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Lin J, Wang S, Wen L, Ye H, Shang S, Li J, Shu J, Zhou P. Targeting peptide-mediated interactions in omics. Proteomics 2023; 23:e2200175. [PMID: 36461811 DOI: 10.1002/pmic.202200175] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Peptide-mediated interactions (PMIs) play a crucial role in cell signaling network, which are responsible for about half of cellular protein-protein associations in the human interactome and have recently been recognized as a new kind of promising druggable target for drug development and disease therapy. In this article, we give a systematic review regarding the proteome-wide discovery of PMIs and targeting druggable PMIs (dPMIs) with chemical drugs, self-inhibitory peptides (SIPs) and protein agents, particularly focusing on their implications and applications for therapeutic purpose in omics. We also introduce computational peptidology strategies used to model, analyze, and design PMI-targeted molecular entities and further extend the concepts of protein context, direct/indirect readout, and enthalpy/entropy effect involved in PMIs. Current issues and future perspective on this topic are discussed. There is still a long way to go before establishment of efficient therapeutic strategies to target PMIs on the omics scale.
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Affiliation(s)
- Jing Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Shaozhou Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Li Wen
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Haiyang Ye
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Shuyong Shang
- Institute of Ecological Environment Protection, Chengdu Normal University, Chengdu, China
| | - Juelin Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Jianping Shu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
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Zhang Y, Wang J, Li W, Guo Y. Rational design of stapled helical peptides as antidiabetic PPARγ antagonists to target coactivator site by decreasing unfavorable entropy penalty instead of increasing favorable enthalpy contribution. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:535-543. [PMID: 36057906 DOI: 10.1007/s00249-022-01616-x] [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: 04/05/2022] [Revised: 08/07/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-activated transcription factor belonging to the nuclear hormone receptor and has been exploited as a well-established druggable target for the treatment of diabetes mellitus (DM). Traditionally, small-molecule compounds have been developed to attack at the ligand site and Ser273 phosphorylation site of PPARγ. In this study, we derived helical peptide segments from the LXXLL motif region of coactivator proteins as antidiabetic PPARγ antagonists, which were expected to competitively disrupt the native interaction between PPARγ and its cognate coactivators by rebinding at PPARγ coactivator site. Structural analysis, dynamics simulation and energetics dissection revealed that these peptides cannot be well folded into active helical structure when splitting from the protein context of their parent coactivators and exhibit a large flexibility and intrinsic disorder in the free state, which would, therefore, incur a considerable entropy penalty upon rebinding to PPARγ. Hydrocarbon stapling strategy was employed to constrain these free coactivator peptides into ordered helical conformation, thus largely minimizing unfavorable entropy penalty but having only a moderate effect on favorable enthalpy contribution. The computational findings were further substantiated by fluorescence-based assays; the binding affinity of three potent SRC1, NCoA6 and p300 coactivator peptides to PPARγ was observed to be improved by 7.2-fold, 4.2-fold and 5.7-fold upon the stapling, which were also measured to have an efficient competitive potency with their unstapled counterparts for PPARγ coactivator site, with CC50 = 0.096, 0.12 and 0.18 μM, respectively.
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Affiliation(s)
- Yang Zhang
- Department of Endocrinology, Affiliated Hospital of Weifang Medical University, Weifang, 261041, China
| | - Jie Wang
- Department of Endocrinology, Affiliated Hospital of Weifang Medical University, Weifang, 261041, China
| | - Wenchao Li
- Department of Endocrinology, Affiliated Hospital of Weifang Medical University, Weifang, 261041, China
| | - Ying Guo
- Department of Endocrinology, Affiliated Hospital of Weifang Medical University, Weifang, 261041, China.
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Zhong H, He J, Yu J, Li X, Mei Y, Hao L, Wu X. Mig6 not only inhibits EGFR and HER2 but also targets HER3 and HER4 in a differential specificity: Implications for targeted esophageal cancer therapy. Biochimie 2021; 190:132-142. [PMID: 34293452 DOI: 10.1016/j.biochi.2021.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/15/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022]
Abstract
The human EGF receptor family plays pivotal roles in physiology and cancer, which contains four closely-related members: HER1/EGFR, HER2, HER3 and HER4. Previously, it was found that the mitogen-inducible gene 6 (Mig6) protein is a negative regulator of EGFR and HER2 by using its S1 segment to bind at the kinase dimerization interface. However, it is still unclear whether the S1 segment can also effectively target HER3 and HER4? Here, we performed a systematic investigation to address this issue. The segment can bind to all the four HER kinases with a varying affinity and moderate selectivity; breaking of the segment into shorter hotspot peptides would largely impair the affinity and selectivity, indicating that the full-length sequence is required for the effective binding of S1 to these kinases. The hs2 peptide, which corresponds to the middle hotspot region of S1 segment, can partially retain the affinity to HER kinases, can moderately compete with S1 segment at the dimerization interfaces, and can mimic the biological function of Mig6 protein to suppress HER4+ esophageal cancer at cellular level. In addition, we also analyzed the binding potency of S1 segment and hs2 peptide to the kinase domains of other five widely documented growth factor receptors (GFRs). It was showed that both the S1 and hs2 cannot effectively interact with these receptors. Overall, the Mig6 is suggested as a specific pan-HER inhibitor, which can target and suppress HER family members with a broad selectivity, but exhibits weak or no activity towards other GFRs.
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Affiliation(s)
- Hai Zhong
- Department of Thoracic Surgery, Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; Department of Cardiothoracic Surgery, Ningbo Yinzhou Second Hospital, Ningbo, 315040, China
| | - Jiajia He
- Department of Hematologic Oncology, Ningbo Yinzhou Second Hospital, Ningbo, 315040, China
| | - Jingjing Yu
- Department of Hematologic Oncology, Ningbo Yinzhou Second Hospital, Ningbo, 315040, China
| | - Xiang Li
- Department of Emergency, Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yuxian Mei
- Department of Urology, Wenling Hospital of Traditional Chinese Medicine, Wenling, 317500, China
| | - Long Hao
- Department of General Surgery, Ningbo Yinzhou Second Hospital, Ningbo, 315040, China
| | - Xu Wu
- Department of Thoracic Surgery, Huiqiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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Liu Q, Zhou J, Gao J, Ma W, Wang S, Xing L. Rational design of EGFR dimerization-disrupting peptides: A new strategy to combat drug resistance in targeted lung cancer therapy. Biochimie 2020; 176:128-137. [DOI: 10.1016/j.biochi.2020.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/13/2020] [Accepted: 07/18/2020] [Indexed: 12/24/2022]
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Xiao D, Fan Z, Jiaqi W, Liu H, Shen L, He B, Zhang M. Rational molecular targeting of the inter-subunit interaction between human cardiac troponin hcTnC and hcTnI using switch peptide-competitive biogenic medicines. Comput Biol Chem 2020; 87:107272. [PMID: 32438115 DOI: 10.1016/j.compbiolchem.2020.107272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 01/19/2023]
Abstract
The human cardiac troponin (hcTn) has been implicated in diverse cardiovascular diseases (CDs). The protein function is regulated by the inter-subunit interaction between the N-terminal domain of hcTnC and the C-terminal switch peptide of hcTnI; disruption of the interaction has been recognized as a potential therapeutic strategy for CDs. Here, we report use of biogenic medicines as small-molecule competitors to directly disrupt the protein-protein interaction by competitively targeting the core binding site (CBS) of hcTnC NTD domain. A multistep virtual screening protocol is performed against a biogenic compound library to identify competitor candidates and competition assay is employed to verify the screening results. Consequently, two compounds Collismycin and Compound e are identified as strong competitors (CC50 < 10 μM) with hcTnI for hcTnC CBS site, while other tested compounds are found to have moderate (CC50 = 10-100 μM), low (CC50 > 100 μM) or no (CC50 = N.D.) potency. The competitor ligands are anchored at the core groove of hcTnC CBS site through aromatic and hydrophobic interactions, while few peripheral hydrogen bonds are formed to further confer specificity for domain-compound recognition. These molecular-level findings would benefit from further in vitro and in vivo studies at cellular and animal levels, which can help to practice the ultimate therapeutic purpose.
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Affiliation(s)
- Danrui Xiao
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Zixun Fan
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Wu Jiaqi
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Hua Liu
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Linghong Shen
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Ben He
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Min Zhang
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China.
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Xu L, Chen Z, Shao K, Wang Y, Cui L, Guo N. Rational discovery of novel type-III FTF antagonists to competitively suppress TIF-2 coactivation in liver cancer. J Recept Signal Transduct Res 2019; 39:304-311. [PMID: 31755335 DOI: 10.1080/10799893.2019.1690513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Linlin Xu
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Zhongming Chen
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Keke Shao
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Yungang Wang
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Leilei Cui
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Naizhou Guo
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
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