A computer screening approach to immunoglobulin superfamily structures and interactions: Discovery of small non-peptidic CD4 inhibitors as novel immunotherapeutics

Abstract

The interaction between CD4 and major histocompatibility complex (MHC) class II proteins is critical for the activation of CD4 ؉ T cells, which are involved in transplantation reactions and a number of autoimmune diseases. In this study we have identified a CD4 surface pocket as a functional epitope implicated in CD4-MHC class II interaction and T-cell activation. A computer-based strategy has been used to screen Ϸ150,000 non-peptidic organic compounds in a molecular data base and to identify a group of compounds as ligands of the proposed CD4 surface pocket. These small organic compounds have been shown to specifically block stable CD4-MHC class II binding, and exhibit significant inhibition of immune responses in animal models of autoimmune disease and allograft transplant rejection, suggesting their potential as novel immunosuppressants. This structurebased computer screening approach may have general implications for studying many immunoglobulin-like structures and interactions that share similar structural features. Furthermore, the results from this study have demonstrated that the rational design of small non-peptidic inhibitors of large protein-protein interfaces may indeed be an achievable goal.Protein-protein interactions are critical events in many biological processes. In general, these interactions involve large interfaces with many intermolecular contacts (1, 2). As such, it has long been a great challenge to design small molecular inhibitors of these surfaces in either peptide or more preferably non-peptide form. Recently, it has been suggested that proteins may actually interact through small critical surfacebinding epitopes, as in the cases of the human growth hormone-(3) and the erythropoietin-receptor complexes (4). These findings raise the intriguing possibility that inhibitors of these small binding epitopes may be sufficient for the effective blockade of large protein-protein interfaces. However, the general validity of this hypothesis and its implication for rational drug design remain to be tested and demonstrated in different biological systems. Undoubtedly, the development of a general approach to inhibit protein-protein interactions will have a tremendous impact on the understanding of the structural basis of these interactions and the design of new therapeutic strategies for many human diseases.An important category of protein-protein interactions are those among the immunoglobulin (Ig) superfamily of molecules, which includes a large group of cell surface structures that are characterized by a conserved Ig-like folding (5). The members of the Ig superfamily mediate diverse biological functions in immunity, particularly in cell surface recognition, and thus are attractive targets for drug design studies. In an attempt to better understand the structural basis of Ig superfamily interactions, we have focused on the interaction between the CD4 protein and the major histocompatibility complex (MHC) class II protein. CD4 is a glycoprotein expressed on the surface of helper T cells,...

Triggering of T Cell Activation via CD4 Dimers

“…This raised the possibility that the weak monomeric CD4-MHC affinity could be overcome by augmenting the avidity of the interaction through CD4 dimerization/oligomerization. Several crystallographic, molecular modeling, biochemical, and functional studies have indicated the involvement of CD4 oligomers in MHC class II binding and/or T cell activation (12,(17)(18)(19)(20)(21)(22). Confirming the crystallographic data, we identified K318 and Q344, two highly conserved residues within the D4 domain, as critical for CD4 dimer formation, assessed biochemically.…”

CD4 Dimers Constitute the Functional Component Required for T Cell Activation

“…The involvement of CD4 oligomers in MHC class II binding and/or T cell activation has been previously suggested, but not proven, by a panoply of crystallographic studies (13,37), molecular modeling studies (reviewed in Ref. 10), functional studies (11,15,24,38), and inhibition of IL-2 production using synthetic peptides (39,40). In addition, CD4 oligomerization has been reported to be critical for an efficient interaction of CD4 with other ligands, such as gp160 or IL-16 (6 -10, 41).…”

Small, Nonpeptide p75NTRLigands Induce Survival Signaling and Inhibit proNGF-Induced Death

“…Virtual (also called in silico) screening of chemical libraries based on the structure of protein-protein interaction sites, ligand-receptor interaction sites, or a series of known small ligands is a potentially powerful approach for the identification of novel lead compounds (for review, see Kurogi and Guner, 2001;Mason et al, 2001;Guner, 2002;Singh et al, 2002;Guner et al, 2004). To date, in the area of modulation of protein-protein interactions, virtual screening has yielded only inhibitors, including compounds inhibiting the interactions of Bak with Bcl-2 (J. L. , Bak with Bcl-x (Enyedy et al, 2001), major histocompatibility complex class II proteins with CD4 (Li et al, 1997), and very late antigen-4 with vascular cell adhesion molecule-1 (Singh et al, 2002). As in the present work, each of these screening studies was predicated on identification of an oligopeptide with the desired function.…”