In silico screening of drug databases for TSE inhibitors

Today, thousands of different chemical compounds are used as drugs for a wealth of different indications. Here, we demonstrate the use of a novel conformational drug database for the search of compounds with a positive influence on Transmissible Spongiform Encephalopathies (TSEs) by using two- and three-dimensional structural similarity to compounds with known effect. Both methods are combined to deduce a list of 16 candidate drugs. The proposal of a small number of putative inhibitors out of about 2300 approved essential drugs allows testing by expensive or time-consuming methods with the advantage that all agents are well known and suitable for use in humans.     

Structure-activity relationship studies on unifiram (DM232) and sunifiram (DM235), two novel and potent cognition enhancing drugs

Structure-activity relationships on two novel potent cognition enhancing drugs, unifiram (DM232, 1) and sunifiram (DM235, 2), are reported. Although none of the compounds synthesised reached the potency of the parent drugs, some fairly active compounds have been identified that may represent new leads to develop other cognition enhancing drugs. An interesting result of this research is the identification of two compounds (13 and 14) that are endowed with amnesing activity (the opposite of the activity of the original molecules) and are nearly equipotent to scopolamine. Moreover, two compounds of the series (5 and 6) were found endowed with analgesic activity on a rat model of neuropathic pain at the dose of 1 mg/kg.     

Determining the Degree of Promiscuity of Extensively Assayed Compounds

In the context of polypharmacology, an emerging concept in drug discovery, promiscuity is rationalized as the ability of compounds to specifically interact with multiple targets. Promiscuity of drugs and bioactive compounds has thus far been analyzed computationally on the basis of activity annotations, without taking assay frequencies or inactivity records into account. Most recent estimates have indicated that bioactive compounds interact on average with only one to two targets, whereas drugs interact with six or more. In this study, we have further extended promiscuity analysis by identifying the most extensively assayed public domain compounds and systematically determining their promiscuity. These compounds were tested in hundreds of assays against hundreds of targets. In our analysis, assay promiscuity was distinguished from target promiscuity and separately analyzed for primary and confirmatory assays. Differences between the degree of assay and target promiscuity were surprisingly small and average and median degrees of target promiscuity of 2.6 to 3.4 and 2.0 were determined, respectively. Thus, target promiscuity remained at a low level even for most extensively tested active compounds. These findings provide further evidence that bioactive compounds are less promiscuous than drugs and have implications for pharmaceutical research. In addition to a possible explanation that drugs are more extensively tested for additional targets, the results would also support a “promiscuity enrichment model” according to which promiscuous compounds might be preferentially selected for therapeutic efficacy during clinical evaluation to ultimately become drugs.     

Approaches to antiviral drug development

At present, only a few drugs have been approved by the FDA for therapy of viral infections in humans. There is a great need for antiviral drugs with increased potency and decreased toxicity, as well as drugs to treat viral diseases for which no drug or vaccine is currently available. Two approaches for development of antiviral drugs are described--an empirical strategy and a rational strategy--with several examples of each. Although many compounds have potent antiviral activity in cell culture, only a small fraction of these will go on to become antiviral drugs for use in humans. At this time, only seven synthetic compounds and alpha interferon have been approved by the FDA for therapy of viral infections in humans. None of these approved drugs are without toxicities, however, and hence there is a great need for antiviral drugs with increased potency and decreased toxicity, as well as for drugs to treat viral diseases for which no drug or vaccine is currently available. Two approaches for the development of antiviral drugs--the empirical and the rational strategies--and their applications and future directions are discussed.     

Current status and future prospects for epigenetic psychopharmacology

Mounting evidence suggest that epigenetic regulation of brain functions is important in the etiology of psychiatric disorders. These epigenetic regulatory mechanisms, such as DNA methylation and histone acetylation, are influenced by many pharmaceutical compounds including psychiatric drugs. It is therefore of interest to investigate how psychiatric drugs are of influence and what the potential is of new epigenetic drugs for psychiatric disorders. With this targeted review we summarize the current state of knowledge in order to provide insight in this developing field. Several traditional psychiatric drugs have been found to alter the epigenome and in a variety of animal studies, experimental compounds with epigenetic targets have been investigated as potential psychiatric drugs. After discussion of the most relevant epigenetic mechanisms we present the evidence for epigenetic effects for the most relevant classes of drugs.     

转运体ABCC4和ABCC5 介导的肿瘤多药耐药研究进展

ABCC4、ABCC5 是ABCC（ATP-binding cassette transporter family class C, ABCC）蛋白转运体家族的成员,介导众多内源性 代谢产物和外源性药物从细胞内向外转运。ABCC4和ABCC5 在体内分布广泛,参与机体对药物和内、外源物质的吸收、分布和 排泄等。ABCC4、ABCC5 的一些突变会引起转运体表达、功能的改变和机体对药物反应的改变。近年研究发现ABCC4、ABCC5 与某些肿瘤的多药耐药相关,转运体的过表达可以引起肿瘤细胞对多种肿瘤化疗药物的耐药性,导致临床化疗效果不佳。本文就 转运体ABCC4和ABCC5 介导的肿瘤多药耐药研究进展进行综述。     

转运体ABCC4和ABCC5介导的肿瘤多药耐药研究进展

：ABCC4、ABCC5是ABCC（ATP-binding cassette transporter family class C, ABCC）蛋白转运体家族的成员,介导众多内源性代谢产物和外源性药物从细胞内向外转运。ABCC4和ABCC5在体内分布广泛,参与机体对药物和内、外源物质的吸收、分布和排泄等。ABCC4、ABCC5的一些突变会引起转运体表达、功能的改变和机体对药物反应的改变。近年研究发现ABCC4、ABCC5与某些肿瘤的多药耐药相关,转运体的过表达可以引起肿瘤细胞对多种肿瘤化疗药物的耐药性,导致临床化疗效果不佳。本文就转运体ABCC4和ABCC5介导的肿瘤多药耐药研究进展进行综述。     

Fast and slow versus strong and weak metal-DNA binding: consequences for anti-cancer activity

The binding of transition metal compounds to nucleic acids is discussed in the perspectives of kinetics and their anticancer activity. Kinetics of ligand exchange is primarily determined by the intrinsic properties of the metal ions, and to a lesser degree by the ligands coordinated already to the metal ion. Metal compounds having ligand-exchange rates of the same order of magnitude as cell-division processes, e.g. many Pt(iIIi), Ru(II) and Ru(III) compounds, are in use as chemotherapeutic drugs. Detailed knowledge of ligand exchange in such compounds is important for design of derivative and entirely new compounds. Metal coordination compounds of metal ions with much faster ligand-exchange reactions interact with DNA in a quite different way, namely primarily by compensation of negative charge of the polyanionic chain and are usually not active as anticancer agents. Examples of our recent work are presented in relation with experiments performed by others on new generations of platinum anti-cancer drugs.     

Microbial transformation of alkaloids

Alkaloids continue to provide mankind with a plethora of medicines, poisons and potions. Because many valuable drugs are derived from such natural compounds, there is much interest in their transformation to provide new compounds or intermediates for the synthesis of new or improved drugs. This review aims to provide a survey of alkaloid transformations, and concerns microbial transformations and microbially expressed recombinant plant enzymes and their biotechnological applications.     

Antiparasitic activity of flavonoids and isoflavones against Cryptosporidium parvum and Encephalitozoon intestinalis

Flavonoids, polyphenolic compounds found in plants, have demonstrated activity against several parasites and can augment the efficacy of other drugs by either increasing the uptake or decreasing the efflux of these drugs. We evaluated 11 of these compounds alone or in combination in order to test the hypothesis that flavonoids are effective against Cryptosporidium parvum and Encephalitozoon intestinalis. Using in vitro cell culture assays, HCT-8 cells or E6 cells were infected with C. parvum and E. intestinalis, respectively, and treated with compounds at doses ranging from 1 to 200 microM. We found that six compounds were active against C. parvum. Naringenin and genistein had the greatest activities with EC(50) of 15 and 25 microM, respectively. Two compounds, quercetin and apigenin, had activity against E. intestinalis at EC(50) of 15 and 50 microM, respectively. The EC(50) of trifluralin, a dinitroaniline compound, was decreased significantly when combined with genistein in an in vitro assay, suggesting that compounds may be used alone on in combination with other moderately active drugs to increase efficacy. In addition, induction of apoptosis by these compounds was studied but not observed to be a significant mechanism of action.     

High-Throughput Screening for the Identification of New Therapeutic Options for Metastatic Pheochromocytoma and Paraganglioma

Drug repurposing or repositioning is an important part of drug discovery that has been growing in the last few years for the development of therapeutic options in oncology. We applied this paradigm in a screening of a library of about 3,800 compounds (including FDA-approved drugs and pharmacologically active compounds) employing a model of metastatic pheochromocytoma, the most common tumor of the adrenal medulla in children and adults. The collection of approved drugs was screened in quantitative mode, testing the compounds in compound-titration series (dose-response curves). Analysis of the dose-response screening data facilitated the selection of 50 molecules with potential bioactivity in pheochromocytoma cells. These drugs were classified based on molecular/cellular targets and signaling pathways affected, and selected drugs were further validated in a proliferation assay and by flow cytometric cell death analysis. Using meta-analysis information from molecular targets of the top drugs identified by our screening with gene expression data from human and murine microarrays, we identified potential drugs to be used as single drugs or in combination. An example of a combination with a synergistic effect is presented. Our study exemplifies a promising model to identify potential drugs from a group of clinically approved compounds that can more rapidly be implemented into clinical trials in patients with metastatic pheochromocytoma or paraganglioma.     

Synthesis and biological evaluation of the natural product komaroviquinone and related compounds aiming at a potential therapeutic lead compound for high-risk multiple myeloma

Alternatives of treatments for multiple myeloma (MM) have become increasingly available with the advent of new drugs such as proteasome inhibitors, thalidomide derivatives, histone deacetylase inhibitors, and antibody drugs. However, high-risk MM cases that are refractory to novel drugs remain, and further optimization of chemotherapeutics is urgently needed.We had achieved asymmetric total synthesis of komaroviquinone, which is a natural product from the plant Dracocephalum komarovi. Similar to several leading antitumor agents that have been developed from natural compounds, we describe the antitumor activity and cytotoxicity of komaroviquinone and related compounds in bone marrow cells. Our data suggested that komaroviquinone-related agents have potential as starting compounds for anticancer drug development.     

THE EFFECT OF NEW DRUGS ON THE RHYTHMIC FUNCTION OF THE HEART

Epinephrine and related drugs (sympathomimetic amines) are the only compounds which effectively increase the rhythmic function of the heart.Effects of two new non-pressor sympathomimetic compounds were observed. One of these compounds, the isopropyl homologue of epinephrine, was found to be about five times more active than epinephrine.From clinical observations on the action of a new cardiac depressant drug, alpha-fagarine, it was concluded that the drug is very effective but that toxic reactions are unpredictable.The potency of alpha-fagarine and related compounds suggests the possible development of chemically related non-toxic drugs having an effective cardiac depressant action.     

Discovery of Anthelmintic Drug Targets and Drugs Using Chokepoints in Nematode Metabolic Pathways

Parasitic roundworm infections plague more than 2 billion people (1/3 of humanity) and cause drastic losses in crops and livestock. New anthelmintic drugs are urgently needed as new drug resistance and environmental concerns arise. A “chokepoint reaction” is defined as a reaction that either consumes a unique substrate or produces a unique product. A chokepoint analysis provides a systematic method of identifying novel potential drug targets. Chokepoint enzymes were identified in the genomes of 10 nematode species, and the intersection and union of all chokepoint enzymes were found. By studying and experimentally testing available compounds known to target proteins orthologous to nematode chokepoint proteins in public databases, this study uncovers features of chokepoints that make them successful drug targets. Chemogenomic screening was performed on drug-like compounds from public drug databases to find existing compounds that target homologs of nematode chokepoints. The compounds were prioritized based on chemical properties frequently found in successful drugs and were experimentally tested using Caenorhabditis elegans. Several drugs that are already known anthelmintic drugs and novel candidate targets were identified. Seven of the compounds were tested in Caenorhabditis elegans and three yielded a detrimental phenotype. One of these three drug-like compounds, Perhexiline, also yielded a deleterious effect in Haemonchus contortus and Onchocerca lienalis, two nematodes with divergent forms of parasitism. Perhexiline, known to affect the fatty acid oxidation pathway in mammals, caused a reduction in oxygen consumption rates in C. elegans and genome-wide gene expression profiles provided an additional confirmation of its mode of action. Computational modeling of Perhexiline and its target provided structural insights regarding its binding mode and specificity. Our lists of prioritized drug targets and drug-like compounds have potential to expedite the discovery of new anthelmintic drugs with broad-spectrum efficacy.     

Identification of selective ligands for human fibrin recognition using high-throughput docking

The ultimate aim of this study is to identify new molecules that are able to recognize polymerized fibrin, which is the main component of a thrombus. These selective ligands can be exposed on the surface of particular nanoparticles used for the targeted delivery of fibrinolytic drugs. The targeted delivery of these drugs is expected to help to keep under control the severe side effects which can occur if the drugs are administered systemically. The study focuses on the application of high-throughput docking methods used to screen a library of thousands of commercial compounds. The aim was to identify molecules that are potentially capable of interacting with the human fibrin γ(312-324) epitope. The best scoring compounds were purchased and tested through fluorimetric assays in order to estimate their affinity toward fibrin. The results show that the protocol proposed here for identifying new compounds of interest may provide a valuable contribution to the discovery of lead molecules for human fibrin recognition.     

Inhibition of in vitro intracellular growth of Trypanosoma cruzi by dicationic compounds

Dicationic compounds, which are derivatives of pentamidine, are being developed for use as antiprotozoal drugs. These compounds bind to the minor groove of DNA and are thought to inhibit DNA-dependent enzymes and thereby prevent cellular replication by protozoans. The objective of this study was to test the ability of a group of these compounds to inhibit the intracellular and extracellular reproduction of Trypanosoma cruzi in vitro. At present, there are few drugs in use capable of inhibiting the intracellular stages of this parasite, and therefore compounds with this ability would be of value. Cultures of mouse fibroblasts were infected and treated with doses of dicationic compounds, and the numbers of parasites released at the end of the 5- to 7-day growth cycle were determined. Five of the compounds tested were found to be effective at inhibiting T. cruzi growth at doses that were not toxic to the host cells. The compound found most effective (DB709) inhibited parasite release at the low concentration of 0.8 ng/ ml, justifying further study. These results suggest that dicationic compounds may have potential as chemotherapy against T. cruzi infection.     

Unified QSAR approach to antimicrobials. Part 2: predicting activity against more than 90 different species in order to halt antibacterial resistance

There are many different kinds of pathogenic bacteria species with very different susceptibility profiles to different antibacterial drugs. One limitation of QSAR models is that they consider the biological activity of drugs against only one species of bacteria. In a previous paper, we developed a unified Markov model to describe the biological activity of different drugs tested in the literature against some antimicrobial species. Consequently, predicting the probability with which a drug is active against different species of bacteria with a single unified model is a goal of major importance. The work described here develops the unified Markov model to describe the biological activity of more than 70 drugs from the literature tested against 96 species of bacteria. We applied linear discriminant analysis (LDA) to classify drugs as active or inactive against the different tested bacterial species. The model correctly classified 199 out of 237 active compounds (83.9%) and 168 out of 200 inactive compounds (84%). Overall training predictability was 84% (367 out of 437 cases). Validation of the model was carried out using an external predicting series, with the model classifying 202 out of 243 (i.e., 83.13%) of the compounds. In order to show how the model functions in practice, a virtual screening was carried out and the model recognized as active 84.5% (480 out of 568) antibacterial compounds not used in the training or predicting series. The current study is an attempt to calculate within a unified framework the probabilities of antibacterial action of drugs against many different species.     

Multi-target spectral moment QSAR versus ANN for antiparasitic drugs against different parasite species

There are many of pathogen parasite species with different susceptibility profile to antiparasitic drugs. Unfortunately, almost QSAR models predict the biological activity of drugs against only one parasite species. Consequently, predicting the probability with which a drug is active against different species with a single unify model is a goal of the major importance. In so doing, we use Markov Chains theory to calculate new multi-target spectral moments to fit a QSAR model that predict by the first time a mt-QSAR model for 500 drugs tested in the literature against 16 parasite species and other 207 drugs no tested in the literature using spectral moments. The data was processed by linear discriminant analysis (LDA) classifying drugs as active or non-active against the different tested parasite species. The model correctly classifies 311 out of 358 active compounds (86.9%) and 2328 out of 2577 non-active compounds (90.3%) in training series. Overall training performance was 89.9%. Validation of the model was carried out by means of external predicting series. In these series the model classified correctly 157 out 190, 82.6% of antiparasitic compounds and 1151 out of 1277 non-active compounds (90.1%). Overall predictability performance was 89.2%. In addition we developed four types of non Linear Artificial neural networks (ANN) and we compared with the mt-QSAR model. The improved ANN model had an overall training performance was 87%. The present work report the first attempts to calculate within a unify framework probabilities of antiparasitic action of drugs against different parasite species based on spectral moment analysis.     

Bioactive compounds from brown seaweeds: Phloroglucinol,fucoxanthin and fucoidan as promising therapeutic agents against breast cancer

Breast cancer is one of the most common cancers among women and its incidence tends to increase year by year. Chemotherapy is an effective treatment for many types of cancer, however its toxicity in normal cells and acquired tumor resistance to the drug used are considered as the main barriers. New strategies have been proposed to increase the success of anticancer drugs namely it combination with natural dietary compounds, decreasing drug dose administered and reducing its toxicity to normal cells. Seaweeds are rich in bioactive compounds and, in Traditional Chinese Medicine and Japanese folk medicine are used to “treat” tumors. Attending to the attractive biological effects of some seaweed several efforts have been made to isolate the bioactive compounds and explore its action mechanisms. Phloroglucinol, fucoxanthin and fucoidan are bioactive compounds present in brown seaweed showing chemopreventive and chemotherapeutic effects against cancer. Several mechanisms namely antioxidant, cell cycle arrest, induction of cell death and inhibition of metastasis and angiogenesis have been mentioned as responsible for it anticancer activity. Beside the promising biological effects of these compounds, synergistic effects with cytotoxic drugs have been less explored. This review focuses on the potential protective and therapeutic effect – mainly against breast cancer – of the bioactive compounds phloroglucinol, fucoxanthin and fucoidan present in the brown seaweeds. Current knowledge about interaction between each of these compounds and the conventional anticancer drugs and the further research opportunities are discussed.