Showing papers in "ChemMedChem in 2009"

Further evidence of the anti-inflammatory effects of silver nanoparticles.

Abstract: The production of pure silver in nanoparticle size has opened new dimensions in the clinical use of this precious metal. We and others have demonstrated previously that silver nanoparticles (nAg) possess efficient antimicrobial activity. Herein we show they may also have significant anti-inflammatory effects in a postoperative peritoneal adhesion model. This finding provides further insight into the biological actions of nAg as well as a potentially novel therapy for peritoneal adhesions in clinical surgery.With the advent of nanoscience, pure silver can now be made into nanometer-sized particles. As a result, we are able to explore the potentially beneficial properties of pure silver. In our previous study using a burn wound model in mice, we demonstrated that besides antibacterial action, silver nanoparticles (nAg) appear to have anti-inflammatory properties. Herein we further confirm the anti-inflammatory effects of nAg and explore their potential clinical application through a postoperative peritoneal adhesion model. We also elucidate the potential mechanism of action of silver. Our in vitro and in vivo experimental findings show that nAg are effective at decreasing inflammation in peritoneal adhesions without significant toxic effects. This study thus provides further evidence for and contributes to the understanding of the anti-inflammatory properties of nAg and may also give a novel therapeutic direction for the prevention of postoperative adhesions.

Discovery of Riociguat (BAY 63-2521): A Potent, Oral Stimulator of Soluble Guanylate Cyclase for the Treatment of Pulmonary Hypertension

Abstract: Soluble guanylate cyclase (sGC) is a key signal-transduction enzyme activated by nitric oxide (NO). Impairments of the NO-sGC signaling pathway have been implicated in the pathogenesis of cardiovascular and other diseases. Direct stimulation of sGC represents a promising therapeutic strategy particularly for the treatment of pulmonary hypertension (PH), a disabling disease associated with a poor prognosis. Previous sGC stimulators such as the pyrazolopyridines BAY 41-2272 and BAY 41-8543 demonstrated beneficial effects in experimental models of PH, but were associated with unfavorable drug metabolism and pharmacokinetic (DMPK) properties. Herein we disclose an extended SAR exploration of this compound class to address these issues. Our efforts led to the identification of the potent sGC stimulator riociguat, which exhibits an improved DMPK profile and exerts strong effects on pulmonary hemodynamics and exercise capacity in patients with PH. Riociguat is currently being investigated in phase III clinical trials for the oral treatment of PH.

Aryloxy Phosphoramidate Triesters: a Technology for Delivering Monophosphorylated Nucleosides and Sugars into Cells

Abstract: Prodrug technologies aimed at delivering nucleoside monophosphates into cells (protides) have proved to be effective in improving the therapeutic potential of antiviral and anticancer nucleosides. In these cases, the nucleoside monophosphates are delivered into the cell, where they may then be further converted (phosphorylated) to their active species. Herein, we describe one of these technologies developed in our laboratories, known as the phosphoramidate protide method. In this approach, the charges of the phosphate group are fully masked to provide efficient passive cell-membrane penetration. Upon entering the cell, the masking groups are enzymatically cleaved to release the phosphorylated biomolecule. The application of this technology to various therapeutic nucleosides has resulted in improved antiviral and anticancer activities, and in some cases it has transformed inactive nucleosides to active ones. Additionally, the phosphoramidate technology has also been applied to numerous antiviral nucleoside phosphonates, and has resulted in at least three phosphoramidate-based nucleotides progressing to clinical investigations. Furthermore, the phosphoramidate technology has been recently applied to sugars (mainly glucosamine) in order to improve their therapeutic potential. The development of the phosphoramidate technology, mechanism of action and the application of the technology to various monophosphorylated nucleosides and sugars will be reviewed.

The Emerging Therapeutic Potential of Histone Methyltransferase and Demethylase Inhibitors

Abstract: Epigenetics is defined as heritable changes to the transcriptome that are independent of changes in the genome. The biochemical modifications that govern epigenetics are DNA methylation and posttranslational histone modifications. Among the histone modifications, acetylation and deacetylation are well characterized, whereas the fields of histone methylation and especially demethylation are still in their infancy. This is particularly true with regard to drug discovery. There is strong evidence that these modifications play an important role in the maintenance of transcription as well as in the development of certain diseases. This article gives an overview of the mechanisms of action of histone methyltransferases and demethylases, their role in the formation of certain diseases, and available inhibitors. Special emphasis is placed on the strategies that led to the first inhibitors which are currently available and the screening approaches that were used in that process.

Tacrine-melatonin hybrids as multifunctional agents for Alzheimer's disease, with cholinergic, antioxidant, and neuroprotective properties.

Abstract: Tacrine-melatonin hybrids were designed and synthesized as new multifunctional drug candidates for Alzheimer's disease. These compounds may simultaneously palliate intellectual deficits and protect the brain against both beta-amyloid (A beta) peptide and oxidative stress. They show improved cholinergic and antioxidant properties, and are more potent and selective inhibitors of human acetylcholinesterase (hAChE) than tacrine. They also capture free radicals better than melatonin. Molecular modeling studies show that these hybrids target both the catalytic active site (CAS) and the peripheral anionic site (PAS) of AChE. At sub-micromolar concentrations they efficiently displace the binding of propidium iodide from the PAS and could thus inhibit A beta peptide aggregation promoted by AChE. Moreover, they also inhibit A beta self-aggregation and display neuroprotective properties in a human neuroblastoma line against cell death induced by various toxic insults, such as A beta(25-35), H(2)O(2), and rotenone. Finally, they exhibit low toxicity and may be able to penetrate the central nervous system according to an in vitro parallel artificial membrane permeability assay for the blood-brain barrier (PAMPA-BBB).

Pharmacological promiscuity: dependence on compound properties and target specificity in a set of recent Roche compounds.

Abstract: What parameters determine promiscuity? A compound's potential for promiscuity (pharmacological activity at multiple targets) may be influenced by molecular parameters such as ionization state, lipophilicity, and molecular weight. In an analysis of recent Roche compounds we found that a positive charge is an important determinant for potential promiscuity; aminergic activity was found to be the main reason for overt promiscuity. The term “pharmacological promiscuity” describes a compound's pharmacological activity at multiple targets. Pharmacological promiscuity is undesired in typical drug discovery projects, which focus on the “one drug–one target” paradigm. Off-target activity can lead to adverse drug reactions, or can obscure pharmacodynamic effects in animal models. Therefore, advanced lead compounds, pharmacological tool compounds, and drug candidates are usually screened against panels of safety-relevant targets to detect unwanted pharmacological activities. To identify determinants of pharmacological promiscuity, we compared the panel screening outcomes of 213 recent Roche compounds with their molecular properties. Pronounced promiscuity was not observed below a threshold Clog P value of 2. For basic compounds, the propensity for weak off-target activity was found to increase with calculated basicities, whereas the potential for strong off-target activity depends more qualitatively on the presence of a positive charge at physiological pH. Compounds originating from projects with an aminergic receptor or transporter as a therapeutic target are particularly prone to promiscuity; the promiscuity of such compounds is mainly caused by their activity at other aminergic targets in the screening panel.

Triclosan Derivatives: Towards Potent Inhibitors of Drug-Sensitive and Drug-Resistant Mycobacterium tuberculosis.

Abstract: Triclosan has been previously shown to inhibit InhA, an essential enoyl acyl carrier protein reductase of mycolic acid biosynthesis, whose inhibition leads to the lysis of Mycobacterium tuberculosis. Using a structure-based drug design approach, a series of 5-substituted derivatives of triclosan was developed. Two groups of triclosan derivatives with alkyl and aryl substituents, respectively, were identified with dramatically enhanced potency against purified InhA. The most efficacious inhibitor displayed an IC50 value of 21 nM, which was 50-fold more potent than triclosan. X-ray crystal structures of InhA in complex with four triclosan derivatives revealed the structural basis for the inhibitory activity. Six selected triclosan derivatives were tested against isoniazid-sensitive and resistant strains of M. tuberculosis. Among those, the best inhibitor had an MIC value of 4.7 µg/mL (13 µM), which represents a tenfold improvement over the bacteriocidal activity of triclosan. A subset of these triclosan analogs was more potent than isoniazid against two isoniazid-resistant M. tuberculosis strains, demonstrating the significant potential for structure-based design in the development of next generation antitubercular drugs.

PAMAM dendrimers mediate siRNA delivery to target Hsp27 and produce potent antiproliferative effects on prostate cancer cells.

Abstract: RNA interference (RNAi) holds great promise for the treatment of inherited and acquired diseases, provided that safe and efficient delivery systems are available. Herein we report that structurally flexible triethanolamine (TEA) core PAMAM dendrimers are able to deliver an Hsp27 siRNA effectively into prostate cancer (PC-3) cells by forming stable nanoparticles with siRNA, protecting the siRNA nanoparticles from enzymatic degradation, and enhancing cellular uptake of siRNA. The Hsp27 siRNA resulted in potent and specific gene silencing of heat-shock protein 27, an attractive therapeutic target in castrate-resistant prostate cancer. Silencing of the hsp27 gene led to induction of caspase-3/7-dependent apoptosis and inhibition of PC-3 cell growth in vitro. In addition, the siRNA-dendrimer complexes are non-cytotoxic under the conditions used for siRNA delivery. Altogether, TEA core PAMAM dendrimer-mediated siRNA delivery, in combination with RNAi that specifically targets Hsp27, may constitute a promising approach for combating castrate-resistant prostate cancer, for which there is no efficacious treatment.

Molecular Modeling and Molecular Dynamics Studies of Hydralazine with Human DNA Methyltransferase 1

Abstract: DNA methyltransferases (DNMTs) are a family of enzymes that methylate DNA at the C5 position of cytosine residues, and their inhibition is a promising strategy for the treatment of various developmental and proliferative diseases, particularly cancers. In the present study, a binding model for hydralazine, with a validated homology model of human DNMT, was developed by the use of automated molecular docking and molecular dynamics simulations. The docking protocol was validated by predicting the binding mode of 2'-deoxycytidine, 5-azacytidine, and 5-aza-2'-deoxycytidine. The inhibitory activity of hydralazine toward DNMT may be rationalized at the molecular level by similar interactions within the binding pocket (e.g., by a similar pharmacophore) as established by substrate-like deoxycytidine analogues. These interactions involve a complex network of hydrogen bonds with arginine and glutamic acid residues that also play a major role in the mechanism of DNA methylation. Despite the different scaffolds of other non-nucleoside DNMT inhibitors such as procaine and procainamide, the current modeling work reveals that these drugs exhibit similar interactions within the DNMT1 binding site. These findings are valuable in guiding the rational design and virtual screening of novel DNMT inhibitors.

Pharmacophore-Based Discovery of Small-Molecule Inhibitors of Protein–Protein Interactions between HIV-1 Integrase and Cellular Cofactor LEDGF/p75

Abstract: The cellular protein lens epithelium-derived growth factor, or transcriptional coactivator p75 (LEDGF/p75), plays a crucial role in HIV integration. The protein-protein interactions (PPIs) between HIV-1 integrase (IN) and its cellular cofactor LEDGF/p75 may therefore serve as targets for the development of new anti-HIV drugs. In this work, a structure-based pharmacophore model for potential small-molecule inhibitors of HIV-1 IN-LEDGF/p75 interaction was developed using the LigandScout software. The 3D model obtained was used for virtual screening of our in-house chemical database, CHIME, leading to the identification of compound CHIBA-3002 as an interesting hit for further optimization. The rational design, synthesis and biological evaluation of four derivatives were then carried out. Our studies resulted in the discovery of a new and more potent small molecule (7, CHIBA-3003) that is able to interfere with the HIV-1 IN-LEDGF/p75 interaction at micromolar concentration, representing one of the first compounds to show activity against these specific PPIs. Docking simulations were subsequently performed in order to investigate the possible binding mode of our new lead compound to HIV-1 IN. This study is a valid starting point for the identification of anti-HIV agents with a different mechanism of action from currently available antiviral drugs.

Recent Approaches to Antifungal Therapy for Invasive Mycoses

Abstract: Invasive fungal infections with primary and opportunistic mycoses have become increasingly common in recent years and pose a major diagnostic and therapeutic challenge. They represent a major area of concern in today's medical fraternity. The occurrence of invasive fungal diseases, particularly in AIDS and other immunocompromised patients, is life-threatening and increases the economic burden. Apart from the previously known polyenes and imidazole-based azoles, newly discovered triazoles and echinocandins are more effective in terms of specificity, yet some immunosuppressed hosts are difficult to treat. The main reasons for this include antifungal resistance, toxicity, lack of rapid and microbe-specific diagnoses, poor penetration of drugs into sanctuary sites, and lack of oral or intravenous preparations. In addition to combination antifungal therapy, other novel antimycotic treatments such as calcineurin signaling pathway blockers and vaccines have recently emerged. This review briefly summarizes recent developments in the pharmacotherapeutic treatment of invasive fungal infections.

Combined Pharmacophore Modeling, Docking, and 3D QSAR Studies of ABCB1 and ABCC1 Transporter Inhibitors

Abstract: Quinazolinones, indolo- and pyrrolopyrimidines with inhibitory effects toward ABCB1 (P-gp) and ABCC1 (MRP1) transporters were studied by pharmacophore modeling, docking, and 3D QSAR to describe the binding preferences of the proteins. The pharmacophore overlays between dual and/or highly selective inhibitors point to binding sites of different topology and physiochemical properties for MRP1 and P-gp. Docking of selective inhibitors into the P-gp binding cavity by the use of a structural model based on the recently resolved P-gp structure confirms the P-gp pharmacophore features identified, and reveals the interactions of some functional groups and atoms in the structures with particular protein residues. The 3D QSAR analysis of the dual-effect inhibitors allows satisfactory prediction of the selectivity index of the compounds and outlines electrostatics as most important for selectivity. The results from the combined modeling approach complement each other and could improve our understanding of the protein-ligand interactions involved, and could aid in the development of highly selective and potent inhibitors of P-gp and MRP1.

Development of novel thiazolopyrimidines as CDC25B phosphatase inhibitors.

Abstract: The development of CDC25 phosphatase inhibitors is an interesting approach toward new antitumor agents, as CDC25 play key roles in cell-cycle regulation and are overexpressed in numerous cancers. We previously reported a novel compound belonging to the thiazolopyrimidine family that inhibits CDC25 activity with an IC(50) value of 13 microM and displays cytotoxic properties against HeLa cells. Structural modifications were subsequently conducted on this new pharmacophore which led to a library of 45 thiazolopyrimidines. Regarding the in vitro effects, 14 compounds inhibit CDC25B with IC(50)<20 microM, with the most efficient inhibitor 44 improving the potency to 4.5 microM. Steady-state kinetics were performed and showed a mixed inhibition pattern for all tested compounds. Furthermore, 44 was able to revert the bypass of genotoxicity-induced G(2) arrest upon CDC25B overexpression, indicating that this compound targets the dual-specificity phosphatase in cultured cells. Finally, the cytotoxic activities of the compounds were determined against two human cancer cell lines. The results indicate that the prostatic LNCaP cell line is more sensitive to these derivatives than the pancreatic adenocarcinoma MiaPaCa-2 line. With its interesting enzymatic and cellular properties, compound 44 appears to be a promising CDC25B inhibitor for further development.

Synthetic Multimeric Heptyl Mannosides as Potent Antiadhesives of Uropathogenic Escherichia coli

Abstract: Urinary tract infections caused by uropathogenic Escherichia coli presents a serious communal and nosocomial health problem initiated by bacterial adhesion to the bladder cells. E. coli expresses fimbriae with a mannose-binding adhesin, FimH, at the tip. Heptyl alpha-D-mannoside (HM) is a nanomolar inhibitor of this lectin, preventing adhesion of type 1-piliated E. coli and reducing bacteria levels in a murine cystitis model. Herein, we described the synthesis of multimeric heptyl-mannosides with valencies ranging from one to four by copper-catalyzed azide alkyne cycloaddition (CuAAC). Biological evaluation of the multivalent compounds revealed an increase in potency compared to HM. Inhibition of bladder cell binding highlighted a promising tetravalent derivative with inhibitory concentrations 6000- and 64-fold lower than mannose and HM respectively.

Classification of organic molecules by molecular quantum numbers.

Abstract: The periodic table classifies elements by increasing atomic number in periods following the principal quantum number, and allows their physicochemical properties to be rationalized. Herein, we propose a related system for organic molecules based on 42 molecular quantum numbers (MQNs), defined here as counts for simple structural features such as atom, bond and ring types, creating a multidimensional grid called MQN space. In analogy to the elements and their isotopes grouped in each entry of the periodic table, MQN isomers have identical MQNs and occupy the same position in MQN space. The MQN system is able to analyze large molecular databases and clusters compounds with similar structure, physicochemical properties and bioactivities, as illustrated for the databases ZINC and GDB-11. Organic molecules can be named by systematic nomenclature, or coded in line notations such as SMILES or InChI. These methods achieve an exact description of the molecular structure, but only provide a unidimensional classification, which is of limited use for analyzing molecular diversity. More recently, chemical space has emerged as a concept to classify large molecular databases. Chemical space is most often represented as a property space whose dimensions measure a combination of structural parameters and predicted physicochemical properties, allowing useful data mining, such as the quest for natural products analogues. While many descriptors of molecular structures and properties of varying complexity are known and may be used for defining chemical space, we set out to test whether a system based only on counts for simple structural features (MQNs) might produce an easily accessible and logical classification system for organic molecules. MQNs were considered counting atoms and bonds, polarity and topology (Table 1). MQNs were determined for the ZINC database, listing 8.4 million organic molecules, and the GDB11 database, listing 26.4 million possible molecules with up to 11 atoms of C, N, O, F, giving a total of 6 501 005 MQN combinations, or MQN bins (Table 2). Molecules with identical MQNs (MQN isomers) were strongly related structural isomers (Figure 1). Principal component analysis (PCA) showed that MQN space organizes molecules by structural types. For ZINC, 73 % of the variability is visible in the PC1/PC2 plane. PC1 mostly represents molecular size (Figure 2 a, and figure S1 in the Supporting Information). Molecules appear in elongated clusters distributed along the ascending diagonal with increasing number of rings (Figure 2 b). The number of rotatable bonds (rbc) representing molecular flexibility, the number of H-bond acceptor sites (hbam, counting nonbonding electron pairs on Nand O-atoms) and the topological surface area (TPSA in ) indicative of polarity, all increase along the descending diagonal (Figure 2 c, d & e). The calculated water–octanol partition coefficient (clog P) follows molecular size and, in part, rings and hbam (Figure 2 f). PCA of GDB-11 shows similar patterns in the PC1/PC2 plane, containing 63 % of the variability (Supporting Information, figure S2/ S3). Interestingly, compounds with similar bioactivities form groups in MQN space. Ranking by MQN distance (calculated as [a] Dr. K. T. Nguyen, L. C. Blum, R. van Deursen, Prof. Dr. J.-L. Reymond Departement of Chemistry and Biochemistry, University of Berne Freiestrasse 3, 3012 Berne (Switzerland) Fax: (+ 41) 31-631-8057 E-mail : jean-louis.reymond@ioc.unibe.ch Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/cmdc.200900317. Table 1. Molecular quantum numbers.

Synthesis, biological evaluation of 1,1-diarylethylenes as a novel class of antimitotic agents.

Abstract: The cytotoxic activities of 23 new isocombretastatin A derivatives with modifications on the B-ring were investigated. Several compounds exhibited excellent antiproliferative activity at nanomolar concentrations against a panel of human cancer cell lines. Compounds isoFCA-4 (2 e), isoCA-4 (2 k) and isoNH(2)CA-4 (2 s) were the most cytotoxic, and strongly inhibited tubulin polymerization with IC(50) values of 4, 2 and 1.5 microM, respectively. These derivatives were found to be 10-fold more active than phenstatin and colchicine with respect to growth inhibition but displayed similar activities as tubulin polymerization inhibitors. In addition, cell cycle arrest in the G(2)/M phase and subsequent apoptosis was observed in three cancer cell lines when treated with these compounds. The disruptive effect of 2 e, 2 k and 2 s on the vessel-like structures formed by human umbilical vein endothelial cells (HUVEC) suggest that these compounds may act as vascular disrupting agents. Both compounds 2 k and 2 s have the potential for further prodrug modification and development as vascular disrupting agents for treatment of solid tumors.

Virtual screening and biological characterization of novel histone arginine methyltransferase PRMT1 inhibitors

Abstract: Lysine and arginine methyltransferases participate in the posttranslational modification of histones and regulate key cellular functions. Protein arginine methyltransferase 1 (PRMT1) has been identified as an essential component of mixed lineage leukemia (MLL) oncogenic complexes, revealing its potential as a novel therapeutic target in human cancer. The first potent arginine methyltransferase inhibitors were recently discovered by random- and target-based screening approaches. Herein we report virtual and biological screening for novel inhibitors of PRMT1. Structure-based virtual screening (VS) of the Chembridge database composed of 328 000 molecules was performed with a combination of ligand- and target-based in silico approaches. Nine inhibitors were identified from the top-scored docking solutions; these were experimentally tested using human PRMT1 and an antibody-based assay with a time-resolved fluorescence readout. Among several aromatic amines, an aliphatic amine and an amide were also found to be active in the micromolar range.

Discovery of a Potent, CNS‐Penetrant Orexin Receptor Antagonist Based on an N,N‐Disubstituted‐1,4‐diazepane Scaffold that Promotes Sleep in Rats

Abstract: Silent Night: Antagonism of the orexin (or hypocretin) system has recently been identified as a novel mechanism for the treatment of insomnia. Herein, we describe discovery of a dual (OX(1)R/OX(2)R) orexin receptor antagonist featuring a 1,4-diazepane central constraint that blocks orexin signaling in vivo. In telemetry-implanted rats, oral administration of this antagonist produced a decrease in wakefulness, while increasing REM and non-REM sleep.

Cytotoxicities and structure-activity relationships of natural and unnatural lamellarins toward cancer cell lines.

Abstract: Twenty-two naturally occurring and three unnatural lamellarins were synthesized and evaluated for their cytotoxicities against cancer cells. Across eleven cancer cell lines derived from six different cancer types, the IC(50) values of these compounds ranged from sub-nanomolar (0.08 nM) to micromolar (>97.0 microM). About one-fourth (6/25) and one-half (11/25) of these lamellarins are more potent than the positive control, etoposide, against at least six different cell lines and three different cell types, respectively. In general, lamellarins D, X, epsilon, M, N, and dehydrolamellarin J are significantly more potent than the other lamellarins. The IC(50) values were used to perform structure-activity relationship (SAR) studies by comparing the cytotoxic activities of several pairs of lamellarin structures that differ in selected substitution patterns. Our results not only reveal the importance of specific hydroxylation or methoxylation patterns for the first time, but also confirm prior findings and clarify some previous uncertainties.

Glycopeptide dendrimers with high affinity for the fucose-binding lectin LecB from Pseudomonas aeruginosa.

Abstract: The fucose-specific lectin LecB is implicated in tissue binding and biofilm formation by the opportunistic pathogen Pseudomonas aeruginosa, which causes severe respiratory tract infections mainly in immunocompromised patients or cancer patients undergoing chemotherapy. With a view to developing multivalent LecB inhibitors as novel antibacterial agents, a combinatorial library containing 15 625 tetravalent C-fucosyl peptide dendrimers with the basic structure (CFuc-X(6)X(5)X(4))(4)(LysX(3)X(2)X(1))(2)LysIleHisNH(2) (CFuc=alpha-L-fucosyl acetic acid, X(1-6)=amino acids, Lys=lysine branching) was screened for lectin binding using on-bead binding assays. Ten tetravalent and three octavalent dendrimers derived from the identified sequences were prepared by solid-phase peptide synthesis (SPPS), cleaved from the resin, and purified by preparative HPLC. Relative affinities of these soluble ligands to LecB were determined by an enzyme-linked lectin assay (ELLA). Strong binding was observed for tetravalent and octavalent ligands, with up to 440-fold enhancement in potency over fucose for the octavalent cationic dendrimer 2G3 (CFuc-LysPro)(8)(LysLeuPhe)(4)(LysLysIle)(2)LysHisIleNH(2)). Mono- and divalent controls showed affinities similar to fucose, highlighting the importance of multivalency for binding. Docking studies showed that the C-fucosyl group of the dendrimers can adopt the same binding mode as fucose itself, with the peptide arms protruding from the binding pocket and establishing specific contacts with the lectin.

Assessing the bioisosterism of the trifluoromethyl group with a protease probe.

Abstract: The bioisosterism of the trifluoromethyl group, namely its capacity to act as a replacement for groups with similar size or shape without substantially altering key biological properties such as binding affinity, remains a controversial issue. Until recently the most accepted idea was that CF3 and isopropyl groups are interchangeable, whereas CF3 was thought to be considerably bulkier than CH3. [1] However, a recent theory supported by careful analysis of van der Waals volumes and shapes of the CF3 group in comparison with various alkyl groups has suggested that CF3 is closer to the ethyl group in terms of steric effect, whereas the isopropyl group is larger. Considering the importance of the CF3 group in medicinal chemistry and drug discovery, we decided to investigate the issue of CF3 bioisosterism further, and to clarify it using an empirical “lock and key” approach. In fact, according to M ller et al. , replacement of alkyl residues by similarly sized fluoroalkyl groups in tight lipophilic pockets neither increases nor decreases binding affinity substantially. Therefore, we decided to exploit a suitable protease pocket as a steric probe to determine how effectively a CF3 group can be accommodated in comparison with methyl, ethyl, and isopropyl groups by measuring the inhibitory potency of the corresponding molecules. The choice of the protease was critical, because the abovelisted groups should be accommodated in a tight and deep hydrophobic pocket that has: 1) high affinity for CF3 and for the selected alkyl groups, 2) stringent steric features that can discriminate between steric size and shape, and 3) the possibility to place such groups in a remote position to minimize the risk of conformational changes in the ligands, or interference by other functions of the ligands or of the protease receptor. We identified the active site of matrix metalloprotease-9 (MMP-9; gelatinase B) as the ideal probe. In fact, MMP-9 has a tunnel-like and relatively shallow hydrophobic S1’ cavity, which is “shorter” than that of MMP-2 (gelatinase A, which is closely related from a structural standpoint). Furthermore, the bottom of the S1’ cavity of MMP-9 is partially blocked by the Arg 424 side chain, thus representing a potentially very selective steric probe for an MMP-9 inhibitor bearing a P1’ appendage with a CF3 group at the w-position. [6] The other challenging issue was the identification of suitable inhibitors. Barbiturates have been shown to be potent and selective inhibitors of several MMPs, including MMP-9. For example, compound A was described as a rather potent inhibitor of MMP-9 (IC50 = 20 nm). [8] Because the synthesis of fluorinated

A Second Generation of Carbamate-Based Fatty Acid Amide Hydrolase Inhibitors with Improved Activity in vivo

Abstract: The fatty acid ethanolamides are a class of signaling lipids that include agonists at cannabinoid and alpha type peroxisome proliferator-activated receptors (PPARalpha). In the brain, these compounds are primarily hydrolyzed by the intracellular serine enzyme fatty acid amide hydrolase (FAAH). O-aryl carbamate FAAH inhibitors such as URB597 are being evaluated clinically for the treatment of pain and anxiety, but interactions with carboxylesterases in liver might limit their usefulness. Here we explore two strategies aimed at overcoming this limitation. Lipophilic N-terminal substitutions, which enhance FAAH recognition, yield potent inhibitors but render such compounds susceptible to attack by broad-spectrum hydrolases and inactive in vivo. By contrast, polar electron-donating O-aryl substituents, which decrease carbamate reactivity, yield compounds, such as URB694, that are highly potent FAAH inhibitors in vivo and less reactive with off-target carboxylesterases. The results suggest that an approach balancing inhibitor reactivity with target recognition produces FAAH inhibitors that display significantly improved drug-likeness.

Design, Synthesis, and Biological Evaluation of Enantiomeric β-N-Acetylhexosaminidase Inhibitors LABNAc and DABNAc as Potential Agents against Tay-Sachs and Sandhoff Disease

Abstract: Combating glycolipid storage disorders: LABNAc was prepared in an efficient 11-step procedure from D-lyxonolactone. The enantiomer DABNAc was also prepared from L-lyxonolactone. Preliminary cellular studies indicate that these compounds may find utility as chemical chaperones for the treatment of Tay-Sachs and Sandhoff diseases. N-Acetylhexosaminidases are of considerable importance in mammals and are involved in various significant biological processes. In humans, deficiencies of these enzymes in the lysosome, resulting from inherited genetic defects, cause the glycolipid storage disorders Tay-Sachs and Sandhoff diseases. One promising therapy for these diseases involves the use of β-N-acetylhexosaminidase inhibitors as chemical chaperones to enhance the enzyme activity above sub-critical levels. Herein we describe the synthesis and biological evaluation of a potent inhibitor, 2-acetamido-1,4-imino-1,2,4-trideoxy-L-arabinitol (LABNAc), in a high-yielding 11-step procedure from D-lyxonolactone. The N-benzyl and N-butyl analogues were also prepared and found to be potent inhibitors. The enantiomers DABNAc and NBn-DABNAc were synthesised from L-lyxonolactone, and were also evaluated. The L-iminosugar LABNAc and its derivatives were found to be potent noncompetitive inhibitors of some β-N-acetylhexosaminidases, while the D-iminosugar DABNAc and its derivatives were found to be weaker competitive inhibitors. These results support previous work postulating that D-iminosugar mimics inhibit D-glycohydrolases competitively, and that their corresponding L-enantiomers show noncompetitive inhibition of these enzymes. Molecular modelling studies confirm that the spatial organisation in enantiomeric inhibitors leads to a different overlay with the monosaccharide substrate. Initial cell-based studies suggest that NBn-LABNAc can act as a chemical chaperone to enhance the deficient enzyme's activity to levels that may cause a positive pharmacological effect. LABNAc, NBn-LABNAc, and NBu-LABNAc are potent and selective inhibitors of β-N-acetylhexosaminidase and may be useful as therapeutic agents for treating adult Tay-Sachs and Sandhoff diseases.

2,3-Dihydro-1-benzofuran derivatives as a series of potent selective cannabinoid receptor 2 agonists: design, synthesis, and binding mode prediction through ligand-steered modeling.

Abstract: We recently discovered and reported a series of N-alkyl-isatin acylhydrazone derivatives that are potent cannabinoid receptor 2 (CB(2)) agonists. In an effort to improve the druglike properties of these compounds and to better understand and improve the treatment of neuropathic pain, we designed and synthesized a new series of 2,3-dihydro-1-benzofuran derivatives bearing an asymmetric carbon atom that behave as potent selective CB(2) agonists. We used a multidisciplinary medicinal chemistry approach with binding mode prediction through ligand-steered modeling. Enantiomer separation and configuration assignment were carried out for the racemic mixture for the most selective compound, MDA7 (compound 18). It appeared that the S enantiomer, compound MDA104 (compound 33), was the active enantiomer. Compounds MDA42 (compound 19) and MDA39 (compound 30) were the most potent at CB(2). MDA42 was tested in a model of neuropathic pain and exhibited activity in the same range as that of MDA7. Preliminary ADMET studies for MDA7 were performed and did not reveal any problems.

CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory.

Abstract: CypScore is an in silico approach for predicting the likely sites of cytochrome P450-mediated metabolism of druglike organic molecules. It consists of multiple models for the most important P450 oxidation reactions such as aliphatic hydroxylation, N-dealkylation, O-dealkylation, aromatic hydroxylation, double-bond oxidation, N-oxidation, and S-oxidation. Each of these models is based on atomic reactivity descriptors derived from surface-based properties calculated with ParaSurf and based on AM1 semiempirical molecular orbital theory. The models were trained with data derived from Bayer Schering Pharma's in-house MajorMetabolite Database with more than 2300 transformations and more than 800 molecules collected from the primary literature. The models have been balanced to allow the treatment of relative intramolecular, intra-chemotype, and inter-chemotype reactivities of the labile sites toward oxidation. The models were evaluated with promising hit rates on three public datasets of varying quality in the annotation of the experimental positions. For 39 well-characterized compounds from 14 in-house lead optimization programs, we could detect at least one major metabolite for the three highest-ranked positions in 87 % of the compounds and overall more than 62 % of all major metabolites, with promising true- to false-positive ratios of 0.9.

Thermodynamic optimisation in drug discovery: a case study using carbonic anhydrase inhibitors.

Abstract: Historically the early stages of drug discovery have been based on finding the highest affinity compounds that bind to the target of interest, with little consideration for the forces driving the binding event. The association constant (Ka) can be defined by the equation DG = RTln Ka, with DG =DH TDS. To fully describe Ka it would therefore be beneficial to characterize both of the thermodynamic terms (DH and DS) that drive this affinity for binding. The importance of separating affinity into its thermodynamic components is emphasized by the ubiquitous “enthalpy/entropy compensation effect”, where large changes in DH and DS tend to be of similar but opposite signs and there is no net change in affinity, despite potentially very different binding mode. It has been proposed by Freire, and Ward & Holdgate that it is advantageous, in terms of both potency and selectivity, to start from an enthalpically-driven lead. It can also be argued that choosing compounds with different binding modes increases the variety of chemical substrate for optimization, therefore reducing the risk of all the compounds encountering the same side effects. These points emphasize the need to measure thermodynamic signatures of lead compounds as early in the drug discovery process as possible. The only method that directly measures the thermodynamics of a binding event in solution is isothermal titration calorimetry (ITC). Even though ITC can give a full thermodynamic signature (DGobs, DHobs, DSobs and KB, obs) from a single experiment, the full utilization of the technique for lead optimization has been hampered by technical limitations requiring substantial quantities of reagents. In addition, data have frequently been collected from optimized, but varied, experimental conditions for a particular system, and without appropriate controls the interpretation of results between studies is difficult. Here, we demonstrate that with recent advances in ITC technology and comparing subtly modified ligands against the same target, under identical conditions, and with X-ray data support, thermodynamic measurements can provide medicinal chemists with another differentiator in their quest to discover the best lead compounds. Moreover, these data are informative to medicinal chemists as they are applicable to situations where a less complete biophysical analysis is possible. We chose human carbonic anhydrase (hCA II) as a favorable system for this investigation as there is already a wealth of both 3D structures and calorimetric data available, which has established this protein as the leading model system. Additionally, the protein binds benzene sulfonamides (BSAs) with a 1:1 stoichiometry and does not undergo gross conformational changes upon binding, providing an essentially thermodynamically closed system that will therefore not complicate interpretation of the binding thermodynamics. The binding of BSA to hCA II is driven mainly through four H bonds from the sulfonamide, two H bonds to the Zn co-factor (which is itself coordinated by three histidine residues: His 94, His 96 and His 119) and two H bonds to Thr 199. The dominance of this sulfonamide interaction means that any changes in the thermodynamics of binding caused by additions to the benzene ring may be small and therefore requires careful experimental design. In addition, the effect that aryl substituents may have in terms of electron-withdrawing effects etc. on the sulfonamide binding must also be considered. ITC analysis was performed on seventeen benzene sulfonamide derivatives (1–17) and three benzylamide para-substituted benzene sulfonamides (18–20) by titration into hCA II. In

Synthesis and Biological Evaluation of Chromium Bioorganometallics Based on the Antibiotic Platensimycin Lead Structure

Abstract: The recent discovery of the natural product platensimycin as a new antibiotic lead structure has triggered the synthesis of numerous organic derivatives for structure-activity relationship studies. Herein, we describe the synthesis, characterization and biological evaluation of the first organometallic antibiotic inspired by platensimycin. Two bioorganometallic compounds containing (eta(6)-pentamethylbenzene)Cr(CO)(3) (2) and (eta(6)-benzene)Cr(CO)(3) (3), linked by an amide bond to the aromatic part of platensimycin, were synthesized. Their antibiotic activities were tested against B. subtilis 168 (Gram positive) and E. coli W3110 (Gram negative) bacterial strains. Both compounds were found to be inactive against E. coli but derivative 2 inhibits B. subtilis growth at a moderate MIC value of 0.15 mM. To test the intrinsic toxicity of chromium, several chromium salts along with {eta(6)-(3-pentamethylphenyl propionic acid)}Cr(CO)(3) (5) and {eta(6)-(3-phenyl propionic acid)}Cr(CO)(3) (6) were tested against both bacterial strains. No activity was observed against E. coli for any of the compounds; B. subtilis growth was not inhibited by Cr(NO(3))(3) and only very weakly by 5, K(2)Cr(2)O(7) and Na(2)CrO(4) at MIC values of 0.5, 0.68 and 1.24 mM, respectively. Compounds 2, 3, 5 and 4 (the pure organic analogue of 2) show similar cytotoxicity against HeLa, HepG2 and HT-29 mammalian cell lines. Furthermore, the cellular uptake and the intracellular distribution of compounds 2, 3 and Cr(NO(3))(3) in B. subtilis were studied using atomic absorption spectroscopy to gain insight in to the possible cellular targets. Compound 2 was found to be readily taken up and distributed almost equally among cytosol, cell debris and cell membrane in B. subtilis.

Small‐Molecule Inhibitors of Store‐Operated Calcium Entry

Abstract: Controlled variation in intracellular calcium concentration is a key component of the immune response signaling pathway in lymphocytes Store-operated calcium entry (SOCE) in these cells provides a prolonged increase in cytoplasmic Ca(2+) concentrations and ultimately leads to the production of pro-inflammatory cytokines Molecules that inhibit SOCE could therefore be useful immunomodulating agents for the treatment of rheumatoid arthritis, psoriasis, inflammatory bowel disease, and other conditions Although the presence of the SOCE signaling pathway in lymphocytes and other cells involved in the immune response has been known for many years, key proteins involved in SOCE were identified only recently The identification of these proteins may further enable the identification of agents that inhibit SOCE without affecting other cellular processes This contribution documents representative examples of the small-molecule inhibitors of SOCE that have been reported to date Where possible, methods that were used to characterize the mechanism of action of the inhibitors are also described

In vitro and in vivo Staining Characteristics of Small, Fluorescent, Aβ42‐Binding D‐Enantiomeric Peptides in Transgenic AD Mouse Models

Abstract: One of the characteristic pathological hallmarks of Alzheimer's disease (AD) are neuritic plaques that consist of amyloid peptide (Abeta) To improve diagnosis and treatment evaluation, neuroimaging tools that make use of Abeta-binding ligands to visualise amyloid plaques are being developed We investigate the in vitro and in vivo characteristics of a series of three D-enantiomeric peptides (D1-D3) that were developed to specifically bind amyloid beta1-42 (Abeta42) in the brains of transgenic AD-model mice We stained brain sections of the mice, injected and infused the mice with these small D-peptides, and examined their staining of Abeta42 in the brain The experiments demonstrate that the D-peptides label all plaques that contain Abeta42 in the brain In contrast, diffuse amyloid beta deposits (which do not contain Abeta42) are not stained by any of the D-peptides The in vivo and in vitro studies demonstrate that the D-peptides label all Abeta42 in the brain, and none of the D-peptides causes inflammation or is taken up by astrocytes or microglia Furthermore, long-term infusion of the peptides does not cause inflammation Together, this demonstrates that these D-peptides might be suitable for use as molecular probes to measure Abeta plaque load in the living brain for early diagnosis of Alzheimer's disease, or to monitor Abeta42 plaque load during disease progression or during treatment

Improved Tricyclic Inhibitors of Trypanothione Reductase by Screening and Chemical Synthesis

Abstract: Trypanothione reductase (TryR) is a key validated enzyme in the trypanothione-based redox metabolism of pathogenic trypanosomes and leishmania parasites. This system is absent in humans, being replaced with glutathione and glutathione reductase, and as such offers a target for selective inhibition. As part of a program to discover antiparasitic drugs, the LOPAC1280 library of 1266 compounds was screened against TryR and the top hits evaluated against glutathione reductase and T. brucei parasites. The top hits included a number of known tricyclic neuroleptic drugs along with other new scaffolds for TryR. Three novel druglike hits were identified and SAR studies on one of these using information from the tricyclic neuroleptic agents led to the discovery of a competitive inhibitor (K(i)=330 nM) with an improved potency against T. brucei (EC(50)=775 nM).