Target-based Approaches Research Articles

BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts.

BackgroundTuberculosis (TB) is the second leading cause of death from a single infectious organism, demanding attention towards discovery of novel anti-tubercular compounds. Natural products or their derivatives have provided more than 50% of all existing drugs, offering a chemically diverse space for discovery of novel drugs.DescriptionBioPhytMol has been designed to systematically curate and analyze the anti-mycobacterial natural product chemical space. BioPhytMol is developed as a drug-discovery community resource with anti-mycobacterial phytomolecules and plant extracts. Currently, it holds 2582 entries including 188 plant families (692 genera and 808 species) from global flora, manually curated from literature. In total, there are 633 phytomolecules (with structures) curated against 25 target mycobacteria. Multiple analysis approaches have been used to prioritize the library for drug-like compounds, for both whole cell screening and target-based approaches. In order to represent the multidimensional data on chemical diversity, physiochemical properties and biological activity data of the compound library, novel approaches such as the use of circular graphs have been employed.ConclusionBioPhytMol has been designed to systematically represent and search for anti-mycobacterial phytochemical information. Extensive compound analyses can also be performed through web-application for prioritizing drug-like compounds. The resource is freely available online at http://ab-openlab.csir.res.in/biophytmol/. Graphical BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts generated using Crowdsourcing. The platform comprises of manually curated data on antimycobacterial natural products along with tools to perform structure similarity and visualization. The platform allows for prioritization of drug like natural products for antimycobacterial drug discovery. Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-014-0046-2) contains supplementary material, which is available to authorized users.

Designing innovative therapies for neuropathic pain: pros and cons of target-based drug discovery.

Designing innovative therapies for neuropathic pain: pros and cons of target-based drug discovery.

Assay suitability for natural product screening: searching for leads to fight Alzheimer's disease.

Phenotypic and target-based approaches represent two principal strategies for identifying new bioactive compounds. In this review, differences between these approaches, as well as strengths and limitations thereof, are described by examples from the therapeutic area of Alzheimer's disease. Some of the central mechanisms of the disease that today are targets of screening campaigns are described. These mechanisms include acetylcholinesterase inhibition, amyloid-based approaches, and oxidative stress. Examples of assays using natural products, either as isolated pure compounds, unpurified or partially purified extracts, are given for each mechanism. Further, the article presents and discusses the pros and cons of both target-based and phenotypic approaches for the chosen mechanisms. In most cases, a thoroughly biology-driven selection of the used assays can be recommended, especially when taking into account the complexity of the disease in question. However, target-based assays also have their justification as long as there is an awareness of what the assay read-out stands for. A clear recommendation is thus for every researcher to critically consider the aim of their bioactivity screening efforts and to adopt the screening strategies most appropriate for the goals set.

Isobenzofuranone derivatives exhibit antileishmanial effect by inhibiting type II DNA topoisomerase and inducing host response.

Leishmania, a protozoan parasite, causes a wide range of human diseases ranging from the localized self-healing cutaneous lesions to fatal visceral leishmaniasis. Toxicity of traditional first line drugs and emergence of drug-resistant strains have worsened the situation. DNA topoisomerase II in kinetoplastid protozoan parasites are of immense interest as drug target because they take part in replication of unusual kinetoplast DNA network. In this study, we have taken target-based therapeutic approaches to combat leishmaniasis. Two isobenzofuranone compounds, viz., (1) 3,5-bis(4-chlorophenyl)-7-hydroxyisobenzofuran-1(3H)-one (JVPH3) and (2) (4-bromo)-3′-hydroxy-5′-(4-bromophenyl)-benzophenone(JVPH4) were synthesized chemically and characterized by NMR and mass spectrometry analysis. Activity of type II DNA topoisomerase of leishmania (LdTOPII) was monitored by decatenation assay and plasmid cleavage assay. The antiparasitic activity of these compounds was checked in experimental BALB/c mice model of visceral leishmaniasis. Isobenzofuranone derivatives exhibited potent antileishmanial effect on both antimony (Sb) sensitive and resistant parasites. Treatment with isobenzofuranone derivatives on promastigotes caused induction of reactive oxygen species (ROS)-mediated apoptosis like cell death in leishmania. Both the compounds inhibited the decatenation activity of LdTOPII but have no effect on bi-subunit topoisomerase IB. Treatment of LdTOPII with isobenzofuranone derivatives did not stabilize cleavage complex formation both in vitro and in vivo. Moreover, treatment with isobenzofuranone derivatives on Leishmania donovani-infected mice resulted in clearance of parasites in liver and spleen by induction of Th1 cytokines. Taken together, our data suggest that these compounds can be exploited as potential antileishmanial agents targeted to DNA topoisomerase II of the parasite.

The discovery of first-in-class drugs: origins and evolution.

Analysis of the origins of new drugs approved by the US Food and Drug Administration (FDA) from 1999 to 2008 suggested that phenotypic screening strategies had been more productive than target-based approaches in the discovery of first-in-class small-molecule drugs. However, given the relatively recent introduction of target-based approaches in the context of the long time frames of drug development, their full impact might not yet have become apparent. Here, we present an analysis of the origins of all 113 first-in-class drugs approved by the FDA from 1999 to 2013, which shows that the majority (78) were discovered through target-based approaches (45 small-molecule drugs and 33 biologics). In addition, of 33 drugs identified in the absence of a target hypothesis, 25 were found through a chemocentric approach in which compounds with known pharmacology served as the starting point, with only eight coming from what we define here as phenotypic screening: testing a large number of compounds in a target-agnostic assay that monitors phenotypic changes. We also discuss the implications for drug discovery strategies, including viewing phenotypic screening as a novel discipline rather than as a neoclassical approach.

The discovery of medicines for rare diseases.

There is a pressing need for new medicines (new molecular entities; NMEs) for rare diseases as few of the 6800 rare diseases (according to the NIH) have approved treatments. Drug discovery strategies for the 102 orphan NMEs approved by the US FDA between 1999 and 2012 were analyzed to learn from past success: 46 NMEs were first in class; 51 were followers; and five were imaging agents. First-in-class medicines were discovered with phenotypic assays (15), target-based approaches (12) and biologic strategies (18). Identification of genetic causes in areas with more basic and translational research such as cancer and in-born errors in metabolism contributed to success regardless of discovery strategy. In conclusion, greater knowledge increases the chance of success and empirical solutions can be effective when knowledge is incomplete.

C-KIT Signaling in Cancer Treatment

Tumor progression is strongly associated with the activity of receptor tyrosine kinases (RTKs) and their intracellular signal transduction pathways, which regulate several cell functions including proliferation, apoptosis, motility, adhesion and angiogenesis. Detailed structural and functional studies of RTKs, including the stem cell factor receptor c-KIT, revealed the complexity of these receptor systems and contributed to development of targeted clinical approaches with relevance in both prognosis and therapy. C-KIT signaling network has been the subject of intense research and pharmaceutical strategies to identify novel target-based approaches for cancer treatment. Evidence that c-KIT signaling promotes cell proliferation and survival, along with the frequency in which this pathway is aberrantly activated in cancer, support the current efforts to identify approaches for its efficient inhibition. C-KIT mutations are associatied with several human malignancies, such as gastrointestinal stromal tumors, acute myeloid leukemia, mast cell leukemia, and melanoma. Novel therapies are developed that target some of the identified genetic defects. It is therefore anticipated that newly-identified genetic markers will acquire a predictive value, that is, the ability to predict differential efficacy of a therapy. This review describes the evolving understanding of c-KIT/SCF axis and their downstream signaling in cancer, and the strategies for c-KIT-directed targeted cancer therapy.

Multi-attribute target-based utilities and extensions of fuzzy measures

We introduce a formal description of the Target-Based Approach to utility theory for the case of n>1 attributes and point out the connections with aggregation-based extensions of capacities. Our discussion provides economic interpretations of different concepts of the theory of fuzzy measures. In particular, we analyze the meaning of extensions of capacities based on n-dimensional copulas. The latter describes stochastic dependence for random vectors of interest in the problem. We also trace the connections between the case of {0,1}-valued capacities and the analysis of “coherent” reliability systems.

ABC transporters in multi-drug resistance and ADME-Tox of small molecule tyrosine kinase inhibitors.

The past decade has seen tremendous efforts in the research and development of new chemotherapeutic drugs using target-based approaches. These efforts have led to the discovery of small molecule tyrosine kinase inhibitors (TKIs). Following the initial approval of imatinib by the US FDA in 2001, more than 15 TKIs targeting different tyrosine kinases have been approved, and numerous others are in various phases of clinical evaluation. Unlike conventional chemotherapy that can cause non-discriminating damage to both normal and cancerous cells, TKIs attack cancer-specific targets and therefore have a more favorable safety profile. However, although TKIs have had outstanding success in cancer therapy, there has been increasing evidence of resistance to TKIs. The enhanced efflux of TKIs by ATP-binding cassette (ABC) transporters over-expressed in cancer cells has been found to be one such important resistance mechanism. Another major drawback of TKI therapies that has been increasingly recognized is the extensive inter-individual pharmacokinetic variability, in which ABC transporters seem to play a major role as well. This review covers recent findings on the interactions of small molecule TKIs with ABC transporters. The effects of ABC transporters on anticancer efficacy and the absorption, distribution, metabolism, excretion, and toxicity (ADME-Tox) of the small molecule TKIs are summarized in detail. Since TKIs have been found to not only serve as substrates of ABC transporters, but also as modulators of these proteins via inhibition or induction, their influence upon ABC transporters and potential role on TKI-drug interactions are discussed as well.

Muddying the Water? Assessing Target-based Approaches in Development Cooperation for Water and Sanitation

In the debate on the post-2015 development agenda, a clear preference exists for simple and quantifiable targets. The water sector provides a useful perspective in which to evaluate the use of this strategy because it has been subject to quantitative target setting since 1976. We critically analyze two early periods of target setting together with their most recent incarnation in the Millennium Development Goals. In so doing, we identify two stories concerning the utility of such a turn to metrics: the first is a perennial and at times justified optimism in target setting, and the second is a more cautionary tale about the dangers of measurement and its tendency to gloss over challenging but significant issues. In addition, we offer some brief conclusions on the implications for the post-2015 agenda and some potential measurement alternatives.

SIRT1 deacetylase is overexpressed in human melanoma and its small molecule inhibition imparts anti-proliferative response via p53 activation

Melanoma causes more deaths than any other skin cancer, and its incidence in the US continues to rise. Current medical therapies are insufficient to control this deadly neoplasm, necessitating the development of new target-based approaches. The objective of this study was to determine the role and functional significance of the class III histone deacetylase SIRT1 in melanoma. We have found that SIRT1 is overexpressed in clinical human melanoma tissues and human melanoma cell lines (Sk-Mel-2, WM35, G361, A375, and Hs294T) compared to normal skin and normal melanocytes, respectively. In addition, treatment of melanoma cell lines A375, Hs294T, and G361 with Tenovin-1, a small molecule SIRT1 inhibitor, resulted in a significant decrease in cell growth and cell viability. Further, Tenovin-1 treatment also resulted in a marked decrease in the clonogenic survival of melanoma cells. Further experiments showed that the anti-proliferative response of Tenovin-1 was accompanied by an increase in the protein as well as activity of the tumor suppressor p53. This increase in p53 activity was substantiated by an increase in the protein level of its downstream target p21. Overall, these data suggest that small molecule inhibition of SIRT1 causes anti-proliferative effects in melanoma cells. SIRT1 appears to be acting through the activity of the tumor suppressor p53, which is not mutated in the majority of melanomas. However, future detailed studies are needed to further explore the role and mechanism of SIRT1 in melanoma development and progression and its usefulness in melanoma treatment.

UCSF Small Molecule Discovery Center: Innovation, Collaboration and Chemical Biology in the Bay Area

The Small Molecule Discovery Center (SMDC) at the University of California, San Francisco, works collaboratively with the scientific community to solve challenging problems in chemical biology and drug discovery. The SMDC includes a high throughput screening facility, medicinal chemistry, and research labs focused on fundamental problems in biochemistry and targeted drug delivery. Here, we outline our HTS program and provide examples of chemical tools developed through SMDC collaborations. We have an active research program in developing quantitative cell-based screens for primary cells and whole organisms; here, we describe whole-organism screens to find drugs against parasites that cause neglected tropical diseases. We are also very interested in target-based approaches for so-called "undruggable", protein classes and fragment-based lead discovery. This expertise has led to several pharmaceutical collaborations; additionally, the SMDC works with start-up companies to enable their early-stage research. The SMDC, located in the biotech-focused Mission Bay neighborhood in San Francisco, is a hub for innovative small-molecule discovery research at UCSF.

Recent Approaches for Studying the Role of Glia

A target-based approach has been used to develop novel drugs in many therapeutic fields. However, this approach remains suboptimal for drug discovery in brain disorders because the target identification in a brain disorder requires a hierarchical integration from in vitro cellular and functional tissue studies to animal models that sustain neuronal and glial complexity. Although glial cells comprise over half of the brain and play important roles in brain function and disease, the intracellular signaling of glial cells remains essentially unexplored. This is because the lack of optimal strategy to selectively activate or deactivate glial signaling has made it difficult to study glial roles. The recent development of approaches using mouse models and enabling the selective activation of cell signaling could be used to assess the role of glial cells in physiology and disease. This review presents how glial G- protein signaling contributes to brain disorders and how the role of glia is investigated.

Prospects on Strategies for Therapeutically Targeting Oncogenic Regulatory Factors by Small-Molecule Agents

Although the Human Genome Project has raised much hope for the identification of druggable genetic targets for cancer and other diseases, this genetic target-based approach has not improved productivity in drug discovery over the traditional approach. Analyses of known human target proteins of currently marketed drugs reveal that these drugs target only a limited number of proteins as compared to the whole proteome. In contrast to genome-based targets, mechanistic targets are derived from empirical research, at cellular or molecular levels, in disease models and/or in patients, thereby enabling the exploration of a greater number of druggable targets beyond the genome and epigenome. The paradigm shift has made a tremendous headway in developing new therapeutic agents targeting different clinically relevant mechanisms/pathways in cancer cells. In this Prospects article, we provide an overview of potential drug targets related to the following four emerging areas: (1) tumor metabolism (the Warburg effect), (2) dysregulated protein turnover (E3 ubiquitin ligases), (3) protein-protein interactions, and (4) unique DNA high-order structures and protein-DNA interactions. Nonetheless, considering the genetic and phenotypic heterogeneities that characterize cancer cells, the development of drug resistance in cancer cells by adapting signaling circuitry to take advantage of redundant pathways or feedback/crosstalk systems is possible. This "phenotypic adaptation" underlies the rationale of using therapeutic combinations of these targeted agents with cytotoxic drugs.

Application of Microarray and Functional-Based Screening Methods for the Detection of Antimicrobial Resistance Genes in the Microbiomes of Healthy Humans

The aim of this study was to screen for the presence of antimicrobial resistance genes within the saliva and faecal microbiomes of healthy adult human volunteers from five European countries. Two non-culture based approaches were employed to obviate potential bias associated with difficult to culture members of the microbiota. In a gene target-based approach, a microarray was employed to screen for the presence of over 70 clinically important resistance genes in the saliva and faecal microbiomes. A total of 14 different resistance genes were detected encoding resistances to six antibiotic classes (aminoglycosides, β-lactams, macrolides, sulphonamides, tetracyclines and trimethoprim). The most commonly detected genes were erm(B), bla TEM, and sul2. In a functional-based approach, DNA prepared from pooled saliva samples was cloned into Escherichia coli and screened for expression of resistance to ampicillin or sulphonamide, two of the most common resistances found by array. The functional ampicillin resistance screen recovered genes encoding components of a predicted AcrRAB efflux pump. In the functional sulphonamide resistance screen, folP genes were recovered encoding mutant dihydropteroate synthase, the target of sulphonamide action. The genes recovered from the functional screens were from the chromosomes of commensal species that are opportunistically pathogenic and capable of exchanging DNA with related pathogenic species. Genes identified by microarray were not recovered in the activity-based screen, indicating that these two methods can be complementary in facilitating the identification of a range of resistance mechanisms present within the human microbiome. It also provides further evidence of the diverse reservoir of resistance mechanisms present in bacterial populations in the human gut and saliva. In future the methods described in this study can be used to monitor changes in the resistome in response to antibiotic therapy.

Tuberculosis drug discovery in the post‐post‐genomic era

The expectation that genomics would result in new therapeutic interventions for infectious diseases remains unfulfilled. In the post-genomic era, the decade immediately following the availability of the genome sequence of Mycobacterium tuberculosis, tuberculosis (TB) drug discovery relied heavily on the target-based approach but this proved unsuccessful leading to a return to whole cell screening. Genomics underpinned screening by providing knowledge and many enabling technologies, most importantly whole genome resequencing to find resistance mutations and targets, and this resulted in a selection of leads and new TB drug candidates that are reviewed here. Unexpectedly, many new targets were found to be ‘promiscuous’ as they were inhibited by a variety of different compounds. In the post-post-genomics era, more advanced technologies have been implemented and these include high-content screening, screening for inhibitors of latency, the use of conditional knock-down mutants for validated targets and siRNA screens. In addition, immunomodulation and pharmacological manipulation of host functions are being explored in an attempt to widen our therapeutic options.

Proteomic screening of molecular targets of crocin

BackgroundTraditional drug discovery approaches are mainly relied on the observed phenotypic changes following administration of a plant extract, drug candidate or natural product. Recently, target-based approaches are becoming more popular. The present study aimed to identify the cellular targets of crocin, the bioactive dietary carotenoid present in saffron, using an affinity-based method.MethodsHeart, kidney and brain tissues of BALB/c mice were homogenized and extracted for the experiments. Target deconvolution was carried out by first passing cell lysate through an affinity column prepared by covalently attaching crocin to agarose beads. Isolated proteins were separated on a 2D gel, trypsinized in situ and identified by MALDI-TOF/TOF mass spectrometry. MASCOT search engine was used to analyze Mass Data.ResultsPart of proteome that physically interacts with crocin was found to consist of beta-actin-like protein 2, cytochrome b-c1 complex subunit 1, ATP synthase subunit beta, tubulin beta-3 chain, tubulin beta-6 chain, 14-3-3 protein beta/alpha, V-type proton ATPase catalytic subunitA, 60 kDa heat shock protein, creatine kinase b-type, peroxiredoxin-2, cytochrome b-c1 complex subunit 2, acetyl-coA acetyltransferase, cytochrome c1, proteasome subunit alpha type-6 and proteasome subunit alpha type-4.ConclusionThe present findings revealed that crocin physically binds to a wide range of cellular proteins such as structural proteins, membrane transporters, and enzymes involved in ATP and redox homeostasis and signal transduction.

Insights into the inhibition and mechanism of compounds against LPS-induced PGE2 production: a pathway network-based approach and molecular dynamics simulations.

In comparison to the current target-based screening approach, it is increasingly evident that active lead compounds based on disease-related phenotypes are more likely to be translated to clinical trials during drug development. That is, because human diseases are in essence the outcome of the abnormal function of multiple genes, especially in complex diseases. Therefore, as a conventional technology in the early phase of active lead compound discovery, computational methods that can connect molecular interactions and disease-related phenotypes to evaluate the efficacy of compounds are in urgently required. In this work, a computational approach that integrates molecular docking and pathway network analysis (network efficiency and network flux) was developed to evaluate the efficacy of a compound against LPS-induced Prostaglandin E2(PGE2) production. The predicted results were then validated in vitro, and a correlation with the experimental results was analyzed using linear regression. In addition, molecular dynamics (MD) simulations were performed to explore the molecular mechanism of the most potent compounds. There were 12 hits out of 28 predicted ingredients separated from Reduning injection (RDN). The predicted results have a good agreement with the experimental inhibitory potency (IC50) (correlation coefficient = 0.80). The most potent compounds could target several proteins to regulate the pathway network. This might partly interpret the molecular mechanism of RDN on fever. Meanwhile, the good correlation of the computational model with the wet experimental results might bridge the gap between molecule-target interactions and phenotypic response, especially for multi-target compounds. Therefore, it would be helpful for active lead compound discovery, the understanding of the multiple targets and synergic essence of traditional Chinese medicine (TCM).

Recent Patents in the Field of Radioprotector Development: Opportunities and Challenges

Ionizing radiation-induced Acute Radiation Syndrome (ARS) can be prevented/treated using radioprotective agents including; radioprotectors, radiomitigators and radio-therapeutics. Most of the radioprotective molecules currently being developed have emerged from classical drug discovery approaches and have certain shortcomings related to efficacy and toxicity. In order to overcome these issues, adoption of new target-based drug development approaches is required. Like other pharmaceutical drug development programs, patents are being used to protect the new radioprotective compounds that provide right of exclusivity to the inventors. In addition to patents, the FDA approval for safety and efficacy is required for the development of radioprotective drugs that is often being done under FDA's animal rule and requires huge amount of funding. However, radiation countermeasure agents considered emergency medicines and not carrying attractive revenue generation opportunities and are often granted 'orphan drug status'. Thus, pharma giants do not take much interest in such molecules that limit the funding options only to the government agencies, which in turn reduces the interest of researchers in this particular area. In addition to their emergency use, these agents could also be employed for clinical radiotherapy purposes and may provide reasonable incentive to the inventor. Thus, encouraging the development of new radioprotective agent with cutting-edge drug discovery approaches needs more public-private partnership ensuring affordable access; that may stimulate researchers to engage in the area of radioprotector development. This article attempts to cover information available so far on the products/patents/major compounds, known in this critical area of development, along with most relevant regulatory issues and future perspectives.

FRET-Based Calcium Imaging: A Tool for High-Throughput/Content Phenotypic Drug Screening in Alzheimer Disease

Perturbed intracellular store calcium homeostasis is suggested to play a major role in the pathophysiology of Alzheimer disease (AD). A number of mechanisms have been suggested to underlie the impairment of endoplasmic reticulum calcium homeostasis associated with familial AD-linked presenilin 1 mutations (FAD-PS1). Without aiming at specifically targeting any of those pathophysiological mechanisms in particular, we rather performed a high-throughput phenotypic screen to identify compounds that can reverse the exaggerated agonist-evoked endoplasmic reticulum calcium release phenotype in HEK293 cells expressing FAD-PS1. For that purpose, we developed a fully automated high-throughput calcium imaging assay using a fluorescence resonance energy transfer–based calcium indicator at single-cell resolution. This novel robust assay offers a number of advantages compared with the conventional calcium measurement screening technologies. The assay was employed in a large-scale screen with a library of diverse compounds comprising 20,000 low-molecular-weight molecules, which resulted in the identification of 52 primary hits and 4 lead structures. In a secondary assay, several hits were found to alter the amyloid β (Aβ) production. In view of the recent failure of AD drug candidates identified by target-based approaches, such a phenotypic drug discovery paradigm may present an attractive alternative for the identification of novel AD therapeutics.