Drug Repositioning for Diabetes Based on 'Omics' Data Mining

Drug repositioning has shorter developmental time, lower cost and less safety risk than traditional drug development process. The current study aims to repurpose marketed drugs and clinical candidates for new indications in diabetes treatment by mining clinical ‘omics’ data. We analyzed data from genome wide association studies (GWAS), proteomics and metabolomics studies and revealed a total of 992 proteins as potential anti-diabetic targets in human. Information on the drugs that target these 992 proteins was retrieved from the Therapeutic Target Database (TTD) and 108 of these proteins are drug targets with drug projects information. Research and preclinical drug targets were excluded and 35 of the 108 proteins were selected as druggable proteins. Among them, five proteins were known targets for treating diabetes. Based on the pathogenesis knowledge gathered from the OMIM and PubMed databases, 12 protein targets of 58 drugs were found to have a new indication for treating diabetes. CMap (connectivity map) was used to compare the gene expression patterns of cells treated by these 58 drugs and that of cells treated by known anti-diabetic drugs or diabetes risk causing compounds. As a result, 9 drugs were found to have the potential to treat diabetes. Among the 9 drugs, 4 drugs (diflunisal, nabumetone, niflumic acid and valdecoxib) targeting COX2 (prostaglandin G/H synthase 2) were repurposed for treating type 1 diabetes, and 2 drugs (phenoxybenzamine and idazoxan) targeting ADRA2A (Alpha-2A adrenergic receptor) had a new indication for treating type 2 diabetes. These findings indicated that ‘omics’ data mining based drug repositioning is a potentially powerful tool to discover novel anti-diabetic indications from marketed drugs and clinical candidates. Furthermore, the results of our study could be related to other disorders, such as Alzheimer’s disease.     

Brain penetrant kinase inhibitors: Learning from kinase neuroscience discovery

A recent review of kinase inhibitors in clinical trials for brain cancer noted differences in the properties of these compounds relative to the mean property parameters associated with drugs marketed for CNS-associated conditions. However, many of these kinase drugs arose from opportunistic observations of brain activity, rather than design or flow schemes focused on optimizing CNS penetration. Thus, this digest examines kinase inhibitors that have been developed specifically for neurodegenerative indications such as Alzheimer’s or Parkinson’s disease, and considers design, flow scheme, and the physicochemical properties associated with compounds that have demonstrated brain penetrance.     

Role of hydrophobicity on the monoamine receptor binding affinities of central nervous system drugs: a quantitative retention-activity relationships analysis using biopartitioning micellar chromatography

Biological action and activity reflect an aspect of the fundamental physicochemical properties of the bioactive compounds. As an alternative to classical QSAR studies, in this work different quantitative retention-activity relationships (QRAR) models are proposed, which are able to describe the role of hydrophobicity on the binding affinity to different brain monoamine receptors (H(1)-histamine, alpha(1)-noradrenergic and 5-HT(2)-serotonergic) of different families of psychotherapeutic drugs. The retention of compounds is measured in a biopartitioning micellar chromatography (BMC) system using Brij-35 mobile phases. The adequacy of the QRAR models developed is due to the fact that both the retention of compounds in BMC and the drug-receptor interaction are described by the same hydrophobic, electronic and steric properties of compounds. The obtained results indicate that, for structurally related compounds that present the same molecular features as the basic pharmacophore, there is a retention range in which compounds present the highest affinity to all of monoamine receptors.     

Thiazole-based chalcones as potent antimicrobial agents. Synthesis and biological evaluation

As part of ongoing studies in developing new antimicrobials, we report the synthesis of a new class of structurally novel derivatives, that incorporate two known bioactive structures a thiazole and chalcone, to yield a class of compounds with interesting antimicrobial properties. Evaluation of antibacterial activity showed that almost all the compounds exhibited greater activity than reference drugs and thus could be promising novel drug candidates.     

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.     

Synthesis and in vitro characterization of platinum(II) anticancer coordinates using FTIR spectroscopy and NCI COMPARE: A fast method for new compound discovery

Platinum-based drugs have been used for several decades to treat various cancers successfully. Cisplatin is the original compound in this class; it cross-links DNA, resulting in cell cycle arrest and cell death via apoptosis. Cisplatin is effective against several tumor types but exhibits toxic side effects; in addition, tumors often develop resistance. An original in vitro approach is proposed to determine whether platinum-based research compounds are good candidates for further study by comparing them to marketed drugs using FTIR spectroscopy and the COMPARE analysis from the NCI. Both methods can produce fingerprints and highlight differences between the compounds, classifying the candidates and revealing promising derivatives.     

In silico studies on marine actinomycetes as potential inhibitors for Glioblastoma multiforme

Glioblastoma multiforme (GBM) is considered to be the most common and often deadly disorder which affects the brain. It is caused by the over expression of proteins such as ephrin type-A receptor 2 (EphA2), epidermal growth factor receptor (EGFR) and EGFRvIII. These 3 proteins are considered to be the potential therapeutic targets for GBM. Among these, EphA2 is reported to be over-expressed in ˜90% of GBM. Herein we selected 35 compounds from marine actinomycetes, 5 in vitro and in vivo studied drug candidates and 4 commercially available drugs for GBM which were identified from literature and analysed by using comparative docking studies. Based on the glide scores and other in silico parameters available in Schrödinger, two selected marine actinomycetes compounds which include Tetracenomycin D and Chartreusin exhibited better binding energy among all the compounds studied in comparative docking. In this study we have demonstrated the inhibition of the 3 selected targets by the two bioactive compounds from marine actinomycetes through in-silico docking studies. Furthermore molecular dynamics simulation were also been performed to check the stability and the amino acids interacted with the 3 molecular targets (EphA2 receptor, EGFR, EGFRvIII) for GBM. Our results suggest that Tetracinomycin D and Chartreusin are the novel and potential inhibitor for the treatment of GBM.     

Comparison of Physical and Chemical Properties of Green and Brown Brazilian Propolis Collected in Minas Gerais,Brazil

Among the 13 types of propolis classified in Brazil according to their physicochemical properties, green propolis and brown propolis are the most commonly found and used. In this work, a comparison of the physicochemical properties of green and brown propolis produced in Minas Gerais, Brazil was performed according to the methodology established by the Brazilian legislation. And, the content of 9 bioactive compounds in the samples was determined by RP-HPLC. GrProp showed a higher content of pinocembrin, artepillin C and baccharin, and a higher quantity of total flavonoids, in comparison with BrwProp. The mechanical mass content in both types of propolis was above the limit established by legislation. However, the other physicochemical parameters were within the limits. The chemical composition, especially the flavonoid content and the free radical (DPPH) scavenger property confer to both types of propolis a promising pharmacological activity.     

Systematic drug repositioning based on clinical side-effects

Drug repositioning helps fully explore indications for marketed drugs and clinical candidates. Here we show that the clinical side-effects (SEs) provide a human phenotypic profile for the drug, and this profile can suggest additional disease indications. We extracted 3,175 SE-disease relationships by combining the SE-drug relationships from drug labels and the drug-disease relationships from PharmGKB. Many relationships provide explicit repositioning hypotheses, such as drugs causing hypoglycemia are potential candidates for diabetes. We built Naïve Bayes models to predict indications for 145 diseases using the SEs as features. The AUC was above 0.8 in 92% of these models. The method was extended to predict indications for clinical compounds, 36% of the models achieved AUC above 0.7. This suggests that closer attention should be paid to the SEs observed in trials not just to evaluate the harmful effects, but also to rationally explore the repositioning potential based on this “clinical phenotypic assay”.     

The potential of click reactions for the synthesis of bioactive triterpenes

Click reactions between alkynes and azides using the privileged scaffold of triterpenes have been of interest for biological chemistry. Many publications deal with the synthesis of novel bioactive molecules; these conjugates have also been used for bioanalytical and diagnostic purposes. As a result, conjugates of better physicochemical properties were obtained; even compounds of improved solubility in water and physiological fluids were made through the introduction of a triazol residue. “Hybrid-structures“, i.e. molecules consisting of two independently bioactive subunits linked by a triazole residue were higher bioactive than their parent compounds but not as active as expected, and with a few exceptions the ultimate breakthrough has not yet been achieved. Only in the synthesis of compounds with anti-leishmanial activity some new and promising lead structures were found. As a consequence, triazole modified triterpenes seem to hold their greatest future prospect rather as diagnostic reagents and molecular probes than as drugs.     

Translating clinical findings into knowledge in drug safety evaluation--drug induced liver injury prediction system (DILIps)

Drug-induced liver injury (DILI) is a significant concern in drug development due to the poor concordance between preclinical and clinical findings of liver toxicity. We hypothesized that the DILI types (hepatotoxic side effects) seen in the clinic can be translated into the development of predictive in silico models for use in the drug discovery phase. We identified 13 hepatotoxic side effects with high accuracy for classifying marketed drugs for their DILI potential. We then developed in silico predictive models for each of these 13 side effects, which were further combined to construct a DILI prediction system (DILIps). The DILIps yielded 60-70% prediction accuracy for three independent validation sets. To enhance the confidence for identification of drugs that cause severe DILI in humans, the "Rule of Three" was developed in DILIps by using a consensus strategy based on 13 models. This gave high positive predictive value (91%) when applied to an external dataset containing 206 drugs from three independent literature datasets. Using the DILIps, we screened all the drugs in DrugBank and investigated their DILI potential in terms of protein targets and therapeutic categories through network modeling. We demonstrated that two therapeutic categories, anti-infectives for systemic use and musculoskeletal system drugs, were enriched for DILI, which is consistent with current knowledge. We also identified protein targets and pathways that are related to drugs that cause DILI by using pathway analysis and co-occurrence text mining. While marketed drugs were the focus of this study, the DILIps has a potential as an evaluation tool to screen and prioritize new drug candidates or chemicals, such as environmental chemicals, to avoid those that might cause liver toxicity. We expect that the methodology can be also applied to other drug safety endpoints, such as renal or cardiovascular toxicity.     

Proposed criteria for assessing the efficacy of cancer reduction by plant foods enriched in carotenoids, glucosinolates, polyphenols and selenocompounds

BACKGROUND AND AIMS: The cancer-protective properties of vegetable consumption are most likely mediated through 'bioactive compounds' that induce a variety of physiologic functions including acting as direct or indirect antioxidants, regulating enzymes and controlling apoptosis and the cell cycle. The 'functional food' industry has produced and marketed foods enriched with bioactive compounds, but there are no universally accepted criteria for judging efficacy of the compounds or enriched foods. SCOPE: Carotenoids, glucosinolates, polyphenols and selenocompounds are families of bioactive compounds common to vegetables. Although numerous studies have investigated the agricultural and human health implications of enriching foods with one or more of these compounds, inadequate chemical identification of compounds, lack of relevant endpoints and inconsistencies in mechanistic hypotheses and experimental methodologies leave many critical gaps in our understanding of the benefits of such compounds. This review proposes a decision-making process for determining whether there is reasonable evidence of efficacy for the both the compound and the enriched food. These criteria have been used to judge the evidence of efficacy for cancer prevention by carotenoids, polyphenols, glucosinolates and selenocompounds. CONCLUSIONS: The evidence of efficacy is weak for carotenoids and polyphenols; the evidence is stronger for glucosinolates and lycopene, but production of enriched foods still is premature. Additionally there is unacceptable variability in the amount and chemical form of these compounds in plants. The evidence of efficacy for selenocompounds is strong, but the clinical study that is potentially the most convincing is still in progress; also the variability in amount and chemical form of Se in plants is a problem. These gaps in understanding bioactive compounds and their health benefits should not serve to reduce research interest but should, instead, encourage plant and nutritional scientists to work together to develop strategies for improvement of health through food.     

An integrated database of flavonoids

Flavonoids are polyphenolic compounds that occur ubiquitously in foods of plant origin. Some of these molecules exhibit various physiological activities. Among existing drugs, there are a huge number of compounds bearing a flavonoid-related skeleton. Because of the relevance for pharmaceutical research, it would be beneficial to collect these compounds into a database. Recently, various databases of chemicals were compiled to help biological and/or chemical research, but no comprehensive database of flavonoids with chemical structures and physicochemical parameters, supposedly related to their activity, is available yet. The aim of this research was to merge the information about flavonoids of plant origin and flavonoids used as medicines into a database. Moreover, predictions of activities against various targets were performed using a virtual screening procedure to demonstrate a possible application of the database for pharmaceutical research.     

Methyl-containing pharmaceuticals: Methylation in drug design

The importance of methyl groups in modulating biological activity, selectivity, solubility, metabolism and pharmacokinetic/pharmacodynamic properties of biologically active molecules is highlighted. The information compiled from selected beneficial cases, focuses mostly on marketed drugs and clinical candidates, and indicates that the methylation strategy has been successful in drug design.     

Database on pharmacophore analysis of active principles, from medicinal plants

Plants continue to be a major source of medicines, as they have been throughout human history. In the present days, drug discovery from plants involves a multidisciplinary approach combining ethnobotanical, phytochemical and biological techniques to provide us new chemical compounds (lead molecules) for the development of drugs against various pharmacological targets, including cancer, diabetes and its secondary complications. In view of this need in current drug discovery from medicinal plants, here we describe another web database containing the information of pharmacophore analysis of active principles possessing antidiabetic, antimicrobial, anticancerous and antioxidant properties from medicinal plants. The database provides the botanical, taxonomic classification, biochemical as well as pharmacological properties of medicinal plants. Data on antidiabetic, antimicrobial, anti oxidative, anti tumor and anti inflammatory compounds, and their physicochemical properties, SMILES Notation, Lipinski's properties are included in our database. One of the proposed features in the database is the predicted ADMET values and the interaction of bioactive compounds to the target protein. The database alphabetically lists the compound name and also provides tabs separating for anti microbial, antitumor, antidiabetic, and antioxidative compounds. AVAILABILITY: http://www.hccbif.info /     

Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer

The cost and time to develop a drug continues to be a major barrier to widespread distribution of medication. Although the genomic revolution appears to have had little impact on this problem, and might even have exacerbated it because of the flood of additional and usually ineffective leads, the emergence of high throughput resources promises the possibility of rapid, reliable and systematic identification of approved drugs for originally unintended uses. In this paper we develop and apply a method for identifying such repositioned drug candidates against breast cancer, myelogenous leukemia and prostate cancer by looking for inverse correlations between the most perturbed gene expression levels in human cancer tissue and the most perturbed expression levels induced by bioactive compounds. The method uses variable gene signatures to identify bioactive compounds that modulate a given disease. This is in contrast to previous methods that use small and fixed signatures. This strategy is based on the observation that diseases stem from failed/modified cellular functions, irrespective of the particular genes that contribute to the function, i.e., this strategy targets the functional signatures for a given cancer. This function-based strategy broadens the search space for the effective drugs with an impressive hit rate. Among the 79, 94 and 88 candidate drugs for breast cancer, myelogenous leukemia and prostate cancer, 32%, 13% and 17% respectively are either FDA-approved/in-clinical-trial drugs, or drugs with suggestive literature evidences, with an FDR of 0.01. These findings indicate that the method presented here could lead to a substantial increase in efficiency in drug discovery and development, and has potential application for the personalized medicine.     

人类非洲锥虫病的治疗研究进展

人类非洲锥虫病是一种被忽视的热带寄生虫病,威胁着撒哈拉以南非洲人民的生命健康。目前临床使用的治疗药物有四种,这些药物副作用多,用药困难并产生了一定的耐药性,因此有必要开发安全有效且利于服用的药物。目前有三类候选药物相继进入临床实验阶段,在不久的将来可能会进入临床应用。另外,还有许多正在研究的治疗药物,包括天然产物、磷酸二酯酶抑制剂、蛋白酶抑制剂、拓扑异构酶抑制剂、亮氨酰t RNA合成酶抑制剂、微管蛋白抑制剂以及一些靶点尚不明确却有很好的锥虫抑制活性的化合物。其中,壳二孢呋喃酮选择性较好,喹啉-3-羧酸类衍生物毒性低,5-硝基-2-呋喃酰胺类化合物对硝呋莫司耐受的锥虫仍有活性。这些研究无疑都为新型抗锥虫药物的出现提供了可能,相信在不久的将来越来越多的药物会在临床使用。     

Chemoinformatic Analysis of GRAS (Generally Recognized as Safe) Flavor Chemicals and Natural Products

Food materials designated as “Generally Recognized as Safe” (GRAS) are attracting the attention of researchers in their attempts to systematically identify compounds with putative health-related benefits. In particular, there is currently a great deal of interest in exploring possible secondary benefits of flavor ingredients, such as those relating to health and wellness. One step in this direction is the comprehensive characterization of the chemical structures contained in databases of flavoring substances. Herein, we report a comprehensive analysis of the recently updated FEMA GRAS list of flavoring substances (discrete chemical entities only). Databases of natural products, approved drugs and a large set of commercial molecules were used as references. Remarkably, natural products continue to be an important source of bioactive compounds for drug discovery and nutraceutical purposes. The comparison of five collections of compounds of interest was performed using molecular properties, rings, atom counts and structural fingerprints. It was found that the molecular size of the GRAS flavoring substances is, in general, smaller cf. members of the other databases analyzed. The lipophilicity profile of the GRAS database, a key property to predict human bioavailability, is similar to approved drugs. Several GRAS chemicals overlap to a broad region of the property space occupied by drugs. The GRAS list analyzed in this work has high structural diversity, comparable to approved drugs, natural products and libraries of screening compounds. This study represents one step towards the use of the distinctive features of the flavoring chemicals contained in the GRAS list and natural products to systematically search for compounds with potential health-related benefits.