Virtual Screening Against α-Cobratoxin

 Virtual Screening Against α-Cobratoxin

Authors: MALEERUK UTSINTONG, TODD T. TALLEY, PALMER W. TAYLOR, ARTHUR J. OLSON, and OPA VAJRAGUPTA. 

In this study, the authors use virtual screening to identify candidates that bind with α-Cobratoxin, a neurotoxin inhibitor of nAChBP. For the target, they utilize three receptor structures: two unbound structures (CTX1 and CTX2) and one bound structure extracted from 1YI5.

They also perform molecular docking with two NMR structures (1LXG and 1LXH) and 1YI5, resulting in three bound structures from the Protein Data Bank. The amino acid sequences and binding sites are similar among these structures, but their shapes differ. The binding poses of the two NMR structures (RMSD = 5.251 Å) vary more than those of AChR (RMSD = 2.665 Å). This difference is attributed to the distinct conditions of solution versus crystal environments. The bound AChR unit in the NMR structure is only a 15-mer peptide from the alpha-1 subunit of AChR (residues 181-198), whereas in the crystal structure of AChBP, five subunits are present, with Ctx bound to the alpha-7 subunit.

Since the crystal structure in 1YI5 provides more detail on the binding mode of Ctx, this structure will be used to further study virtual screening. Three crystal structures are referenced: two unbound (CTX1, CTX2) and one bound (1YI5). The unbound structures contain 71 ordered residues seen in electron density, while the bound structure has only 68 residues. These missing residues, located at the tip of the Cbtx loop III, do not contribute significantly to the interaction between Cbtx and the AChBP molecule, as also reported by Bourne et al., who state that residues 67-71 and loop III weakly contribute to Cbtx binding.

The study uses CTX1, CTX2, and 1YI5 as templates for virtual screening, with the bound region on chain C of 1YI5 validating the Cbtx template. Chain H of 1YI5 represents bound Cbtx and will be reconstructed using Swiss-PdbViewer.

All prepared Cbtx structures will be re-docked to chain C of AChBP, showing that Cbtx proteins can be used for virtual screening, as all prepared proteins bind to active sites. During virtual screening, the compounds will be clustered and ranked; each cluster will contain compounds with similar 3D structures. Out of 175 compounds with an energy cut-off of -8.72 kcal/mol, each was ranked according to binding energy. Lipinski’s rule of five is also considered during the virtual screening.

Following virtual screening, the study will use in vivo tests to investigate the binding capacity of these compounds. Among the 1,990 compounds from the NCI database, NSC121865 shows strong potential as a new treatment for snake bites. Additionally, three hits (NSC42258, NSC121865, NSC134754) show potential but require further modification to enhance pharmacological properties.