Homology analysis between the β chains of C3 molecules from H. sapiens and D. rerio. The FASTA sequences CO3_HUMAN and Q3MU74_DANRE were obtained from the UniProt database (http://www.uniprot.org), and their similarity and identity were evaluated on the Espript platform (http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi). Similar amino acid sequences in the two species are shown in red, and the similarity of the secondary structures is shown by the symbols β, α and η.

Comparative analysis on the C3-molecule β chains from D. rerio and H. sapiens. (a,b) Representation of C3 proteoforms (residues 1-645) from D. rerio and H. sapiens showing similar peptide sequences between species, as identified in blue; (c) structural and physicochemical characteristics of the C3 β-chain MG4 and MG5 domains in three-dimensional form showing the properties of amino acid residues in terms of hydrophobicity and positive and negative charges; (d) graphs showing the distribution of these amino acids according to area in Å; the networks are numbered and correlated with the color of the residuals; (e) distribution of hydrogen bond networks in the MG4 and MG5 domains; the circle drawn shows in detail the regions of the binding site based on the PDB model: 2QKI. In (f), the distribution of areas according to charges and hydrophobicity, on the surface between the ligand and the receptor at the binding site, is shown in detail, and in (g) the charge and hydrophobicity properties of Cp40 are exhibited. The numerical sequences refer to the colors that represent each network of hydrogen bonds.

Virtual screening for the detection of the best D. rerio Cp40–C3 interaction. (a) Docking shows the specific interaction (Model 8, in red) between Cp40 and the active site, as well as between the MG4 and MG5 domains of the D. rerio C3 β chain. Other interactions/models outside the circle are unspecific links; (b) H. sapiens C3 β chain docking showing two model-specific interactions (7 and 10) and other non-specific bindings; (c) shows the top ten interactions based on cavitation and blind docking; (*) represents H. sapiens values and (#) shows model 8#, selected according to position associated with the Cp40 activity site and the compstatin 2QKI crystallographic model. (c.1) Interaction of Cp40 with the main C3 binding amino acid residues in the orthosteric binding pocket between the MG4 and MG5 domains of Model 8#. (d) Docking based on the amino acid sequence of Model 8 (d.1) shows three interactions: model 0 (blue), based on prediction according to template-based blind docking; compstatin linked to C3 of H. sapiens (red), based on model 2QKI; and model 2 (yellow), chosen from the positions and values shown in the (e). The chains overlap between H. sapiens (purple) and D. rerio (grey), and the MG4 and MG5 domains distinguish the two domains. The numeric sequences refer to the colors that represent each docking interaction model.

In silico analysis of the peptide–protein interaction between the peptide Cp40 and the C3 molecule of D. rerio and H. sapiens. (a,a.1) Structure of the C3/Cp40 complex of H. sapiens and the structural alignment of the β chain of the homologous molecule of D. rerio (purple); (I) comparison of the binding of Cp40 to the domains MG4 and MG5 of the β ring in H. sapiens (purple) and D. rerio (yellow); (b,c) docking of the protein–binder interaction between C3 and Cp40 in the two species; (b.1,c.1) spatial interaction of Cp40 at the binding site; (d) redocking, showing the flexibility of the peptide Cp40 at the C3 binding site of D. rerio; (d.1,d.2) the two main interactions with greatest binding force, obtained through the FlexPepDock platform; (d.3) graph of RMSD (x-axis) vs. score (y-axis) of the ten models created through simulations; (e,f) main interactions of amino acid residues from the pocket of the β chain and the Van der Waals binding force, with binder residues: (e) D. rerio and (f) H. sapiens. The PDB C3 file for D. rerio was built in the Swiss model, using the reference 5fo8 of H. sapiens, and the Hdock Serve platform for docking. Macroglobulin domain (MG); binding domain (LNK); cleavage site of the alpha chain (NT); anchor (hydrogen bridge binding to the MG7 domain).

Comparative structural alignment between D. rerio and H. sapiens C5aR1. The FASTA sequences C5AR1_HUMAN and C5AR1_DANRE were obtained from the UNIPROT database (http://www.uniprot.org), and their similarity and identity were analyzed on the Espript platform (http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi). Similar amino acid sequences in the two species are shown in red, and the similarity of the secondary structure is shown by the symbols β, α and η.

Comparative analysis of C5aR1 from D. rerio and H. sapiens. (a,b) C5aR1 proteoforms from D. rerio and H. sapiens showing similar peptide sequences identified in blue; (c) structural and physicochemical characteristics of C5aR1, showing charge and hydrophobicity; (c.1) arrows point to the C5aR1 cavitation and show the PMX205 receptor binding pockets and (d) the volume of the pockets; (e) structural and physicochemical characteristics of C5aR1 in three-dimensional form, showing the properties of amino acid residues in terms of hydrophobicity and positive and negative charges; the graphs (f) show the distribution of these amino acids according to the area in Å; (g) distribution of hydrogen bond networks. The numerical sequences refer to the colors that represent each network of hydrogen bonds.

Virtual screening for the detection of the best D. rerio PMX205–C5aR1 interaction. (a) Docking showing specific interactions inside the drawn circle and non-specific ones outside the circle; (b) anchoring of PMX205-C5aR1 from H. sapiens showing model 1# specific interaction and other non-specific binding; (c) shows the top ten transients with regard to cavitation and blind docking; (*) H. sapiens values and (#) Model 1 selected through the position associated with PMX205 activity site based on crystallographic model 6C1R; (d) docking based on the amino acid sequence of Model 1# (Figure (c)), showing eight specific interactions inside the circle and two outside the circle representing nonspecific simulations from D. rerio; (e) for H. sapiens, all interactions were specific; (f) shows the values used for choosing the best interaction. (*) H. sapiens values. The numeric sequences refer to the colors that represent each docking interaction model.

In silico analysis of the interaction of PMX205 with C5aR1 in D. rerio and H. sapiens. (a) 3D structure of PMX205 in the mol2 format of the ChemSpider database; (b) structural overlap of H. sapiens C5aR1 (grey) and homologous molecule of D. rerio (blue); (I) comparison of the PMX205–C5aR1 interaction between H. sapiens (purple) and D. rerio (pink); (c,c.1,d,d.1) docking of protein–binder interaction between C5aR1 and PMX205; (c.2,d.2) interaction of PMX205 with the binding site, in detail; (c.3,d.3) main amino acid residues of the receptors of H. sapiens (c.3) and D. rerio (d.3) and Van der Waals binding force with binder residues. The PDB C5aR1 file for D. rerio was built in the Swiss model, using the reference based on the crystallographic model 6C1R of H. sapiens, and the CB-Dock platform for docking.