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National Research Council (US). Health and Medicine: Challenges for the Chemical Sciences in the 21st Century. Washington (DC): National Academies Press (US); 2004.

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Health and Medicine: Challenges for the Chemical Sciences in the 21st Century.

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1New Tools and Approaches for Discovery, Diagnostics, and Prevention

With recent advances in the chemical sciences there has been an explosion of information in genomics, proteomics, informatics, and high-throughput screening. This has led to an ever increasing need for new tools and approaches to effectively create and manage the large amounts of information that are being obtained in the postgenomic era. Concomitant with the increase in biological information, interdisciplinary fields have emerged in the chemical sciences in order to fully exploit all areas of research. One such field, systems biology, does not use the traditional reductionist approach to chemical problems. Instead the scientist looks at biological problems as the whole of its components, which is made possible by the various technological advances in the chemical sciences.

DNA SEQUENCING

New tools and technology in the chemical sciences have advanced DNA sequencing. The automated florescent DNA sequencer has led to the completion of the human genome project. There has been roughly a 6,000-fold increase in the throughput of DNA sequencing with a significant decrease in cost from its inception in 1986. There are current efforts to increase the throughput another 3,000-to 6,000-fold, which can be accomplished by single molecule DNA sequencing. This new approach will open the world of genomes to comparative analysis, which in turn will allow predictive and preventative medicine based on an individual’s specific genomic makeup (see Sidebar 1.1).

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Sidebar 1.1

The DNA Sequencing Revolution. Excerpt from “Systems Biology and Global Analytical Techniques”, Leroy Hood, The Institute for Systems Biology Since the 1986 publication of the automated fluorescent DNA prototype, an increase of approximately (more...)

There are other new and innovative approaches to DNA sequencing in development. The 2002 Nobel Prize winner in physiology, Sydney Brenner, has developed a technique whereby a million cDNA sequences can be affixed on separate beads and amplified for 16 to 20 base pairs simultaneously in a flow cell. This results in roughly a million sequences in about six hours. This particular technique is important in analyzing a discreet transcriptome of a particular cell type. Another innovative approach to genome sequencing developed in the laboratory of Leroy Hood uses inkjet technology to synthesize oligonucleotide arrays. The current model has the ability to synthesize 60 to 70 mers in very high yield in a short time. This technology may lead to the synthesis of large genes or even gene families.

DNA NANOTECHNOLOGY

An emerging field that is attempting to exploit the information content of DNA is DNA-based nanofabrication. The idea is to achieve instructed fabrication by using the information contained in DNA to construct higher-order complexes and to control motion by using the chemical properties of the DNA. There are a number of examples of using DNA scaffolds to demonstrate controllable molecular motions. One such example used a DNA structural motif termed the “paranemic crossover” that was able to rotate 180 degrees depending on which oligonucleotide was added to the solution. DNA nanotechnology is a promising new field of science that certainly will lead to powerful new approaches to chemical and biological problems.

NUCLEIC ACID THERAPEUTICS

Nucleic acid therapeutics was first proposed using antisense technology in the late 1970s. This technology has since evolved into preclinical and clinical trials. Antisense DNA binds to target mRNA through Watson-Crick pairing, which prevents the RNA from being translated into protein. The formation of a DNA-RNA heteroduplex initiates the enzyme RNase H to cleave the RNA portion of the heteroduplex. While theoretically sound, the advancement of this technology has been very slow. A newer approach using antisense employs the mechanism of RNA interference (RNAi). RNAi uses the ability of higher eukaryotic cells to cleave double-stranded RNA, presumably in defense of a viral infection. The double-stranded RNA is enzymatically cleaved into smaller fragments known as small interfering RNAs (siRNAs), which in turn initiate the cleavage of the mRNA that corresponds with the sequence of the siRNAs. RNAi technology is still not completely elucidated. In order for this technology to be effectively incorporated into a viable therapeutic alternative, RNAs must be inhibited from inducing an interferon response in the cell.

COMBINATORIAL CHEMISTRY

Combinatorial chemistry has emerged as one of the most productive new approaches to drug discovery. The technology of creating and testing large amounts of compounds to ascertain which ones contain the desired biological activity has spawned many new approaches to synthesis and design. It can provide access to ligands to probe a biological process (e.g., ligands that inhibit a target protein of interest, promote a phenotype of interest, or act as a sensor). Many new assays have been developed to effectively screen molecular libraries. The screens typically are immunoassays, enzyme reactions, cell-based assays, or any number of other specialized tests chosen for the specific disease or molecule being studied. The synthetic process in combinatorial chemistry usually employs many automated techniques, such as robotics, to synthesize thousands of unique chemical compounds or oligonucleotides with predetermined atomic structure that are categorized in a database or library. The ultimate goal of this technology in the area of health and medicine is to enable researchers to pursue rational drug design, whether using molecular libraries to discover new drugs or in oligonucleotide therapeutics. Combinatorial methods are now also being employed in the biotechnology sector in the areas of proteomics and bioinformatics.

STRUCTURAL PROTEOMICS

One of the fields of science that is benefiting the most from recent advances in the chemical sciences is structural proteomics, which is the global analysis of proteins. There are presently only about 15,000 structures deposited in the Protein Data Bank, of which roughly 4,000 represent unique protein folds spanning 1,500 protein families. Although these numbers are growing every day, the predicted number of protein families in our proteome is on the order of 20,000–50,000. These numbers depict the challenge that lies ahead for chemists and biologists in understanding the complex mechanisms in the human body. There are only a limited number of proteins that have been marketed due to structure-based discovery techniques. Timely access to molecular structures has historically been one of the major drawbacks. Parallel processing, miniaturization, and automation have greatly decreased the amount of time it takes from protein purification to structure determination. In particular, the use of robotics, nano- and picoliter-scale crystallization techniques, and high-throughput automated imaging systems to detect viable crystals has greatly increased the speed at which protein structures are elucidated. In nuclear magnetic resonance spectroscopy there has been limited success with automated structure determination programs. There have also been new advances in pulse sequences that greatly reduce the number of scans needed to obtain structural data under certain conditions, thereby decreasing costly data acquisition time. In addition, innovative tandem mass spectrometry techniques allow detailed characterization of proteins without having to undergo the potentially painstaking task of structure determination. These advances have dramatically improved efforts to look for biologically active compounds that thwart disease.

PROTEIN EXPRESSION ANALYSIS

Since there is no analog to polymerase chain reaction (PCR) for proteins, it is difficult to analyze the expression patterns of proteins in response to various phenotypic conditions. New techniques using mass spectrometry have been able to help associate protein expression with genomic DNA in response to various cellular stressors. A technique called “isotope coded affinity tagging” (ICAT) in combination with mass spectrometry was used by Leroy Hood and colleagues to analyze the galactose expression system and create a snapshot of the global interactions of a series of different systems present in a yeast cell. A protein engineering technique called Expressed Protein Ligation has been developed that introduces sequences of unnatural amino acids, posttranslational modifications, and biophysical probes into proteins of any size through the chemoselective addition of a peptide to a recombinant protein (see Sidebar 1.2).

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Sidebar 1.2

Genetic Code Expansion. Excerpt from “Biotechnology”, Peter G. Schultz, The Scripps Research Institute Every known form of life has the same genetic code containing the same common 20 amino acids, with a few rare exceptions. Logical questions (more...)

PROTEIN STRUCTURE ANALYSIS

Although protein structure determination is critical to understanding the process of an enzyme, it often does not adequately address real-time protein-protein interactions in vivo, which is imperative when attempting to decipher the inner workings of the cell. Co-expression tags can aid in detecting protein localization and interactions in the cell. Barbara Imperiali and colleagues have developed a new, less obtrusive class of expression probes that bind lanthanide ions to impart luminescent effects. This enables these co-expressed proteins to be monitored by protein-protein interaction assays. The small size of these probes aids in minimizing any steric interactions between the probe and the proteins of interest.

MICROFLUIDICS

To circumvent the increasing cost and increase the efficiency of research and development in health and medicine, there is an increasing trend toward miniaturizing reactions and reaction conditions. Microfluidics is the study of reaction conditions and fluid flow in microenvironments. Many scientists are investigating this type of “lab on a chip” technology where compounds can undergo complicated reaction schemes in a microenvironment. This new technology affords the possibility of having multiple laboratory functions, such as purification, immobilization, sorting, and detection, carried out on a single chip, enabling the capacity to perform multiple parallel analyses in a faster and often more accurate microreaction.

MOLECULE DELIVERY

One of the challenges in studying intracellular interactions is successfully delivering the molecule of interest to its site of action. There have been many new approaches and advances in this arena. One such advance is in the area of caged phosphopeptides. Phosphopeptides that represent phosphorylation sites in various kinases have been designed to examine the effect of the liberated phosphopeptide on cell migration. Typically, the phosphopeptides can be cleaved by photolysis of the cage upon migrating to the site of action in the cell. Although promising, there is still much research to be done before this approach can be widely used in medicine. There are many new and innovative approaches to drug delivery that are currently under investigation.

Copyright © 2004, National Academy of Sciences.
Bookshelf ID: NBK92227

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