Chapter 2: Combinatorial chemistry

Combinatorial chemistry is a branch of chemistry that focuses on the development of chemical synthesis procedures that enable the preparation of a large number of compounds in a single proceeding, ranging from tens to thousands or even millions. Combinations, collections of individual compounds, or chemical structures that are manufactured by computer software are all examples of the types of compound libraries that can be created. The production of peptides and small molecules can both be accomplished through the application of combinatorial chemistry.

Additionally, combinatorial chemistry encompasses the strategies that enable the discovery of valuable components that are contained inside libraries. The methodologies that are utilized in combinatorial chemistry can also be utilized in other fields besides chemistry.

The primary objective of combinatorial chemistry is to compile libraries consisting of an extremely large number of compounds and to determine which of these compounds have the potential to be utilized as pharmaceuticals or agricultural chemicals. The utilization of high-throughput screening, which is able to evaluate the output at a scale that is enough, is therefore essential.

Combinatorial chemistry may be traced back to the 1960s, when a researcher at Rockefeller University named Bruce Merrifield began exploring the solid-phase synthesis of peptides. Although combinatorial chemistry has only been seriously taken up by industry since the 1990s, its roots can be found as far back as the 1960s. It is possible to rapidly produce a large number of compounds by the synthesis of peptides using a combinatorial approach. There are 8,000 (203) different options that can be created by using the twenty natural amino acids, for instance, in a tripeptide. Furka came up with a "split and mix" method, which was eventually adopted, and solid-phase procedures for tiny molecules were discovered later.

When it comes to the pharmaceutical sector, combinatorial chemistry in its current version has most likely had the most significant impact available. As part of their efforts to enhance the activity profile of a chemical, researchers develop a "library" consisting of a wide variety of compounds that are connected to one another. An industrial method to combinatorial synthesis has been developed as a result of advancements in robotics. This approach has made it possible for businesses to routinely generate more than 100,000 new and unique molecules per year.

A "virtual library" is a computational enumeration of all possible structures of a given pharmacophore with all available reactants. This is done by researchers in order to manage the huge number of structural options that are available. A library of this kind may contain anywhere from thousands to millions of 'virtual' chemicals or compounds. For the purpose of actual synthesis, the researcher will choose a subset of the "virtual library" based on a number of different computations and criteria (for more information, see ADME, computational chemistry, and QSAR).

The solid-phase synthesis that Merrifield created serves as the foundation for the combinatorial split-mix synthesis, also known as split and pool synthesis. When a combinatorial peptide library is created by synthesizing twenty amino acids (or other types of building blocks), the solid support in the form of beads is divided into twenty equal sections. A separate amino acid is then coupled to each section after this step has been completed. The mixing of all of the elements constitutes the third phase. A cycle is made up of these three stepping stones. Simply repeating the steps in the cycle is all that is required to get the desired result of elongating the peptide chains.

The synthesis of a dipeptide library, which uses the same three amino acids as building blocks in both cycles, serves as an illustration of the technique. There are two amino acids that are ordered in a different order in each of the components that make up this library. Within the picture, the circles that are yellow, blue, and red respectively show the amino acids that are utilized in couplings. Divergent arrows illustrate the process of creating equal amounts of solid support resin (shown by green circles), vertical arrows indicate the process of coupling, and convergent arrows illustrate the process of mixing and homogenizing the support's various components.

As can be seen in the image, nine dipeptides are produced over the two cycles of the synthetic process. Twenty-seven tripeptides and eighty-one tetrapeptides would be produced during the third and fourth cycles, respectively.

A number of remarkable characteristics are possessed by the "split-mix synthesis":

The year 1990 saw the publication of three different groups' descriptions of methods for the preparation of peptide libraries using biological processes. The following year, Fodor et al. presented a remarkable approach for the synthesis of peptide arrays on thin glass slides.

In order to expedite the process of peptide array creation, Mario Geysen and his colleagues came up with a technique known as "parallel synthesis." They achieved the synthesis of 96 peptides by using plastic rods (pins) that had the solid support coated at the ends of the rods. Within the wells of a microtiter plate, the pins were submerged in the solution of reagents that had been deposited there originally. One of the most common applications of this technology is through the utilization of automatic parallel synthesizers. In spite of the fact that the parallel technique is significantly slower than the real combinatorial one, it has the advantage of being able to precisely determine which peptide or other molecule forms on each different pin.

In order to combine the benefits of split-mix synthesis and parallel synthesis, additional processes were created. For the procedure that was reported by two different groups, the solid support was encased in permeable plastic capsules, and a radiofrequency tag was attached to each capsule. The tag carried the code of the compound that was going to be created inside the capsule. In a manner that was analogous to the split-mix method, the procedure was carried out. During the split stage, on the other hand, the capsules were sent out to the various response vessels in accordance with the codes that were read from the RF tags that were attached to the capsules.

The term "string synthesis" refers to a separate approach that was developed by Furka and colleagues for the same or similar aim. The capsules did not include any code when using this method. They are then inserted into the reaction vessels in a stringed configuration, similar to how pearls are strung together in a necklace setting. The location of the capsules on the strings is used to store not only the contents of the capsules but also the identities of the capsules themselves. In accordance with predetermined guidelines, the capsules are re-distributed among the new strings following each step of the coupling process.

The synthesis and biological evaluation of small compounds of interest have traditionally been a time-consuming and difficult step in the process of drug discovery. In recent decades, combinatorial chemistry has evolved as a method that may rapidly and effectively synthesize a huge variety of possible compounds.

tiny molecules that could be used as drugs. A typical synthesis results in the production of a single target molecule at the conclusion of a synthetic scheme. Furthermore, each step in a synthesis results in the production of a single product. During a combinatorial synthesis, it is feasible to synthesize a huge library of compounds by employing identical reaction conditions. These molecules can then be tested for their biological activity. This is conceivable when only a single starting material is used. Following this, the pool of products is divided into three equal pieces, each of which contains each of the three products. After that, each of the three individual pools is reacted with another unit of reagent B, C, or D, which results in the production of nine distinct compounds from the three that were previously produced. Following this, the procedure is continued until the necessary quantity of building blocks is added, which results in the production of a large number of compounds. In order to successfully synthesize a library of compounds using a multi-step synthesis, it is necessary to utilize efficient reaction methods. However, if conventional purification methods are utilized after each reaction step, both yields and efficiency would suffer.

There are potential answers that can be found through solid-phase synthesis that eliminate the requirement for the standard quenching and purification procedures that are typically utilized in synthetic chemistry. The process begins with adhering a beginning molecule to a solid support, which is often an insoluble polymer. Subsequently, further reactions are carried out, and the end product is purified before being cleaved from the solid support. Because the molecules of interest are bonded to a solid substrate, it is possible to reduce the purification process after each reaction to a single filtration/wash step. This eliminates the need for the laborious liquid-liquid extraction and solvent evaporation stages that are involved in the majority of synthetic chemistry. In addition, the utilization of heterogeneous reactants allows for the utilization of excess reagents to accelerate the conclusion of slow reactions, which additionally has the potential to enhance yields. The removal of excess chemicals can be accomplished with simple washing, eliminating the requirement for extra purification procedures such as...