The Use of Combinatorial Chemistry in Organic Chemistry

Introduction

In before, progression of drug discovery was not very efficient because the process of synthesizing a molecule in traditional method was time consuming and costly and only one molecule could be synthesized at each time [1]. Therefore, combinatorial chemistry, a new technique in pharmaceutical industries is greatly applied to produce large number of varies compound with similar structures from a set of building blocks at a time under same reaction conditions and they are organized as chemical libraries [2]. This method was first found at late 1980s by Mario Geyson’s study about the peptide synthesis on solid supports and followed by Bruce Merrifield who won the Nobel Prize for his study about the solid-phase synthesis [3]. This technique also allowed this large population of molecules to be screened in a biological test to identify the biologically active compound [2]. Generally, there are two types of combinatorial chemistry including solid phase synthesis and solution phase synthesis which both of them showed different production methodologies and applied in drug discovery and drug design [4].

Solid phase synthesis

In solid phase synthesis, the compounds are typically synthesized on a solid support [3]. The solid support must be chemical inert to every reagent and have the ability to swell to allow permeation of reagents to the binding site in the resin during reaction [4]. The most common used solid supports are polystyrene resin, polyacrylamide resins as well as glass and ceramic bead used for high temperature reaction [5]. The library of molecules produced is generally attached to the solid support with the aid of a linker [6]. A linker must remain stable under reaction conditions. Besides, the protecting groups are sometimes included during synthesis to avoid polymerization of unbounded molecules to the non-reactive side on the linker [7]. This type of synthesis can usually be done via split-and-mix synthesis or parallel unit synthesis methods [8].

Split-mix-synthesis

Split-and-mix synthesis aimed to produce large libraries of product and the resulting library is described as ‘one bead, one compound’ type [5]. The first step is preparing a solid-phase support such as polymer resin beads and attaches the compounds to polymer beads by reacting to the linker [2,8]. Then, the resin is split equally then coupled with one of the building block from the prepared reagents [2,8]. Each portion of resins are combined and mixed in a vessel after washing [2,8]. In the next step, the mixture of resins is divided into equally parts and treated with one of the building block from the other prepared reagents again in second reaction [2,8]. The steps can be repeated as many times as wanted thus resulting products obtained will be more and more and they are all categorized as a same library. As a result, it has an advantage of producing large libraries which can contain 103 to 105 compounds [1].

Parallel synthesis

This method of synthesis is quite similar to the split-and-mix synthesis. It can be used on either solution-phase or solid phase synthesis [8]. This synthesis starts by reacting the separated starting compound with one of the building blocks of reagent and then split into partitions [7]. Each partition of previous product is further reacted with one of the next incoming building blocks of different reagents [7]. The parallel synthesis is usually conducted by using huge numbers of vessel of tube that arranged in a parallel way [9]. The advantages of parallel synthesis are the structure of compounds in each vessel can be known at any time and the resulting products are pure because they are reacted independently [9].

Solution phase synthesis

Most of the organic syntheses are conducted in solution phase synthesis in which the reaction takes place in a solution by using a soluble support instead of solid support [7]. The common soluble supports used are linear polymers such as polyethylene glycol (PEG) and dendrimers [10]. Mishra et al. said PEG has the ability to present in either solid or liquid phase at room temperature and show varies solubility in aqueous and organic solvent, thus it is used in solution phase synthesis [4]. Sometimes, compounds that have fluorinated group are also used as one of the support due to its ability to partition selectively out of both aqueous and organic solutions [6]. The solution phase synthesis works by reacting the substrate with the mixture of several known building blocks in a mixture to get a pool of products with similar characteristics [6]. Parallel unit synthesis can also be applied in this synthesis to remove the problem of polymerization between the individual reagents when mixture of reagents is put into the solution [4]. The advantage of this type of synthesis is that no attachment or detachment steps onto the support required if compared to solid phase synthesis [11].

Screening

Since large numbers of molecules are produced from both solid and solution phase syntheses, a screening process was developed to test and identify the ‘useful’ or biologically active compound from those libraries [5]. The most common used screening type is high throughput screening (HTS) that could access the activity of a sample against a biological target and identify the active compound from it [2]. HTS is possible to screen 10 to 100 arrays of samples simultaneously and a screening of 100,000 assays per days is known as Ultra High Throughput Screening (UHTS) [12]. The libraries are usually set up in parallel assays by placing each bead into well of the microtiter plate and then screened to identify the most active compound [6]. Besides, the screenings can also apply the fluorescent assay technique by selecting the active compound based on their colours [13]. On the other sides, virtual screening is another one of the screening methods used in drug discovery by checking the activity of compounds based on the three-dimensional of the chemical structure [14]. Both HTS and virtual screening play an important role in pharmaceutical research because of their ability to screen a large scale of compounds simultaneously [15].

Encoding

Since there will be lots of active molecules chosen out from the libraries after screening, it is important to determine each molecule’s identity to prevent mix up by using encoding process [16]. In before, spatial encoding was the very earliest encoding method used but it was then taken over by more advanced encoding strategies due to its limitation in which only suitable for smaller libraries [16]. The examples of current encoding methods include positional encoding, chemical encoding and electronic encoding [7]. Positional encoding works by checking back to the synthesis process so that the identity of the compounds can be determined based on their physical position in the rack [17]. Apart from that, the chemical encoding only works for peptide type libraries. It starts by generating the large number of RNA sequence in a solution and passing the solution through an affinity column with ligands inside it, then the RNA sequence eluted will be identified [7, 16]. Lastly, an electronic encoding method use a device called a radiofrequency (rf) memory tag by attaching it to the synthetic platform where the synthesis occurred [17]. It is made up of a silicon chip that consist of unique codes, a rectifying circuit that converts the rf energy to electrical energy and an antenna that helps to transmit the code to the computer linked [16]. By reading the chips and analyzing the codes sent, the identity of library members can be determined [17].

Conclusion

Combinatorial chemistry is one of the most important fields that really beneficial in pharmaceutical and medical sector especially on the drug discovery application. It can impact these sectors by increasing the efficiency of research work and reducing the cost needed in drug research. It was because of the power of combinatorial methods that can create or diverse numerous chemical libraries such as peptides, oligomers, organic molecules and others in a time [18]. However, there are stills a lots of potential advancement which can be done in this area in terms of synthesis and screening. The scientists believe that the new and modern combinatorial chemistry may lead to huge discovery and development in next-generation drugs.

References

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