In silico design of glyco-D,L-peptide antiviral molecules

Abstract Background most licensed antiviral drugs are nucleoside analogs. A recent research focuses on blocking a virus from entering the cells in the viral cell adsorption/entry stage. In this entry mechanism the glycans present on the viral surface play a fundamental role. Homochiral L-peptides acting this fusion mechanism have shown some inhibition of viral infection. Peptides with regularly alternating enantiomeric sequence (L,D-peptides) can assume structures, which are not accessible to the corresponding homochiral molecules. Further, L,D-peptides are less sensitive to the enzymatic digestion. Aim in silico design a L,D-peptide with a high affinity for the viral surface glycans, and consequently able to interfere with its fusion mechanism. Methods a 3α,6α-Mannopentaose (3-6MP) molecule was used to simulate a viral surface glycan. Molecular Dynamics (MD) simulations of 3-6MP and D,L-peptide in water are performed using the force field AMBER12-GLYCAM06i. The binding constant was evaluated from trajectories. The D,L-peptide molecule was modified over the sequence, the length, the terminals and finally glycosylated to attain a very high binding constant value for 3-6MP. In addition, the specific interaction between T lymphocyte CD4 glycoprotein and HIV envelope gp120 glycoprotein was studied through MD simulations between a D,L-peptide, bounded to a typical CD4 glycan, and a highly conserved HIV gp120 glycan. Results in the case of interaction with 3-6MP molecule, the very effective molecule obtained was H-D-Trp-L-Pro-D-Asn-L-Pro-D-Trp-L-Pro-D-Asn-L-Pro-OH where the Asn residues in position 3 and 7 are glycosylated with alpha-D-Mannopyranosyl-(1->3)-[alpha-D-mannopyranosyl-(1->6)]-alpha-D-mannopyranosyl-(1->4)-N-acetyl-beta-D-glucopyranosyl-(1->4)-N-acetyl-beta-D-glucopyranosyl-1-OH. In the case of interaction with HIV envelope, the very effective molecule obtained, able to antagonize the CD4 glycoprotein, was H-D-Trp-L-Pro-D-Asn-L-Pro-D-Trp-L-Pro-D-Asn-L-Pro-OH where the Asn residue in position 3 is glycosylated with alpha-D-galactopyranosyl-(1->4)-N-acetyl-beta-D-glucopyranosyl-(1->2)-alpha-D-Mannopyranosyl-(1->3)-[alpha-D-galactopyranosyl-(1->4)-N-acetyl-beta-D-glucopyranosyl-(1->2)-alpha-D-Mannopyranosyl-(1->6)]-beta-D-mannopyranosyl-(1->4)-N-acetyl-beta-D-glucopyranosyl-(1->4)-N-acetyl-beta-D-glucopyranosyl-1-OH Conclusion these glycosylated D,L-peptide molecules are very promising representatives of a new class of antiviral agents.