Biomedical Chemistry: Research and Methods 2024, 7(3), e00235

Modified Knottins as Potential Inhibitors of HCV NS3 Protease

A.V. Talanova*, D.S. Shcherbinin, E.F. Kolesanova, A.V. Veselovsky

Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia; *e-mail: bionasty@mail.ru

Keywords: HCV NS3/4A protease; knottin; MCOTI-II; molecular dynamics; molecular modeling

DOI:10.18097/BMCRM00235

The whole version of this paper is available in Russian.

Knottins form a group of peptides containing approximately 30 amino acid residues. Their structures are stabilized by three disulfide bonds forming a characteristic ‘pseudo-knotted’ structure. Several modifications in knottin from Momordica cochinchinensis were made to convert it to inhibitor of human hepatitis C (HCV) NS3 protease. These modifications of the knottin template included deletion of several residues from the N-terminus, replacement of residues in- and outside the inhibitor loop and replacement of certain L-amino acids by their D-stereoisomers. Binding energy values for protein-knottin complexes were estimated by MM-GBSA methods. Two designed knottins showed high stability in knottin-protease HCV complexes and values of binding energy comparable with known peptide inhibitors from crystal structures.
Figure 1. (A) Structure of the knottin trypsin inhibitor from Momordica cochinchinensis (MCoTI-II) and (B) MCOTI-II (blue) and 4A1V (yellow) inhibitory loops overlay. The knottin residue names are underlined.

Figure 2. Root Mean Square Deviation of the modified knottins during molecular dynamics simulation of protein–knottin complexes: black (KIT-1), red (KIT-2), green (KIT-3), deep-blue (KIT-4) and turquoise (KIT-5) lines, yellow and brown - peptide NS3 inhibitors.

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Table 1. Sequences of designed knottins. Modifications in KITs in comparison to MCOTI-II are in Italic.

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Table 2. Free binding energy of modified knottins and peptide inhibitors with HCV NS3 protease.

FUNDING

The work was performed within the framework of the Program for Basic Research in the Russian Federation for a long-term period (2021-2030) (№ 122030100170-5).

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