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Huang W, Zhou Y, Pan C, Zhang X, Zhao H, Shen L. Molecular modeling and rational design of disulfide-stapled self-inhibitory peptides to target IL-17A/IL-17RA interaction. J Mol Recognit 2023:e3045. [PMID: 37415317 DOI: 10.1002/jmr.3045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/31/2023] [Accepted: 06/20/2023] [Indexed: 07/08/2023]
Abstract
Interleukin-17A (IL-17A) is a pro-inflammatory cytokine implicated in diverse autoimmune and inflammatory disorders such as psoriasis and Kawasaki disease. Mature IL-17A is a homodimer that binds to the extracellular type-III fibronectin D1:D2-dual domain of its cognate IL-17 receptor A (IL-17RA). In this study, we systematically examined the structural basis, thermodynamics property, and dynamics behavior of IL-17RA/IL-17A interaction and computationally identified two continuous hotspot regions separately from different monomers of IL-17A homodimer that contribute significantly to the interaction, namely I-shaped and U-shaped segments, thus rendered as a peptide-mediated protein-protein interaction (PmPPI). Self-inhibitory peptides (SIPs) are derived from the two segments to disrupt IL-17RA/IL-17A interaction by competitively rebinding to the IL-17A-binding pocket on IL-17RA surface, which, however, only have a weak affinity and low specificity for IL-17RA due to lack of the context support of intact IL-17A protein, thus exhibiting a large flexibility and intrinsic disorder when splitting from the protein context and incurring a considerable entropy penalty when rebinding to IL-17RA. The U-shaped segment is further extended, mutated and stapled by a disulfide bridge across its two strands to obtain a number of double-stranded cyclic SIPs, which are partially ordered and conformationally similar to their native status at IL-17RA/IL-17A complex interface. Experimental fluorescence polarization assays substantiate that the stapling can moderately or considerably improve the binding affinity of U-shaped segment-derived peptides by 2-5-fold. In addition, computational structural modeling also reveals that the stapled peptides can bind in a similar mode with the native crystal conformation of U-shaped segment in IL-17RA pocket, where the disulfide bridge is out of the pocket for avoiding intervene of the peptide binding.
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Affiliation(s)
- Weihua Huang
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
| | - Yang Zhou
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
| | - Chunhua Pan
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
| | - Xin Zhang
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
| | - Huijun Zhao
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
| | - Lili Shen
- Department of Pediatrics, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, China
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Wang X, Hou D, Dai W, Gao W, Ju S, Cao H, Zhang L, Wang G, Guo Y, Chen S, Tian H, Li Z. Derivation of Self-inhibitory Helical Peptides to Target Rho-kinase Dimerization in Cerebrovascular Malformation: Structural Bioinformatics Analysis and Peptide Binding Assay. Mol Inform 2016; 35:262-7. [PMID: 27492240 DOI: 10.1002/minf.201501022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/25/2016] [Indexed: 11/08/2022]
Abstract
Rho-kinase dimerization is essential for its kinase activity and biological function; disruption of the dimerization has recently been established as a new and promising therapeutics strategy for cerebrovascular malformation (CM). Based on Rho-kinase dimer crystal structure we herein combined in silico analysis and in vitro assay to rationally derive self-inhibitory peptides from the dimerization interface. Three peptides namely Hlp1, Hlp2 and Hlp3 were successfully designed that have potential capability to rebind at the dimerization domain of Rho-kinase. Molecular dynamics (MD) simulations revealed that these peptides are helically structured when bound to Rho-kinase, but exhibit partially intrinsic disorder in unbound state. Binding free energy (BFE) analysis suggested that the peptides have a satisfactory energetic profile to interact with Rho-kinase. The computational findings were then substantiated by fluorescence anisotropy assays, conforming that the helical peptides can bind tightly to Rho-kinase with affinity KD at micromolar level. These designed peptides are considered as lead molecular entities that can be further modified and optimized to obtain more potent peptidomimetics as self-competitors to disrupt Rho-kinase dimerization in CM.
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Affiliation(s)
- Xuyang Wang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital, Shanghai, 200233, China
| | - Dianqi Hou
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, 200080, China
| | - Weiwei Dai
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Wenwei Gao
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital, Shanghai, 200233, China
| | - Shiming Ju
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital, Shanghai, 200233, China
| | - Heli Cao
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital, Shanghai, 200233, China
| | - Lin Zhang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital, Shanghai, 200233, China
| | - Gan Wang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital, Shanghai, 200233, China
| | - Yan Guo
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital, Shanghai, 200233, China
| | - Shiwen Chen
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital, Shanghai, 200233, China
| | - Hengli Tian
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital, Shanghai, 200233, China. ,
| | - Zhiqiang Li
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated 6th People's Hospital South Campus, Shanghai, 201400, China.
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