Rational Design of De Novo CCL2 Binding Peptides

Abstract

Chronic levels of inflammation lead to autoimmune diseases such as rheumatoid arthritis and atherosclerosis. A key molecular mediator responsible for the progression of these diseases is Chemokine C–C motif ligand 2 (CCL2), a homodimerized cytokine that dissociates into monomeric form and binds to the CCR2 receptor. CCL2, also known as monocyte chemoattractant protein‐1 (MCP‐1), attracts monocytes to migrate to areas of injury and mature into macrophages, leading to positive feedback inflammation with further release of proinflammatory molecules such as IL‐1β and TNF‐α. Sequestering CCL2 to prevent its binding to CCR2 may prevent this inflammatory activity. Prior work adapted an α‐helical CCL2‐binding peptide (WKNFQTI) from murine CCR2 through extracellular loop analysis. Here, higher‐affinity peptide binders are computationally designed through homology modeling and energy calculations, yielding an 11‐amino acid peptide with high binding affinity. In addition, Rosetta mutations improves binding affinity in silico with blockage of the CCL2 dimerization site. Future work in analyzing binding kinetics and in vivo inflammation abrogation will confirm the accuracy of computational modeling techniques in de novo rational design of CCL2 cytokine binders.

Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives

“…Aguas et al, subjected the binding site peptide sequence obtained from murine CCR2 to a series of homology models, energy calculations and Rosetta mutations to block chemokine C–C motif ligand 2 (CCL2) binding to the CCR2 receptor and proposed an 11 aa-long CCL2 blocking peptide (Aguas et al 2023 ). Mimics of the kinase-inhibitory region of Suppressors of Cytokine Signaling 1 (KIR-SOCS1) have been proposed for many inflammation-related diseases, and the peptidomimetic PS5 has been reported to downregulate the expression of NADPH oxidase (NOX1 and NOX4) and proinflammatory genes, and to reduce plaque size, lipid content and monocyte/macrophage accumulation in vivo (Manna et al 2020 , 2021a , b ).…”

Self-Assembling Peptides with Insulin-Like Growth Factor Mimicry

“…The hydrogen bonds were collected and summed for each frame for each residue using the CPPTRAJ H-bond command as described previously. 47 Non-H-bond intermolecular contacts were defined as two non-H atoms, one on each molecule, within 3 Å of each other and were collected per frame using the CPPTRAJ contact command. The Gibbs free energy of the model was estimated by using the sum of van der Waals and electrostatic interactions between all molecules within the simulation box.…”

“…Hydrogen bonds were defined as interactions between an H atom on either the ligand or receptor and an N or an O atom on the opposite molecule within 3 Å of each other. The hydrogen bonds were collected and summed for each frame for each residue using the CPPTRAJ H-bond command as described previously . Non-H-bond intermolecular contacts were defined as two non-H atoms, one on each molecule, within 3 Å of each other and were collected per frame using the CPPTRAJ contact command.…”

“…The systems were energy-minimized and equilibrated as described previously. 47 Production MD simulations were performed using an NPT ensemble with the temperature set at 310 K and pressure set at 1 atm.…”

“…The simulation box was solvated with TIP3P water and ionized with sodium and chloride ions to achieve a neutral pH. The systems were energy-minimized and equilibrated as described previously . Production MD simulations were performed using an NPT ensemble with the temperature set at 310 K and pressure set at 1 atm.…”