships. Experimental validation confirmed the designed peptide's binding ability to AR and VHL. Transdermal microneedle patching technology was seamlessly integrated for the peptide PROTAC drug delivery in androgenic alopecia treatment. In summary, our approach provides a generic method for generating peptide PROTACs and offers a practical application for designing potential therapeutic drugs for androgenetic alopecia. This showcases the potential of interdisciplinary approaches in advancing drug development and personalized medicine.
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Affiliation(s)
- Bohan Ma
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Donghua Liu
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhe Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Dize Zhang
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yanlin Jian
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Kun Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Tianyang Zhou
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yibo Gao
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yizeng Fan
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jian Ma
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yang Gao
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yule Chen
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Si Chen
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Jing Liu
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiang Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Lei Li
- Department of Urology, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710049, China
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Danishuddin, Jamal MS, Song KS, Lee KW, Kim JJ, Park YM. Revolutionizing Drug Targeting Strategies: Integrating Artificial Intelligence and Structure-Based Methods in PROTAC Development. Pharmaceuticals (Basel) 2023; 16:1649. [PMID: 38139776 PMCID: PMC10747325 DOI: 10.3390/ph16121649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
PROteolysis TArgeting Chimera (PROTAC) is an emerging technology in chemical biology and drug discovery. This technique facilitates the complete removal of the target proteins that are "undruggable" or challenging to target through chemical molecules via the Ubiquitin-Proteasome System (UPS). PROTACs have been widely explored and outperformed not only in cancer but also in other diseases. During the past few decades, several academic institutes and pharma companies have poured more efforts into PROTAC-related technologies, setting the stage for several major degrader trial readouts in clinical phases. Despite their promising results, the formation of robust ternary orientation, off-target activity, poor permeability, and binding affinity are some of the limitations that hinder their development. Recent advancements in computational technologies have facilitated progress in the development of PROTACs. Researchers have been able to utilize these technologies to explore a wider range of E3 ligases and optimize linkers, thereby gaining a better understanding of the effectiveness and safety of PROTACs in clinical settings. In this review, we briefly explore the computational strategies reported to date for the formation of PROTAC components and discuss the key challenges and opportunities for further research in this area.
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Affiliation(s)
- Danishuddin
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | | | - Kyoung-Seob Song
- Department of Medical Science, Kosin University College of Medicine, 194 Wachi-ro, Yeongdo-gu, Busan 49104, Republic of Korea;
| | - Keun-Woo Lee
- Division of Life Science, Department of Bio & Medical Big-Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
- Angel i-Drug Design (AiDD), 33-3 Jinyangho-ro 44, Jinju 52650, Republic of Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Yeong-Min Park
- Department of Integrative Biological Sciences and Industry, Sejong University, 209, Neugdong-ro, Gwangjin-gu, Seoul 05006, Republic of Korea
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