Structural basis for the binding of the cancer targeting scorpion toxin, ClTx, to the vascular endothelia growth factor receptor neuropilin-1

Gagan Sharma; Carolyne B Braga; Kai-En Chen; Xinying Jia; Venkatraman Ramanujam; Brett M Collins; Roberto Rittner; Mehdi Mobli

doi:10.1016/j.crstbi.2021.07.003

Structural basis for the binding of the cancer targeting scorpion toxin, ClTx, to the vascular endothelia growth factor receptor neuropilin-1

Curr Res Struct Biol. 2021 Aug 2:3:179-186. doi: 10.1016/j.crstbi.2021.07.003. eCollection 2021.

Authors

Gagan Sharma¹, Carolyne B Braga^{1

2}, Kai-En Chen³, Xinying Jia¹, Venkatraman Ramanujam¹, Brett M Collins³, Roberto Rittner², Mehdi Mobli¹

Affiliations

¹ Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia.
² Chemistry Institute, University of Campinas, P.O. Box 6154, 13083-970, Campinas, SP, Brazil.
³ Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.

Abstract

Chlorotoxin (ClTx) is a 36-residue disulfide-rich peptide isolated from the venom of the scorpion Leiurus quinquestriatus. This peptide has been shown to selectively bind to brain tumours (gliomas), however, with conflicting reports regarding its direct cellular target. Recently, the vascular endothelial growth factor receptor, neuropilin-1 (NRP1) has emerged as a potential target of the peptide. Here, we sought to characterize the details of the binding of ClTx to the b1-domain of NRP1 (NRP1-b1) using solution state nuclear magnetic resonance (NMR) spectroscopy. The 3D structure of the isotope labelled peptide was solved using multidimensional heteronuclear NMR spectroscopy to produce a well-resolved structural ensemble. The structure points to three putative protein-protein interaction interfaces, two basic patches (R14/K15/K23 and R25/K27/R36) and a hydrophobic patch (F6/T7/T8/H10). The NRP1-b1 binding interface of ClTx was elucidated using ¹⁵N chemical shift mapping and included the R25/K27/R36 region of the peptide. The thermodynamics of binding was determined using isothermal titration calorimetry (ITC). In both NMR and ITC measurements, the binding was shown to be competitive with a known NRP1-b1 inhibitor. Finally, combining all of this data we generate a model of the ClTx:NRP1-b1 complex. The data shows that the peptide binds to the same region of NRP1 that is used by the SARS-CoV-2 virus for cell entry, however, via a non-canonical binding mode. Our results provide evidence for a non-standard NRP1 binding motif, while also providing a basis for further engineering of ClTx to generate peptides with improved NRP1 binding for future biomedical applications.

Keywords: Chlorotoxin; Disulfide-rich peptide; Heteronuclear NMR; ITC; NRP1.