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The fluorescence thermal shift (FTS) method is a biophysical technique that can improve productivity in a structural genomics pipeline and provide a fast and easy platform for identifying ligands in protein function or drug discovery screening. The technique has gained widespread popularity in recent years due to its broad-scale applicability, throughput, and functional relevance. FTS is based on the principle that a protein unfolds at a critical temperature that depends upon its intrinsic stability. A probe that will fluoresce when bound to hydrophobic surfaces is used to monitor protein unfolding as temperature is increased. In this manner, conditions or small molecules that affect the thermal stability of a protein can be identified. Herein, principles, protocols, data analysis, and special considerations of FTS screening as performed for the Center for Structural Genomics of Infectious Diseases (CSGID) pipeline are described in detail. The CSGID FTS screen is designed as a high-throughput 384-well assay to be performed on a robotic platform; however, all protocols can be adapted to a 96-well format that can be assembled manually. Data analysis can be performed using a simple curve fitting of the fluorescent signal using a Boltzmann or double Boltzmann equation. A case study of 100 proteins screened against Emerald Biosystem's ADDit⠪ library is included as discussion. [ABSTRACT FROM AUTHOR]

Natural products play an essential role in our everyday life as almost all antibiotics or anti-cancer compounds currently in clinical use are either natural products or derivatives thereof. Mainly due to increasing resistance against these antibiotics there is an urgent need for novel bioactive natural products and several strategies are currently in use to find new compounds. In this chapter insects are suggested as a new and very promising source for novel secondary metabolite-producing bacteria and fungi. Whereas entomopathogenic fungi have been known for quite some time as potent producers of different bioactive compounds and have been used in traditional Chinese medicine for more than 2000 years, almost nothing is known about the underlying biochemistry and molecular biology that is involved in the biosynthesis of such compounds. Similarly, entomopathogenic bacteria have only been proven to be a rich source of interesting compounds during the last 20 years and recent genome sequencing projects have revealed their great potential as secondary metabolite producers. Furthermore, bacteria that live in symbiosis with insects have also been shown to be a rich source of potent natural products which have to be explored in the future in more detail. [ABSTRACT FROM AUTHOR]

Embryonic stem cells (ESCs) are recognized by the general public mainly as a possible source of cellular replacement therapy and transplantation. However, the usefulness of ESCs and ESC-derived tissue cell types for cell-based in vitro test systems in drug screening and toxicity was already recognized early after the discovery of ESCs in the late 1980s. In the present chapter, the employment of ESCs in cell-based test systems is described in the light of state-of-the-art methods in the field of drug discovery, and the advantages and disadvantages of the applications are discussed. The possible use of ESCs in the drug development process is illustrated by three examples: (1) the use of ESCs for basic research in early developmental biology, (2) the embryonic stem cell test for embryotoxicity, and (3) the use of ESC-derived cardiomyocytes for detection of cardiac toxicity. Potential applications of human ESCs, induced pluripotent stem cells (IPS cells), and personalized medicine are described in the last part. [ABSTRACT FROM AUTHOR]

Significant advancements in stem cell research have provided important information on stem cell biology and offer great promise for developing novel successful stem cell-based medical treatments. Further investigations appear to be necessary to translate the basic knowledge into clinical therapeutic applications in humans. The identification of specific biomarkers to each type of adult stem/progenitor cells relative to their more committed and mature progeny is important for the characterization of their specific physiological functions. [ABSTRACT FROM AUTHOR]

1. One in 10 adults has subjective tinnitus, and for 1 in 100 adults, tinnitus severely affects their quality of life. 2. Despite the significant unmet clinical need for a safe and effective drug targeting tinnitus relief, there is currently not a single FDA-approved drug on the market. 3. Since in some individuals, tinnitus causes irritability, agitation, stress, depression, insomnia, and interferes with normal life, even a drug that produces a small but significant effect would have a huge therapeutic impact. 4. A glimpse of hope is appearing in the near future, as some pharmaceutical industries now have compounds targeting tinnitus in their pipeline. 5. If these compounds finally reach the market, they will set a new era that will revolutionize the treatment of tinnitus. [ABSTRACT FROM AUTHOR]

In this chapter we will briefly reiterate critical aspects of solution nuclear magnetic resonance (NMR) spectroscopy approaches and their applications in drug discovery. These approaches are essentially based on a number of NMR techniques that have been developed to monitor and characterize intermolecular interactions. By way of examples, we will illustrate the unique advantages that these techniques offer when employed in conjunction with fragment-based ligand design, especially when tackling challenging drug targets. [ABSTRACT FROM AUTHOR]

Heterocyclic structures are an integral part of numerous drugs and natural products and there is a considerable interest in efficient methods for their synthesis. A variety of multicomponent reactions (MCRs) provide access to heterocyclic structures such as isocyanide based MCRs, dicarbonyl derivative and cycloaddition MCRs. MCR-derived heterocycles are typically prepared in few, versatile and atom efficient synthetic steps and exhibit anticancer, antioxidant and antimicrobial properties. [ABSTRACT FROM AUTHOR]

Tumor resistance to chemotherapeutic DNA damaging agents, such as cisplatin, is an obstacle in the treatment of many cancers, including lung and ovarian. Resistance is influenced by nucleotide excision repair (NER) catalyzed removal of cisplatin-DNA lesions. NER is the primary pathway used by the cells in the repair of helix-distorting cisplatin lesions; therefore, inhibition of NER may increase the efficacy of cisplatin treatment. More specifically, the recognition and verification of DNA damage by NER is a critical step in the pathway, making it an ideal target for inhibition. Recognition of DNA damage occurs primarily through two proteins, Xeroderma Pigmentosum Group A (XPA) and replication protein A (RPA). XPA has been shown to have a role exclusively in NER, thus making it a highly specific target for inhibition that will lead to a decrease in NER and an increase in sensitivity to cisplatin treatment. RPA is a single-stranded DNA-binding protein that has roles in NER as well as in other metabolic pathways, including DNA replication and recombination. We have developed a high-throughput (HT) assay for XPA/RPA binding to DNA and screened libraries of small molecules to identify compounds capable of interrupting the protein/DNA interaction, an effort that has lead to the identification of small molecule inhibitors of both RPA and XPA. These inhibitors have been validated in secondary in vitro screens and structure–activity relationships were determined for one class of inhibitors. Further development of this class of compounds is anticipated to display cytostatic/cytotoxic activity and sensitize cells to cisplatin therapy. [ABSTRACT FROM AUTHOR]

This case study illustrates how the determination of multiple co-crystal structures of the protein tyrosine kinase c-Abl was used to support drug discovery efforts leading to the design of nilotinib, a newly approved therapy for imatinib-intolerant and – resistant chronic myelogenous leukemia. Chronic myelogenous leukemia (CML) results from the BCR-Abl onco-protein, which possesses a constitutively activated Abl tyrosine kinase domain. Although many chronic-phase CML patients treated with imatinib as first-line therapy maintain excellent, durable responses, patients who have progressed to advanced-stage CML frequently fail, or lose their response to therapy, often due to the emergence of drug-resistant mutants of the protein. More than 60 such point mutations have been detected in imatinib-resistant patients. We determined the crystal structures of wild-type and mutant Abl kinase in complex with imatinib and other small molecule Abl inhibitors, with the aim of understanding the molecular basis for resistance and to aid in the design and optimization of inhibitors active against the resistance mutants. These results are presented in a way which illustrates the approaches used to generate multiple structures, the type of information that can be gained and the way this information is used to support drug discovery. [ABSTRACT FROM AUTHOR]

The problems associated with neglected diseases are often compounded by increasing incidence of antibiotic resistance. Patient negligence and abuse of antibiotics has lead to explosive growth in cases of tuberculosis, with some M. tuberculosis strains becoming virtually untreatable. Structure-based drug development is viewed as cost-effective and time-consuming method for discovery and development of hits to lead compounds. In this review we will discuss the suitability of fragment-based methods for developing new chemotherapeutics against neglected diseases, providing examples from our tuberculosis programme. [ABSTRACT FROM AUTHOR]

In this paper we present a methodology for evaluating the confidence in the prediction of a physicochemical or biological property. Identifying unreliable compounds΄ predictions is crucial for the modern drug discovery process.This task is accomplished by the combination of the method of prediction with a self-organizing map. In this way, the method is able to segregate unconfident predictions as well as confident predictions. We applied the method to four different data sets, and we obtained significant differences in the average predictions of our segregation. This approach constitutes a novel way for evaluating confidence, since it not only looks for extrapolation situations but also it identifies interpolation problems. [ABSTRACT FROM AUTHOR]

An abstract of the article "Towards quantitative biology: Integration of biological information to elucidate disease pathways and to guide drug discovery," by Hans Peter Fischer is presented.