Genetic and genomic approaches to identify and study the targets of bioactive small molecules

Natural and synthetic bioactive small molecules form the backbone of modern therapeutics. These drugs primarily exert their effect by targeting cellular host or foreign proteins that are critical for the progression of disease. Therefore, a crucial step in the process of recognizing valuable new drug leads is identification of their protein targets; this is often a time consuming and difficult task. This report is intended to provide a comprehensive review of recent developments in genetic and genomic approaches to overcome the hurdle of discovering the protein targets of bioactive small molecules.     

Identification of the cellular targets of bioactive small organic molecules using affinity reagents

The elucidation of molecular targets of bioactive small organic molecules remains a significant challenge in modern biomedical research and drug discovery. This tutorial review summarizes strategies for the derivatization of bioactive small molecules and their use as affinity probes to identify cellular binding partners. Special emphasis is placed on logistical concerns as well as common problems encountered during such target identification experiments. The roadmap provided is a guide through the process of affinity probe selection, target identification, and downstream target validation.     

Multiple-injection technique for isolating a target protein from multicomponent mixtures

An integrated chromatographic process comprising ion exchange (IEC) and hydrophobic interaction chromatography (HIC) for isolating a target protein form multicomponent mixtures has been analyzed. The model mixture contained immunoglobulin G that was the key product of the separation process, cytochrome C and ovalbumin. The adsorption characteristics and the mass transport kinetics of the model proteins have been determined along with their dependencies on the operating variables such as pH, temperature and the salt concentration for IEC as well as HIC media. Limitations of the process efficiency resulting from kinetic effects, solubility constraints and the necessity of the mobile phase exchange between chromatographic steps have been discussed. To improve the performance of the integrated process the multiple-injection technique has been suggested. This technique consisted in loading feed mixtures dissolved in a good solvent onto the column by several small-volume injections under conditions of strong protein adsorption. It allowed diminishing interactions between the sample-solvent and protein and elimination of undesired effects such as band splitting and band broadening. For the process design and optimization a dynamic model has been used accounting for thermodynamics and kinetics of the process. The optimization results indicated superiority of the multiple-injection technique over standard isocratic injections in terms of the process yield and productivity.     

RigFit: A new approach to superimposing ligand molecules

If structural knowledge of a receptor under consideration is lacking, drug design approaches focus on similarity or dissimilarity analysis of putative ligands. In this context the mutual ligand superposition is of utmost importance. Methods that are rapid enough to facilitate interactive usage, that allow to process sets of conformers and that enable database screening are of special interest here. The ability to superpose molecular fragments instead of entire molecules has proven to be helpful too. The RigFit approach meets these requirements and has several additional advantages. In three distinct test applications, we evaluated how closely we can approximate the observed relative orientation for a set of known crystal structures, we employed RigFit as a fragment placement procedure, and we performed a fragment-based database screening. The run time of RigFit can be traded off against its accuracy. To be competitive in accuracy with another state-of-the-art alignment tool, with which we compare our method explicitly, computing times of about 6s per superposition on a common day workstation are required. If longer run times can be afforded the accuracy increases significantly. RigFit is part of the flexible superposition software FlexS which can be accessed on the WWW [http://cartan.gmd.de/FlexS].     

Facile zeolite induced Fischer-indole synthesis: a new approach to bioactive natural product rutaecarpine

Starting from glutaric anhydride (5) we have demonstrated an elegant six-step practical synthesis of bioactive natural product rutaecarpine (1a) via o-amidoglutaranilic acid formation, esterification, chemoselective ester reduction, intramolecular dehydrative cyclizations, hydrazone formation and zeolite induced Fischer-indole synthesis with 53% overall yield. The conditions employed in the present synthesis are mild, efficient and general.     

Conformational sampling of bioactive molecules: a comparative study

The necessity to generate conformations that sample the entire conformational space accessible to a given molecule is ubiquitous in the field of computer-aided drug design. Protein-ligand docking, 3D database searching, and 3D QSAR are three commonly used techniques that depend critically upon the quality and diversity of the generated conformers. Although there are a wide range of conformational search algorithms available, the extent to which they sample conformational space is often unclear. To address this question, we conducted a robust comparison of the search algorithms implemented in several widely used molecular modeling packages, including Catalyst, Macromodel, Omega, MOE, and Rubicon as well as our own method, stochastic proximity embedding (SPE). We found that SPE used in conjunction with conformational boosting, a heuristic for biasing conformational search toward more extended or compact geometries, along with Catalyst, are significantly more effective in sampling the full range of conformational space compared to the other methods, which show distinct preferences for either more extended or more compact geometries.     

Photo-affinity labeling strategies in identifying the protein ligands of bioactive small molecules: examples of targeted synthesis of drug analog photoprobes

The discovery of many new targets by chemical genetics has frequently exploited the fact that their biologically active chemical ligands were reactive and thus could covalently bind to their protein target(s). When experimental compounds or therapeutic agents with unidentified mechanisms of action do not contain reactive groups that can covalently label the putative site of molecular action, it may be possible to create a reactive photo-affinity probe if there is sufficient knowledge of the structure-activity relationship of the chemical series. Two specific examples are presented. These include the use of photo-affinity probes in the identification of the mechanism of action of synthetic oxazolidinones, a class of novel acting antibiotics and in the identification of a novel target for the insulin-sensitizing thiazolidinediones. Developments in photo-affinity labeling and combinatorial library design now imply that the parallel incorporation of photo-probes into screening library design could, at least in principle, greatly facilitate reverse pharmacological and chemical genetics approaches to protein target discovery.     

Ligand-regulated peptides: a general approach for modulating protein-peptide interactions with small molecules

We engineered a novel ligand-regulated peptide (LiRP) system where the binding activity of intracellular peptides is controlled by a cell-permeable small molecule. In the absence of ligand, peptides expressed as fusions in an FKBP-peptide-FRB-GST LiRP scaffold protein are free to interact with target proteins. In the presence of the ligand rapamycin, or the nonimmunosuppressive rapamycin derivative AP23102, the scaffold protein undergoes a conformational change that prevents the interaction of the peptide with the target protein. The modular design of the scaffold enables the creation of LiRPs through rational design or selection from combinatorial peptide libraries. Using these methods, we identified LiRPs that interact with three independent targets: retinoblastoma protein, c-Src, and the AMP-activated protein kinase. The LiRP system should provide a general method to temporally and spatially regulate protein function in cells and organisms.     

From small charged molecules to oligomers: a semiempirical approach to the modeling of actual mobility in free solution

According to Stokes' treatment, the ionic mobility of particles, which are small with respect to Debye length, is usually considered to be proportional to the nominal charge and inversely proportional to the hydrodynamic radius. Experimentally, it is well known, however, that the ionic mobility of a small multicharged molecule does not depend linearly on its nominal charge in a wide range. This behavior can be accounted for by a condensation of the charge or a modification of the friction coefficient with the charge. This paper presents a semiempirical modeling of the actual mobility based on the assumption of additivity of frictional contributions pertaining to the uncharged molecular backbone and to each charged or uncharged moiety. Condensation of the charge was not considered. The model first appeared to be suitable for multicharged analytes having a characteristic dimension smaller than the Debye length, such as benzene polycarboxylic acids and polysulfated disaccharides. This approach was then adapted to account for the actual mobilities of singly and evenly charged oligomers (N-mers) having a dimension smaller than or similar to the Debye length. Rather good experimental agreement was obtained for polyalanines and polyglycines (N < or = 6), fatty acid homologs, fully sulfonated polystyrene oligomers (N < or = 13), and polycytidines (N < or = 10). Especially the influence of the polymerization degree on the mobility of oligomers having identical charge densities was clarified. It is also shown that the electrophoretic contribution to the overall friction coefficient increases linearly with the nominal charge but hardly depends on the chemical nature of the charged moieties. This model should be of interest to evaluate the role of various physicochemical phenomena (hydrodynamic and electrophoretic frictions, hydrodynamic coupling, charge condensation) involved in the migration of charged oligomers.     

A new approach to enantiopure C3-symmetric molecules

Chiral base chemistry has been used to create three chiral centres in one pot on a C3-symmetric substrate. The potential of this new approach to C3-symmetric molecules is exemplified by the creation of an enantiopure C3v-symmetric triol, triphosphane and tripyridine. A ruthenium complex of the last compound has been studied by X-ray crystallography.     

Development of new quinoline-based photo-labile groups for photo-regulation of bioactive molecules

A series of quinoline-based photo-removable protecting (caging) groups were synthesized for the development of new chemical tools to photo-regulate bioactive molecules in living cells and tissues with improved properties. Compared with the recently developed 8-bromo-7-hydroxyquinolinyl (BHQ) chromophore, change of the bromine substituent to a pyridine group led to a new photo-labile group (3′-PyHQ) with an increased water solubility, a lower self-fluorescence, and a higher photolysis efficiency. It was proposed that the replacement of a halogen group by a pyridine-like heterocycle may provide a general strategy to improve the existing photo-caging groups.     

‘Catch and release’ cascades: a resin-mediated three-component cascade approach to small molecules

The application of a ‘catch and release’ approach to palladium-catalysed multi-component cascade reactions leads to diverse libraries of pharmacologically interesting small molecules in high yield and with excellent purity.     

Hypercrosslinking: new approach to porous polymer monolithic capillary columns with large surface area for the highly efficient separation of small molecules

Monolithic polymers with an unprecedented surface area of over 600 m(2)/g have been prepared from a poly(styrene-co-vinylbenzyl chloride-co-divinylbenzene) precursor monolith that was swollen in 1,2-dichloroethane and hypercrosslinked via Friedel-Crafts reaction catalyzed by ferric chloride. Both the composition of the reaction mixture used for the preparation of the precursor monolith and the conditions of the hypercrosslinking reaction have been varied using mathematical design of experiments and the optimized system validated. Hypercrosslinked monolithic capillary columns contain an array of small pores that make the column ideally suited for the high efficiency isocratic separations of small molecules such as uracil and alkylbenzenes with column efficiencies reproducibly exceeding 80,000 plates/m for retained compounds. The separation process could be accelerated while also improving peak shape through the use of higher temperatures and a ternary mobile phase consisting of acetonitrile, tetrahydrofuran, and water. As a result, seven compounds were well separated in less than 2 min. These columns also facilitate separations of peptide mixtures such as a tryptic digest of cytochrome c using a gradient elution mode which affords a sequence coverage of 93%. A 65 cm long hypercrosslinked capillary column used in size exclusion mode with tetrahydrofuran as the mobile phase afforded almost baseline separation of toluene and five polystyrene standards.     

A new approach to construct a doubly interpenetrated microporous metal-organic framework of primitive cubic net for highly selective sorption of small hydrocarbon molecules

A new approach has been realized to construct a three‐dimensional doubly interpenetrated cubic metal–organic framework Zn₂(PBA)₂(BDC) ? (DMF)₃(H₂O)₄ ( UTSA‐36 , HPBA=4‐(4‐pyridyl) benzoic acid, H₂BDC=1,4‐benzenedicarboxylic acid) through the self‐assembly of the pyridylcarboxylate linker 4‐(4‐pyridyl) benzoate and bicarboxylate linker 1,4‐benzenedicarxylate with paddle‐wheel [Zn₂(COO)₄]. The activated UTSA‐36 a exhibits highly selective gas sorption of C₂H₆, C₂H₄ and C₂H₂ over CH₄ with the Henry law’s selectivities of 11 to 25 in the temperature range of 273 to 296 K attributed to the unique 3D intersected pore structure of about 3.1 to 4.8 Å within the framework, indicating that UTSA‐36 a is a potentially very useful and promising microporous material for such industrially important separation of C₂ hydrocarbons over methane.     

Chemical dimerizers and three-hybrid systems: scanning the proteome for targets of organic small molecules

The integration of technological advances in areas as diverse as chemical biology, proteomics, genomics, automation, and bioinformatics has led to the emergence of novel screening paradigms for analyzing the molecular basis of drug action. This review summarizes recent advances in three-hybrid technologies and their application to the characterization of small molecule-protein interactions and proteome-wide identification of drug receptors.     

"Click-made" biaryl-linker improving efficiency in protein labelling for the membrane target protein of a bioactive compound

We report on the design, synthesis and assessment of a novel biaryl-linked (BArL) molecular probe for the exploration of low-abundant target proteins for bioactive compounds based on the activity based protein profiling (ABPP) approach. Surprisingly, the performance of the BArL probe was better than that of the stepwise tagging approach that is considered to be the most effective method used in ABPP study.     

Polyisocyanides as a new alignment medium to measure residual dipolar couplings for small organic molecules

Polyisocycanides were found to give anisotropic molecular alignment in the magnetic field and are useful to measure residual dipolar couplings (RDCs) from analytes, e.g. strychnine. They show less quadrupolar splitting of the deuterated solvent signal compared with other liquid crystal systems such as Poly-γ-benzyl-L-glutamate (PBLG) and hence less undesired line broadening.     

A three-hybrid approach to scanning the proteome for targets of small molecule kinase inhibitors

In this study, we explored the application of a yeast three-hybrid (Y3H)-based compound/protein display system to scanning the proteome for targets of kinase inhibitors. Various known cyclin-dependent kinase (CDK) inhibitors, including purine and indenopyrazole analogs, were displayed in the form of methotrexate-based hybrid ligands and deployed in cDNA library or yeast cell array-based screening formats. For all inhibitors, known cell cycle CDKs as well as novel candidate CDK-like and/or CDK-unrelated kinase targets could be identified, many of which were independently confirmed using secondary enzyme assays and affinity chromatography. The Y3H system described here may prove generally useful in the discovery of candidate drug targets.