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PubMed2006

Rational design approaches to chemical libraries for hit identification.

Sequencing of the human genome along with developments in combinatorial synthesis and high-throughput biological screening provide unparallel opportunities to drug discovery. It has been noted that the increased number of synthesized and annotated compounds did not yield the expected increase in number of viable drug candidates. To address this problem, several novel computation technologies have emerged for making combinatorial library design cost-effective. Of particular interest for the modern drug discovery are the structure-based or target-based methods that use structural information about target proteins and their small molecule ligands. In this work, we provide an overview of selected advances in computational algorithms for the rational selection of molecule libraries for the synthesis, with emphasis on structure-based approaches. These include a fusion of scaffold-linking method and combinatorial library design, pharmacophore matching and informative library design, and search by 3-D tree topological descriptors.

Combinatorial Chemistry Techniques↗
PubMedDate not supplied

Focused combinatorial library design based on structural diversity, druglikeness and binding affinity score.

The advent of focused library and virtual screening has reduced the disadvantage of combinatorial chemistry and changed it to a realizable and cost-effective tool in drug discovery. Usually, genetic algorithms (GAs) are used to quickly finding high-scoring molecules by sampling a small subset of the total combinatorial space. Therefore, scoring functions play essential roles in focused library design. Reported here is our initial attempt to establish a new approach for generating a target-focused library using the combination of the scores of structural diversity and binding affinity with our newly improved drug-likeness scoring functions. Meanwhile, a software package, named LD1.0, was developed on the basis of the new approach. One test on a cyclooxygenase (COX)2-focused library successfully reproduced the structures that have been experimentally studied as COX2-selective inhibitors. Another test is on a peroxisome proliferator-activated receptors gamma-focused library design, which not only reproduces the key fragments in the approved (thiazolidinedione) TZD drugs, but also generates some new structures that are more active than the approved drugs or published ligands. Both of the two tests took approximately 15% of the running time of the ordinary molecular docking method. Thus, our new approach is an effective, reliable, and practical way for building up a properly sized focused library with a high hit rate, novel structure, and good ADME/T profile.

Algorithms↗
PubMed2005

Discovery of acetylcholinesterase peripheral anionic site ligands through computational refinement of a directed library.

The formation of beta-amyloid plaques in the brain is a key neurodegenerative event in Alzheimer's disease. Small molecules capable of binding to the peripheral anionic site of acetylcholinesterase (AChE) have been shown to inhibit the AChE-induced aggregation of the beta-amyloid peptide. Using the combination of a computational docking model and experimental screening, five compounds that completely blocked the amyloidogenic effect of AChE were rapidly identified from an approximately 200-member library of compounds designed to disrupt protein-protein interactions. Critical to this docking model was the inclusion of two explicit water molecules that are tightly bound to the enzyme. Interestingly, none of the tested compounds inhibited the related enzyme butyrylcholinesterase (BuChE) up to their aqueous solubility limits. These compounds are among the most potent inhibitors of amyloid beta-peptide aggregation and are equivalent only to propidium, a well-characterized AChE peripheral anionic site binder and aggregation inhibitor.

Acetylcholinesterase↗
PubMed2004

Specific inhibition of human cytomegalovirus glycoprotein B-mediated fusion by a novel thiourea small molecule.

A novel small molecule inhibitor of human cytomegalovirus (HCMV) was identified as the result of screening a chemical library by using a whole-virus infected-cell assay. Synthetic chemistry efforts yielded the analog designated CFI02, a compound whose potency had been increased about 100-fold over an initial inhibitor. The inhibitory concentration of CFI02 in various assays is in the low nanomolar range. CFI02 is a selective and potent inhibitor of HCMV; it has no activity against other CMVs, alphaherpesviruses, or unrelated viruses. Mechanism-of-action studies indicate that CFI02 acts very early in the replication cycle, inhibiting virion envelope fusion with the cell plasma membrane. Mutants resistant to CFI02 have mutations in the abundant virion envelope glycoprotein B that are sufficient to confer resistance. Taken together, the data suggest that CFI02 inhibits glycoprotein B-mediated HCMV virion fusion. Furthermore, CFI02 inhibits the cell-cell spread of HCMV. This is the first study of a potent and selective small molecule inhibitor of CMV fusion and cell-cell spread.

Animals↗
PubMedDate not supplied

A Multimeric Synthetic Peptide Combinatorial Library.

We describe here a novel type of synthetic peptide library, named Multimeric Synthetic Peptide Combinatorial Library (M-SPCL), where multiple small peptide ligands are tied together in the same molecule. The advantage of using small peptides in the form of M-SPCL is two-fold: first, the high density assembly of the sequences on the branching scaffold leads to signal amplification, thereby effectively lowering the binding threshold for the selection of ligands; second, to interfere with protein-protein interactions, multimericity has been shown to be a desirable feature per se. The M-SPCL is prepared by solid-phase peptide synthesis, based on the structure of Multiple Antigen Peptides. When prepared in Positional Scanning format [C. Pinilla, J. Appel, P. Blanc and R.A. Houghten. 1992. BioTechniques 13: 901-905], selection is based on the amplified interaction of a single residue in a sequence-defined position. The usefulness of the new library was demonstrated by the selection of octameric peptides, which inhibit the binding of the cytokine human interleukin-6 to its receptor, with an apparent nanomolar affinity. Tetrameric, but not dimeric, branched peptides with the same sequences were also active with comparable affinity. The success of this approach is noteworthy, since screening of the corresponding monomeric pentapeptide SPCL did not lead to the selection of any inhibitory compound in the same system.

Amino Acid Sequence↗
PubMed1997

Construction, exploitation and evolution of a new peptide library displayed at high density by fusion to the major coat protein of filamentous phage.

The amino-terminus of the major coat protein (PVIII) of filamentous phage can be extended, up to 6-7 residues, without interfering with the phage life cycle. We have constructed a library of approximately ten millions different phage each displaying a different octapeptide joined to the amino-terminus of the 2700 copies of PVIII. Most of the resulting clones are able to produce infective particles. This molecular repertoire constituted by the periodic regular decoration of the phage filament surface, can be utilized to search elements that bind proteins or relatively small organic molecules like the textile dye Cibacron blue. By sequential growth cycles we have performed a library evolution experiment to select phage clones that have a growth advantage in the absence of any requirement for binding a specific target. The consensus of the best growers reveals a Pro rich sequence with large hydrophobic residues at position 7 and Asn at position 1 of the random peptide insert. We propose that the assembly secretion process is favoured in phages displaying this family of peptides since they fit the groove between two adjacent PVIII subunits by making advantageous molecular contacts on the phage surface.

Amino Acid Sequence↗
PubMed1999

Molecular forceps from combinatorial libraries prevent the farnesylation of Ras by binding to its carboxyl terminus.

INTRODUCTION: Ras is one of the major oncogenes. In order to function properly it has to undergo post-translational processing at its carboxyl terminus. It has been shown that inhibitors of farnesyl transferase, the first enzyme in the processing chain, can suppress the transforming activity of oncogenic Ras. RESULTS: We have identified molecular forceps, branched peptidic molecules, from combinatorial libraries that bind to the carboxyl terminus of Ras and interfere with its farnesylation without inhibiting the farnesyl transferase. The active molecules were selected by a screening against the carboxy-terminal octapeptide of Ras. CONCLUSIONS: The implications of our findings are twofold. First, we demonstrate that it is possible to prevent enzymatic transformations by blocking the enzyme's access to its substrate using a synthetic small molecule to mask the substrate. Second, we show that it is feasible to derive molecules from combinatorial libraries that bind a specific epitope on a protein by selecting these molecules with the isolated peptide epitope.

Alkyl and Aryl Transferases↗
PubMed1996

Glubodies: randomized libraries of glutathione transferase enzymes.

BACKGROUND: The immunoglobulin framework has been mutagenized to engineer recombinant libraries of proteins as potential diagnostics and novel catalysts, although the often shallow binding cleft may limit the utility of this framework for binding diverse small organic molecules. By contrast, the glutathione S-transferase (GST) family of enzymes contains a deep binding cleft, which has evolved to accommodate a broad range of hydrophobic xenobiotics. We set out to determine whether GST molecules with novel ligand-binding characteristics could be produced by random mutagenesis of segments of the binding cleft. RESULTS: We have identified two ligand-recognition segments (LRSs) in human GST P1, which are near the active site in the folded protein, but have characteristics indicating that the integrity of their sequence is not essential for the overall structure or activity of the protein. Libraries of GST P1-derived proteins were produced by substituting randomized sequences for an LRS or inserting random sequences into an LRS. The recombinant proteins in the libraries, collectively designated as 'glubodies,' generally retain enzymatic activity but differ markedly both from each other and from the parent enzyme in sensitivity to inhibition by diverse small organic compounds. In some instances, a glubody is inhibited by completely novel structures. CONCLUSIONS: We have shown that a non-antibody framework can be used to create large libraries of proteins with a wide range of binding specificities for small organic molecules. The glubodies provide a rich source of data for correlating the structural and functional features of proteins relevant to ligand binding. The criteria applied for identifying an LRS in GST P1 are generally applicable to other protein frameworks.

Amino Acid Sequence↗
PubMed2004

Molecule-specific imaging with mass spectrometry and a buckminsterfullerene probe: application to characterizing solid-phase synthesized combinatorial libraries.

We employ a newly developed buckminsterfullerene (C(60)) primary ion beam with time-of-flight secondary ion mass spectrometry to create molecule-specific images of resin particles employed in the solid-phase synthesis of peptide combinatorial libraries. This new cluster ion source, when operated at an incident energy of 20 keV, is remarkably effective at desorbing small peptides directly from a polymer surface and opens new possibilities for characterizing large arrays of diverse sets of molecules. In addition, the C(60) ion beam may be focused to a spot of 1.5 microm in diameter, enabling molecule-specific images of single 100 microm resin particles to be acquired. We report three significant aspects associated with utilizing the C(60) projectile that show how this technology can be taken to a more advanced level, especially when compared to results obtained with more conventional atomic primary ions. First, the useful yield of molecular ions is generally observed to be enhanced by at least 3 orders of magnitude over those previously possible. Second, the energy dissipation process associated with the C(60) impact is most efficient at desorbing molecules on soft substrates such as polymer surfaces rather than harder substrates such as metals or semiconductors. Third, there is a greatly reduced tendency for insulating surfaces to build up excess charge, obviating the need for charge compensation. Using a small five-member peptide library as a model, we show that by utilizing the focusing properties of the C(60) beam, it is possible to assay the surface composition of 100-microm polymer beads at a rate of up to 10 particles/s. Moreover, even at the picomole level, there are enough sequence ions in the mass spectrum to determine a unique composition. The results illustrate the ability to quickly assay large libraries without the use of tags and suggest the strategy may be applicable to a range of high-throughput experiments.

Combinatorial Chemistry Techniques↗
PubMed2005

Small molecule inhibitors of dynamin I GTPase activity: development of dimeric tyrphostins.

Dynamin I is a GTPase enzyme required for endocytosis and is an excellent target for the design of potential endocytosis inhibitors. Screening of a library of tyrphostins, in our laboratory, against the GTPase activity of dynamin I gave rise to a microM potent lead, 2-cyano-3-(3,4-dihydroxyphenyl)thioacrylamide (1, IC50 70 microM). Our initial investigations suggested that only the dimeric form of 1 displayed dynamin I GTPase inhibitory activity. Subsequent synthetic iterations were based on dimeric analogues and afforded a number of small molecules, low microM potent, inhibitors of dynamin I GTPase, in particular, symmetrical analogues with a minimum of two free phenolic -OHs: catechol-acrylamide (9) (IC50= 5.1 +/- 0.6 microM), its 3,4,5-trihydroxy congener (10) (IC50= 1.7 +/- 0.2 microM), and the corresponding 3-methyl ether (11) (IC50= 9 +/- 3 microM). Increasing the length of the central alkyl spacer from ethyl to propyl (22-24) afforded essentially identical activity with IC50's of 1.7 +/- 0.2, 1.7 +/- 0.2, and 5 +/- 1 microM, respectively. No decrease in activity was noted until the introduction of a hexyl spacer. Our studies highlight the requirement for two free amido NHs with neither the mono-N-methyl (86) nor the bis-N-methyl (87) analogues inhibiting dynamin I GTPase. A similar effect was noted for the removal of the nitrile moieties. However, modest potency was observed with the corresponding ester analogues of 9-11: ethyl ester (90), propyl ester (91), and butyl ester (92), with IC50's of 42 +/- 3, 38 +/- 2, and 61 +/- 2 microM, respectively. Our studies reveal the most potent and promising dynamin I GTPase inhibitor in this series as (22), which is also known as BisT.

Animals↗
PubMed2006

Towards erythropoietin mimicking small molecules.

Small molecules potentially mimicking the hormone erythropoietin have been discovered by screening of a library of rationally designed multicomponent reaction molecules in a functional cell-based assay.

Animals↗
PubMed2006

Selection of a phage-displayed peptide recognized by monoclonal antibody directed blocking the site of hepatitis C virus E2 for human CD81.

The human CD81 (hCD81) molecule has been identified as a putative receptor for hepatitis C virus (HCV). HCV envelope glycoprotein 2 (E2) most likely plays a pivotal role in binding to host cells by interacting with the hCD81 molecule. In this study, a phage-displayed peptide library was used to select small peptides with anti-hCD81 monoclonal antibody JS-81. The output/input ratio of phages increased about 91 fold after the third round of selection. Eight of the 30 phage clones selected from the phage library showed specific binding to the anti-hCD81 by enzyme linked immunosorbent assay (ELISA). Competitive inhibition test further demonstrated that HCV E2 could significantly inhibit the binding of a positive phage clone to anti-hCD81 JS-81. Exogenous small peptide ATWVCGPCT contained by the positive phage clones showed aligned with the hCD81 sequence from 153-161 by sequence analyses. These results suggest that the selected ATWVCGPCT is a novel hCD81-like small peptide, which can block the binding site of HCV E2 for hCD81. It may be of further application on development of antiviral agents targeting the stage of HCV entry.

Amino Acid Sequence↗
PubMed2000

RNA aptamers to S-adenosylhomocysteine: kinetic properties, divalent cation dependency, and comparison with anti-S-adenosylhomocysteine antibody.

To explore the potential of RNA aptamers as small-molecule discriminating devices, we have characterized the properties of aptamers selected from a library of approximately 10(14) variants through their interaction with S-adenosylhomocysteine (SAH, AdoHcy). Competition studies with SAH and azaSAM analogues revealed that the Hoogsteen face of adenine is the main contributor to binding, whereas specificity for SAH is conferred by a secondary contact point at or near the sulfur/thioether of homocysteine (Hcy). Binding specificities were determined by both affinity chromatography and a novel method designed for the biosensor. The kinetic properties of individual aptamers, including the "classic" ATP aptamer that also emerged in our selection, were studied by biosensor analysis. Association rates were slow, but the complexes were stable, suggesting micro- to submicromolar affinities. A solution affinity of approximately 0.1 microM was found for the strongest binding variant under the conditions used for selection (5 mM Mg(2+)). Systematic studies of the effect of Mg(2+) and Mn(2+) on binding, however, revealed that the affinity of the aptamers could be substantially improved, and at optimized conditions of Mn(2+) the affinity of one of the aptamers approached that of an anti-SAH antibody with similar/identical binding specificity. Comparisons with the MAb suggest that the on rate is the limiting factor for high-affinity binding by these aptamers, and comparison with a truncated aptamer shows that shortening of RNA constructs may alter binding kinetics as well as sensitivity to ions.

Adenine↗
PubMed2003

Small-molecule switches for zinc finger transcription factors.

We have developed a general approach to generate selective small-molecule switches for zinc finger transcription factors based on the notion of structural complementation. A small molecule, 2-(4'-quinoline)benzimidazole (7), was identified by screening of a heterocycle library, which functionally rescues a structurally compromised transcription factor C7-F116A/H125G-VP16. Compound 7 induces the activity of the mutant zinc finger in a luciferase-based transactivation assay by about 18-fold at 100 muM concentration. Surface plasmon resonance measurements revealed that compound 7 enhances the affinity between the mutant C7 and its cognate DNA sequence by 16-fold while a structurally analogous compound, 2-(2'-naphthyl)benzimidazole (8), showed no affinity enhancement, indicating there is a specific interaction between compound 7 and the mutant zinc finger. Taken together, these results suggest that the partial affinity recovery of the mutant transcription factor may be the mechanism for the functional rescue of the zinc finger transcription factor by compound 7.

Amino Acid Sequence↗
PubMed2000

Discovery of novel, potent, and selective small-molecule CCR5 antagonists as anti-HIV-1 agents: synthesis and biological evaluation of anilide derivatives with a quaternary ammonium moiety.

The search for new small-molecule CCR5 antagonists by high-throughput screening (HTS) of the Takeda chemical library using [(125)I]RANTES and CHO/CCR5 cells led to the discovery of lead compounds (A, B) with a quaternary ammonium or phosphonium moiety, which were synthesized to investigate new MCP-1 receptor antagonists. A series of novel anilide derivatives 1 with a quaternary ammonium moiety were designed, synthesized, and tested for their CCR5 antagonistic activity. Through the optimization of lead compounds, we have found N,N-dimethyl-N-[4-[[[2-(4-methylphenyl)-6, 7-dihydro-5H-benzocyclohepten-8-yl]carbonyl]amino]benzyl]tetrahydr o-2 H-pyran-4-aminium chloride (1r, TAK-779) as a highly potent and selective nonpeptide CCR5 antagonist with a IC(50) value of 1.4 nM in the binding assay. Compound 1r also inhibited the replication of macrophage (M)-tropic HIV-1 (Ba-L strain) in both MAGI-CCR5 cells and PBMCs with EC(50) values of 1.2 and 3.7 nM, respectively. The synthesis and structure-activity relationships of 1r and its related compounds are detailed.

Amides↗
PubMed2000

MALDI-TOF MS analysis of a library of polymerizable cyclodextrin derivatives.

Polymerizable cyclodextrin derivatives (PCDs) have been proposed as candidates for use in dental therapeutics (Bowen, 1996; Bowen and Reed, 1997). Here, PCD "libraries" were synthesized by quasi-random reactions of 6 moles of methacrylic anhydride plus 6 moles of cyclic glutaric anhydride per mole of beta-cyclodextrin (BCD) in solution. BCD has 21 reactive sites on each of its molecules. These proportions were based on probability calculations, which predicted that the products should have a minimum of 2 polymerizable substituents and acidic ligand groups on practically every one of the diverse product molecules. Matrix-assisted laser desorption/ionization (MALDI) time of flight (TOF) mass spectrometry (MS) gave valuable information regarding the masses of molecular ions representing the molecules that made up the PCD libraries. For the MALDI-TOF MS analyses, small samples were analyzed by the successive application of 3 solutions to the sample holder: the matrix in acetone, the products in water, and sodium trifluoroacetate in water. The resulting spectra had > 40 envelopes of mass peaks above background. The ionic-abundance peak heights had quasi-Gaussian configurations, with central peaks having masses in the neighborhood of 2000 g/mol (Daltons). Regardless of structural permutations within each peak, the range of these peaks was between about 1500 g/mol and 2900 g/mol. This range of masses was in accord with, but perhaps somewhat more narrow than, that predicted by the statistical method, which was based on equal reactivity of all hydroxyl groups. Analysis by MALDI-TOF MS gave valuable data regarding the masses, structures, and characteristics of the products formed and provided unanticipated information to facilitate improvements in future PCD syntheses.

Acetone↗
PubMed2002

The application of multi-component reactions in drug discovery.

Multi-component reactions (MCRs) enable the facile, automated and high throughput generation of small organic molecules. MCRs have been used to create diversity oriented and biased combinatorial libraries, to accomplish the synthesis of highly complex natural products as well as for the large-scale production of drug candidates. This provides medicinal chemists with a powerful tool to create novel chemical diversity, matching the space of biological targets with relevant chemistry. The discovery of novel MCRs has become an increasingly active area of research, yielding novel chemical scaffolds for drug discovery efforts.

Animals↗
PubMed2001

The design and synthesis of noncovalent factor Xa inhibitors.

Thrombosis is a major cause of mortality in the industrialized world. Therefore, the control of blood coagulation has become a major target for new therapeutic agents. One attractive approach is the inhibition of factor Xa (fXa), the enzyme directly responsible for thrombin generation. In this review we describe our approaches in the design and synthesis of small molecule, noncovalent fXa inhibitors. Rational drug design and selective screening of our GPIIb/IIIa library afforded several lead compounds for our fXa program. Following-up the leads in the isoxazoline series led to potent fXa inhibitors such as SF303 and SK509 with only one basic group. The isoxazole series was then designed to remove the chiral center in the isoxazoline ring, and this effort led to SA862 which has subnanomolar fXa affinity. Optimizing the core structure generated a series of novel five-membered ring heterocycles substituted with benzamidine, which are potent fXa inhibitors. Further optimization in the pyrazole series resulted in the discovery of fXa inhibitors such as SN429 with picomolar fXa affinity. Efforts to improve the oral bioavailability by lowering the basicity of these compounds, while simultaneously maintaining potency against fXa, culminated in the discovery of DPC 423. DPC 423 was selected for clinical evaluation as a potent and orally bioavailable fXa inhibitor.

Animals↗