RSSHow to cope with the quest for new antibiotics.
Source
Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, Camerino (MC), Italy.
Abstract
Since their introduction in therapy, antibiotics have played an essential role in human society, saving millions of lives, allowing safe surgery, organ transplants, cancer therapy. Antibiotics have also helped to elucidate several biological mechanisms and boosted the birth and growth of pharmaceutical companies, generating profits and royalties. The golden era of antibiotics and the scientific and economical drive of big pharma towards these molecules is long gone, but the need for effective antibiotics is increased as their pipelines dwindle and multi-resistant pathogenic strains spread. Here we outline some strategies that could help meet this emergency and list promising new targets.
Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Large-scale analysis of UPR-mediated apoptosis in human cells.
Source
Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
Abstract
The historic distinction between academic- and industry-driven drug discovery, whereby academicians worked to identify therapeutic targets and pharmaceutical companies advanced probe discovery, has been blurred by an academic high-throughput chemical genomic revolution. It is now common for academic labs to use biochemical or cell-based high-throughput screening (HTS) to investigate the effects of thousands or even hundreds of thousands of chemical probes on one or more targets over a period of days or weeks. To support the efforts of individual investigators, many universities have established core facilities where screening can be performed collaboratively with large chemical libraries managed by highly trained HTS personnel and guided by the experience of computational, medicinal, and synthetic organic chemists. The identification of large numbers of promising hits from such screens has driven the need for independent labs to scale down secondary in vitro assays in the hit to lead identification process. In this chapter, we will describe the use of luminescent and quantitative reverse transcription real-time PCR (qRT-PCR) technologies that permit evaluation of the expression patterns of multiple unfolded protein response (UPR) and apoptosis-related genes, and simultaneously evaluate proliferation and cell death in 96- or 384-well format.
Copyright © 2011 Elsevier Inc. All rights reserved.
- PMID:
- 21329794
- [PubMed - indexed for MEDLINE]
Functions and regulation of the 70kDa ribosomal S6 kinases.
Source
Ludwig Institute for Cancer Research, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0660, USA.
Abstract
The 70kDa ribosomal protein S6 kinases, S6K1 and S6K2 are two highly homologous serine/threonine kinases that are activated in response to growth factors, cytokines and nutrients. The S6 kinases have been linked to diverse cellular processes, including protein synthesis, mRNA processing, glucose homeostasis, cell growth and survival. Studies in model organisms have highlighted the roles that S6K activity plays in a number of pathologies, including obesity, diabetes, ageing and cancer. The importance of S6K function in human diseases has led to the development of S6K-specific inhibitors by a number of companies, offering the promise of improved tools with which to study these enzymes and potentially the effective targeting of deregulated S6K signalling in patients. Here we review the current literature on the role of S6Ks in the regulation of cell growth, survival and proliferation downstream of various signalling pathways and how their dysregulation contributes to the pathogenesis of human diseases.
Copyright © 2010 Elsevier Ltd. All rights reserved.
Optimization and high-throughput screening of antimicrobial peptides.
Source
Membrane Sciences, 3550 General Atomics Court, San Diego, CA 92121, USA. sylvieb@sanfordburnham.org
Abstract
While a well-established process for lead compound discovery in for-profit companies, high-throughput screening is becoming more popular in basic and applied research settings in academia. The development of combinatorial libraries combined with easy and less expensive access to new technologies have greatly contributed to the implementation of high-throughput screening in academic laboratories. While such techniques were earlier applied to simple assays involving single targets or based on binding affinity, they have now been extended to more complex systems such as whole cell-based assays. In particular, the urgent need for new antimicrobial compounds that would overcome the rapid rise of drug-resistant microorganisms, where multiple target assays or cell-based assays are often required, has forced scientists to focus onto high-throughput technologies. Based on their existence in natural host defense systems and their different mode of action relative to commercial antibiotics, antimicrobial peptides represent a new hope in discovering novel antibiotics against multi-resistant bacteria. The ease of generating peptide libraries in different formats has allowed a rapid adaptation of high-throughput assays to the search for novel antimicrobial peptides. Similarly, the availability nowadays of high-quantity and high-quality antimicrobial peptide data has permitted the development of predictive algorithms to facilitate the optimization process. This review summarizes the various library formats that lead to de novo antimicrobial peptide sequences as well as the latest structural knowledge and optimization processes aimed at improving the peptides selectivity.
High content screening for inhibitors of protein interactions and post-translational modifications in primary cells by proximity ligation.
Source
Molecular Medicine, Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Dag Hammarskjölds Väg 20, S-751 85 Uppsala, Sweden. karl-johan.leuchowius@genpat.uu.se
Abstract
The cost of developing new drugs is a major obstacle for pharmaceutical companies and academia with many drugs identified in the drug discovery process failing approval for clinical use due to lack of intended effect or because of severe side effects. Since the early 1990 s, high throughput screening of drug compounds has increased enormously in capacity but has not resulted in a higher success rate of the identified drugs. Thus, there is a need for methods that can identify biologically relevant compounds and more accurately predict in vivo effects early in the drug discovery process. To address this, we developed a proximity ligation-based assay for high content screening of drug effects on signaling pathways. As a proof of concept, we used the assay to screen through a library of previously identified kinase inhibitors, including six clinically used tyrosine kinase inhibitors, to identify compounds that inhibited the platelet-derived growth factor (PDGF) receptor beta signaling pathway in stimulated primary human fibroblasts. Thirteen of the 80 compounds were identified as hits, and the dose responses of these compounds were measured. The assay exhibited a very high Z' factor (0.71) and signal to noise ratio (11.7), demonstrating excellent ability to identify compounds interfering with the specific signaling event. A comparison with regular immunofluorescence detection of phosphorylated PDGF receptor demonstrated a far superior ability by the in situ proximity ligation assay to reveal inhibition of receptor phosphorylation. In addition, inhibitor-induced perturbation of protein-protein interactions of the PDGF signaling pathway could be quantified, further demonstrating the usefulness of the assay in drug discovery.
Manufacturing peptides as active pharmaceutical ingredients.
Source
Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain.
Abstract
BACKGROUND:
Today, there are more than 40 peptides on the pharmaceutical world market and more than 100 in several clinical phases. Although in the past the pharmaceutical industries had reduced their interest in peptides research, in recent decades, they have rekindled their interest in peptides as a result of contemporary novel technological accomplishments, strategic developments, advances in the areas of formulation and enhanced drug delivery technology of peptides. Thus, eight new peptide drugs that could previously have been characterized as difficult to prepare on the large scale required by industry, have entered the pharmaceutical market at the new millennium.
DISCUSSION:
The manufacturing of most of these drugs has benefited from new technological advances. Traditional and most modern techniques have been applied to the manufacture of these new entries.
CONCLUSION:
Recent accomplishments, together with the traditional benefits of peptides (high biological activity, high specificity and low toxicity), have led pharmaceutical companies to re-focus their attention on peptide-based agents. Therefore, several serious diseases can be treated using the potential next generation of peptide drugs.
- PMID:
- 21425973
- [PubMed - indexed for MEDLINE]
IgG glycosylation analysis.
Source
Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands.
Abstract
A multitude of monoclonal IgG antibodies directed against a variety of therapeutic targets is currently being developed and produced by biotechnological companies. The biological activity of IgGs is modulated by the N-glycans attached to the fragment crystallizable (Fc) part. For example, lack of core-fucoses on these N-glycans may lead to a drastic enhancement of antibody-mediated cellular cytotoxicity. Moreover, sialylation of Fc N-glycans determines the immunosuppressive properties of polyclonal IgG from human blood, which stimulates research into Fc glycosylation of human plasma IgG in various disease settings. This review presents and evaluates the different approaches which are used for IgG glycosylation analysis: N-glycans may be enzymatically or chemically released from purified IgG, prior to chromatographic or mass spectrometric analysis. Moreover, IgGs may be treated with endoproteinases such as trypsin, followed by glycosylation analysis at the glycopeptide level, which is generally accomplished by HPLC with ESI-MS. Alternatively, intact IgGs or fragments thereof obtained by enzymatic cleavages in the hinge region and by reduction may be analyzed by a large number of analytical techniques, including MS and chromatography or CE.
Studies on nonsense mediated decay reveal novel therapeutic options for genetic diseases.
Source
Laboratory of Molecular Oncology and National Genomics and Transcriptomics Facility, Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad-500 076, India. bashyam@cdfd.org.in
Abstract
Scientific breakthroughs have often led to commercially viable patents mainly in the field of engineering. Commercialization in the field of medicine has been restricted mostly to machinery and engineering on the one hand and therapeutic drugs for common chronic ailments such as cough, cold, headache, etc, on the other. Sequencing of the human genome has attracted the attention of pharmaceutical companies and now biotechnology has become a goldmine for commercialization of products and processes. Recent advances in our understanding of basic biological processes have resulted in the opening of new avenues for treatment of human genetic diseases, especially single gene disorders. A significant proportion of human genetic disorders have been shown to be caused due to degradation of transcripts for specific genes through a process called nonsense mediated decay (NMD). The modulation of NMD provides a viable therapeutic option for treatment of several genetic disorders and therefore has been a good prospect for patenting and commercialization. In this review the molecular basis for NMD and attempts to treat genetic diseases which result from NMD are discussed.
Peptide-based drug design: here and now.
Source
Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, USA.
Abstract
After many years of stagnation, peptide therapeutics once again became the focus of innovative drug development efforts backed up by venture funds and biotechnology companies. Designer peptide drugs overcome the unattractive pharmacological properties of native peptides and protein fragments and frequently feature nonnatural amino acid or backbone replacements, cyclic or multimeric structures, or peptidic or nonpeptidic delivery modules. With their high specificity and low toxicity profile, biologicals offer viable alternatives to small molecule therapeutics. The development ofpeptide drugs requires specific considerations of this family of biopolymers. Historically, peptide vaccines to viral infections and antibacterial peptides led the way in clinical development, but recently many other diseases have been targeted, including the big sellers AIDS, cancer, and Alzheimer's disease. This book gives practical advice to the most important steps in peptide-based drug development such as isolation, purification, characterization, interaction with targets, structural analysis, stability studies, assessment of biodistribution and pharmacological parameters, sequence modifications, and high throughput screening. This brief overview provides historical background for each of the listed techniques and diseases.
Artificial restriction DNA cutter for site-selective scission of double-stranded DNA with tunable scission site and specificity.
Source
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. komiyama@mkomi.rcast.u-tokyo.ac.jp
Abstract
The artificial restriction DNA cutter (ARCUT) method to cut double-stranded DNA at designated sites has been developed. The strategy at the base of this approach, which does not rely on restriction enzymes, is comprised of two stages: (i) two strands of pseudo-complementary peptide nucleic acid (pcPNA) anneal with DNA to form 'hot spots' for scission, and (ii) the Ce(IV)/EDTA complex acts as catalytic molecular scissors. The scission fragments, obtained by hydrolyzing target phosphodiester linkages, can be connected with foreign DNA using DNA ligase. The location of the scission site and the site-specificity are almost freely tunable, and there is no limitation to the size of DNA substrate. This protocol, which does not include the synthesis of pcPNA strands, takes approximately 10 d to complete. Thesynthesis and purification of the pcPNA, which are covered by a related protocol by the same authors, takes an additional 7 d, but pcPNA can also be ordered from custom synthesis companies if necessary.
Solid-phase synthesis of pseudo-complementary peptide nucleic acids.
Source
Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. komiyama@mkomi.rcast.u-tokyo.ac.jp
Abstract
Pseudo-complementary peptide nucleic acid (pcPNA) is a DNA analog in which modified DNA bases 2,6-diaminopurine (D) and 2-thiouracil (U(s)) 'decorate' a poly[N-(2-aminoethyl)glycine] backbone, together with guanine (G) and cytosine (C). One of the most significant characteristics of pcPNA is its ability to effect double-duplex invasion of predetermined DNA sites inducing various changes in the biological and the physicochemical properties of the DNA. This protocol describes solid-phase synthesis of pcPNA. The monomers for G and C are commercially available, but the monomers for D and U(s) need to be synthesized (or can be ordered to custom synthesis companies). Otherwise, the procedure is the same as that employed for Boc-strategy synthesis of conventional PNA. This protocol, if the synthesis of D and U(s) monomers is not factored in, takes approximately 7 d to complete.
Strategic paradigm shifts in the antimicrobial drug discovery process of the 21st century.
Source
Department of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA. leq2001@med.cornell.edu
Abstract
The numbers of global infections produced by bacterial strains that are resistant to single and multiple antimicrobial drugs are on the rise. Concomitant with this alarming upward trend, there is a clear downward trend in the intent and determination of pharmaceutical companies to develop novel antimicrobials. One of the pressing goals to confront the twenty first century's public health challenges brought about by the escalating antibacterial drug resistance problem is the development of an armamentarium of new chemotherapeutic agents. Two interconnected strategic paradigm shifts in the drug discovery process that are anticipated to facilitate the achievement of this goal are discussed herein. One is an antimicrobial to anti-infective (ATA) paradigm shift. The other is a shift from a target candidate prioritization (TCP) paradigm that is dominated by an essential target preference criterion to an alternative paradigm that relies on a less restrictive criterion, one that does not exclude conditionally essential targets. Examples of conditionally essential targets for the development of anti infectives include the enzymes involved in the biosynthesis of small molecule virulence effectors such as non ribosomal peptide polyketide derived iron scavenging siderophores. Siderophores are utilized for iron uptake by many pathogenic bacteria, including Mycobacterium and Yersinia species. The recent progress towards developing inhibitors of siderophore biosynthesis is discussed herein.
Design of synthetic antibody libraries.
Source
Tel-Aviv University, Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Green Building, Room 202, Ramat Aviv 69978, Israel. benhar@post.tau.ac.il
Abstract
Antibody libraries came into existence 15 years ago when the accumulating sequence data of immunoglobulin genes and the advent of polymerase chain reaction technology made it possible to clone antibody gene repertoires. Since then, virtually hundreds of antibody libraries have been constructed, employing limitless maneuvers from the antibody engineering molecular bag of tricks towards the crucial parameters that determine library quality, library size, diversity and robustness. Phage and additional display and screening technologies were applied to pan out desired binding specificities from antibody libraries. Several biotech companies established themselves as key operators in the multibillion-dollar field of recombinant antibody technology. Out of nineteen FDA-approved therapeutic antibodies, one was isolated from an antibody library and many more are in various stages of clinical evaluation. This review highlights key milestones in the short history of antibody libraries and attempts to predict the future impact of antibody libraries on drug discovery.
Genomics basics: DNA structure, gene expression, cloning, genetic mapping, and molecular tests.
Source
Division of Hematology, Mayo Clinic, Rochester, MN 55905, USA. tefferi.ayalew@mayo.edu
Abstract
Genomics is the study of the structure and function of the human genome including genes and their surrounding DNA sequences. The over 3 billion base pairs of the human genome have now been sequenced and approximately 25,000 genes acknowledged. However, only 1% of the entire genome has been assigned to protein coding and decades more work is anticipated to define the functional relevance of noncoding DNA as well as the basis and consequences of sequence variations among individuals. For medical scientists, the focus remains on discovering both disease-causing and disease-susceptibility genes. For pharmaceutical companies, the opportunity to develop molecularly targeted therapy is not going unnoticed. For the practicing physician, the prospect of genomic medicine that incorporates molecular diagnosis and pathogenesis-targeted therapy requires basic understanding of terminology and concepts in molecular biology and the corresponding laboratory tests.
Antibacterial drug discovery and structure-based design.
Source
Evotec UK, 111 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK. john.barker@evotec.com
Abstract
Bacterial resistance continues to develop and pose a significant threat, both in hospitals and, more recently, in the community. A focus on other therapeutic areas by the larger pharmaceutical companies has left a shortfall in the pipeline of novel antibacterials. Recently, many new structures have been studied by structure-genomics initiatives, delivering a wealth of targets to consider. Using the tools of structure-based design, antibacterial discovery must exploit these targets to accelerate the process of drug discovery.
A plethora of targets, a paucity of drugs: progress towards the development of novel chemotherapies for human African trypanosomiasis.
Source
Wellcome Centre for Molecular Parasitology, The Anderson College, University of Glasgow, Glasgow, UK.
Abstract
Human African trypanosomiasis is a major health problem in large regions of Africa. Current chemotherapeutic options are limited and far from ideal. A diverse range of drug targets has been identified and validated in trypanosomes. These include several organelles (glycosomes, acidocalcisomes, kinetoplast) that are not represented in the mammalian host and biochemical pathways that differ significantly from host counterparts (carbohydrate metabolism, protein and lipid modification, response to oxidative stress, cell cycle). However, there has been little progress in developing novel drugs. Pharmaceutical companies are unwilling to invest in the development of drugs for a market that comprises some of the worlds poorest people. This review highlights some of the most attractive drug targets in trypanosomes.
- PMID:
- 15482108
- [PubMed - indexed for MEDLINE]
Biodegradable water absorbent synthesized from bacterial poly(amino acid)s.
Source
National Institute of Advanced Industrial Science and Technology, Higashi 1-1-1, Tsukuba, Ibaraki 305-8565, Japan. m.kunioka@aist.go.jp
Abstract
Biodegradable hydrogels prepared by gamma-irradiation from microbial poly(amino acid)s have been studied. pH-Sensitive hydrogels were prepared by the gamma-irradiation of poly(gamma-glutamic acid) (PGA) produced by Bacillus subtilis and poly(epsilon-lysine) (PL) produced by Streptomyces albulus in aqueous solutions. When the gamma-irradiation dose was 19 kGy or more, and the concentration of PGA in water was 2 wt.-% or more, transparent hydrogels could be produced. For the 19 kGy dose, the produced hydrogel was very weak, however, the specific water content (wt. of absorbed water/wt. of dry hydrogel) of this PGA hydrogel was approximately 3,500. The specific water content decreased to 200, increasing when the gamma-irradiation dose was over 100 kGy. Under acid conditions or upon the addition of electrolytes, the PGA hydrogels shrunk. The PGA hydrogel was pH-sensitive and the change in the volume of the hydrogel depended on the pH value outside the hydrogel in the swelling medium. This PGA hydrogel was hydrodegradable and biodegradable. A new novel purifier reagent (coagulant), made from the PGA hydrogels, for contaminated turbid water has been found and developed by Japanese companies. A very small amount of this coagulant (only 2 ppm in turbid water) with poly(aluminum chloride) can be used for the purification of turbid water. A PL aqueous solution also can change into a hydrogel by gamma-irradiation. The specific water content of the PL hydrogel ranged from 20 to 160 depending on the preparation conditions. Under acid conditions, the PL hydrogel swelled because of the ionic repulsion of the protonated amino groups in the PL molecules. The rate of enzymatic degradation of the respective PL hydrogels by a neutral protease was much faster than the rate of simple hydrolytic degradation.
Virtual screening of virtual libraries.
Source
GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
Abstract
Virtual screening of virtual libraries (VSVL) is a rapidly changing area of research. Great efforts are being made to produce better algorithms, selection methods and infrastructure. Yet, the number of successful examples in the literature is not impressive, although the quality of work certainly is high. Why is this? One reason is that these methods tend to be applied at the lead generation stage and therefore there is a large lead-time before successful examples appear in the literature. However, any computational chemist would confirm that these methods are successful and there exists a glut of start-up companies specialising in virtual screening. Moreover, the scientific community would not be focussing so much attention on this area if it were not yielding results. Even so, the paucity of literature data is certainly a hindrance to the development of better methods. The VSVL process is unique within the discovery process, in that it is the only method that can screen the > 10(30) genuinely novel molecules out there. Already, some VSVL methods are evaluating 10(13) compounds, a capacity that high throughput screening can only dream of. There is a huge potential advantage for the company that develops efficient and effective methods, for lead generation, lead hopping and optimization of both potency and ADME properties. To do this, it requires more than the software, it requires confidence to exploit the methodology, to commit synthesis on the basis of it, and to build this approach into the medicinal chemistry strategy. It is a fact that these tools remain quite daunting for the majority of scientists working at the bench. The routine use of these methods is not simply a matter of education and training. Integration of these methods into accessible and robust end user software, without dilution of the science, must be a priority. We have reached a coincidence, where several technologies have the required level of maturity predictive computational chemistry methods, algorithms that manage the combinatorial explosion, high throughput crystallography and ADME measurements and the massive increase in computational horsepower from distributed computing. The author is confident that the synergy of these technologies will bring great benefit to the industry, with more efficient production of higher quality clinical candidates. The future is bright. The future is virtual!
- PMID:
- 12774691
- [PubMed - indexed for MEDLINE]
Functional proteomics: mapping protein-protein interactions and pathways.
Source
MDS-Proteomics, Toronto, Ontario, Canada. dfigeys@mdsp.com
Abstract
The function of a protein is defined by its interactions with other proteins and molecules. Mapping of protein interactions can highlight new functionalities for a known protein or can even define the function of novel proteins. With the draft sequence of the human genome now available, it is possible to perform high-throughput mapping of protein-protein interactions in humans, which is termed as functional proteomics. The developments in functional proteomics are particularly timely since pharmaceutical companies are searching for technologies that will strengthen their genomic efforts and prioritize their drug discovery pipeline. In this article we review recent developments in functional proteomics.
- PMID:
- 12139305
- [PubMed - indexed for MEDLINE]
Alpha 4 integrin antagonists.
Source
Department of Bioorganic Chemistry, Genentech Inc., 1 DNAWay, MS18, Francisco, CA 94080, USA. davej@gene.com
Abstract
The accumulation of leukocytes in various organs contributes to the pathogenesis of a number of human autoimmune diseases such as asthma, rheumatoid arthritis, Crohn s disease, ulcerative colitis, hepatitis C, and multiple sclerosis. The inflammatory processes leading to tissue damage and disease are mediated in part by the alpha4 integrins, alpha4beta1 and alpha4beta7, expressed on the leukocyte cell surface. These glycoprotein receptors modulate cell adhesion via interaction with their primary ligands, vascular cell adhesion molecule (VCAM) and mucosal addressin cell adhesion molecule (MAdCAM), expressed in the affected tissue. Upon binding, the combined integrin/CAM interactions at the cell surface result in firm adhesion of the leukocyte to the vessel wall followed by entry into the affected tissue. Elevated cell adhesion molecule (CAM) expression in various organs has been linked with several autoimmune diseases. Monoclonal antibodies specific for alpha4 integrins or their CAM ligands can moderate inflammation in animal models suggesting such inhibitors may be useful for treating human inflammatory diseases. The alpha4 integrins have become well validated drug targets for pharmaceutical companies and numerous publications describing alpha4 integrin antagonists have recently appeared. This article discusses the rationale for targeting alpha4 integrins for the treatment of autoimmune disorders and reviews some currently known antagonists. The methods used to identify lead molecules and the progress of selected antagonists toward becoming new drugs will is also discussed. (131 references).
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