Modeling of both shared and distinct interactions between MIF and its homologue D-DT with their common receptor CD74

Abstract

D-dopachrome tautomerase (D-DT) shares amino acid sequence similarity, structural architecture and biological activity with the cytokine MIF. Recent studies show that the two protein homologues also bind to the same cell surface receptor, CD74, to activate the ERK1/2 pathway that ultimately leads to pro-inflammatory and pro-survival gene expression. We recently showed that RTL1000 and DRa1-MOG-35-55, two biological drugs with potent anti-inflammatory properties that treat experimental autoimmune encephalomyelitis (EAE) in mice, bind to the cell surface receptor CD74 with high affinity and compete with MIF for binding to the same regions of CD74. Computational modeling of MIF and RTL1000 binding interactions with CD74 predicted the presence of three CD74 binding regions for each MIF homotrimer. Through a similar approach we have now expanded our work to study the D-DT (MIF2) interaction with CD74 that is mainly defined by three elements scattered throughout the disordered regions of the interacting molecules. The model predicted: a) a hydrophobic cradle between CD74 and D-DT consisting of N-terminal tyrosine residues of three CD74 monomers arranged in a planar alignment interacts with aromatic amino acid residues located in the disordered D-DT C-terminus; b) a triad consisting of the E103 residue on one D-DT monomer in close contact with R179 and S181 on one chain of the CD74 trimer forms an intermolecular salt bridge; and c) amino acid residues on the C-terminus random coil of CD74 chain C form a long interacting area of ~500Å2 with a disordered region of D-DT chain B. These three binding elements were also present in MIF/CD74 binding interactions, with involvement of identical or highly similar amino acid residues in each MIF homotrimer that partner with the exact same residues in CD74. Topologically, however, the location of the three CD74 binding regions of the D-DT homotrimer differs substantially from that of the three MIF binding regions. This key difference in orientation appears to derive from a sequence insertion in D-DT that topologically limits binding to only one CD74 molecule per D-DT homotrimer, in contrast to predicted binding of up to three CD74 molecules per MIF homotrimer. These results have implications for the manner in which D-DT and MIF compete with each other for binding to the CD74 receptor and for the relative potency of DRa1-MOG-35-55 and RTL1000 for competitive inhibition of D-DT and MIF binding and activation through CD74.

MIF family cytokines in cardiovascular diseases and prospects for precision-based therapeutics

“…To date only an NMR structure of a truncated CD74 ectodomain has been reported [126] and there is evidence that the CD74 intramembrane domain provides crucial three-dimensional stabilization for the protein. Computational modeling studies support the possibility of a dodecamer involving either MIF:CD74 or MIF-2:CD74 (Figure 5E) [114, 127] and mutational data support aspects of this working model [127, 128]. Strong interest in MIF-pathway based interventions is further prompted by the possibility that such agents could be applied in a pharmacogenomic approach to modulate MIF signaling.…”

A selective small-molecule inhibitor of macrophage migration inhibitory factor-2 (MIF-2), a MIF cytokine superfamily member, inhibits MIF-2 biological activity

“…MIF-1 interacts with disordered residues at the N-and C-terminal end of the CD74 ectodomain through contacts close to the MIF-1 C terminus. Modeling studies further suggest that the MIF-1 and MIF-2 homologs may utilize the same amino acid residues to bind to CD74 (53). The binding of 4-CPPC to MIF-2 and ensuing conformational change in the MIF-2 C-terminal region reduces MIF-2/CD74 interaction and presumably abrogates productive signal transduction.…”

“…Structural differences between MIF-1 and MIF-2 have been suggested to result in distinct modes of receptor engagement because of a short amino acid sequence insertion in MIF-2, leading to dissimilarity in stoichiometry (53,54). Although one MIF-2 homotrimer may be limited to binding only one CD74 molecule per trimer, the MIF-1 homotrimers may bind three separate CD74 molecules (54).…”

Structural Plasticity in the C-Terminal Region of Macrophage Migration Inhibitory Factor-2 Is Associated with an Induced Fit Mechanism for a Selective Inhibitor

“…4 Experimental three-dimensional structures of MIF-1 and MIF-2 with their receptor, CD74, have yet to be determined, though molecular models are available for both complexes. 11,12 Chemical modifications, site-directed mutagenesis, and recent structural modeling studies indicate that CD74 activation is dependent on residues at the interface between two subunits, outside the catalytic cavity of the MIF proteins. 9,11–13 Recent mechanistic insights into the MIF-1-induced activation of CD74 showed that the activation process is dynamically controlled by an allosteric site that is found on one side of the solvent channel.…”