- Introduction
- History
- Natural Drug Leads
- Combinatorial Approach
- Discoveries
- Conclusion
- References
- Contact Us
Combinatorial Methods
Combinatorial chemistry essentially means reacting a set of starting chemicals in all possible combinations. Traditionally, chemists make compounds one at a time, step by step. If the synthesis of a compound requires numerous steps, the intermediate compounds are usually purified after each step. On the other hand, when chemists use combinatorial methods they will always be making many different compounds at the same time often in the same reaction vessel. The purification steps are usually faster and less complicated compared to the traditional methods.
Typically, circular chemicals are used as a starting point for a library. Hundreds of different side-branches can be added to the various chemical groups poking out of the circle or in other words one of a large number of possible building blocks is added to each of several variable sites on a molecule.
Small plastic beads have traditionally been used as a scaffold to attach the molecular building blocks upon in stepwise reactions. These plastic beads can be easily washed between each step to purify the intermediate compound using chemically resistant porous bags resembling tea bags or columns resembling coffee filters.
Two different methods exist for rapidly creating thousands of molecules from only a few starting materials. "Split and Mix" synthesis is the fastest method of producing many compounds with a minimal number of starting materials and reaction vessels. The basic principle is explained in the following example: Starting with three batches of beads, in three separate containers, one reacted with building block "a," one with "b," and one with "c." The three beads are washed and then mixed and split into the three vessels. Each vessel contains all three types of beads. Addition of another building block to each vessel (a in container 1, b in container 2, and c in container 3) yields 9 different molecules across the three vessels. Another round of washing, mixing, and splitting, puts each of the 9 molecules in each of the three vessels. Adding another building block results in a total of 27 different molecules. By continuing this process, millions of uinque molecules can be created very quickly.
The parallel synthesis method involves multiple reaction vessels and attachment of each building block in a stepwise function. Typically a plate with 96 individual wells is used, with beads attached to each well. The advantage of parallel synthesis is that the composition of each compound is known, but generally, the split and mix procedure can generate many more compounds in the same amount of time. This method is used typically when generating libraries of under 10000 molecules.
Typically, circular chemicals are used as a starting point for a library. Hundreds of different side-branches can be added to the various chemical groups poking out of the circle or in other words one of a large number of possible building blocks is added to each of several variable sites on a molecule.
Small plastic beads have traditionally been used as a scaffold to attach the molecular building blocks upon in stepwise reactions. These plastic beads can be easily washed between each step to purify the intermediate compound using chemically resistant porous bags resembling tea bags or columns resembling coffee filters.
Two different methods exist for rapidly creating thousands of molecules from only a few starting materials. "Split and Mix" synthesis is the fastest method of producing many compounds with a minimal number of starting materials and reaction vessels. The basic principle is explained in the following example: Starting with three batches of beads, in three separate containers, one reacted with building block "a," one with "b," and one with "c." The three beads are washed and then mixed and split into the three vessels. Each vessel contains all three types of beads. Addition of another building block to each vessel (a in container 1, b in container 2, and c in container 3) yields 9 different molecules across the three vessels. Another round of washing, mixing, and splitting, puts each of the 9 molecules in each of the three vessels. Adding another building block results in a total of 27 different molecules. By continuing this process, millions of uinque molecules can be created very quickly.
The parallel synthesis method involves multiple reaction vessels and attachment of each building block in a stepwise function. Typically a plate with 96 individual wells is used, with beads attached to each well. The advantage of parallel synthesis is that the composition of each compound is known, but generally, the split and mix procedure can generate many more compounds in the same amount of time. This method is used typically when generating libraries of under 10000 molecules.
These examples illustrate the main limitation of combinatorial chemistry. The simplicity of combinatorial chemistry is also one of its drawbacks. Only certain types of compounds can bind to plastic beads, and only a fairly limited number of reactions can be used in these repetitive steps. This means that only certain types of substances can be made using combinatorial chemistry. One of the challenges facing combinatorial chemists is to develop new reactions and new classes of substances that can be applied in simple and repetitive steps.
To overcome the limitation of the small number of reactions that can be performed on beads, chemists have developed methods of performing combinatorial chemistry in solution where a vast range of reactions can be performed. Other chemists have combined molecular biology with combinatorial chemistry. They introduce different combinations of genes into microorganisms, turning each batch of microorganism into an individual bioreactor.
To overcome the limitation of the small number of reactions that can be performed on beads, chemists have developed methods of performing combinatorial chemistry in solution where a vast range of reactions can be performed. Other chemists have combined molecular biology with combinatorial chemistry. They introduce different combinations of genes into microorganisms, turning each batch of microorganism into an individual bioreactor.
Detecting Active Compounds
After any combinatorial synthesis whether split and mix, parallel or solution, the products need to be identified, tested, and screened for the sought-after activity against the intended biological target, which could be an antibody, a receptor or other biological target molecule such as the Human Immunodeficiency Virus.
Identification of compounds can easily be accomplished by detecting the exact molecular weight (using a mass spectrometer) or the electronic environment of particular atoms (using a nuclear magnetic resonance (NMR) machine). There is just enough of a chemical on a standard bead for identification using these methods. Some methods work with the chemical attached to the bead; for others the ‘linker’ that holds the chemical to the bead must be sheared with light or acid or base. Tags can also be used to detect active sites through fluorescence and absorbance spectra or fluorescence resonance energy transfer (FRET).
Combinatorial chemists can create thousands of compounds in just days. They need rapid and inexpensive ways of screening such large numbers of compounds. Consequently they developed robotics and automated methods to help them with these screenings. This need to be able to rapidly screen huge numbers of compounds has spawned its own discipline known as high throughput screening. Combinatorial chemistry would not be manageable or efficient without it.
After initial detection of active molecules, the library size is decreased to those containing activity. One way of whittling down library size is to bring in the practitioners of rational drug design -- scientists who use the shape and structure of the target to deduce which one chemical key will fit the protein lock. Smaller libraries are also more suited to the later stages of drug discovery.
The first chemical that shows promise in drug testing rarely ends up being the final drug. Instead there is a period of optimization, in which hundreds of variants of the original ‘lead’ chemical are made and tested. Combinatorial chemistry can be used to make more variants more rapidly. Usually one or more of the variants is an improvement on the original lead chemical.
In summary, combinatorial synthesis is a process which rapidly produces many different compounds by using a few starting reagents and varying the reactions used. The objective is to build a large library of compounds from a starting "scaffold" to interact with specific biological targets. From this library, the most potent hits can then be isolated for further testing and development, eventually leading to a finished product to begin clinical trials.
Identification of compounds can easily be accomplished by detecting the exact molecular weight (using a mass spectrometer) or the electronic environment of particular atoms (using a nuclear magnetic resonance (NMR) machine). There is just enough of a chemical on a standard bead for identification using these methods. Some methods work with the chemical attached to the bead; for others the ‘linker’ that holds the chemical to the bead must be sheared with light or acid or base. Tags can also be used to detect active sites through fluorescence and absorbance spectra or fluorescence resonance energy transfer (FRET).
Combinatorial chemists can create thousands of compounds in just days. They need rapid and inexpensive ways of screening such large numbers of compounds. Consequently they developed robotics and automated methods to help them with these screenings. This need to be able to rapidly screen huge numbers of compounds has spawned its own discipline known as high throughput screening. Combinatorial chemistry would not be manageable or efficient without it.
After initial detection of active molecules, the library size is decreased to those containing activity. One way of whittling down library size is to bring in the practitioners of rational drug design -- scientists who use the shape and structure of the target to deduce which one chemical key will fit the protein lock. Smaller libraries are also more suited to the later stages of drug discovery.
The first chemical that shows promise in drug testing rarely ends up being the final drug. Instead there is a period of optimization, in which hundreds of variants of the original ‘lead’ chemical are made and tested. Combinatorial chemistry can be used to make more variants more rapidly. Usually one or more of the variants is an improvement on the original lead chemical.
In summary, combinatorial synthesis is a process which rapidly produces many different compounds by using a few starting reagents and varying the reactions used. The objective is to build a large library of compounds from a starting "scaffold" to interact with specific biological targets. From this library, the most potent hits can then be isolated for further testing and development, eventually leading to a finished product to begin clinical trials.