Targeting stem cell signaling pathways for drug discovery: advances in the Notch and Wnt pathways

Signaling pathways transduce extracellular stimuli into cells through molecular cascades to regulate cellular functions.In stem cells,a small number of pathways,notably those of TGF-?/BMP,Hedgehog,Notch,and Wnt,are responsible for the regulation of pluripotency and differentiation.During embryonic development,these pathways govern cell fate specifications as well as the formation of tissues and organs.In adulthood,their normal functions are important for tissue homeostasis and regeneration,whereas aberrations result in diseases,such as cancer and degenerative disorders.In complex biological systems,stem cell signaling pathways work in concert as a network and exhibit crosstalk,such as the negative crosstalk between Wnt and Notch.Over the past decade,genetic and genomic studies have identified a number of potential drug targets that are involved in stem cell signaling pathways.Indeed,discovery of new targets and drugs for these pathways has become one of the most active areas in both the research community and pharmaceutical industry.Remarkable progress has been made and several promising drug candidates have entered into clinical trials.This review focuses on recent advances in the discovery of novel drugs which target the Notch and Wnt pathways.     

Human embryonic stem cell technologies and drug discovery

Development of new drugs is costly and takes huge resources into consideration. The big pharmaceutical companies are currently facing increasing developmental costs and a lower success‐rate of bringing new compounds to the market. Therefore, it is now of outmost importance that the drug‐hunting companies minimize late attritions due to sub‐optimal pharmacokinetic properties or unexpected toxicity when entering the clinical programs. To achieve this, a strong need to test new candidate drugs in assays of high human relevance in vitro as early as possible has been identified. The traditionally used cell systems are however remarkably limited in this sense, and new improved technologies are of greatest importance. The human embryonic stem cells (hESC) is one of the most powerful cell types known. They have not only the possibility to divide indefinitely; these cells can also differentiate into all mature cell types of the human body. This makes them potentially very valuable for pharmaceutical development, spanning from use as tools in early target studies, DMPK or safety assessment, as screening models to find new chemical entities modulating adult stem cell fate, or as the direct use in cell therapies. This review illustrates the use of hESC in the drug discovery process, today, as well as in a future perspective. This will specifically be exemplified with the most important cell type for pharmaceutical development—the hepatocyte. We discuss how hESC‐derived hepatocyte‐like cells could improve this process, and how these cells should be cultured if optimized functionality and usefulness should be achieved. J. Cell. Physiol. 219: 513–519, 2009. © 2009 Wiley‐Liss, Inc.     

Toxicogenomics in drug discovery: from preclinical studies to clinical trials

Gene expression analysis applied to toxicology studies, also referred to as toxicogenomics, is rapidly being embraced by the pharmaceutical industry as a useful tool to identify safer drugs in a quicker, more cost-effective manner. Studies have already demonstrated the benefits of applying gene expression profiling towards drug safety evaluation, both for identifying mechanisms underlying toxicity, as well as for providing a means to identify safety liabilities early in the drug discovery process. Furthermore, toxicogenomics has the potential to better identify and assess adverse drug reactions of new drug candidates or marketed products in humans. While much still remains to be learned about the relevance and the application of gene expression changes in human toxicology, the next few years should see gene expression technologies applied to more stages and more programs of the drug discovery and development process. This review will focus on how toxicogenomics can or has been applied in drug discovery and development, and will discuss some of the challenges that still remain.     

The changing landscape of antiparasitic drug discovery for veterinary medicine

Changes in economic imperatives in the pharmaceutical industry have led to a wave of consolidation, which has had the unintended side effect of shrinking the resource devoted to antiparasitic drug discovery in animal health companies. Scientific changes have altered the way in which drugs could be discovered in the future. New science and business models will need to be implemented to address the demand for innovative antiparasitic drugs in veterinary medicine. Novel drugs are needed to combat drug resistance and for currently non-addressed problems. At the center of the future for this field, however, lies the need for more support into the basic research on the biology of parasites.     

Drug discovery for malaria: a very challenging and timely endeavor

The prevalence of resistance to known antimalarial drugs has resulted in the expansion of antimalarial drug discovery efforts. Academic and nonprofit institutions are partnering with the pharmaceutical industry to develop new antimalarial drugs. Several new antimalarial agents are undergoing clinical trials, mainly those resurrected from previous antimalarial drug discovery programs. Novel antimalarials are being advanced through the drug development process, of course, with the anticipated high failure rate typical of drug discovery. Many of these are summarized in this review. Mechanisms for funding antimalarial drug discovery and genomic information to aid drug target selection have never been better. It remains to be seen whether ongoing efforts will be sufficient for reducing malaria burden in the developing world.     

High-throughput screening assay for the identification of compounds regulating self-renewal and differentiation in human embryonic stem cells

High-throughput screening (HTS) of chemical libraries has become a critical tool in basic biology and drug discovery. However, its implementation and the adaptation of high-content assays to human embryonic stem cells (hESCs) have been hampered by multiple technical challenges. Here we present a strategy to adapt hESCs to HTS conditions, resulting in an assay suitable for the discovery of small molecules that drive hESC self-renewal or differentiation. Use of this new assay has led to the identification of several marketed drugs and natural compounds promoting short-term hESC maintenance and compounds directing early lineage choice during differentiation. Global gene expression analysis upon drug treatment defines known and novel pathways correlated to hESC self-renewal and differentiation. Our results demonstrate feasibility of hESC-based HTS and enhance the repertoire of chemical compounds for manipulating hESC fate. The availability of high-content assays should accelerate progress in basic and translational hESC biology.     

Recent Advances in Drug Repositioning for the Discovery of New Anticancer Drugs

Drug repositioning (also referred to as drug repurposing), the process of finding new uses of existing drugs, has been gaining popularity in recent years. The availability of several established clinical drug libraries and rapid advances in disease biology, genomics and bioinformatics has accelerated the pace of both activity-based and in silico drug repositioning. Drug repositioning has attracted particular attention from the communities engaged in anticancer drug discovery due to the combination of great demand for new anticancer drugs and the availability of a wide variety of cell- and target-based screening assays. With the successful clinical introduction of a number of non-cancer drugs for cancer treatment, drug repositioning now became a powerful alternative strategy to discover and develop novel anticancer drug candidates from the existing drug space. In this review, recent successful examples of drug repositioning for anticancer drug discovery from non-cancer drugs will be discussed.     

Will the ubiquitin system furnish as many drug targets as protein kinases?

Protein phosphorylation and protein ubiquitination regulate most aspects of cell life, and defects in these control mechanisms cause cancer and many other diseases. In the past decade, protein kinases have become one of the most important classes of drug targets for the pharmaceutical industry. In contrast, drug discovery programs that target components of the ubiquitin system have lagged behind. In this Perspective, we discuss the reasons for the delay in this pipeline, the drugs targeting the ubiquitin system that have been developed, and new approaches that may popularize this area of drug discovery in the future.     

Drugs against leishmaniasis: a synergy of technology and partnerships

To date, there are no vaccines against any of the major parasitic diseases, and chemotherapy is the main weapon in our arsenal. There is an urgent need for better drugs against Leishmania. With the completion of the human genome sequence and soon that of Leishmania, for the first time we have the opportunity to identify novel chemotherapeutic treatments. This requires the exploitation of a variety of technologies. The major challenge is to take the process from discovery of drug candidates all the way along the arduous path to the marketplace. A crucial component will be the forging of partnerships between the pharmaceutical industry and publicly funded scientists to ensure that the promise of the current revolution in biology lives up to our hopes and expectations.     

Drug resistance plasmids

Conclusion The discovery of chemotherapeutic agents brought remarkable progress to the practice of medicine and to human and animal hygiene. In addition, improved sanitation and preventive medicine have protected human beings from infectious diseases caused by known pathogenic bacteria. As a result, the types of bacteria that play leading roles in infectious diseases have changed. These microoganisms readily cause infection, they are parasitic, and they carry multiple drug resistance as a result of the use of chemotherapeutic agents. Thus, mutiply resistant organisms have become prevalent and particular strains have become stabilized in hospitals and farms.The presence of conjugative (R) and nonconjugative (r) resistance plasmids in these bacterial strains has compounded the problems for the practice of medicine, livestock hygiene, and the fish culture industry. Rapid acquisition of drug resistance by bacteria and delays in finding new drugs have created new biological hazards for human beings.The discovery of resistance plasmids opened new research fields in genetics and molecular biology; it became clear that multiply resistant bacteria could develop quickly and spread rapidly all over the world. The genes governing replication, self-regulation, conjugal transmission and drug resistance, including transposon, are the most fascinating problems in biology. And the prevalence of drug resistance plasmids has broadened our perspective on the role that genetic exchanges play in the natural history of bacterial species.     

Antimalarial chemotherapy: young guns or back to the future?

The burgeoning global problem of malaria is largely due to the emergence of parasite resistance to our limited armamentarium of antimalarial drugs. The recognition of this impending disaster at the international level and the engagement of the pharmaceutical industry promise a more optimistic future for antimalarial drug development. This is particularly exciting when considering the advances in our understanding of parasite biology, which are currently being fuelled by the malaria genome project. This article discusses recent developments in the area of antimalarial drug discovery and evaluation. New advances, based on traditional antimalarial drug classes including the quinolines, peroxides and antifolates (‘back to the future’), are discussed, followed by a presentation of some novel targets (‘young guns’) that have been shown to be good candidates for chemotherapeutic attack.     

Efficiency of antisense oligonucleotide drug discovery

The costs for discovering and developing new drugs continue to escalate, with current estimates that the average cost is more than $800 million for each new drug brought to the market. Pharmaceutical companies are under enormous pressure to increase their efficiency for bringing new drugs to the market by third-party payers, shareholders, and their patients, and at the same time regulators are placing increased demands on the industry. To be successful in the future, pharmaceutical companies must change how they discover and develop new drugs. So far, new technologies have done little to increase overall efficiency of the industry and have added additional costs. Platform technologies such as monoclonal antibodies and antisense oligonucleotides have the potential of reducing costs for discovery of new drugs, in that many of the steps required for traditional small molecules can be skipped or streamlined. Additionally the success of identifying a drug candidate is much higher with platform technologies compared to small molecule drugs. This review will highlight some of the efficiencies of antisense oligonucleotide drug discovery compared to traditional drugs and will point out some of the current limitations of the technology.     

Perspective from the heart: The potential of human pluripotent stem cell‐derived cardiomyocytes

Human pluripotent stem cells (hPSC) are self‐renewing cells with the potential to differentiate into a variety of human cells. They hold great promise for regenerative medicine and serve as useful in vitro models for studying human biology. For the past few years, there is vast interest in applying these cells to advance cardiovascular medicine. Human cardiomyocytes can be readily generated from hPSC and they have been characterized extensively with regards to molecular and functional properties. They have been transplanted into animal models of cardiovascular diseases and also shown to be potentially useful reagents for drug discovery. Yet, despite great progress in this field, significant technical hurdles remain before these cells could be used clinically or for pharmaceutical research and development. Further research using novel approaches will be required to overcome these bottlenecks. J. Cell. Biochem. 114: 39–46, 2012. © 2012 Wiley Periodicals, Inc.     

UV-induced interaction between p38 MAPK and p53 serves as a molecular switch in determining cell fate

p53 plays a fundamental role in the maintenance of genome integrity after DNA damage, deciding whether cells repair and live, or die. However, the rules that govern its choice are largely undiscovered. Here we show that the functional relationship between p38 and p53 is crucial in defining the cell fate after DNA damage. Upon low dose ultraviolet (UV) radiation, p38 and p53 protect the cells from apoptosis separately. Conversely, they function together to favor apoptosis upon high dose UV exposure. Taken together, a UV-induced, dose-dependent interaction between p38 and p53 acts as a switch to determine cell fate.

Structured summary

MINT-8050838: p53 (uniprotkb:P02340) physically interacts (MI:0915) with p38 (uniprotkb:P47811) by anti bait coimmunoprecipitation (MI:0006)MINT-8050948: p53 (uniprotkb:P04637) physically interacts (MI:0915) with p38 (uniprotkb:P47811) by anti tag coimmunoprecipitation (MI:0007)     

Network pharmacology and drug discovery

The pharmaceutical industry has historically relied on particular families of 'druggable' proteins against which to develop compounds with desired actions. But proteins rarely function in isolation in and outside the cell; rather, proteins operate as part of highly interconnected cellular networks. Network pharmacology is an emerging area of pharmacology which utilizes network analysis of drug action. By considering drug actions in the context of the cellular networks, network analysis promises to greatly increase our knowledge of the mechanisms underlying the multiple actions of drugs. Network pharmacology can provide new approaches for drug discovery for complex diseases. This review introduced the recent progress of network pharmacology and its importance to understand the mechanism of drug actions and drug discovery.     

Peptide deformylase is a potential target for anti-Helicobacter pylori drugs: reverse docking, enzymatic assay, and X-ray crystallography validation

Colonization of human stomach by the bacterium Helicobacter pylori is a major causative factor for gastrointestinal illnesses and gastric cancer. However, the discovery of anti-H. pylori agents is a difficult task due to lack of mature protein targets. Therefore, identifying new molecular targets for developing new drugs against H. pylori is obviously necessary. In this study, the in-house potential drug target database (PDTD, http://www.dddc.ac.cn/tarfisdock/) was searched by the reverse docking approach using an active natural product (compound 1) discovered by anti-H. pylori screening as a probe. Homology search revealed that, among the 15 candidates discovered by reverse docking, only diaminopimelate decarboxylase (DC) and peptide deformylase (PDF) have homologous proteins in the genome of H. pylori. Enzymatic assay demonstrated compound 1 and its derivative compound 2 are the potent inhibitors against H. pylori PDF (HpPDF) with IC50 values of 10.8 and 1.25 microM, respectively. X-ray crystal structures of HpPDF and the complexes of HpPDF with 1 and 2 were determined for the first time, indicating that these two inhibitors bind well with HpPDF binding pocket. All these results indicate that HpPDF is a potential target for screening new anti-H. pylori agents. In addition, compounds 1 and 2 were predicted to bind to HpPDF with relatively high selectivity, suggesting they can be used as leads for developing new anti-H. pylori agents. The results demonstrated that our strategy, reverse docking in conjunction with bioassay and structural biology, is effective and can be used as a complementary approach of functional genomics and chemical biology in target identification.     

抗凋亡蛋白Mcl-1及其抑制剂的研究进展

骨髓细胞白血病蛋白Mcl-1是Bcl-2家族蛋白中重要的抗凋亡蛋白成员,其在多种恶性肿瘤(急性细胞性白血病、多发性骨髓瘤等)中都具有高表达的特点,导致肿瘤细胞对传统化疗药物及Bcl-2抑制剂产生耐药性。Mcl-1作为抗肿瘤药物研发的重要靶点正日益受到相关研究人员的关注,其中Mcl-1新型抑制剂以及联合抑制剂的研究取得了较大进展。本文将对Mcl-1蛋白结构和功能以及相关抑制剂的研究做更深入的分析和总结。     

Polypharmacology and supercomputer-based docking: opportunities and challenges

Polypharmacology, the ability of drugs to interact with multiple targets, is a fundamental concept of interest to the pharmaceutical industry in its efforts to solve the current issues of the rise in the cost of drug development and decline in productivity. Polypharmacology has the potential to greatly benefit drug repurposing, bringing existing pharmaceuticals on the market to treat different ailments quicker and more affordably than developing new drugs, and may also facilitate the development of new, potent pharmaceuticals with reduced negative off-target effects and adverse side effects. Present day computational power, when combined with applications such as supercomputer-based virtual high-throughput screening (docking) will enable these advances on a massive chemogenomic level, potentially transforming the pharmaceutical industry. However, while the potential of supercomputing-based drug discovery is unequivocal, the technical and fundamental challenges are considerable.     

Time for a change: addressing R&D and commercialization challenges for antibacterials

The antibacterial therapeutic area has been described as the perfect storm. Resistance is increasing to the point that our hospitals encounter patients infected with untreatable pathogens, the overall industry pipeline is described as dry and most multinational pharmaceutical companies have withdrawn from the area. Major contributing factors to the declining antibacterial industry pipeline include scientific challenges, clinical/regulatory hurdles and low return on investment. This paper examines these challenges and proposes approaches to address them. There is a need for a broader scientific agenda to explore new approaches to discover and develop antibacterial agents. Additionally, ideas of how industry and academia could be better integrated will be presented. While promising progress in the regulatory environment has been made, more streamlined regulatory paths are still required and the solutions will lie in global harmonization and clearly defined guidance. Creating the right incentives for antibacterial research and development is critical and a new commercial model for antibacterial agents will be proposed. One key solution to help resolve both the problem of antimicrobial resistance (AMR) and lack of new drug development are rapid, cost-effective, accurate point of care diagnostics that will transform antibacterial prescribing and enable more cost-effective and efficient antibacterial clinical trials. The challenges of AMR are too great for any one group to resolve and success will require leadership and partnerships among academia, industry and governments globally.