Design, synthesis and biological activity of a targeted library of potential tryptase inhibitors

We have designed, synthesized, and tested two small collections of potential tryptase inhibitors. The first library consists of diversely N-substituted 3-aminopiperidin-2-ones 6, and the second (compounds 7) was prepared by dimerising compounds 6 through the 3-amino function using diverse carbon chains. We have established efficient routes for obtaining 6 both in solution and on solid supports. We have also compared the dimerisation on-resin and in solution. Four of the compounds showed a high degree of tryptase inhibition at 1 microM, but none surpassed the tryptase inhibition activity of BABIM.     

Synthesis and screening of a molecularly imprinted polymer library targeted for penicillin G

A library of molecularly imprinted polymers (MIPs) was synthesized by radical bulk polymerization using the beta-lactam antibiotic penicillin G as the template. Diversity of the library was obtained by combining various functionalized monomers and cross-linkers and by varying the stoichiometry and the concentration of the components in the prepolymerization mixtures. The library was screened for selectivity to penicillin G by a radioligand binding assay and was compared to a corresponding control library. The best MIP candidate, showing the highest selectivity for penicillin G, was prepared from methacrylic acid and trimethylolpropane trimethacrylate as the functionalized monomer and cross-linker, respectively. Cross-reactivity studies with other beta-lactam antibiotics showed a low cross-reactivity of penicillin V (15%), ampicillin (16%), and amoxicillin (19%). Nafcillin and oxacillin showed less cross-reactivity (<1%). Cross-reaction with a cephalosporin antibiotic (cephapirin) and structurally nonrelated antibiotics (chloramphenicol, tetracycline, dapsone, and erythromycin) was less than 0.01%.     

Parallel synthesis and antimalarial screening of a 4-aminoquinoline library

Due to growing problems with drug resistance, there is an outstanding need for new, cost-effective drugs for the treatment of malaria. The 4-aminoquinolines have provided a number of useful antimalarials, and Plasmodium falciparum, the causative organism for the most deadly form of human malaria, is generally slow to develop resistance to these drugs. Therefore, diverse screening libraries of quinolines continue to be useful for antimalarial drug discovery. We report herein the development of an efficient method for producing libraries of 4-aminoquinolines variant in the side chain portion of the molecule. The effects of these substitutions were evaluated by screening this library for activity against P. falciparum, revealing four potent compounds active against drug-resistant strains.     

Strategy for discovering chemical inhibitors of human cyclophilin a: focused library design, virtual screening, chemical synthesis and bioassay

The discovery of cyclophilin A (CypA) inhibitor is now of special interest in the treatment of immunological disorders. In this work, using a strategy integrating focused combinatorial library design, virtual screening, chemical synthesis, and bioassay, a series of novel small molecular CypA inhibitors have been discovered. First, using the fragments taken from our previously discovered CypA inhibitors (Bioorg. Med. Chem. 2006, 14, 2209-2224) as building blocks, we designed a focused combinatorial library containing 255 molecules employing the LD1.0 program (J. Comb. Chem. 2005, 7, 398-406) developed by us. Sixteen compounds (1a-e, 2a-b, 3a-b, and 4a-g) were selected by using virtual screening against the X-ray crystal structure of CypA as well as druglike analysis for further synthesis and bioassay. All these sixteen molecules are CypA binders with binding affinities (K(D) values) ranging from 0.076 to 41.0 microM, and five of them (4a, 4c, and 4e-g) are potent CypA inhibitors with PPIase inhibitory activities (IC(50) values) of 0.25-6.43 microM. The hit rates for binders and inhibitors are as high as 100% and 31.25%, respectively. Remarkably, both the binding affinity and inhibitory activity of the most potent compound increase approximately 10 times than that of the most active compound discovered previously. The high hit rate and the high potency of the new CypA inhibitors demonstrated the efficiency of the strategy for focused library design and screening. In addition, the novel chemical entities reported in this study could be leads for discovering new therapies against the CypA pathway.     

A model of the human M2 muscarinic acetylcholine receptor

The M₂ muscarinic acetylcholine receptor belongs to the family of rhodopsin like G-Protein Coupled Receptors. This subtype of muscarinic receptors is of special interest because it bears, aside from an orthosteric binding site, also an allosteric binding site. Based on the X-ray structure of bovine rhodopsin a complete homology model of the human M₂ receptor was developed. For the orthosteric binding site point mutations and binding studies with different agonists and antagonists are available. This knowledge was utilized for an initial verification of the M₂ model. Allosteric modulation of activity is mediated by structurally different ligands such as gallamine, caracurine V salts or W84 (a hexamethonium-derivative). Caracurine V derivatives with different affinities to M₂ were docked using GRID-fields. Subsequent molecular dynamics simulations yielded different binding energies based on diverse electrostatic and lipophilic interactions. The calculated affinities are in good agreement to experimentally determined affinities.     

On homology modeling of the M2 muscarinic acetylcholine receptor subtype

Twelve homology models of the human M₂ muscarinic receptor using different sets of templates have been designed using the Prime program or the modeller program and compared to crystallographic structure (PDB:3UON). The best models were obtained using single template of the closest published structure, the M₃ muscarinic receptor (PDB:4DAJ). Adding more (structurally distant) templates led to worse models. Data document a key role of the template in homology modeling. The models differ substantially. The quality checks built into the programs do not correlate with the RMSDs to the crystallographic structure and cannot be used to select the best model. Re-docking of the antagonists present in crystallographic structure and relative binding energy estimation by calculating MM/GBSA in Prime and the binding energy function in YASARA suggested it could be possible to evaluate the quality of the orthosteric binding site based on the prediction of relative binding energies. Although estimation of relative binding energies distinguishes between relatively good and bad models it does not indicate the best one. On the other hand, visual inspection of the models for known features and knowledge-based analysis of the intramolecular interactions allows an experimenter to select overall best models manually.     

Acetylcholinesterase immobilized on modified magnetic beads as a tool for screening a compound library

Acetylcholinesterase (AChE) from Electrophorus electricus was immobilized on the surface of amino-modified magnetic beads (AChE-MB), and its activity evaluated by the quantification of acetylcholine hydrolysis. A reference mixture composed of AChE binders (galanthamine and a probe coumarin, K _i = 0.031 ± 0.010 μM) and non-binders (ketamine and propranolol) was used to probe the fishing assay. The performance of the bioconjugation assay was demonstrated with a library of 12 reference coumarins from which two ligands were directly identified by LC-MS/MS in a single assay, demonstrating the usefulness of this approach.

A bioconjugate-screening assay with AChE-modified magnetic beads was developed to direct identification of AChE binders, in mixtures, by LC-MS/MS. A reference mixture of twelve coumarins was used and, the two ligands were identified.

     

Rational principles of compound selection for combinatorial library design

It is practically impossible in a short period of time to synthesize and test all compounds in any large exhaustive chemical library. We discuss rational approaches to selecting representative subsets of virtual libraries that help direct experimental synthetic efforts for both targeted and diverse library design. For targeted library design, we consider principles based on the similarity to lead molecules. In the case of diverse library design, we discuss algorithms aimed at the selection of both diverse and representative subsets of the entire chemical library space. We illustrate methodologies with several practical examples.     

Regioselective synthesis and initial evaluation of a folate receptor targeted rhaponticin prodrug

To improve the therapeutic effect of rhaponticin(RHA),a folate receptor(FR) targeted RHA prodrug was designed and regioselectively synthesized by utilizing a hydrophilic peptide spacer linked to folic acid(FA) via a releasable disulfide linker.A series of biological evaluation was investigated in vitro and in vivo.The positive results of biological investigations warrant further preclinical study before this novel targeted chemotherapeutic is considered for clinical investigation.     

Combinatorial organic materials research (COMR): design,synthesis and screening of a 225-membered materials library of liquid crystalline fluorinated p-quaterphenyls

The rapid solution phase synthesis of novel liquid crystalline materials is demonstrated by utilising combinatorial and parallel methods for the preparation of a library of 225 differently fluorinated 4,4"-dipropyl-p-quaterphenyls. Chemical diversity was introduced into the growing oligomers via a convergent synthetic sequence of iodinations and Suzuki cross-couplings by using various fluorinated phenyl building blocks. A highly efficient rapid parallel purification method was developed that provided HPLC-pure library members in amounts sufficient for the characterization of bulk properties.     

Dendrimer-based prodrugs: design, synthesis, screening and biological evaluation

Dendrimers are a new class of artificial macromolecules with well-defined hyperbranched structures which enable bio-active molecules such as drugs to be presented in a highly multi-valent fashion. Covalent conjugation of drugs to the surface of dendrimers can be easily achieved either by direct chemical reactions between dendrimers and drug molecules including esterification and amidation or through cleavable linkers, depending on the functional groups on the surface of dendrimers. The pharmacological properties of these dendrimer-based prodrugs such as biocompatibility, biodistribution, biostability, bioadhesion and biopermeability can be modulated by further modifying dendrimers with specific functional molecules to fit a specific medicinal purpose. In this mini-review, recent advances on the use of dendrimers as prodrug nano-scaffolds were briefly demonstrated. The design and synthesis of dendrimer-based prodrugs as well as screening their intrinsic properties in biological systems were fully discussed.     

The synthesis and biological characterization of a ceramide library

A facile synthesis of a combinatorial ceramide library and their activities in the NF-kappaB pathway and in apoptosis induction/prevention were demonstrated. A novel NF-kappaB activating molecule was discovered among ceramide containing beta-galactose, and the structural requirements of ceramides for apoptosis induction was elucidated.     

Tubulin targeted antimitotic agents based on adamantane lead compound: synthesis,SAR and molecular modeling

1. Download : Download high-res image (173KB)
2. Download : Download full-size image

     

The design and synthesis of a herbicide targeted library of N-[1-(1,3-benzoxazol-2-yl)alkyl]-6-alkyl-1,3,5-triazine-2,4-diamines

Amino acids were immobilised by attaching them via a carbamate linker to Wang resin. These intermediates were converted to 1-(1,3-benzoxazol-2-yl)alkanamines over three steps, followed by coupling with 4-alkyl-6-chloro-1,3,5-triazine-2-amines to furnish the desired N-[1-(1,3-benzoxazol-2-yl)alkyl]-6-alkyl-1,3,5-triazine-2,4-diamines. Physico-chemical property profiles were used to support design and development of a combinatorial library. The synthetic methodology described herein was validated with the production of a herbicide targeted library of 300 members.