Herein, we compared the ability of linear and cyclic peptides generated in silico to target different protein sites: internal pockets and solvent-exposed sites. We selected human lysozyme (HuL) as a model target protein combined with the computational evolution of linear and cyclic peptides. The sequence evolution of these peptides was based on the PARCE algorithm. The generated peptides were screened based on their aqueous solubility and HuL binding affinity. The latter was evaluated by means of scoring functions and atomistic molecular dynamics (MD) trajectories in water, which allowed prediction of the structural features of the protein-peptide complexes. The computational results demonstrated that cyclic peptides constitute the optimal choice for solvent exposed sites, while both linear and cyclic peptides are capable of targeting the HuL pocket effectively. The most promising binders found in silico were investigated experimentally by surface plasmon resonance (SPR), nuclear magnetic resonance (NMR), and electrospray ionization mass spectrometry (ESI-MS) techniques. All tested peptides displayed dissociation constants in the micromolar range, as assessed by SPR; however, both NMR and ESI-MS suggested multiple binding modes, at least for the pocket binding peptides. A detailed NMR analysis confirmed that both linear and cyclic pocket peptides correctly target the binding site they were designed for.

Cantarutti, C., Vargas, M., Dongmo Foumthuim, C., Dumoulin, M., La Manna, S., Marasco, D., et al. (2021). Insights on peptide topology in the computational design of protein ligands: The example of lysozyme binding peptides. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 23(40), 23158-23172 [10.1039/d1cp02536h].

Insights on peptide topology in the computational design of protein ligands: The example of lysozyme binding peptides

Santambrogio C.;Grandori R.;
2021

Abstract

Herein, we compared the ability of linear and cyclic peptides generated in silico to target different protein sites: internal pockets and solvent-exposed sites. We selected human lysozyme (HuL) as a model target protein combined with the computational evolution of linear and cyclic peptides. The sequence evolution of these peptides was based on the PARCE algorithm. The generated peptides were screened based on their aqueous solubility and HuL binding affinity. The latter was evaluated by means of scoring functions and atomistic molecular dynamics (MD) trajectories in water, which allowed prediction of the structural features of the protein-peptide complexes. The computational results demonstrated that cyclic peptides constitute the optimal choice for solvent exposed sites, while both linear and cyclic peptides are capable of targeting the HuL pocket effectively. The most promising binders found in silico were investigated experimentally by surface plasmon resonance (SPR), nuclear magnetic resonance (NMR), and electrospray ionization mass spectrometry (ESI-MS) techniques. All tested peptides displayed dissociation constants in the micromolar range, as assessed by SPR; however, both NMR and ESI-MS suggested multiple binding modes, at least for the pocket binding peptides. A detailed NMR analysis confirmed that both linear and cyclic pocket peptides correctly target the binding site they were designed for.
Articolo in rivista - Articolo scientifico
Algorithms; Amino Acid Sequence; Binding Sites; Muramidase; Nuclear Magnetic Resonance, Biomolecular; Peptides; Peptides, Cyclic; Protein Binding; Spectrometry, Mass, Electrospray Ionization; Surface Plasmon Resonance; Ligands; Molecular Dynamics Simulation;
English
23158
23172
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Cantarutti, C., Vargas, M., Dongmo Foumthuim, C., Dumoulin, M., La Manna, S., Marasco, D., et al. (2021). Insights on peptide topology in the computational design of protein ligands: The example of lysozyme binding peptides. PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 23(40), 23158-23172 [10.1039/d1cp02536h].
Cantarutti, C; Vargas, M; Dongmo Foumthuim, C; Dumoulin, M; La Manna, S; Marasco, D; Santambrogio, C; Grandori, R; Scoles, G; Soler, M; Corazza, A; Fortuna, S
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/367224
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