A workflow for in silico design of hIL-10 and ebvIL-10 inhibitors using well-known miniprotein scaffolds

Abstract

The over-expression of immune-suppressors such as IL-10 is a crucial landmark in both tumor progression, and latent viral and parasite infection. IL-10 is a multifunctional protein. Besides its immune-cell suppressive function, it also promotes B-cell tumorigenesis of lymphomas and melanoma. Human pathogens like unicellular parasites and viruses that remain latent inside B cells promote the over-expression of hIL-10 upon infection, which inhibits cell-mediated immune surveillance, and at the same time mediates B cell proliferation. The B-cell specific oncogenic latent virus Epstein-Barr virus (EBV) encodes a viral homologue of hIL-10 (ebvIL-10), expressed during lytic viral proliferation. Once expressed, ebvIL-10 inhibits cell-mediated immune surveillance, assuring EBV re-infection. During long-term latency, EBV-infected B cells over-express hIL-10 to assure B-cell proliferation, occasionally inducing EBV-mediated lymphomas. The amino acid sequences of hIL-10 and ebvIL-10 are more than 80% identical and thus have a very similar tridimensional structure. Based on their published crystallographic structures bound to their human receptor IL10R1, we report a structure-based design of hIL-10 and ebvIL-10 inhibitors based on 3 loops from IL10R1 that establish specific hydrogen bonds with the two IL10s. We have grafted these loops onto a permissible loop in three well-known miniprotein scaffolds—the Conus snail toxin MVIIA, the plant-derived trypsin inhibitor EETI, and the human appetite modulator AgRP. Our computational workflow described in detail below was invigorated by the negative and positive controls implemented, and therefore paves the way for future in vitro and in vivo validation assays of the IL-10 inhibitors engineered.

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Acknowledgements

This work was supported by the Universidad Nacional Autonoma de Mexico (UNAM) through a DGTIC-UNAM-SC16-1-IG-46 grant, which allowed us to use the Miztli Supercomputer at UNAM, plus the Bilateral Cooperation Conacyt-Conicyt Mexico-Chile 205466, and Fordecyt 272894 grants awarded to SAA. Other support was given by the Centro de Investigación Científica y Educación Superior de Ensenada, Baja California (CICESE) through an internal grant awarded to GP. SD received a Consejo Nacional de Ciencia y Tecnología (CONACYT) graduate scholarship to pursue Master in Science studies, which derived in this publication.

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Correspondence to Sergio A. Aguila or Genaro Pimienta.

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Fig. S1
figure7

Simulated annealing schematic explanation. This supplementary figure is a schematic explanation of how the simulated annealing, followed by a Boltzmann distribution plot allowed us to chose the representative (energetically-most stable) mutated scaffold model (GIF 159 kb)

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Dueñas, S., Aguila, S.A. & Pimienta, G. A workflow for in silico design of hIL-10 and ebvIL-10 inhibitors using well-known miniprotein scaffolds. J Mol Model 23, 118 (2017). https://doi.org/10.1007/s00894-017-3276-1

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Keywords

  • IL-10 inhibition
  • Knottin
  • Loop grafting
  • Miniprotein scaffold
  • Oncovirus and cancer