New Strategies For Drug Discovery Research Articles

New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters

Genome sequencing of Streptomyces, myxobacteria, and fungi showed that although each strain contains genes that encode the enzymes to synthesize a plethora of potential secondary metabolites, only a fraction are expressed during fermentation. Interest has therefore grown in the activation of these cryptic pathways. We review current progress on this topic, describing concepts for activating silent genes, utilization of “natural” mutant-type RNA polymerases and rare earth elements, and the applicability of ribosome engineering to myxobacteria and fungi, the microbial groups known as excellent searching sources, as well as actinomycetes, for secondary metabolites.

Fragment screening of cyclin G-associated kinase by weak affinity chromatography

Fragment-based drug discovery (FBDD) has become a new strategy for drug discovery where lead compounds are evolved from small molecules. These fragments form low affinity interactions (dissociation constant (KD) = mM − μM) with protein targets, which require fragment screening methods of sufficient sensitivity. Weak affinity chromatography (WAC) is a promising new technology for fragment screening based on selective retention of fragments by a drug target. Kinases are a major pharmaceutical target, and FBDD has been successfully applied to several of these targets. In this work, we have demonstrated the potential to use WAC in combination with mass spectrometry (MS) detection for fragment screening of a kinase target—cyclin G-associated kinase (GAK). One hundred seventy fragments were selected for WAC screening by virtual screening of a commercial fragment library against the ATP-binding site of five different proteins. GAK protein was immobilized on a capillary HPLC column, and compound binding was characterized by frontal affinity chromatography. Compounds were screened in sets of 13 or 14, in combination with MS detection for enhanced throughput. Seventy-eight fragments (46 %) with KD < 200 μM were detected, including a few highly efficient GAK binders (KD of 2 μM; ligand efficiency = 0.51). Of special interest is that chiral screening by WAC may be possible, as two stereoisomeric fragments, which both contained one chiral center, demonstrated twin peaks. This ability, in combination with the robustness, sensitivity, and simplicity of WAC makes it a new method for fragment screening of considerable potential.

Identification of Molecular Mechanism for Actions of Existing Medicines and Its Application for Drug Development

As a new strategy for drug discovery and development, we propose here the establishment of drug re-profiling strategy. In this strategy, the actions of existing medicines, whose safety and pharmacokinetic effects in humans have been confirmed already, are examined comprehensively at the molecular level and the results are used for the development of new medicines. For example, identification of the mechanisms underlying the side effects of medicines enables us to develop safer drugs. The results can also be used for developing existing drugs for use as medicines in treatment of other diseases. Promoting this research strategy could provide breakthroughs in drug discovery and development by pharmaceutical companies.

New strategies for drug discovery in tropical forests based on ethnobotanical and chemical ecological studies

Ethnopharmacological relevanceHypotheses from ethnobotany and chemical ecology can increase our ability to predict the pharmaceutical potential of tropical flora. In order to illustrate how bioprospecting studies can benefit from the incorporation of these hypotheses, especially in tropical dry forests, we discuss evidence from ethnobotanical studies that examine hypotheses about the ecology of plant defense against herbivory. Materials and methodsWe focus on two hypotheses regarding defense patterns in plants—the plant apparency hypothesis and the resource availability hypothesis—and analyze how these can help us understand the use of medicinal plants by traditional communities. ResultsThe evidence suggests that medicinal plants in the dry forest are a rich source of drugs in which phenolic compounds, especially tannins, are directly responsible for the therapeutic activity. Phenolic compounds and their potential therapeutic activity are likely good candidates for bioprospecting efforts. ConclusionWe believe that following strategies to link ethnobotanical and chemical ecological approaches will increase the efficiency of bioprospecting studies in tropical forests.

New sources of drugs for hematologic malignancies

AbstractAdvancing novel therapeutic agents for the treatment of malignancy into the marketplace is an increasingly costly and lengthy process. As such, new strategies for drug discovery are needed. Drug repurposing represents an opportunity to rapidly advance new therapeutic strategies into clinical trials at a relatively low cost. Known on-patent or off-patent drugs with unrecognized anticancer activity can be rapidly advanced into clinical testing for this new indication by leveraging their known pharmacology, pharmacokinetics, and toxicology. Using this approach, academic groups can participate in the drug discovery field and smaller biotechnology companies can “de-risk” early-stage drug discovery projects. Here, several scientific approaches used to identify drug repurposing opportunities are highlighted, with a focus on hematologic malignancies. In addition, a discussion of the regulatory issues that are unique to drug repurposing and how they impact developing old drugs for new indications is included. Finally, the mechanisms to enhance drug repurposing through increased collaborations between academia, industry, and nonprofit charitable organizations are discussed.

Drug discovery and development focusing on existing medicines: drug re-profiling strategy

As a new strategy for drug discovery and development, I focus on drug re-profiling as a way to identify new treatments for diseases. In this strategy, the actions of existing medicines, whose safety and pharmacokinetic effects in humans have already been confirmed clinically and approved for use, are examined comprehensively at the molecular level and the results used for the development of new medicines. This strategy is based on the fact that we still do not understand the underlying mechanisms of action of many existing medicines, and as such the cellular responses that give rise to their main effects and side effects are yet to be elucidated. To this extent, identification of the mechanisms underlying the side effects of medicines offers a means for us to develop safer drugs. The results can also be used for developing existing drugs for use as medicines for the treatment of other diseases. Promoting this research strategy could provide breakthroughs in drug discovery and development.

Editorial [Hot Topic: New Strategy for Drug Discovery Using Monoclonal Antibody (Guest Editor: Yukihiro Shoyama)

Editorial [Hot Topic: New Strategy for Drug Discovery Using Monoclonal Antibody (Guest Editor: Yukihiro Shoyama)

Single cell trapping and DNA damage analysis using microwell arrays

With a direct link to cancer, aging, and heritable diseases as well as a critical role in cancer treatment, the importance of DNA damage is well-established. The intense interest in DNA damage in applications ranging from epidemiology to drug development drives an urgent need for robust, high throughput, and inexpensive tools for objective, quantitative DNA damage analysis. We have developed a simple method for high throughput DNA damage measurements that provides information on multiple lesions and pathways. Our method utilizes single cells captured by gravity into a microwell array with DNA damage revealed morphologically by gel electrophoresis. Spatial encoding enables simultaneous assays of multiple experimental conditions performed in parallel with fully automated analysis. This method also enables novel functionalities, including multiplexed labeling for parallel single cell assays, as well as DNA damage measurement in cell aggregates. We have also developed 24- and 96-well versions, which are applicable to high throughput screening. Using this platform, we have quantified DNA repair capacities of individuals with different genetic backgrounds, and compared the efficacy of potential cancer chemotherapeutics as inhibitors of a critical DNA repair enzyme, human AP endonuclease. This platform enables high throughput assessment of multiple DNA repair pathways and subpathways in parallel, thus enabling new strategies for drug discovery, genotoxicity testing, and environmental health.

Angiogenic Factors Stimulate Growth of Adult Neural Stem Cells

BackgroundThe ability to grow a uniform cell type from the adult central nervous system (CNS) is valuable for developing cell therapies and new strategies for drug discovery. The adult mammalian brain is a source of neural stem cells (NSC) found in both neurogenic and non-neurogenic zones but difficulties in culturing these hinders their use as research tools [1], [2], [3], [4], [5], [6].Methodology/Principal FindingsHere we show that NSCs can be efficiently grown in adherent cell cultures when angiogenic signals are included in the medium. These signals include both anti-angiogenic factors (the soluble form of the Notch receptor ligand, Dll4) and pro-angiogenic factors (the Tie-2 receptor ligand, Angiopoietin 2). These treatments support the self renewal state of cultured NSCs and expression of the transcription factor Hes3, which also identifies the cancer stem cell population in human tumors. In an organotypic slice model, angiogenic factors maintain vascular structure and increase the density of dopamine neuron processes.Conclusions/SignificanceWe demonstrate new properties of adult NSCs and a method to generate efficient adult NSC cultures from various central nervous system areas. These findings will help establish cellular models relevant to cancer and regeneration.

Reverse‐phase protein arrays for application‐orientated cancer research

A detailed and quantitative analysis of disease-relevant signaling will greatly contribute to our understanding of tumorigenesis and cancer progression, and thus open new strategies for drug discovery. However, throughput and sensitivity of currently established methods available for proteome profiling do not comply with the needs of clinical research such as high sample capacity and low sample consumption. Protein microarrays emerged as a promising alternative to analyze the abundance of proteins and their phosphorylation status on a high-throughput level. Here we summarize recent methodological advancements in the field of reverse-phase protein arrays and demonstrate their potential for clinical research as well as for in vitro applications.

Recent progress in fragment-based lead discovery

Fragment-based methods have emerged as a new strategy for drug discovery. The main advantages are that useful starting points for lead identification for most targets can be identified from a relatively small (typically 1000-member) library of low molecular weight compounds. The main constraints are the need for a method that can reliably detect weak binding and strategies for evolving the fragments into larger lead compounds. The approach has been validated recently as series of compounds from various programs have entered clinical trials. Current new developments are focussing on application of the methods to targets where conventional HTS fails and to integration of fragments alongside HTS for more druggable targets. Here, we provide a brief summary of the key elements of fragment-based lead discovery (FBLD), review recent progress and provide a perspective on the challenges that remain for the field.

Searching For the Hinge of E3 Ubiquitin Ligase Machinery with MD Simulations

In Cullin-RING E3 ubiquitin ligases, substrate binding proteins, such as VHL-box, SOCS-box or the F-box proteins, recruit substrates for ubiquitination, accurately positioning and orienting the substrates for ubiquitin transfer. Yet, how the E3 machinery precisely positions the substrate is unclear. We performed molecular dynamics simulations for seven substrate binding proteins: Skp2, Fbw7, β-TrCP1, Cdc4, pVHL, SOCS2, and SOCS4, in the unbound form and bound to Skp1 or Elongin C. All seven proteins have two domains: one binds to the substrate; the other to E3 ligase modules Skp1/Elongin C. In all seven cases, the flexible inter-domain linker serves as a hinge rotating the substrate binding domain, optimally and accurately positioning it for ubiquitin transfer. A conserved proline is noticed in the linker of all seven proteins. The prolines pucker substantially and the pucker is associated with the backbone rotation toward the E2/ubiquitin. We further observed that the linker flexibility could be regulated allosterically by binding events associated with either domain. Thus searching for the allosteric sites to regulate the flexibility could provide a new strategy for drug discovery targeting the ubiquitin system. This project has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes of Health, under contract number NO1-CO-12400.

Human embryonic stem cell and embryonic germ cell lines

Undifferentiated human embryonic stem (ES) cells and embryonic germ (EG) cells can be cultured indefinitely and yet maintain the potential to form many or all of the differentiated cells in the body. Human ES and EG cells provide an exciting new model for understanding the differentiation and function of human tissue, offer new strategies for drug discovery and testing, and promise new therapies based on the transplantation of ES and EG cell-derived tissues.

Human embryonic stem cell technology.

Undifferentiated human embryonic stem (ES) cells can be cultured indefinitely and yet maintain the potential to form almost every cell in the adult human body. Therefore ES cells provide a model for understanding the differentiation and function of human tissue, offer new strategies for drug discovery and testing, and have the potential to provide new transplantation therapies for the treatment of a wide variety of human diseases. In this article, we describe the origin and properties of human ES cells, distinguish ES cells from other pluripotent stem cell lines, and discuss their implications for basic research and human medicine.