Jürgen Bajorath

Integration of virtual and high-throughput screening.

High-throughput and virtual screening are important components of modern drug discovery research. Typically, these screening technologies are considered distinct approaches, as one is experimental and the other is theoretical in nature. However, given their similar tasks and goals, these approaches are much more complementary to each other than often thought. Various statistical, informatics and filtering methods have recently been introduced to foster the integration of experimental and in silico screening and maximize their output in drug discovery. Although many of these ideas and efforts have not yet proceeded much beyond the conceptual level, there are several success stories and good indications that early-stage drug discovery will benefit greatly from a more unified and knowledge-based approach to biological screening, despite the many technical advances towards even higher throughput that are made in the screening arena.

B7-H4, a Molecule of the B7 Family, Negatively Regulates T Cell Immunity

We identify a B7 family molecule, B7-H4, by protein sequence analysis and comparative molecular modeling. While B7-H4 mRNA is widely distributed in mouse and human peripheral tissues, cell surface expression of B7-H4 protein is limited and shows an inducible pattern on hematopoietic cells. Putative receptor of B7-H4 can be upregulated on activated T cells. By arresting cell cycle, B7-H4 ligation of T cells has a profound inhibitory effect on the growth, cytokine secretion, and development of cytotoxicity. Administration of B7-H4Ig into mice impairs antigen-specific T cell responses whereas blockade of endogenous B7-H4 by specific monoclonal antibody promotes T cell responses. B7-H4 thus may participate in negative regulation of cell-mediated immunity in peripheral tissues.

Molecular modeling and functional mapping of B7-H1 and B7-DC uncouple costimulatory function from PD-1 interaction.

B7-H1 and B7-DC are ligands for PD-1, a receptor implicated in negative regulation of T and B cell functions. These ligands, however, also costimulate T cell responses. It remains elusive whether or not costimulation is mediated through PD-1. By comparative molecular modeling and site-directed mutagenesis, we found that nonconserved residues between these ligands on the A′GFCC′C′′ face mediate interaction with PD-1. This indicates significant structural heterogeneity of the interactions between PD-1 and its ligands. Importantly, ligand mutants with abolished PD-1 binding capacity could still costimulate proliferation and cytokine production of T cells from normal and PD-1–deficient mice. Our results reveal unique binding characteristics of B7-H1 and B7-DC and provide direct evidence for an independent costimulatory receptor other than PD-1.

Solution structure of human CTLA-4 and delineation of a CD80/CD86 binding site conserved in CD28.

The structure of human CTLA-4 reveals that residues Met 99, Tyr 100 and Tyr 104 of the M99 YPPPY104 motif are adjacent to a patch of charged surface residues on the A‘GFCC’ face of the protein. Mutation of these residues, which are conserved in the CTLA-4/CD28 family, significantly reduces binding to CD80 and/or CD86, implicating this patch as a ligand binding site.

Identification of CD44 Residues Important for Hyaluronan Binding and Delineation of the Binding Site

CD44 is a widely distributed cell surface protein that plays a role in cell adhesion and migration. As a proteoglycan, CD44 is also implicated in growth factor and chemokine binding and presentation. The extracellular region of CD44 is variably spliced, giving rise to multiple CD44 isoforms. All isoforms contain an amino-terminal domain, which is homologous to cartilage link proteins. The cartilage link protein-like domain of CD44 is important for hyaluronan binding. The structure of the link protein domain of TSG-6 has been determined by NMR. Based on this structure, a molecular model of the link-homologous region of CD44 was constructed. This model was used to select residues for site-specific mutagenesis in an effort to identify residues important for ligand binding and to outline the hyaluronan binding site. Twenty-four point mutants were generated and characterized, and eight residues were identified as critical for binding or to support the interaction. In the model, these residues form a coherent surface the location of which approximately corresponds to the carbohydrate binding sites in two functionally unrelated calcium-dependent lectins, mannose-binding protein and E-selectin (CD62E).

Molecular organization, structural features, and ligand binding characteristics of CD44, a highly variable cell surface glycoprotein with multiple functions

CD44 is a type I transmembrane protein and member of the cartilage link protein family. It is involved in cell‐cell and cell‐matrix interactions and signal transduction. Several CD44 ligands have been identified. CD44 is a major cell surface receptor for hyaluronan, a component of the extracellular matrix. It is implicated in diseases such as cancer and inflammation and therefore intensely studied. A characteristic feature of CD44 is the occurrence of many isoforms that are expressed in a cell‐specific manner and differentially glycosylated. Although a number of CD44 isoforms have been characterized, the structural diversity of CD44 makes it often challenging to study (isoform‐specific) CD44‐ligand interactions at the molecular level of detail. The structural organization and ligand binding characteristics of CD44 are focal points of this review. On the basis of recent structural and mutagenesis studies, details of the CD44‐hyaluronan interaction are beginning to be understood. Proteins 2000;39:103–111.

CD6—ligand interactions: a paradigm for SRCR domain function?

The scavenger receptor cysteine-rich (SRCR) superfamily, which includes proteins expressed by leukocytes, can be subdivided into groups A and B. Group B contains the lymphocyte cell-surface receptor CD6. This article reviews recent progress in understanding the interaction between CD6 and its ligand, activated leukocyte cell adhesion molecule (ALCAM). Analysis of the CD6-ALCAM interaction may help to understand how other SRCR domains bind to their ligands.

New methodologies for ligand-based virtual screening.

Computational screening of compound databases has become increasingly popular in pharmaceutical research. Virtual screening approaches can roughly be divided into target structure-based screening (often referred to as docking) and screening using active compounds as templates (ligand-based virtual screening). Ligand-based screening techniques essentially focus on comparative molecular similarity analysis of compounds with known and unknown activity, regardless of the methods or algorithms used. In this review, we first provide an overview of widely used ligand-based virtual screening approaches including various database filters and then discuss recent trends in this field and new methodological developments.

Cell surface receptors and their ligands: in vitro analysis of CD6-CD166 interactions.

CD6 is a cell surface receptor belonging to the scavenger receptor cysteine‐rich (SRCR) protein superfamily (SRCRSF). It specifically binds activated leukocyte cell adhesion molecule (ALCAM, CD166), a member of the immunoglobulin (Ig) superfamily (IgSF). CD166 was among the first molecules identified as a ligand for an SRCRSF receptor, and the CD6‐CD166 interaction was the first interaction characterized involving SRCRSF and IgSF proteins. We focus here on what has been learned about the specifics of the CD6‐CD166 interaction from in vitro analysis. The studies are thought to provide an instructive example for the analysis of interactions between single‐path transmembrane cell surface proteins. Using soluble recombinant forms, the extracellular binding domains of receptor and ligand have been identified and characterized in a variety of assay systems. Both CD6 and CD166 have been subjected to intense mutagenesis and monoclonal antibody (mAb) binding studies and residues critical for their interaction have been identified. The availability of structural prototypes of both superfamilies has made it possible to map the binding site in CD166 and, more recently, in CD6 and compare these regions to epitopes of mAbs that block, or do not block, the interaction. In addition, the molecular basis of observed cross‐species receptor‐ligand interactions could be rationalized. These studies illustrate the value of structural templates for the interpretation of sequence and mutagenesis analyses. Proteins 2000;40:420–428.

Computational analysis of ligand relationships within target families.

Computational tools for the large-scale analysis and prediction of ligand-target interactions and the identification of small molecules having different selectivity profiles within target protein families complement research in chemical genetics and chemogenomics. For computational analysis and design, such tasks require a departure from the traditional focus on single targets, hit identification, and lead optimization. Recently, studies have been reported that profile compounds in silico against arrays of targets or systematically map ligand-target space. In order to identify small molecular probes that are suitable for chemical genetics applications, molecular diversity needs to be viewed in a way that partly differs from principles guiding conventional library design.