Investigation of cyclic ligands inhibiting CD2-CD58 interactions using molecular dynamics and molecular docking approaches

Laurence Leherte, Axel Petit, Denis Jacquemin, Daniel Vercauteren, Adèle Laurent

Research output: Contribution to conferencePoster

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Abstract

The CD2-CD58 protein-protein interaction is known to favor the recognition of antigen presenting cells by T cells. Molecular Dynamics (MD) and molecular docking calculations are carried out to study the structural, energetics, and dynamical properties of three known cyclic CD58 ligands, named P6 [1-3], P7 [1,4], and RTD-c [3]. Each ligand, connected via turn inducers, mimics the C and F β-strands of protein CD2. The MD analyses focus on the location of the ligands on the surface of CD58 and on the direct and water-mediated hydrogen bonds (Hbonds) they form with that receptor. Ligand P6, with a sequence close to the experimental β-strands of CD2, presents characteristics that explain its higher experimental affinity, e.g., the lower mobility and flexibility at the CD58 surface, and the larger number and occurrence frequency of ligand-CD58 Hbonds. For the two other ligands, the structural modifications lead to changes in the binding pattern with CD58 and its dynamics. In parallel, a large set of molecular docking calculations, carried out with various search spaces and docking algorithms, are compared to provide a consensus view of the preferred ligand binding modes. The analysis of the ligand side chain locations yields results that are consistent with the CD2-CD58 crystal structure and suggest various binding modes of the experimentally identified hot spot of the ligands, i.e., Tyr86. P6 is shown to form a number of contacts that are also present in the experimental CD2-CD58 structure.
This work is supported by the Wallonie-Bruxelles International (WBI) and the Belgian National Foundation for Scientific Research (FNRS), by the French Ministry of Foreign and European Affairs, and by the Ministry of
Higher Education and Research, in the framework of the Hubert Curien partnerships (PHC Tournesol “DoIFAD” #40638PL).

References
1) Gokhale A, Weldeghiorghis ThK, Taneja V, Satyanarayanajois D (2011) Conformationally constrained peptides from CD2 to modulate protein-protein interactions between CD2 and CD58. J Med Chem 54:5307-5319
2) Gokhale A, Kanthala S, Latendresse J, Taneja V, Satyanarayana SD (2013) Immunosuppression by co-stimulatory molecules: Inhibition of CD2-CD48/CD58 interaction by peptides from CD2 to suppress progression of collagen-induced arthritis in mice. Chem Biol Drug Des 82:106-118
3) Sable R, Durek T, Taneja V, Craik DJ, Pallerla S, Gauthier T, Jois S (2016) Constrained cyclic peptides as immunomodulatory inhibitors of the CD2:CD58 protein-protein interaction. ACS Chem Biol 11:2366-2374
4) Gokhale AS, Sable R, Walker JD, McLaughlin L, Kousoulas KG, Satyanarayana SD (2015) Inhibition of cell adhesion and immune responses in the mouse model of collagen-induced arthritis with a peptidomimetic that blocks CD2-CD58
interface interactions. Biopolymers 104:733-742
Original languageEnglish
Publication statusPublished - 23 Nov 2018
EventAnnual One-Day Meeting on Medicinal Chemistry - MedChem2018 - UNamur, Namur, Belgium
Duration: 23 Nov 201823 Nov 2018

Meeting

MeetingAnnual One-Day Meeting on Medicinal Chemistry - MedChem2018
CountryBelgium
CityNamur
Period23/11/1823/11/18

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  • Projects

    DoIFAD: Design Of peptide Inhibitors Fighting Autoimmune Disease

    LEHERTE, L., Laurent, A. D., Vercauteren, D. & Jacquemin, D.

    1/01/1831/12/19

    Project: Research

    CÉCI – Consortium of high performance computing centers

    CHAMPAGNE, B., Lazzaroni, R., Geuzaine , C., Chatelain, P. & Knaepen, B.

    1/01/1831/12/19

    Project: Research

    Equipment

  • Activities

    • 4 Hosting a researcher
    • 1 Participation in conference

    Adèle D. Laurent

    Laurence Leherte (Host)

    18 Feb 201920 Feb 2019

    Activity: Hosting a visitor typesHosting a researcher

    Annual One-Day Meeting on Medicinal Chemistry - MedChem2018

    Laurence Leherte (Poster)

    23 Nov 2018

    Activity: Participating in or organising an event typesParticipation in conference

    Adèle D. Laurent

    Laurence Leherte (Host)

    17 Sep 201820 Sep 2018

    Activity: Hosting a visitor typesHosting a researcher

    Cite this

    Leherte, L., Petit, A., Jacquemin, D., Vercauteren, D., & Laurent, A. (2018). Investigation of cyclic ligands inhibiting CD2-CD58 interactions using molecular dynamics and molecular docking approaches. Poster session presented at Annual One-Day Meeting on Medicinal Chemistry - MedChem2018, Namur, Belgium.