Combinatorial target-guided ligand assembly: identification of potent subtype-selective c-Src inhibitors

The consequences of translational and rotational entropy lost by small molecules on binding to proteins

When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entropy barrier from the increase in binding affinities that results when two fragments of known affinity and known binding mode are joined together. The paper reviews the relatively rare number of examples where good quality data is available. From the analysis of this data, we estimate that the barrier to binding, due to the loss of rigid-body entropy, is 15-20 kJ/mol, i.e. around 3 orders of magnitude in affinity at 298 K. This large barrier explains why it is comparatively rare to observe multiple fragments binding to non-overlapping adjacent sites in enzymes. The barrier is also consistent with medicinal chemistry experience where small changes in the critical binding regions of ligands are often poorly tolerated by enzymes.

Development of protein-detecting microarrays and related devices

There is great interest in the development of devices capable of monitoring the levels and post-translational modification states of hundreds or thousands of proteins simultaneously. One way to do this would be to create protein-detecting microarrays roughly akin to the DNA microarrays that are used for genome-wide expression studies. Two major challenges must be addressed before practical devices of this type become available. One is the development of high-throughput methods for the isolation of protein-binding compounds that will act as capture molecules in the array. The second is the optimization of methods that register binding of target proteins to the immobilized ligands in a sensitive and quantitative fashion. Progress in these areas, and some of the challenges remaining, are reviewed in this article.

A pH sensitive colorometric assay for the high-throughput screening of enzyme inhibitors and substrates: a case study using kinases

We have developed an uncoupled, pH sensitive kinase assay that can be used for high-throughput screening of potential inhibitors or for determining substrate specificity. Kinases catalyze the transfer of a gamma-phosphoryl group from ATP to an appropriate hydroxyl acceptor with the release of a proton. This assay is based on the detection of this proton using an appropriately matched buffer/indicator system. The assay was used to measure the activity of four readily available kinases, including hexokinase, glucokinase, glycerokinase, and pyruvate kinase, which was run in the reverse direction. We also went on to screen a small series of mono- and diphosphonucleotides for inhibition of hexokinase as well as a modest set of potential hexokinase substrates. We determined sucrose to be a modest substrate for hexokinase with a K(m) of 1.8 +/- 0.2 mM, a k(cat) of 142 +/- 3 min(-1), and a V(max) that is 15% of that for glucose. Given the importance of kinases in a diverse array of biological functions and disease states, there is a need for a simple, rapid assay system. We feel this assay will lend itself well to meet this end. This method should be applicable to many other enzymatic reactions which involve a change in pH.

Peptide chips for the quantitative evaluation of protein kinase activity

Peptide chips are an emerging technology that could replace many of the bioanalytical methods currently used in drug discovery, diagnostics, and cell biology. Despite the promise of these chips, their development for quantitative assays has been limited by several factors, including a lack of well-defined surface chemistries to immobilize peptides, the heterogeneous presentation of immobilized ligands, and nonspecific adsorption of protein to the substrate. This paper describes a peptide chip that overcomes these limitations, and demonstrates its utility in activity assays of the nonreceptor tyrosine kinase c-Src. The chip was prepared by the Diels-Alder-mediated immobilization of the kinase substrate AcIYGEFKKKC-NH(2) on a self-assembled monolayer of alkanethiolates on gold. Phosphorylation of the immobilized peptides was characterized by surface plasmon resonance, fluorescence, and phosphorimaging. Three inhibitors of the enzyme were quantitatively evaluated in an array format on a single, homogeneous substrate.

Tyrosylprotein sulfotransferase inhibitors generated by combinatorial target-guided ligand assembly

Tyrosylprotein sulfotransferases (TPSTs) catalyze the sulfation of tyrosine residues within secreted and membrane-bound proteins. The modification modulates protein-protein interactions in the extracellular environment. Here we use combinatorial target-guided ligand assembly to discover the first known inhibitors of human TPST-2.

Recent advances in chemical approaches to the study of biological systems

A number of novel chemical methods for studying biological systems have recently been developed that provide a means of addressing biological questions not easily studied with other techniques. In this review, examples that highlight the development and use of such chemical approaches are discussed. Specifically, strategies for modulating protein activity or protein-protein interactions using small molecules are presented. In addition, methods for generating and utilizing novel biomolecules (proteins, oligonucleotides, oligosaccharides, and second messengers) are examined.

An inhibitor of the human UDP-GlcNAc 4-epimerase identified from a uridine-based library: a strategy to inhibit O-linked glycosylation

The biological study of O-linked glycosylation is particularly problematic, as chemical tools to control this modification are lacking. An inhibitor of the UDP-GlcNAc 4-epimerase that synthesizes UDP-GalNAc, the donor initiating O-linked glycosylation, would be a powerful reagent for reversibly inhibiting O-linked glycosylation. We synthesized a 1338 member library of uridine analogs directed to the epimerase by virtue of substrate mimicry. Screening of the library identified an inhibitor with a K(i) value of 11 microM. Tests against related enzymes confirmed the compound's specificity for the UDP-GlcNAc 4-epimerase. Inhibitors of a key step of O-linked glycan biosynthesis can be discovered from a directed library screen. Progeny thereof may be powerful tools for controlling O-linked glycosylation in cells.

High-throughput antibody isolation

To define the proteome of an organism, there is a need for robust and reproducible methods for the quantitative detection of all the polypeptides in a cell. High-density arrays of receptors specific for each of the polypeptides in a complex sample hold great promise for the analysis of complex protein mixtures. Because of their high affinity, specificity and their ability to bind to virtually any protein, antibodies appear particularly promising as the receptor element in protein-detection arrays. For proteomic-scale analyses, the ability to isolate and produce antibodies en masse to large numbers of target molecules is critical. A variety of systems for the high-throughput isolation of antibodies from combinatorial libraries are being developed and are outlined in this review. However, there are several other important considerations to be borne in mind before such systems can realistically be applied on a large scale.

Protein-protein interfaces: mimics and inhibitors

Many biological processes are mediated by specific molecular recognition between proteins. However, the thermodynamic and structural 'rules' for such recognition are incompletely understood, as is the potential for inhibition by small molecules. Recent progress has included the discovery of small-molecule inhibitors for several targets important in cancer.

Combinatorial libraries and biological discovery

Combinatorial chemistry has become a popular tool for the preparation of collections of compounds that can be used to find inhibitors and substrates for different protein targets. It has evolved to provide small molecule libraries, which, with the concomittant use of affinity chromatography, gene expression profiling and complementation, can be used to identify compounds and their protein targets in biological systems, including the neurological system.

Synthesis and biological evaluation of vancomycin dimers with potent activity against vancomycin-resistant bacteria: target-accelerated combinatorial synthesis

Based on the notion that dimerization and/or variation of amino acid 1 of vancomycin could potentially enhance biological activity, a series of synthetic and chemical biology studies were undertaken in order to discover potent antibacterial agents. Herein we describe two ligation methods (disulfide formation and olefin metathesis) for dimerizing vancomycin derivatives and applications of target-accelerated combinatorial synthesis (e.g. combinatorial synthesis in the presence of vancomycin's target Ac2-L-Lys-D-Ala-D-Ala) to generate libraries of vancomycin dimers. Screening of these compound libraries led to the identification of a number of highly potent antibiotics effective against vancomycin-suspectible, vancomycin-intermediate resistant and, most significantly, vancomycin-resistant bacteria.

A library approach to the generation of bisubstrate analogue sulfotransferase inhibitors

[reaction: see text]. A library of potential bisubstrate analogue inhibitors (1) targeting sulfotransferase enzymes was generated by the chemoselective ligation of the PAPS mimic 2 with a panel of 447 aldehydes. Preliminary screening has identified compounds that inhibit estrogen sulfotransferase (EST), an enzyme relevant to breast cancer.

Chemical genetic approaches for the elucidation of signaling pathways

New chemical methods that use small molecules to perturb cellular function in ways analogous to genetics have recently been developed. These approaches include both synthetic methods for discovering small molecules capable of acting like genetic mutations, and techniques that combine the advantages of genetics and chemistry to optimize the potency and specificity of small-molecule inhibitors. Both approaches have been used to study protein function in vivo and have provided insights into complex signaling cascades.

Src inhibitors: genomics to therapeutics

Following the milestone discoveries that identified Src as the first known protein tyrosine kinase and as a prototype oncogene, as well as Src transgenic studies to validate it as a promising therapeutic target for osteoporosis, intense efforts are being made to create Src inhibitor drugs. Drug discovery strategies focused on both the non-catalytic and catalytic domains of Src have successfully resulted in promising Src inhibitor lead compounds with potential therapeutic applications for osteoporosis, cancer, and other diseases. Some noteworthy examples of Src inhibitors are described, and their chemical diversity, structure-based design, and biological activities in vitro and in vivo are illustrated. The potency, selectivity, and in vivo efficacy of key Src inhibitors are being investigated in molecular, cellular and animal models. Consequently, Src inhibitor drug development is imminent, and current studies are well-poised to achieve the ultimate milestone of a Src inhibitor therapeutic.

Molecular complexity and its impact on the probability of finding leads for drug discovery

Using a simple model of ligand-receptor interactions, the interactions between ligands and receptors of varying complexities are studied and the probabilities of binding calculated. It is observed that as the systems become more complex the chance of observing a useful interaction for a randomly chosen ligand falls dramatically. The implications of this for the design of combinatorial libraries is explored. A large set of drug leads and optimized compounds is profiled using several different properties relevant to molecular recognition. The changes observed for these properties during the drug optimization phase support the hypothesis that less complex molecules are more common starting points for the discovery of drugs. An extreme example of the use of simple molecules for directed screening against thrombin is provided.

Library design for NMR-based screening

Recent advances in NMR-based screening methods have made it possible to screen larger libraries of molecules with higher throughput. However, experience shows that intelligent library design is important if NMR screening is to succeed in aiding our discovery of potent and useful lead compounds. This review presents the current state-of-the-art methodologies for designing primary and follow-up libraries for NMR screening. Diversity, drug-likeness and combinatorial libraries are discussed, and the inherent pitfalls of the NMR approach are addressed.

Protein microarrays: prospects and problems

Protein microarrays are potentially powerful tools in biochemistry and molecular biology. Two types of protein microarrays are defined. One, termed a protein function array, will consist of thousands of native proteins immobilized in a defined pattern. Such arrays can be utilized for massively parallel testing of protein function, hence the name. The other type is termed a protein-detecting array. This will consist of large numbers of arrayed protein-binding agents. These arrays will allow for expression profiling to be done at the protein level. In this article, some of the major technological challenges to the development of protein arrays are discussed, along with potential solutions.

The copper-mediated cross-coupling of phenylboronic acids and N-hydroxyphthalimide at room temperature: synthesis of aryloxyamines

[figure: see text] A novel route to aryloxyamines via the copper-mediated cross-coupling of N-hydroxyphthalimide and phenylboronic acids is reported. The reaction is mediated by selected copper(I) and (II) salts in the presence of pyridine and is tolerant of several functional groups on the phenylboronic acid. The phthallmide group is removed using hydrazine to afford the corresponding aryloxyamine.

Design of adenosine kinase inhibitors from the NMR-based screening of fragments

A strategy is described for designing high-affinity ligands using information derived from the NMR-based screening of fragments. The method involves the fragmentation of an existing lead molecule, identification of suitable replacements for the fragments, and incorporation of the newly identified fragments into the original scaffold. Using this technique, novel substituents were rapidly identified and incorporated into lead inhibitors of adenosine kinase that exhibited potent in vitro and in vivo activities. This approach is a valuable strategy for modifying existing leads to improve their potency, bioavailability, or toxicity profile and thus represents a useful technique for lead optimization.

Src inhibitors: drugs for the treatment of osteoporosis, cancer or both?

Src was one of the first proto-oncogenes to be identified and is a prototype of non-receptor type tyrosine kinases. The role of Src in bone metabolism first became apparent in Src-deficient mice and has been confirmed using low-molecular-weight Src inhibitors in animal models of osteoporosis. At the cellular level, it is well established that Src plays an important role in proliferation, and adhesion and motility. In addition, recent data indicate an involvement of Src in cell survival and intracellular trafficking in various specialized cell types. These new findings suggest that Src inhibitors might have therapeutic value in the suppression of tumor growth, tumor angiogenesis and bone resorption.

Chemical genetics: ligand-based discovery of gene function

Chemical genetics is the study of gene-product function in a cellular or organismal context using exogenous ligands. In this approach, small molecules that bind directly to proteins are used to alter protein function, enabling a kinetic analysis of the in vivo consequences of these changes. Recent advances have strongly enhanced the power of exogenous ligands such that they can resemble genetic mutations in terms of their general applicability and target specificity. The growing sophistication of this approach raises the possibility of its application to any biological process.

Site-directed ligand discovery

We report a strategy (called "tethering") to discover low molecular weight ligands ( approximately 250 Da) that bind weakly to targeted sites on proteins through an intermediary disulfide tether. A native or engineered cysteine in a protein is allowed to react reversibly with a small library of disulfide-containing molecules ( approximately 1,200 compounds) at concentrations typically used in drug screening (10 to 200 microM). The cysteine-captured ligands, which are readily identified by MS, are among the most stable complexes, even though in the absence of the covalent tether the ligands may bind very weakly. This method was applied to generate a potent inhibitor for thymidylate synthase, an essential enzyme in pyrimidine metabolism with therapeutic applications in cancer and infectious diseases. The affinity of the untethered ligand (K(i) approximately 1 mM) was improved 3,000-fold by synthesis of a small set of analogs with the aid of crystallographic structures of the tethered complex. Such site-directed ligand discovery allows one to nucleate drug design from a spatially targeted lead fragment.

A "traceless" Staudinger ligation for the chemoselective synthesis of amide bonds

[reaction: see text] Here we report a novel modification of our previously reported "Staudinger ligation" that generates an amide bond from an azide and a specifically functionalized phosphine. This method for the selective formation of an amide bond, which does not require the orthogonal protection of distal functional groups, should find general utility in synthetic and biological chemistry.