Potential Self-Peptide Inhibitors of the SARS-CoV-2 Main Protease

Abstract

The SARS-CoV-2 main protease (M pro ) plays an essential role in viral replication, cleaving viral polyproteins into functional proteins. This makes M pro an important drug target. M pro consists of an N-terminal catalytic domain and a C-terminal α-helical domain (M pro C). Previous studies have shown that peptides derived from a given protein sequence (self-peptides) can affect the folding and, in turn, the function of that protein. Since the SARS-CoV-1 M pro C is known to stabilize its M pro and regulate its function, we hypothesized that SARS-CoV-2 M pro C-derived self-peptides may modulate the folding and the function of SARS-CoV-2 M pro . To test this, we studied the folding of M pro C in the presence of various selfpeptides using coarse-grained structure-based models and molecular dynamics simulations. In these simulations of M pro C and one selfpeptide, we found that two self-peptides, the α1-helix and the loop between α4 and α5 (loop4), could replace the equivalent native sequences in the M pro C structure. Replacement of either sequence in full-length M pro should, in principle, be able to perturb M pro function albeit through different mechanisms. Some general principles for the rational design of self-peptide inhibitors emerge: The simulations show that prefolded self-peptides are more likely to replace native sequences than those which do not possess structure. Additionally, the α1-helix self-peptide is kinetically stable and once inserted rarely exchanges with the native α1-helix, while the loop4 self-peptide is easily replaced by the native loop4, making it less useful for modulating function. In summary, a prefolded α1derived peptide should be able to inhibit SARS-CoV-2 M pro function.

A Perspective on Interdicting in Protein Misfolding for Therapeutic Drug Design: Modulating the Formation of Nonlocal Contacts in α-Synuclein as a Strategy against Parkinson’s Disease

“…A very important question in this context is whether the segments predicted by the SCM could function as FIPs without chemical modification or a minimal one, for example to ensure solubility. Self-peptides have been shown experimentally to affect the folding mechanism of several globular proteins. − Moreover, incubation with self-peptide p(250–257) predicted by the SCM to be involved in the formation of the dominant early contact of p53, has been shown to seriously disrupt its folding leading to its conversion into an amyloid-like isoform . Also, incubation with self-peptide 105–124 of RNAase A, containing the SCM predicted most stable primary contact segment 116–120, and also segment 106–110 included in the second-best primary contact 106–110, suffices to almost completely shut down the folding process .…”

“…Following these pioneering efforts, the field of protein folding-based drug design now constitutes an active area of research. , Within the field, considerable efforts have been devoted to investigate the possibility of developing therapeutic strategies against neuropathogenic misfolding, including successful experiments employing nonpeptidic small molecules . The specific approach of employing self-peptides (i.e., fragments of the native sequence) to study and modulate protein folding also has a long and fruitful history. − Within this context, we recently proposed the folding interdiction approach, in which specific target segments are predicted employing the Sequential Collapse Model (SCM), − relying on its predicted existence of a very few specific early contacts whose formation constitutes Nature’s shortcut to protein folding . The predicted target segments are called folding interdiction target regions (FITR) .…”