Chemical genetics

Definition:Chemical genetics involves using small molecules to manipulate and therefore better understand biological systems. While in this context, small does not have a concrete definition, small molecules are typically organic molecules that, because of their structure and composition, bind to proteins and allow modification of gene expression. The molecules used may be either man-made or isolated from natural sources. Depending on the nature and needs of the experiment, this may be done at the molecular, cellular, or organismic level.

Chemical genetics as a field is a relatively recent development, with many of the tools and data needed to systematize its research only arising since 1990. However, many of the important developments and discoveries of small molecules central to the field date from before this time. Continuing research allows scientists to better understand the workings of those discoveries.

Basic Principles

Genes work by encoding for proteins, and in chemical genetics, the small molecules used are designed or chosen in order to target those proteins. While genetic manipulation and experimentation has been a part of the field of genetics since Gregor Mendel’s experiments with plants and establishment of the laws of heredity, chemical genetics differs from classical genetics in that it focuses on targeting the proteins rather than the genes themselves.

Chemical genetics has several advantages over classical genetics in its study and application. These advantages are largely linked to the fact that chemical genetics is typically done with simple organisms. The smaller scale allows for better concentration on a single effect. In addition, the effect is often reversible; whether or not that is the case is easier to ascertain on a smaller scale. Finally, using cell-based chemical-genetics testing avoids the problem of long gestation and generation times that come with animal and human testing. The major disadvantage of chemical genetics is that it can be unclear from testing how usable a potential treatment is. It can be difficult to find or create a molecule that will only react with one target, so there is a possibility of small molecules having unintended side effects.

The two basic types of research in the field are called forward and reverse chemical genetics. In forward chemical genetics, as in forward classical genetics, the research looks from the phenotype (outward appearance of a trait) of interest to the genotype (genetic coding for a trait), but in chemical genetics, that continues from the genotype to the encoded protein. In experimentation, a number of small molecules are added to cells or animals to be observed for the desired effect. The next step is to identify the protein to which the small molecules have bound themselves.

With reverse chemical genetics, research begins with the protein. The small molecule being used is added to a sample of the pure protein, with the result placed into a cell or animal. The resulting phenotype is observed and analyzed.

Chemical genetics also features many of the same elements and processes as drug discovery. In drug discovery, however, the molecules used must be screened for safety because of their potential use in living humans or other animals. In chemical genetics, the initial focus is on effects, and the nature of many experiments, at either the cellular or the molecular level, means that the ongoing viability of the cell is not necessarily a primary concern, and therefore human-subject protocols are not in play.

Core Concepts

Chemical genetics is a systemic method of making discoveries that previously were more the result of serendipity. A stepwise process, along with powerful libraries and computing tools, can find and eliminate potential candidates for an experiment much more quickly than was possible in the past.

Forward Chemical Genetics and Target Identification. In a forward chemical genetics experiment, the goal is to find the protein that will react with a small molecule. In order to do this, a plate is prepared with a number of wells that will hold the experimental bacteria. Into each of these wells a different small molecule is placed. The small molecule is immobilized and then tested to determine which, if any, of the proteins in the bacteria it bonded with. Research into the best way to immobilize a molecule is ongoing, with researchers seeking a route that does not involve doing anything to the small molecule itself.

Compound Libraries. In order to determine which small molecule will have the desired effect on a protein, numerous suspects must be tested. Part of the reason for the expansion of the field of chemical genetics has been both the growing number of molecules found for scientists to use and the increasing amount of data resulting from their effects. As more experiments are done, the knowledge base regarding the effects of particular small molecules widens. Ideally, researchers would have access to the small molecules that might affect a target, and all of these molecules would be available for possible use and could be tested.

Typically, scientists working in the science industry have had access to a much wider range of these molecules than those working in other fields. However, organizations have worked to close that gap. The National Human Genome Research Institute, a branch of the National Institutes of Health (NIH), announced plans to develop a wide library of five hundred thousand small molecules, held across a number of centers, for use by researchers.

Reverse Chemical Genetics. In reverse chemical genetics, the goal is to find which small molecule, after binding to the protein, will have the desired effect on a system or an organism. To do this, a purified form of the protein needs to be created, which then needs to be combined separately with each of the small molecules of interest. These combinations are then monitored in the cell to see if the desired phenotype occurs.

Chemical Genomics.Finding a small molecule that affects a protein in the desired way is only the first step. The molecule must have the potential to interact with numerous proteins other than the desired target. Once inside a living organism, the molecule may react in unexpected ways, and the disruption of the biological pathway may have some unforeseen detrimental impacts. Any discoveries yielded by chemical genetics must still be put to real-world use in order to determine if they are effective and if their side effects outweigh the benefit of the treatment. Numerous pathways in the body require proteins; one of the goals of chemical genetics is finding a way to activate or deactivate each and every one of them.

Applications Past and Present

Drug Discovery—Pain Relief. While the scientific discipline of chemical genetics is relatively new, the application of the principles underlying the field is thousands of years old. A great deal of the research in the field has been and continues to be focused on the development of compounds that affect the human body and can alleviate or cure illnesses. Early humans used various plants as medicines; chemical genetics provides even greater tools for determining the action of these plants and isolating and or purifying active compounds for use as pharmaceuticals.

A drug more than a century old provides a useful example for understanding the workings of small molecules and chemical genetics. First discovered in 1853, aspirin was synthesized by placing an acetyl group on salicylic acid, which was isolated from the bark of the white willow tree. In 1897, Felix Hoffmann, working for the company Bayer, was able to synthesize the compound, and in 1899, it began to be sold commercially. Aspirin has been and remains one of the most popular drugs taken, both by itself and combined with other ingredients in pill form, in part because of its utility. In addition to its original purpose as a pain reliever, aspirin has been found to have use as an anti-inflammatory and a fever reducer and to reduce certain heart risks. At the same time, it does have side effects, such as heartburn, stomach pain, nausea, and vomiting. These are among the reasons there are a number of other over-the-counter pain relievers, some of which avoid the side effects of aspirin, such as acetaminophen. The negative effects of aspirin were worse before it was chemically manufactured. In fact, part of the reason for Hoffmann’s interest in synthesizing aspirin in the manner he did was that his father had been taking salicylic acid only, but it severely upset his stomach.

Aspirin was in use for many years before its mechanisms were understood. However, by using chemical-genetics techniques, scientists have been able to develop a better understanding of why aspirin has its anti-inflammatory and pain-relieving effects, as well as its unpleasant side effects. Aspirin works by binding to cyclooxygenase-1 (COX-1, or sometimes just COX), a naturally occurring enzyme that catalyzes the formation of prostaglandins (PGs), which are molecules produced by the body that cause inflammation. The binding action prevents inflammation from occurring. At the same time, PGs produced by the COX-1 pathway are also involved in protecting the lining of the stomach, kidney function, and blood clotting. The inhibition of this pathway can therefore cause stomach pain, kidney disease, or blood thinning in certain cases.

The British pharmacologist John Robert Vane did a great deal of the research that accounts for the knowledge of the mechanism of aspirin. In the course of his research, he also laid some of the groundwork for the discovery of other COX pathways. Vane’s research also contributed to the development of ACE inhibitors, another small-molecule treatment, which are used to treat high blood pressure and heart failure.

One of the pathways discovered by Vane was COX-2, which led to a new class of pain-relieving drugs known as COX-2 inhibitors. These strong anti-inflammatory drugs were used as treatments for arthritis and were used off-label to treat other forms of pain. Because of the adverse effects that can accompany aspirin use, the hope was that these new drugs would provide pain relief without the gastrointestinal side effects. While the drugs are able to provide pain relief, they are accompanied by elevated risk of heart attack and stroke; therefore, several of the approved COX-2 inhibitors have been pulled off the market, and the remaining ones carried a warning. However, research into the potential applications of these small molecules remained ongoing.

A third enzyme, known as COX-3, has also been discovered, and there was some speculation that it might explain the pharmaceutical action of acetaminophen (Tylenol). However, strong evidence has suggested that it does not play a significant role in PG production in humans, although it appeared to have some effect in dogs; thus, it was believed to potentially have some utility in veterinary medicine.

Drug Discovery—Immune Suppressors. Other drug treatments have played significant roles in the development of chemical genetics. Several immunosuppressant drugs were isolated from fungal samples and ultimately played a central role in successful organ transplantation. These drugs include cyclosporine A, rapamycin, and tacrolimus, also known as FK-506.

Drug Discovery—Cancer Treatments.The idea of a “cure for cancer” is discussed less often than before as the public comes to understand that cancer is, in fact, a disease with many different forms. Accordingly, many different strategies are being tried to target various strains of cancers that grow throughout the body, with some treatments arising from chemical genetics.

For example, one early attempt at treatment used chemical-genetics techniques to target MEK, an enzyme that contributes to cell division. The treatment significantly reduced tumor growth while avoiding some of the toxic effects common in cancer drugs with less specific targets. MEK continues to be a subject of research for the treatment of various cancers. One emerging prospect in many cases is combination therapy to inhibit a second molecular pathway at the same time, as many cancers mutate to avoid a single treatment. As an example, one treatment for melanoma targets the BRAF protein, as mutations of the BRAF gene have been strongly linked with development of cancer. However, it has been observed that after prolonged treatment, more of the BRAF protein is produced. Therefore, a prospective treatment option is combining the current treatment with an MEK inhibitor with the goal of preventing the increased production.

The use of small molecules in cancer treatments is likely to have some strong benefits for the field as a whole due to the utility of the large database of information on small molecules and proteins established by the National Cancer Institute’s Initiative for Chemical Genetics.

Drug Discovery—Infectious Disease.While many pharmaceuticals focus on targets in the human body, another target of chemical genetics is the foreign invaders that doctors and patients seek to counter. For example, malaria, which is spread by mosquitoes infected with a pathogen, has proved difficult to contain. Researchers studying the disease found an enzyme called PfSUB1 that breaks protein bonds, leading to a crucial step in the spread of disease once a host is infected. Several chemical screenings of thousands of possibilities yielded some candidate molecules to inhibit the activity of PfSUB1. A drug called NITD609, developed at the Novartis Institute for Tropical Diseases, yielded promising results in early testing.

Hepatitis C treatment has also proved challenging. Drugs used to combat hepatitis C often have harsh side effects, such as flulike symptoms, and patients sometimes cease to respond to treatments. Screening tests yielded cyclosporine A as a drug candidate, as it inhibited replication of the viral cells. However, the known side effects of cyclosporine A make use of the drug undesirable, prompting researchers to focus on other candidates from the cyclosporine drug family.

Plant Genomics. The original subjects of classical genetics research, plants have a continued place in the field of chemical genetics. Plants might prove especially useful for chemical-genetics purposes because they have genomes much larger than those of humans and because many of those genes repeat. As a result, the introduction of small molecules can more easily help determine the function of various genes than a classical approach, as it allows single genes that are duplicates to be targeted simultaneously rather than individually.

Social Context and Future Prospects

The growth of chemical genetics has been facilitated by the sequencing of the human genome and by the increased computing power that allows for increasingly large, fast databases of information on the various proteins and molecules that are used in chemical-genetics testing. Chemical genetics provides a means of conducting large-scale testing and research for the action of large numbers of compounds on large numbers of proteins. As medical science identifies the various mechanisms of disease, more opportunities for the potential use of small molecules are likely to emerge.

However, while chemical genetics has yielded important advances, there have been some highly publicized setbacks. Introduced to the market in the late 1990s and early 2000s, the small molecules used as COX-2 inhibitors had great success in treating arthritis pain, and they were ultimately prescribed for some off-label uses, including pain relief from migraines and after operations. However, the action of the small molecules also seemed to produce a dramatic rise in heart attacks and strokes. Merck took Vioxx off the market in September 2004, and a scandal subsequently ensued when facts emerged that the company had ignored and possibly concealed strong evidence of the risks of taking the medication. Litigation resulted in the release of documents that revealed the depths of the problem, and the company paid $4.85 billion to thousands of litigants who had been harmed. The FDA requested that Pfizer take Bextra off the market in April 2005 because of similar concerns, and ultimately, the company paid billions in a settlement over deceptive marketing practices.

While Vioxx and Bextra, both popular drugs, are no longer available, some physicians believe that, for certain patients, the benefits of the powerful pain relievers would outweigh the heart risks that have been found. However, the impact of the cases went far beyond those who suffered as a result of the side effects of a drug from a class that had once seemed promising. The scandal surrounding the COX-2 inhibitors remained in the news years later, and the issues raised with the recall of these drugs eroded public trust in the pharmaceutical industry. While the small-molecule products produced by chemical genetics can have powerful effects, their use in humans means that undesirable effects can happen when these molecules connect elsewhere. Only with a better understanding of the full field and the workings of the proteins targeted will the field of chemical genetics reach its full potential.

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