Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative `Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed `3interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

Rationalization and prediction of drug resistant mutations in targets for clinical anti-tubercular drugs

Resistance to therapy limits the effectiveness of drug treatment in many diseases. Drug resistance can be considered as a successful outcome of the bacterial struggle to survive in the hostile environment of a drug-exposed cell. An important mechanism by which bacteria acquire drug resistance is through mutations in the drug target. Drug resistant strains (multi-drug resistant and extensively drug resistant) of Mycobacterium tuberculosis are being identified at alarming rates, increasing the global burden of tuberculosis. An understanding of the nature of mutations in different drug targets and how they achieve resistance is therefore important. An objective of this study is to first decipher sequence as well as structural bases for the observed resistance in known drug resistant mutants and then to predict positions in each target that are more prone to acquiring drug resistant mutations. A curated database containing hundreds of mutations in the 38 drug targets of nine major clinical drugs, associated with resistance is studied here. Mutations have been classified into those that occur in the binding site itself, those that occur in residues interacting with the binding site and those that occur in outer zones. Structural models of the wild type and mutant forms of the target proteins have been analysed to seek explanations for reduction in drug binding. Stability analysis of an entire array of 19 mutations at each of the residues for each target has been computed using structural models. Conservation indices of individual residues, binding sites and whole proteins are computed based on sequence conservation analysis of the target proteins. The analyses lead to insights about which positions in the polypeptide chain have a higher propensity to acquire drug resistant mutations. Thus critical insights can be obtained about the effect of mutations on drug binding, in terms of which amino acid positions and therefore which interactions should not be heavily relied upon, which in turn can be translated into guidelines for modifying the existing drugs as well as for designing new drugs. The methodology can serve as a general framework to study drug resistant mutants in other micro-organisms as well.

New Catalytic Methods for the Preparation of Tryptophans and Pyrroloindolines: Total Synthesis of (+)-Naseseazines A and B and (–)-Aspergilazine A

Tryptophan and unnatural tryptophan derivatives are important building blocks for the total synthesis of natural products, as well as the development of new drugs, biological probes, and chiral small molecule catalysts. This thesis describes various catalytic methods for the preparation of tryptophan derivatives as well as their functionalization and use in natural product total synthesis.

Herein, the tandem Friedel–Crafts conjugate addition/asymmetric protonation reaction between 2-substituted indoles and methyl 2-acetamidoacrylate to provide enantioenriched trytophans is reported. This method inspired further work in the area of transition metal catalyzed arylation reactions. We report the development of the coppercatalyzed arylation of tryptamine and tryptophan derivatives. The utility of these transformations is highlighted in the five-step syntheses of the natural products (+)-naseseazine A and B. Further work on the development of a mild and general Larock indolization protocol to access unnatural tryptophans is also discussed.

The price of innovation: new estimates of drug development costs.

The research and development costs of 68 randomly selected new drugs were obtained from a survey of 10 pharmaceutical firms. These data were used to estimate the average pre-tax cost of new drug development. The costs of compounds abandoned during testing were linked to the costs of compounds that obtained marketing approval. The estimated average out-of-pocket cost per new drug is 403 million US dollars (2000 dollars). Capitalizing out-of-pocket costs to the point of marketing approval at a real discount rate of 11% yields a total pre-approval cost estimate of 802 million US dollars (2000 dollars). When compared to the results of an earlier study with a similar methodology, total capitalized costs were shown to have increased at an annual rate of 7.4% above general price inflation.

Malignant pleural mesothelioma: current treatments and emerging drugs

Background: Malignant pleural mesothelioma (MPM) is an uncommon disease whose incidence is increasing worldwide over the past 30 years. Surgical resection and radiotherapy represent the standard treatment in patient with resectable MPM. Chemotherapy is also necessary to reduce incidence of distant metastases, but the optimal setting of treatment (neoadjuvant, adjuvant and intrapleural) is not clarified. For the patients with unresectable MPM, the combination cisplatin and pemetrexed or ralitrexed is the standard treatment as supported by a Phase III study. Better understanding of molecular pathways involved in MPM has enabled inclusion of new drugs targeted against pathways responsible for proliferation, cell survival and angiogenesis. Objective: This review discusses the current treatment option, the specific signal pathways activated in MPM and the novel agents under evaluation in clinical trials. Methods: We use for this article abstracts, papers, oral presentations from ASCO and the website http://www.clinical-trials.gov. Results/conclusion: This review summarizes the activity of chemotherapy and of new agents under evaluation in clinical trials. The better understanding of molecular pathways activated in MPM will hopefully provide new therapeutic options for these patients in the future.

The effects of new topical treatments on management of glaucoma in Scotland:An examination of ophthalmological health care

Background: The management of glaucoma has been changed in the past decade by the introduction of new drugs. The impact of these changes on clinical care of patients was examined by examining operation and prescribing rates for glaucoma in four geographical areas of Scotland for the years 1994 to 1999. Methods: A retrospective analysis of national health statistics: primary care prescribing data, hospital derived operation rates, consultant numbers, optometrist numbers, and eye test data, expressed by estimated population at risk of glaucoma. The outcome measures were prescribing volume and cost for glaucoma medications, and operation rates, corrected for population estimated to be at risk of glaucoma (PEG), for trabeculectomy, for Scotland as a whole, and for four geographical "regions" (north east, south east, central, and south west Scotland). Results: Prescribed items per 1000 population estimated to have glaucoma (PEG) increased by 24.9% between 1994 and 1999. This was above the general increase in prescribing in Scotland (17.8%). This increase varied in the four health regions evaluated (14.3% to 31.9%). Prescribing of topical ß blockers increased little (6.4%), but there was a large increase in the use of new products (topical prostaglandins, carbonic anhydrase inhibitors, and a agonists), at the expense of miotics (47.7% fall), and older sympathomimetics. This change in prescribing pattern was accompanied by a 61.5% increase in cost (range 42.2% to 73.4% in the four regions). New drugs accounted for more than half of total glaucoma expenditure in 1999. Operation rates (corrected for PEG) fell by 45.9% (range 43.1 to 58.6%) between 1994 and 1999. Other indicators suggested increased activity in ophthalmic areas (for example, cataract operations, eye tests, numbers of optometrists and ophthalmic surgeons all increased). Within north east Scotland operation rates decreased and prescribing increased less than in other regions, both from lowest regional baseline in 1994. Conclusions: The introduction of new drug classes has had dramatic effects on the prescribing of glaucoma treatments. There has been a decline in older treatments and an increase in new agents, which has been associated with a large reduction in operation rates for glaucoma in Scotland over 6 years. Comparison of prescribing and operation data indicates regional differences in healthcare delivery for glaucoma.

Antitussive drugs--past, present, and future

Cough remains a serious unmet clinical problem, both as a symptom of a range of other conditions such as asthma, chronic obstructive pulmonary disease, gastroesophageal reflux, and as a problem in its own right in patients with chronic cough of unknown origin. This article reviews our current understanding of the pathogenesis of cough and the hypertussive state characterizing a number of diseases as well as reviewing the evidence for the different classes of antitussive drug currently in clinical use. For completeness, the review also discusses a number of major drug classes often clinically used to treat cough but that are not generally classified as antitussive drugs. We also reviewed a number of drug classes in various stages of development as antitussive drugs. Perhaps surprising for drugs used to treat such a common symptom, there is a paucity of well-controlled clinical studies documenting evidence for the use of many of the drug classes in use today, particularly those available over the counter. Nonetheless, there has been a considerable increase in our understanding of the cough reflex over the last decade that has led to a number of promising new targets for antitussive drugs being identified and thus giving some hope of new drugs being available in the not too distant future for the treatment of this often debilitating symptom.

Connectivity mapping using a combined gene signature from multiple colorectal cancer datasets identified candidate drugs including existing chemotherapies

BACKGROUND: While the discovery of new drugs is a complex, lengthy and costly process, identifying new uses for existing drugs is a cost-effective approach to therapeutic discovery. Connectivity mapping integrates gene expression profiling with advanced algorithms to connect genes, diseases and small molecule compounds and has been applied in a large number of studies to identify potential drugs, particularly to facilitate drug repurposing. Colorectal cancer (CRC) is a commonly diagnosed cancer with high mortality rates, presenting a worldwide health problem. With the advancement of high throughput omics technologies, a number of large scale gene expression profiling studies have been conducted on CRCs, providing multiple datasets in gene expression data repositories. In this work, we systematically apply gene expression connectivity mapping to multiple CRC datasets to identify candidate therapeutics to this disease.

RESULTS: We developed a robust method to compile a combined gene signature for colorectal cancer across multiple datasets. Connectivity mapping analysis with this signature of 148 genes identified 10 candidate compounds, including irinotecan and etoposide, which are chemotherapy drugs currently used to treat CRCs. These results indicate that we have discovered high quality connections between the CRC disease state and the candidate compounds, and that the gene signature we created may be used as a potential therapeutic target in treating the disease. The method we proposed is highly effective in generating quality gene signature through multiple datasets; the publication of the combined CRC gene signature and the list of candidate compounds from this work will benefit both cancer and systems biology research communities for further development and investigations.

Development of new approaches for the synthesis and decoding of one-bead one-compound cyclic peptide libraries

La plupart des processus cellulaires et biologiques reposent, à un certain niveau, sur des interactions protéine-protéine (IPP). Leur manipulation avec des composés chimiques démontre un grand potentiel pour la découverte de nouveaux médicaments. Malgré la demande toujours croissante en molécules capables d’interrompre sélectivement des IPP, le développement d’inhibiteurs d’IPP est fortement limité par la grande taille de la surface d’interaction. En considérant la nature de cette surface, la capacité à mimer des structures secondaires de protéines est très importante pour lier une protéine et inhiber une IPP. Avec leurs grandes capacités peptidomimétiques et leurs propriétés pharmacologiques intéressan-tes, les peptides cycliques sont des prototypes moléculaires de choix pour découvrir des ligands de protéines et développer de nouveaux inhibiteurs d’IPP. Afin d’exploiter pleinement la grande diversité accessible avec les peptides cycliques, l’approche combinatoire «one-bead-one-compound» (OBOC) est l’approche la plus accessible et puissante. Cependant, l’utilisation des peptides cycliques dans les chimiothèques OBOC est limitée par les difficultés à séquencer les composés actifs après le criblage. Sans amine libre en N-terminal, la dégradation d’Edman et la spectrométrie de masse en tandem (MS/MS) ne peuvent pas être utilisées. À cet égard, nous avons développé de nouvelles approches par ouverture de cycle pour préparer et décoder des chimiothèques OBOC de peptides cycliques. Notre stratégie était d’introduire un résidu sensible dans le macrocycle et comme ancrage pour permettre la linéarisation des peptides et leur largage des billes pour le séquençage par MS/MS. Tout d’abord, des résidus sensibles aux nucléophiles, aux ultraviolets ou au bromure de cyanogène ont été introduits dans un peptide cyclique et leurs rendements de clivage évalués. Ensuite, les résidus les plus prometteurs ont été utilisés dans la conception et le développement d’approches en tandem ouverture de cycle / clivage pour le décodage de chimiothèques OBOC de peptides cycliques. Dans la première approche, une méthionine a été introduite dans le macrocycle comme ancrage pour simultanément permettre l’ouverture du cycle et le clivage des billes par traitement au bromure de cyanogène. Dans la seconde approche, un résidu photosensible a été utilisé dans le macrocycle comme ancrage pour permettre l’ouverture du cycle et le clivage suite à une irradiation aux ultraviolets. Le peptide linéaire généré par ces approches peut alors être efficacement séquencé par MS/MS. Enfin, une chimiothèque OBOC a été préparée et criblée la protéine HIV-1 Nef pour identifier des ligands sélectifs. Le développement de ces méthodologies permttra l’utilisation de composés macrocycliques dans les chimiothèques OBOC et constitue une contribution importante en chimie médicinale pour la découverte de ligands de protéines et le développement d’inhibiteurs d’IPP.

Novel ruthenium complexes as potential drugs for Chagas`s disease: enzyme inhibition and in vitro/in vivo trypanocidal activity

Background and purpose: The discovery of the pharmacological functions of nitric oxide has led to the development of NO donor compounds as therapeutic agents. A new generation of ruthenium NO donors, cis-[Ru(NO)(bpy)(2)L]X(n) , has been developed, and our aim was to show that these complexes are able to lyse Trypanosoma cruzi in vitro and in vivo. Experimental approach: NO donors were incubated with T. cruzi and their anti-T. cruzi activities evaluated as the percentage of lysed parasites compared to the negative control. In vivo, trypanocidal activity was evaluated by observing the levels of parasitaemia, survival rate and elimination of amastigotes in mouse myocardial tissue. The inhibition of GAPDH was monitored by the biochemical reduction of NAD+ to NADH. Key results: The NO donors cis-[Ru(NO)(bpy)(2)L]X(n) presented inhibitory effects on T. cruzi GAPDH (IC(50) ranging from 89 to 153 mu M). The crystal structure of the enzyme shows that the inhibitory mechanism is compatible with S-nitrosylation of the active cysteine (cys166) site. Compounds cis-[Ru(NO)(bpy)(2)imN](PF(6))(3) and cis-[Ru(NO)(bpy)(2)SO(3)]PF(6), at a dose of 385 nmol center dot kg-1, yielded survival rates of 80 and 60%, respectively, in infected mice, and eradicated any amastigotes from their myocardial tissue. Conclusions and implications: The ruthenium compounds exhibited potent in vitro and in vivo trypanocidal activities at doses up to 1000-fold lower than the clinical dose for benznidazole. Furthermore, one mechanism of action of these compounds is via the S-nitrosylation of Cys166 of T. cruzi GAPDH. Thus, these compounds show huge potential as candidates for the development of new drugs for the treatment of Chagas`s disease. This article is commented on by Machado et al., pp. 258-259 of this issue. To view this commentary visit http://dx.doi.org/10.1111/j.1476-5381.2010.00662.x and to view a related paper in this issue by Guedes et al. visit http://dx.doi.org/10.1111/j.1476-5381.2010.00576.x.

Randomised controlled trials and 'unexpected' adverse events associated with newly released drugs : improvements in pharmacovigilance systems are necessary for real-time identification of patient safety risks

Adverse drug events are one of the major causes of morbidity in developed countries, yet the drugs involved in these events have been trialled and approved on the basis of randomised controlled trials (RCTs), regarded as the study design that will produce the best evidence.

Though the focus on adverse drug events has been primarily on processes and outcomes associated with the use of these approved drugs, attention needs to be directed to the way in which the RCT study design is structured. The implementation of controls to achieve internal validity in RCTs may be the very controls that reduce external validity, and contribute to the levels of adverse drug events associated with the release of a new drug to the wider patient population.

An examination of these controls, and the effects they can have on patient safety, underscore the importance of knowing about how the clinical trials of a drug are undertaken, rather than relying only on the recorded outcomes.

As the majority of new drugs are likely to be prescribed to older patients who have one or more comorbidities in addition to that targeted by a new drug, and as the RCTs of those drugs typically under-represent the elderly and exclude patients with multiple comorbidities, timely assessment of drug safety signals is essential.

It is unlikely that regulatory jurisdictions will undertake a reassessment of safety issues for drugs that are already approved. Instead, reliance has been placed on adverse drug event reporting systems. Such systems have a very low reporting rate, and most adverse drug events remain unreported, to the eventual cost to patients and healthcare systems.

This makes it essential for near real-time systems that can pick up safety signals as they occur, so that modifications to the product information (or removal of the drug) can be implemented.

Pathways to new drug discovery in neuropsychiatry

There is currently a crisis in drug discovery for neuropsychiatric disorders, with a profound, yet unexpected drought in new drug development across the spectrum. In this commentary, the sources of this dilemma and potential avenues to redress the issue are explored. These include a critical review of diagnostic issues and of selection of participants for clinical trials, and the mechanisms for identifying new drugs and new drug targets. Historically, the vast majority of agents have been discovered serendipitously or have been modifications of existing agents. Serendipitous discoveries, based on astute clinical observation or data mining, remain a valid option, as is illustrated by the suggestion in the paper by Wahlqvist and colleagues that treatment with sulfonylurea and metformin reduces the risk of affective disorder. However, the identification of agents targeting disorder-related biomarkers is currently proving particularly fruitful. There is considerable hope for genetics as a purist, pathophysiologically valid pathway to drug discovery; however, it is unclear whether the science is ready to meet this promise. Fruitful paradigms will require a break from the orthodoxy, and creativity and risk may well be the fingerprints of success.

Auranofin: repurposing an old drug for a golden new age

Drug discovery, development and registration is an expensive and time-consuming process associated with a high failure rate [Pessetto et al. (Mol Cancer Ther 12:1299-1309, 2013), Woodcock and Woosley (Annu Rev Med 59:1-12, 2008)]. Drug 'repurposing' is the identification of new therapeutic purposes for already approved drugs and is more affordable and achievable than novel drug discovery [Pessetto et al. (Mol Cancer Ther 12:1299-1309, 2013)]. Auranofin is a drug that is approved for the treatment of rheumatoid arthritis but is being investigated for potential therapeutic application in a number of other diseases including cancer, neurodegenerative disorders, HIV/AIDS, parasitic infections and bacterial infections [Tejman-Yarden et al. (Antimicrob Agents Chemother 57:2029-2035, 2013)]. The main mechanism of action of auranofin is through the inhibition of reduction/oxidation (redox) enzymes that are essential for maintaining intracellular levels of reactive oxygen species. Inhibition of these enzymes leads to cellular oxidative stress and intrinsic apoptosis [Pessetto et al. (Mol Cancer Ther 12:1299-1309, 2013), Fan et al. (Cell Death Dis 5:e1191, 2014), Fiskus et al. (Cancer Res 74:2520-2532, 2014), Marzano et al. (Free Radic Biol Med 42:872-881, 2007)]. Drugs such as auranofin that have already been approved for human use [Tejman-Yarden et al. (Antimicrob Agents Chemother 57:2029-2035, 2013)] can be brought into clinical use for other diseases relatively quickly and for a fraction of the cost of new drugs.

New antimicrobial therapies used against fungi present in subgingival sites-A brief review

Although the main reservoir of Candida spp. is believed to be the buccal mucosa, these microorganisms can coaggregate with bacteria in subgingival biofilm and adhere to epithelial cells. The treatment of periodontal disease includes scaling and root planning (SR?) associated with proper oral hygiene. However, some patients may have negative responses to different therapeutic procedures, with a continuous loss of insertion, so the use of antimicrobials is needed as an adjuvant to SRP treatment. The use of a broad-spectrum antibiotic, such as tetracycline and metronidazole, as an aid in periodontal treatment has also been a factor for the development of superinfections by resistant bacteria and Candida species, even in patients with HIV. In the dental practice, the most commonly used antifungals are nystatin and fluconazole. However, the introduction of new drugs like the next generation of azoles is essential before the onset of emergent species in periodontal disease. Plants are good options for obtaining a wide variety of drugs. This alternative could benefit a large population that uses plants as a first treatment option. Plants have been used in medicine for a long time and are extensively used in folk medicine, because they represent an economic alternative, are easily accessible and are applicable to various diseases. Herein, we briefly review the literature pertaining the presence of Candida sp. in periodontal pockets, the conventional antifungal resistance and new therapies that include natural antifungal agents are reviewed. (C) 2011 Elsevier Ltd. All rights reserved.

Structure determination of hydroxytrypargine: A new tetrahydro-beta-carboline toxin from the venom of the spider Parawixia bistriata

A new, highly active tetrahydro-p-carboline toxin from the spider Parawixia bistriata, the most-common species of social spider occurring in Brazil, was isolated. The new toxin was identified as 1,2,3,4-tetrahydro-6-hydroxy-beta-carboline (= N-[3-(2,3,4,9-tetrahydro-6-hydroxy-1H-pyrido[3,4-b]indol-1-yl)propyl]guanidine; 3). This type of alkaloid, not common among spider toxins, was found to be the most-potent constituent of the spider's chemical weaponry to kill prey. When P bistriata catch arthropods in their web, they apparently attack their prey in groups of many individuals injecting their venoms. In vivo toxicity assays with 3 demonstrated a potent lethal effect to honeybees, giving rise to clear neurotoxic effects (paralysis) before death. The compound's toxicity (LD50 value) was determined to be ca. 8 ng/g of honeybee. The investigation of the pharmacological properties and neurotoxic actions of 3 may be used in the future for the development of new drugs to be applied for pest control in agriculture.