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Innovations in Combating Infectious Diseases
Opportunities in Therapeutics and Diagnostics through Application of Proteomics, Genomics, Nanotechnology, and Novel Sources of Lead Generation

Publication Date: June 2010
Publisher: Business Insights
Pages: 250

Infectious disease is not merely a problem of the past; despite significant breakthroughs achieved during the last century in the development of antibiotic, antiviral, and antiparasitic drugs and vaccines, the eradication or even control of many infectious diseases has not been accomplished.

Of particular current concern are the problems of rapidly developing drug resistance, emerging disease, re-emerging disease, the threat of bioterrorism, and the speed of reaction to the appearance of virulent strains posing pandemic threats. Furthermore, the effective treatment of infectious diseases is dependent on accurate and rapid diagnosis, and this in itself can present significant challenges, especially in cases where the disease progression is poorly understood or has long asymptomatic latency (such as prion diseases).

Successful drugs and vaccines against infectious agents that put millions of people at risk have potentially lucrative markets. The key to developing those drugs is to understand the pathogenic process and gain insight into where and how it can best be interrupted. This report makes a detailed and comprehensive analysis of the cutting edge of research aiming to reveal how bacteria, viruses, fungi, and prions infect and affect their hosts. It also assesses the new technologies and techniques that are being used to design and develop the anti-infective drugs and diagnostic methods of the 21st century.

Key features of this report

This report presents a snapshot of how new technologies and approaches are being applied to the discovery of new drug targets, vaccine candidates, lead compounds, and novel delivery systems that will enhance diagnostics and therapeutics across the whole range of infectious diseases:

  • How proteomics is being used to identify biomarkers for new diagnostics in infectious diseases
  • How proteomics is being used to identify novel targets for drug discovery and vaccine development in infectious diseases
  • The impact of genomics on the search for novel targets for infectious disease drug discovery
  • Novel natural sources for lead generation in infectious diseases
  • Lead optimization techniques relevant to infectious diseases
  • How the application of nanobiotechnology is impacting on drug discovery and drug delivery in infectious diseases

Scope of this report

  • Gain awareness of the most significant areas of unmet need for anti-infective drug development.
  • Build knowledge of the most promising diagnostics research - ripe for commercialization - for MRSA and community-acquired infections, bacterial meningitis, periodontal disease, and innovative ways for predicting outcome in hepatitis infections.
  • Discover how proteomics and genomics are making an increasing impact on drug development programs, and how important infectious agents can be tackled by drug and vaccine approaches.
  • Identify the new opportunities for small and large biotechnology based companies to undertake vaccine development based on proteomic and genomic studies

Key Market Issues

  • More accurate and rapid diagnostics will remain a pressing need combating prion diseases, sexually transmitted diseases, HIV, hospital-acquired infections and bioterrorism threats.
  • Diagnostics is a big area that is ripe for more commercial development, particularly for diagnostic kits that are fast and simple to operates by unskilled personnel, making them amenable to the point-of-care use.
  • Personalized medicine will remain a priority; drug treatments need to be more tailored and efficient with fewer side effects, less frequent dosing, and faster action..
  • Using genomics to monitor and carry out surveillance of infectious disease will become more important and more necessary, so that new outbreaks, spread of disease, and danger of pandemics can be better monitored and predicted by global warning systems.
  • The need to identify, monitor, and respond to bioterrorism will continue to drive research into lethal viral infections such as small pox and ebola, and bacterial diseases such as anthrax and plague.

Key findings from this report

  • Drug development, vaccine development, and novel approaches to therapeutics are needed urgently for bacterial, viral, fungal, and prion diseases, which cause high morbidity and mortality in both the developing and the developed world.
  • To date, there has been an intensive research effort to use proteomics to detect, identify, characterize, and validate biomarkers and protein signatures in diagnostics for many different infectious diseases but validation and commercialization has so far proved relatively elusive.
  • Drug resistance, emerging infections and the threat of bioterrorism make the understanding of virulence factors and disease pathogenesis essential to form a springboard from which to launch drug discovery programs.
  • Genomics is being applied to drug discovery across the spectrum of infectious diseases, whether they are caused by bacteria, viruses, fungi, parasites, or prions. Genomic data can be used in public health surveillance and monitoring of infectious diseases, particularly when there is a threat of a pandemic or bioterrorist attack.
  • Novel sources of lead compounds to screen against newly discovered targets are much needed; natural sources have already provided the starting point for several successful anti-infectives, and many sources remain to be explored.

Key questions answered

  • Which areas of drug development in infectious disease could have the greatest impact?
  • How can the relatively new technology of proteomics be used to develop leads for drug development?
  • How are proteomic techniques being used in the design and production of modern diagnostic tools for infectious diseases?
  • How are genomic technologies changing the way lead compounds are generated and providing ideas for innovative targeted drugs?
  • In which bacteria, viral, fungal and prion diseases are fundamental research efforts showing the most potential for identifying compounds suitable for drug development?

Contents

  • Executive Summary
    • The need for new therapeutic approaches in infectious diseases
    • Proteomics in the design of novel diagnostics for infectious diseases
    • Proteomic methods in infectious disease drug discovery
    • Genomics and its impact on drug discovery in infectious diseases
    • Natural sources of drug leads for infectious diseases
    • Lead optimization in infectious disease drug discovery
    • Applications of nanotechnology in infectious diseases
  • Chapter 1 The need for new therapeutic approaches in infectious diseases
    • Summary
    • Introduction
    • Why do we need continuing drug development?
    • Major areas of unmet need in infectious disease
    • Report scope
  • Chapter 2 Proteomics in the design of novel diagnostics for infectious diseases
    • Summary
    • Introduction
    • An overview of techniques in proteomics
    • Separation techniques
    • Two-dimensional gel electrophoresis (2D-GE)
    • Separation using SELDI Protein Chip technology
    • Identification techniques
    • Mass spectrometry
    • Bottom up and top down techniques
    • Targeted proteomics using western blots and MS
    • Antibody and aptamer microarray technology in proteomics
    • Allied technology: glycan arrays
    • Limitations of proteomic techniques
    • Limitations of MALDI-TOF
    • The need to be aware of artifacts
    • The limitations of shotgun proteomics
    • MALDI approaches - profiling and imaging
    • Protein, antibody, and aptamer arrays
    • Diagnostics in infectious diseases using proteomic techniques
    • Bacterial infections, proteomics, and diagnosis
    • MRSA and community- and hospital-acquired infections
    • Diagnosing bacterial meningitis and conjunctivitis
    • Faster and easier diagnosis of tuberculosis
    • Proteomics in the diagnosis of periodontal disease
    • Proteomics in the detection of bacteria that pose bioterrorist threats
    • Using proteome microarrays to identify plague
    • Diagnosis of anthrax using the host blood proteome
    • Parasitic infections, proteomics, and diagnosis
    • Developing diagnostic biomarkers for parasitic infections
    • Proteomic diagnostics for fungal infections
    • Proteomics in the detection of viral infections
    • SARS diagnosis using proteomics
    • Hepatitis prognosis using proteomics
    • New diagnostics for prion diseases
    • Conclusions
  • Chapter 3 Proteomic methods in infectious disease drug discovery
    • Summary
    • Introduction
    • Proteomics in target identification and lead discovery in infectious diseases
    • Using proteomics in drug discovery for parasitic diseases
    • Malaria - using proteomics to map parasitic gene expression
    • Liver fluke infections
    • Echinococcus multilocularis
    • Leishmaniasis
    • Entamoeba histolytica
    • Proteomics and antiviral discovery
    • HIV
    • Influenza
    • Hepatitis B
    • Proteomics in the discovery of novel antibacterial drug targets
    • Drug discovery for nosocomial infections
    • Targeting bacteria that affect the gut
    • Applying proteomics to rare bacterial diseases
    • Proteomics and drug discovery for bacterial meningitis
    • Proteomics and drug discovery in tuberculosis
    • Potential therapeutics for bioterrorist threats
    • Proteomics in antifungal drug discovery
    • Proteomics in the generation of new vaccine candidates
    • Antibacterial vaccines
    • Towards a new vaccine for tuberculosis
    • Antibiotic strains of Staphylococcus aureus
    • Clostridium difficile
    • Fungal vaccines
    • Parasitic vaccines
    • Leishmania amastigotes
    • Toxoplasma gondii
    • Schistosomiasis
    • Malaria
    • Viral vaccines
    • Proteomics and HIV vaccine approaches
    • Influenza vaccine strategies
    • Conclusions
  • Chapter 4 Genomics and its impact on drug discovery in infectious diseases
    • Summary
    • Introduction
    • Using genomics to identify new drug targets in infectious diseases
    • Using genomics to target pathogen factors
    • Ligand-based chemogenomic approaches
    • Using genomics to target host factors
    • Novel genomic approaches to therapeutics in infectious diseases
    • RNA interference
    • Ribozymes and flexizymes
    • Replicons
    • Genomics in antiviral drug discovery
    • Genomics and influenza
    • Background to influenza
    • Key development areas
    • How genomics can be applied
    • Genomics and HIV
    • Background to HIV
    • Key development areas
    • Genomics and flavivirus infection
    • Background to flaviviruses
    • Key development areas
    • Genomics and hepatitis C
    • Background to hepatitis C
    • Key development areas
    • Genomics and emerging viral disease
    • SARS-associated coronavirus
    • Nipah virus
    • Dengue
    • Genomics in antibacterial drug discovery
    • General approaches to the discovery of new antibiotics
    • Targeting metabolic networks
    • Genomics in antiparasitic drug discovery
    • Malaria
    • In silico profiling and novel antimalarial candidates
    • Targeting host cell factors
    • Evolutionary patterning
    • Kinetoplastid diseases
    • Toxoplasmosis
    • Schistosomiasis
    • Key development areas
    • Genomic characterization of parasitic pathogens
    • Trypanosomatids
    • Malaria
    • Schistosomiasis
    • Genomics in antifungal drug discovery
    • Genomic insights into prion diseases
    • Genomics in epidemiological surveillance and monitoring
    • Genomic strategies for designing novel infectious disease vaccines
    • Terrorist activity with bioagents: genomic and combined strategies for control
    • Conclusions
  • Chapter 5 Natural sources of drug leads for infectious diseases
    • Summary
    • Introduction
    • Drugs from natural sources worldwide
    • Asia and Africa Science Platform Program
    • Japan-China Joint Medical Workshop on Drug Discoveries and Therapeutics
    • 2008
    • Drugs from China
    • Drugs from natural sources: research in other developing countries
    • Yemen
    • Cameroon
    • Kenya
    • Nigeria
    • Brazil
    • Peru
    • Antibiotics from natural sources
    • Antibacterials from plants
    • Antimicrobials from endophytes
    • Antimicrobials from other sources
    • Antiviral drugs from natural sources
    • Potential of phenolics of natural origin as anti-HIV agents
    • Medicinal plant extracts and activity against herpes simplex
    • Effect of sulfated astragalus polysaccharide on the cellular infectivity of infectious bursal disease virus
    • Antiviral compound derived from the plant Melia azedarach
    • Antifungal drugs from natural sources
    • Antifungal agents derived from plants
    • Activity of isoxazolidinone-containing compounds in the treatment of serious mycoses
    • Antiparasitic agents from natural sources
    • Artemisinin
    • Other antimalarial drug candidates from natural sources
    • Plant-derived antimalarial agents: new leads and efficient
    • phytomedicines
    • Cytotoxic and antiplasmodial compounds from the roots of
    • Strophioblachia fimbricalyx
    • Antiplasmoidal alkaloids from Cassia siamea
    • Marine actinomycetes against human malaria
    • Non-malarial parasitic diseases: leishmania and trypanosomes
    • Biosurfactants and derivation from natural sources
    • Potential applications of biosurfactants in medicine
    • Probiotic bacteria and biosurfactants for nosocomial infection control
    • Antimicrobial biosurfactants from marine Bacillus circulans
    • Pseudomonas aeruginosa rhamnolipids disperse Bordetella
    • bronchiseptica biofilms
  • Chapter 6 Lead optimization in infectious disease drug discovery
    • Summary
    • Introduction
    • What is lead optimization?
    • How is lead optimization conducted?
    • Lead optimization is a cyclical process
    • New drugs for old
    • Lead optimization can make or break drug discovery
    • The outcome of the lead optimization process
    • Techniques used in lead optimization
    • Lead optimization in infectious diseases
    • In silico tools
    • Using in silico tools in drug discovery for tuberculosis
    • Using in silico tools in drug discovery for malaria
    • Using in silico tools in HIV drug discovery
    • High content cellular imaging in infectious diseases
    • Application to bacterial diseases
    • Toxicogenomics-based assays in infectious diseases
    • What is the difference between toxicogenetics and toxicogenomics?
    • Genetic susceptibility factors in infectious diseases
    • Crystallographic approaches in infectious diseases
    • Antibiotic drug discovery
    • HIV drug discovery
    • Intelligent design in infectious diseases
    • Partnerships, databases, and networks
    • The TDR Drug Targets Database
    • TDR Activities
    • TDR achievements and goals
    • The Helminth Drug Initiative
    • HDI activities
    • HDI achievements and goals
    • The Drugs for Neglected Diseases initiative (DNDi)
    • DNDi achievements to date
    • Conclusions
  • Chapter 7 Applications of nanotechnology in infectious diseases
    • Summary
    • Introduction
    • The use of nanotechnology in diagnosis
    • Quantum dot probes
    • Synthetic polymers
    • Nanochips
    • The use of nanotechnology in novel therapeutics for infectious diseases
    • Novel delivery methods for antibiotics
    • Using bacteriophages to deliver drugs
    • Targeting of bacteriophage systems using polymeric nanostructures
    • Aerosol delivery systems
    • Photodynamic therapy systems
    • Nanoemulsions and nanoparticles
    • Biofilms
    • Biofilm infections in cystic fibrosis
    • Biofilm infections related to catheters
    • Biofilm infections on prosthetic devices
    • Novel therapeutic development strategies
    • Peptide therapeutics
    • Use of nanotechnology to combat tuberculosis
    • Use nanotechnology to combat pneumonia
    • Use of nanotechnology to combat malaria
    • Use of nanotechnology to combat Sin Nombre hantavirus infection
    • Using nanotechnology to target fungal infections
    • Candidiasis
    • New nanovaccine strategies for infectious diseases
    • Delivering nanovaccines by injection
    • Mucosal delivery
    • Gene vaccines
    • Novel drug delivery using nanotechnology
    • Nanotubes
    • Polyphosphazenes and delivery of vaccine antigens
    • Solid lipid nanoparticles
    • Conclusions
    • Bibliography
    • Glossary
    • Index
  • List of Figures
    • Figure 2.1: Overview of proteomics
    • Figure 2.2: Standard proteomic approaches
    • Figure 2.3: Two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) workflow
    • Figure 2.4: Example of SELDI-TOF workflow
    • Figure 2.5: Sites of the body usually affected by MSRA infections
    • Figure 2.6: Pulmonary TB
    • Figure 2.7: Trichonomas vaginalis in a Pap smear
    • Figure 3.8: Distribution of proteins produced at different life-cycle stages of Plasmodium falciparum
    • Figure 3.9: Clostridium difficile colonies on a blood agar plate
    • Figure 4.10: Structure-activity relationship homology flowchart
    • Figure 4.11: Novel antiviral strategies based on the HCV life cycle
    • Figure 4.12: Target identification via pathogen and host genome sequencing
    • Figure 4.13: Emergence of MRSA in the US
    • Figure 4.14: Phylogenetic reconstruction based on orthologous glycerol kinase sequences
    • Figure 4.15: Timeline of antifungal drug development
    • Figure 6.16: Summary of techniques used in lead optimization
    • Figure 6.17: Attrition rates and current drug R&D pipeline for neglected diseases
    • Figure 7.18: Relationship of nanobiotechnology to nanomedicine and other biotechnologies
    • Figure 7.19: Schematic representation of a drug-carrying bacteriophage
    • Figure 7.20: Biofilm maturation
    • Figure 7.21: Single-walled carbon nanotube bundles (SWNT) with adsorbed antibody presenting that antibody to T-cells Table 2.1: Advantages and disadvantages of SELDI
  • List of Tables
    • Table 2.2: Advantages and disadvantages of MALDI
    • Table 2.3: Deaths in the UK annually since 1990 from CJD of all known causes

 

 

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