Analysis of a high-throughput screening data set using potency-scaled molecular similarity algorithms

Molecular similarity methods for ligand-based virtual screening (VS) generally do not take compound potency as a variable or search parameter into account. We have incorporated a logarithmic potency scaling function into two conceptually distinct VS algorithms to account for relative compound potency during search calculations. A high-throughput screening (HTS) data set containing cathepsin B inhibitors was analyzed to evaluate the effects of potency scaling. Sets of template compounds were randomly selected from the HTS data and used to search for hits having varying potency levels in the presence or absence of potency scaling. Enrichment of potent compounds in small subsets of the HTS data set was observed as a consequence of potency scaling. In part, observed enrichments could be rationalized as a result of recentering chemical reference space on a subspace populated by potent compounds. Our findings suggest that VS calculations using multiple reference compounds can be directed toward the preferential detection of potent database hits by scaling compound contributions according to potency differences.     

Design,Synthesis, and Evaluation of Dihydropyranopyrazole Derivatives as Novel PDE2 Inhibitors for the Treatment of Alzheimer’s Disease

Phosphodiesterase 2 (PDE2) has been regarded as a novel target for the treatment of Alzheimer’s disease (AD). In this study, we obtained (R)-LZ77 as a hit compound with moderate PDE2 inhibitory activity (IC₅₀ = 261.3 nM) using a high-throughput virtual screening method based on molecular dynamics. Then, we designed and synthesized 28 dihydropyranopyrazole derivatives as PDE2 inhibitors. Among them, compound (+)-11h was the most potent PDE2 inhibitor, with an IC₅₀ value of 41.5 nM. The molecular docking of PDE2-(+)-11h reveals that the 4-(trifluoromethyl)benzyl)oxyl side chain of the compound enters the H-pocket and forms strong hydrophobic interactions with L770/L809/F862, which improves inhibitory activity. The above results may provide insight for further structural optimization of highly potent PDE2 inhibitors and may lay the foundation for their use in the treatment of AD.     

Synthesis and structure-activity relationship of N-arylrolipram derivatives as inhibitors of PDE4 isozymes

Structure activity studies of N-phenylrolipram derivatives have led to the identification of highly potent PDE4 inhibitors. The potential of these inhibitors for cellular activity was routinely assessed in an assay of fMLP induced oxidative burst in human eosinophils. Since first generation PDE4 inhibitors have been plagued with a number of unwanted side effects, parallel structure activity studies for competition with the [3H]-rolipram binding site in rat brain were performed. In this fashion 5-[4-(3-cyclopentyloxy-4-methoxyphenyl)-2-oxo-pyrrolidin-1-yl]-3-(3-methoxybenzyloxy)benzoic acid N',N'-dimethylhydrazide (22) was identified as a potent inhibitor of PDE4 which exhibits >1000 fold selectivity versus PDE3, and is a nanomolar inhibitor in all the cellular assays tested. Studies on the stereoselectivity of PDE4 inhibition of this class of rolipram based compounds revealed, that for example (S)-11 is a more potent inhibitor than (R)-11. This effect can also be observed in primary human cells where the (S)-enantiomer is about 10 fold more potent than the corresponding (R)-enantiomer.     

A PDE6δ‐KRas Inhibitor Chemotype with up to Seven H‐Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2

Small‐molecule inhibition of the interaction between the KRas oncoprotein and the chaperone PDE6δ impairs KRas spatial organization and signaling in cells. However, despite potent binding in vitro (K _D<10 nm ), interference with Ras signaling and growth inhibition require 5–20 μm compound concentrations. We demonstrate that these findings can be explained by fast release of high‐affinity inhibitors from PDE6δ by the release factor Arl2. This limitation is overcome by novel highly selective inhibitors that bind to PDE6δ with up to 7 hydrogen bonds, resulting in picomolar affinity. Their release by Arl2 is greatly decreased, and representative compounds selectively inhibit growth of KRas mutated and ‐dependent cells with the highest activity recorded yet. Our findings indicate that very potent inhibitors of the KRas‐PDE6δ interaction may impair the growth of tumors driven by oncogenic KRas.     

Evaluation of Pseudomonas aeruginosa deacetylase LpxC inhibitory activity of dual PDE4-TNFalpha inhibitors: a multiscreening approach

In this study, we have focused on the implication of a multiscreening approach in the evaluation of Pseudomonas aeruginosa deacetylase LpxC inhibitory activity of dual PDE4-TNFalpha inhibitors. A genetic function approximation (GFA) directed quantitative structure-activity relationship (QSAR) model was developed for LpxC inhibition on the basis of reported biological activity (Kline and Andersen, J. Med. Chem. 2002, 45, 3112-3129). Subsequently, reported PDE4-TNFalpha inhibitors (Klienman and Campbell, J. Med. Chem. 1998, 41, 266-270) were screened using the QSAR model. Whereby, the compounds were predicted to have equipotent activity with the most potent compound in reported LpxC inhibitor series. A docking analysis of these compounds carried out on the LpxC homology model corroborated the initial results. The compounds were then validated using surface electronic properties analysis and subjected to an adsorption, distribution, metabolism, excretion, and toxicity filter. Taken together, a multiscreening strategy was used to validate potential leads for LpxC inhibition.     

Toward the identification of the cardiac cGMP inhibited-phosphodiesterase catalytic site

Cyclic nucleotide phosphodiesterases (PDEs) comprise a complex group of enzymes; five major PDE families or classes with distinctive properties have been identified. Among these a great deal of interest has recently been focused on the so called cGMP-inhibited low K_m cAMP phosphodiesterase (cGI PDE) or PDE III. A number of positive inotropic agents, including the well-known milrinone, display a specific inhibition of PDE III as primary mechanism of action. Recent studies have been carried out to develop a pharmacophore model of the PDE III active site. We therefore performed molecular modelling and 3D-SAR studies so as to better define structural requirements for potent and selective enzymatic inhibition. The DISCO (DIStance COmparison) strategy has been applied on a set of compounds taken from literature and a milrinone analogue previously synthesized by us, all of which are characterized by a marked inotropic effect but with varying degrees of enzyme selectivity. A common pharmacophoric model was derived, validated and considered as starting point to perform a 3D-SAR study using the GRID force field and PCA (Principal Component Analysis) with the aim of rationally designing more selective inhibitors. This paper presents the results of this theoretical approach.     

Comparative molecular field analysis (CoMFA) for phosphodiesterase (PDE) IV inhibitors

A comparative molecular field analysis (CoMFA) for phosphodiesterase (PDE) IV inhibitors has been performed to correlate their chemical structures with their observed biological activity. In this study, CoMFA model based on docking mode for active site of PDE IV can describe the relative change in magnitude of the steric and electrostatic fields as a function of the compounds. Pyridine N-oxide and pyridine group of each compound are aligned toward the metal ion in S2-sub pocket of PDE IV. The study provided a statistically valid model with good correlation and predictive power, and consequently we identified some key features that may be used to design new derivatives.     

Syntheses and Vasodilatory Activities of New Pyrazolo [ 4,3-d ] pyrimidin-7-ones

IntroductionAdenosine 3′,5′-cyclic monophosphate (cAMP)and guanosine 3′,5′-cyclic monophosphate(cGMP) areubiquitous second messengers that mediate biologicalresponses to a variety of extracellular cues, includinghormones, neurotransmitters, chemokines…     

Rational inhibitor design and iterative screening in the identification of selective plasmodial cyclin dependent kinase inhibitors

New chemical classes of compounds must be introduced into the malaria drug development pipeline in an effort to develop new chemotherapy options for the fight against malaria. In this review we describe an iterative approach designed to identify potent inhibitors of a kinase family that collectively functions as key regulators of the cell cycle. Cyclin-dependent protein kinases (CDKs) are attractive drug targets in numerous diseases and, most recently, they have become the focus of rational drug design programs for the development of new antimalarial agents. Our approach uses experimental and virtual screening methodologies to identify and refine chemical inhibitors and increase the success rate of discovering potent and selective inhibitors. The active pockets of the plasmodial CDKs are unique in terms of size, shape and amino acid composition compared with those of the mammalian orthologues. These differences exemplified through the use of screening assays, molecular modeling, and crystallography can be exploited for inhibitor design. To date, several classes of compounds including quinolines and oxindoles have been identified as selective inhibitors of the plasmodial CDK7 homologue, Pfmrk. From these initial studies and through the iterative rational drug design process, more potent, selective, and most importantly, chemically unique compound classes have been identified as effective inhibitors of the plasmodial CDKs and the malarial parasite.     

Discovery of a novel acyl-CoA: cholesterol acyltransferase inhibitor: the synthesis, biological evaluation, and reduced adrenal toxicity of (4-phenylcoumarin)acetanilide derivatives with a carboxylic acid moiety

As a part of our research for novel potent and orally available acyl-CoA: cholesterol acyltransferase (ACAT) inhibitors that can be used as anti-atherosclerotic agents, we recently reported the discovery of the (4-phenylcoumarine)acetanilide derivative 1. However, compound 1 showed adrenal toxicity in animal models. In order to search for safer ACAT inhibitors that do not have adrenal toxicity, we examined the inhibitory activity of ACAT in human macrophage and adrenal cells. The introduction of a carboxylic acid moiety on the pendant phenyl ring and the adjustment of the lipophilicity led to the discovery of (2E)-3-[7-chloro-3-[2-[[4-fluoro-2-(trifluoromethyl)phenyl]amino]-2-oxoethyl]-6-methyl-2-oxo-2H-chromen-4-yl]phenyl]acrylic acid (21e), which showed potent ACAT inhibitory activity in macrophages and a selectivity of around 30-fold over adrenal cells. In addition, compound 21e showed high adrenal safety in guinea pigs.     

Synthesis and Evaluation of PDE5 Inhibitory Activity of Novel Pyrido[2＇,1＇：5,1]pyrazolo[4,3-d]pyrimidin-4-one Derivatives

Novel pyridopyrazolopyrimidinone derivatives were designed and synthesized as potential PDE5 inhibitors. The target compounds demonstrated significant inhibitory activity against human platelet PDE5, but less potent than sildenafil.     

Analytical selenoamino acid studies by chromatography with interfaced atomic mass spectrometry and atomic emission spectral detection

Consumption of selenium enriched plants or yeast-based nutritional supplements has been reported to provide anticarcinogenic benefits which are selenium compound dependent. Separation and identification of these selenium compounds is critical to understand the activity. Plants and yeast convert inorganic selenium in the soil or growth media into organoselenium compounds, probably following a route similar to the sulfur assimilatory pathway. Non-volatile selenium compounds produced include selenoamino acids, some of which have shown anticarcinogenic activity. Volatile compounds produced by chemical reaction of involatile precursors have also been found. An ion pair chromatographic method with ICP-MS detection for the separation of selenoamino acid standards potentially present in real samples is given. The method allows separation of selenoamino acids including such analytes as the cis-trans isomers of Se-1-propenyl-dl-selenocysteine. The method also provides the capability of determining the presence of selenoxides and possibly selenones, and tracking of other functionalities and reactions by selective derivatization. Alternatively, selenoamino acids are treated with ethylchloroformate to produce stable volatile derivatives which are amenable to GC separation with element specific atomic emission detection (GC-AED). Results of total selenium determination and speciation of selenium enriched yeast-based nutritional supplements, selenium enriched allium vegetables and bioremediation samples are presented.     

Redox inactivation of human 15-lipoxygenase by marine-derived meroditerpenes and synthetic chromanes: archetypes for a unique class of selective and recyclable inhibitors

The selective inhibition of human 15-lipoxygenase (15-hLO) could serve as a promising therapeutic target for the prevention of atherosclerosis. A screening of marine sponges revealed that crude extracts of Psammocinia sp. exhibited potent 15-hLO inhibitory activity. Bioassay-guided fractionation led to the isolation of chromarols A-E (8-12) as potent and selective inhibitors of 15-hLO. An additional 22 structurally related compounds, including meroditerpenes from the same Psammocinia sp. (3, 4, 13-16) and our pure compound repository (17, 18), commercially available tocopherols (19-24), and synthetic chromanes (25-32), were evaluated for their ability to inhibit human lipoxygenases. The 6-hydroxychromane moiety found in chromarols A-D was identified as essential for the selective redox inhibition of 15-hLO. Furthermore, the oxidized form of the 6-hydroxychromane could be reduced by ascorbate, suggesting a potential regeneration pathway for these inhibitors in the body. This pharmacophore represents a promising paradigm for the development of a unique class of recyclable 15-hLO redox inhibitors for the treatment of atherosclerosis.     

Drug Design,Synthesis and Biological Evaluation of Heterocyclic Molecules as Anti-Inflammatory Agents

Non-steroidal anti-inflammatory drugs (NSAIDs) are generally utilized for numerous inflammatory ailments. The long-term utilization of NSAIDs prompts adverse reactions such as gastrointestinal ulceration, renal dysfunction and hepatotoxicity; however, selective COX-2 inhibitors prevent these adverse events. Various scientific approaches have been employed to identify safer COX-2 inhibitors, as in any case, a large portion of particular COX-2 inhibitors have been retracted from the market because of severe cardiovascular events. This study aimed to develop and synthesize a novel series of indomethacin analogues with potential anti-inflammatory properties and fewer side effects, wherein carboxylic acid moiety was substituted using DCC/DMAP coupling. This study incorporates the docking of various indomethacin analogues to detect the binding interactions with COX-2 protein (PDB ID: 3NT1). MD simulation was performed to measure the stability and flexibility of ligand–protein interactions at the atomic level, for which the top-scoring ligand–protein complex was selected. These compounds were evaluated in vitro for COX enzymes inhibition. Likewise, selected compounds were screened in vivo for anti-inflammatory potential using the carrageenan-induced rat paw oedema method and their ulcerogenic potential. The acute toxicity of compounds was also predicted using in silico tools. Most of the compounds exhibited the potent inhibition of both COX enzymes; however, 3e and 3c showed the most potent COX-2 inhibition having IC50 0.34 µM and 1.39 µM, respectively. These compounds also demonstrated potent anti-inflammatory potential without ulcerogenic liability. The biological evaluation revealed that the compound substituted with 4-nitrophenyl was most active.     

Analytical selenoamino acid studies by chromatography with interfaced atomic mass spectrometry and atomic emission spectral detection

Consumption of selenium enriched plants or yeast-based nutritional supplements has been reported to provide anticarcinogenic benefits which are selenium compound dependent. Separation and identification of these selenium compounds is critical to understand the activity. Plants and yeast convert inorganic selenium in the soil or growth media into organoselenium compounds, probably following a route similar to the sulfur assimilatory pathway. Non-volatile selenium compounds produced include selenoamino acids, some of which have shown anticarcinogenic activity. Volatile compounds produced by chemical reaction of involatile precursors have also been found. An ion pair chromatographic method with ICP-MS detection for the separation of selenoamino acid standards potentially present in real samples is given. The method allows separation of selenoamino acids including such analytes as the cis-trans isomers of Se-1-propenyl-dl-selenocysteine. The method also provides the capability of determining the presence of selenoxides and possibly selenones, and tracking of other functionalities and reactions by selective derivatization. Alternatively, selenoamino acids are treated with ethylchloroformate to produce stable volatile derivatives which are amenable to GC separation with element specific atomic emission detection (GC-AED). Results of total selenium determination and speciation of selenium enriched yeast-based nutritional supplements, selenium enriched allium vegetables and bioremediation samples are presented. Received: 16 February 1998 / Revised: 4 June 1998 / Accepted: 9 June 1998     

Synthesis, crystal structure and biological activity of beta-carboline based selective CDK4-cyclin D1 inhibitors

The design, synthesis and biological activity of a series of non-planar dihydro-beta-carboline and beta-carboline-based derivatives of the toxic anticancer agent fascaplysin is presented. We show these compounds to be selective inhibitors of CDK4 over CDK2 with an IC50 (CDK4-cyclin D1) = 11 micromol for the best compound in the series 4d. The crystallographic analysis of some of the compounds synthesised (3b/d and 4a-d) was carried out, in an effort to estimate the structural similarities between the designed inhibitors and the model compound fascaplysin.     

Development of a novel high-throughput assay for the investigation of GlyT-1b neurotransmitter transporter function

The glycine transporter (GlyT-1b) is a Na(+)/Cl(-)-dependent electrogenic transporter which mediates the rapid re-uptake of glycine from the synaptic cleft. Based on its tissue distribution, GlyT-1 has been suggested to co-localise with the NMDA receptor where it may modulate the concentration of glycine at its co-agonist binding site. This data has led to GlyT-1 inhibitors being proposed as targets for disorders such as schizophrenia and cognitive dysfunction. Radiolabelled uptake assays (e.g. [(3)H]glycine) have been traditionally used in compound screening to identify glycine transporter inhibitors. While such an assay format is useful for testing limited numbers of compounds, the identification of novel glycine uptake inhibitors requires a functional assay compatible with high-throughput screening (HTS) of large compound libraries. Here, the authors present the development of a novel homogenous cell-based assay using the FLIPR membrane potential blue dye (Molecular Devices) and FLEXstation. Pharmacological data for the GlyT-1 inhibitors Org 24598 and ALX 5407 obtained using this novel electrogenic assay correlated well with the conventional [(3)H]-glycine uptake assay format. Furthermore, the assay has been successfully miniaturised using FLIPR(3) and therefore has the potential to be used for high-throughput screening.     

Chip-based high-throughput screening of herbal medicines

At present, high-throughput screening (HTS) programs in drug discovery rely mainly on compound libraries from combinational chemistry. Similarly, natural flora has been used as a prominent origin for new and potent herbal drugs. Herbal medicines have been used worldwide for thousands of years to cure many diseases. As such, herbal secondary metabolites show a remarkable structural diversity that supplements chemically synthesized compound analogs in drug discovery screening. Unfortunately, there is often a considerable deterioration in the quality of herbal drugs in such screening programs as there are time-consuming manual processes involved in the isolation of active ingredients from the highly complex mixtures of herbal plant products. The quality and quantity of herbal samples are critical for the success of HTS programs. In the recent past, there have been substantial improvements in HTS due to the miniaturization and integration of microchip (e.g., Herbochip(?), DNA chip, protein chip, cell chip, etc.)-based technologies so as to design herbal drugs that compete with synthetic drug analogs. Here we will review various technologies used for HTS of herbal medicines. Finally, we will summarize our efforts to develop a novel chip-based HTS assay to explore the antioxidant and radioprotective properties of herbal plants.     

Extraction and validation of substructure profiles for enriching compound libraries

Compounds known to be potent against a specific protein target may potentially contain a signature profile of common substructures that is highly correlated to their potency. These substructure profiles may be useful in enriching compound libraries or for prioritizing compounds against a specific protein target. With this objective in mind, a set of compounds with known potency against six selected kinases (2 each from 3 kinase families) was used to generate binary molecular fingerprints. Each fingerprint key represents a substructure that is found within a compound and the frequency with which the fingerprint occurs was then tabulated. Thereafter, a frequent pattern mining technique was applied with the aim of uncovering substructures that are not only well represented among known potent inhibitors but are also unrepresented among known inactive compounds and vice versa. Substructure profiles that are representative of potent inhibitors against each of the 3 kinase families were thus extracted. Based on our validation results, these substructure profiles demonstrated significant enrichment for highly potent compounds against their respective kinase targets. The advantages of using our approach over conventional methods in analyzing such datasets and its application in the mining of substructures for enriching compound libraries are presented.     

An empirical process for the design of high-throughput screening deck filters

A process for objective identification and filtering of undesirable compounds that contribute to high-throughput screening (HTS) deck promiscuity is described. Two methods of mapping hit promiscuity have been developed linking SMARTS-based structural queries with historical primary HTS data. The first compares an expected assay hit rate to actual hit rates. The second examines the propensity of an individual compound to hit multiple assays. Statistical evaluation of the data indicates a correlation between the resultant functional group filters and compound promiscuity. These data corroborate a number of commonly applied filters as well as producing some unexpected results. Application of these models to HTS collection triage reduced the number of in-house compounds considered for screening by 12%. The implications of these findings are further discussed in the context of the HTS screening set and combinatorial library design as well as compound acquisition.