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He Q, Xu S, Ma X, Ling T, Feng W, Lu X, Liu W, Chen Z. Coupled folding-upon-binding of human tumor suppressor MIG6 to lung cancer EGFR kinase domain and molecular trimming/stapling of MIG6-derived β-hairpins to target the coupling event. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:17-25. [PMID: 36547692 DOI: 10.1007/s00249-022-01624-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Human epidermal growth factor receptor (EGFR) is involved in strong association with malignant proliferation, which has been shown to play a central role in the development and progression of non-small cell lung cancer and other solid tumors. The tumor-suppressor protein MIG6 is a negative regulator of EGFR kinase activity by binding at the activation interface of asymmetric dimer of EGFR kinase domain to disrupt EGFR dimerization and then inactivate the kinase. The protein adopts two discrete fragments 1 and 2 to directly interact with EGFR. It is revealed that the MIG6 fragment 2 is intrinsically disordered in free unbound state, but would fold into a well-structured β-hairpin when binding to EGFR, thus characterized by a so-called coupled folding-upon-binding process, which can be regarded as a compromise between favorable direct readout and unfavorable indirect readout. Here, a 23-mer F2P peptide was derived from MIG6 fragment 2, trimmed into a 17-mer tF2P peptide that contains the binding hotspot region of the fragment 2, and then constrained with an ordered hairpin conformation in free unbound state by disulfide stapling, finally resulting in a rationally stapled/trimmed stF2P peptide that largely minimizes the unfavorable indirect readout effect upon its binding to EGFR kinase domain, with affinity improved considerably upon the trimming and stapling/trimming. These rationally designed β-hairpin peptides may be further exploited as potent anti-lung cancer agents to target the activation event of EGFR dimerization.
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Affiliation(s)
- Quan He
- Department of Respiratory and Critical Care Medicine, Zhenjiang Hospital of Integrated Traditional Chinese and Western Medicine, Zhenjiang, 212000, China
| | - Shuanglan Xu
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province, Kunming, 650021, China
| | - Xiaomei Ma
- Department of Respiratory and Critical Care Medicine, Zhenjiang Hospital of Integrated Traditional Chinese and Western Medicine, Zhenjiang, 212000, China
| | - Ting Ling
- Department of Respiratory and Critical Care Medicine, Zhenjiang Hospital of Integrated Traditional Chinese and Western Medicine, Zhenjiang, 212000, China
| | - Weiqi Feng
- Department of Respiratory and Critical Care Medicine, Zhenjiang Hospital of Integrated Traditional Chinese and Western Medicine, Zhenjiang, 212000, China
| | - Xuzhi Lu
- Department of Respiratory and Critical Care Medicine, Zhenjiang Hospital of Integrated Traditional Chinese and Western Medicine, Zhenjiang, 212000, China
| | - Weihua Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Zi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing, 210029, China.
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Qiao Z, Wang S. Directed Molecular Engineering of Mig6 Peptide Selectivity between Proto-oncogene ErbB Family Receptor Tyrosine Kinases. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0102-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Yu X, Zhang A, Sun G, Li X. Molecular selectivity design of mitogen-inducible gene-derived phosphopeptides between oncogenic HER kinases. J Mol Graph Model 2020; 99:107661. [PMID: 32574989 DOI: 10.1016/j.jmgm.2020.107661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/23/2020] [Accepted: 05/29/2020] [Indexed: 11/28/2022]
Abstract
Mitogen-inducible gene (MIG) is a natural negative regulator of the oncogenic HER kinase signaling by binding at the activation interface of kinase domain to disrupt the kinase dimerization. In this study, we systematically examine the binding structures, dynamics and energetics of MIG region 2 to four HER kinases based on their crystal or modeled complex structures, and identify an 8-mer phosphopeptide segment pYpY from the core strand sequence of MIG region 2 as the binding hotspot of MIG protein to HER kinases. We demonstrate that the small pYpY phosphopeptide can partially restore the binding affinity of full-length MIG protein, but exhibit a moderate selectivity over different HER kinases (S = 2.3-fold). In addition, the two phosphotyrosine residues pTyr394 and pTyr395 play an essential role in MIG-HER binding; dephosphorylation of them would fully eliminate the binding capability. A machine evolution algorithm is used to optimize the wild-type pYpY phosphopeptide, aiming to simultaneously improve affinity for these kinases and to maximize the affinity gap between different kinases. Consequently, a population is computationally evolved as selective phosphopeptide candidates; the dissociation constants of four representatives with HER kinases are systematically determined using binding affinity analysis, from which their selectivity is derived. The designed pYpYp3 phosphopeptide possesses a high selectivity over different HER kinases (S = 4.8-fold) and satisfactory affinity profile to these kinase (KD = 140-1000 μM). Structural analysis observes that the global binding modes of pYpYp3 to different kinases are roughly consistent, but its local conformation may vary considerably, thus conferring specificity to the phosphopeptide.
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Affiliation(s)
- Xiuli Yu
- Department of Radiotherapy, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Aiying Zhang
- Orthopaedic Trauma, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Guoyu Sun
- Intensive Care Unit, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Xuebo Li
- Department of Radiotherapy, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China.
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