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

Cristina Cantarutti; M. Cristina Vargas; Cedrix J. Dongmo Foumthuim; Mireille Dumoulin; Sara La Manna; Daniela Marasco; Carlo Santambrogio; Rita Grandori; Giacinto Scoles; Miguel A. Soler; Alessandra Corazza; Sara Fortuna

doi:10.1039/D1CP02536H

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

Cristina Cantarutti,

*^a M. Cristina Vargas,

^b Cedrix J. Dongmo Foumthuim,

^ac Mireille Dumoulin,^d Sara La Manna,^e Daniela Marasco,^e Carlo Santambrogio,^f Rita Grandori,^f Giacinto Scoles,^a Miguel A. Soler,

^ag Alessandra Corazza^a and Sara Fortuna

*^agh

Author affiliations

* Corresponding authors

^a Department of Medicine, University of Udine, Piazzale M. Kolbe 4, 33100 – Udine, Italy
E-mail: cristina.cantarutti@uniud.it, s.fortuna@units.it

^b Departamento de Física Aplicada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Unidad Mérida, Apartado Postal 73 “Cordemex”, Mérida, Mexico

^c Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Campus Scientifico – Via Torino 155, 30172 Mestre, Italy

^d Centre for Protein Engineering, InBios, Department of Life Sciences, University of Liege, Liege, Belgium

^e Department of Pharmacy – University of Naples “Federico II”, Naples, Italy

^f Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy

^g Italian Institute of Technology (IIT), Via Melen – 83, B Block, 16152 – Genova, Italy

^h Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy

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.

Physical Chemistry Chemical Physics

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

Abstract

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

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