Combinatorial part (3) Dr.Asmaa (2).pptx

Al-Nahrain University /College Of Pharmacy Organic Pharmaceutical Chemistry IV 𝟏𝒔𝒕 semester - Fifth Stage Combinatorial Chemistry Part (3) Assistant lecturer. Asmaa Adnan Assistant lecturer. Kanar Muthana Department Of Pharmaceutical Chemistry Most ordinary synthetic chemistry takes place in sol...

Al-Nahrain University /College Of Pharmacy Organic Pharmaceutical Chemistry IV 𝟏𝒔𝒕 semester - Fifth Stage Combinatorial Chemistry Part (3) Assistant lecturer. Asmaa Adnan Assistant lecturer. Kanar Muthana Department Of Pharmaceutical Chemistry Most ordinary synthetic chemistry takes place in solution. When a reaction must be modified to accommodate a solid support, it takes time and resources to develop and optimize the reaction conditions. Many reactions cannot ever be run on solid supports because of poor yields or failed reactions.  For these reasons, there has been much interest in using solution-phase chemistry for the preparation of combinatorial libraries (development of Amazing-Mixture). Unlike one-bead which result in one-compound synthesis , solutionphase combinatorial chemistry often leads to a mixture of products.  Imagine reacting a set of 10 amines with 10 acid chlorides, all in one flask, and with the reactants and conditions chosen so that no reaction of amines with amines or chlorides with chlorides occurs, only reactions between amines and chlorides.  The result would be a mixture of 100 amides, one for each possible combination of amine and acid chloride.  The resulting mixture could then be tested for activity.  If activity is found, smaller subsets of amines and chlorides can be tested to eventually find the structure(s) responsible for activity.  The yields of products in such mixture-based experiments are often found to be about 90% or better.  Figure below shows an example of a four-component reaction that yields, after appropriate further transformation of the intermediate product, a mixture of carboxylic acids, esters, pyrroles, 1,4benzodiazepine-2,5-diones. • Difficulty of removing unwanted material. • Purification at each step is necessary. • Other practical problems. Comparison between solid phase and solution phase chemistry Comparison between solid phase and solution phase chemistry Soluble Polymers The difference between solid-phase chemistry and solution-phase chemistry is the use of soluble polymers as a support for the product in solution-phase chemistry . Types of soluble polymers: A. PEG: HO-𝐶𝐻2𝐶𝐻2O-[𝐶𝐻2𝐶𝐻2O-]n- 𝐶𝐻2𝐶𝐻2-OH • Each molecule of PEG has an OH group at either end. • It is a common vehicle in many pharmaceutical preparations. • Depending on the degree of polymerization. PEG can be liquid or solid at room temperature and show varying degrees of solubility in aqueous and organic solvents. B. Dendrimers: These are large, highly branched molecules with terminal amino groups that can be used like the OH groups of PEG for the attachment of products. Soluble Polymers C. Fluorous phases: are a form of "liquid Teflon," consisting mainly of long chains of (-𝐶𝐹2-) groups attached to a silicon atom. When these phases are used as a soluble support for synthesis, the resulting product can be readily separated from any organic solvents and reaction by-products by extracting the reaction mixture with fluorocarbon solvents. D. Complementary DNA as "support " Harvard researchers reported that we can "encourage" pairs of molecules in solution to react under mild conditions, by attaching short strands of complementary DNA or RNA to the structures to "zip" the structures together and promote reaction. Identification of structures from combinatorial synthesis 1- Recursive deconvolution • Method of identifying the active component in a mixture. • Quicker than separately synthesizing all possible components. • Need to retain samples before each mix and split stage. Example: Consider all 27 tripeptides synthesized by the mix and split strategy from glycine, alanine, and valine. • 9 Possible tripeptides in active mixture. • All end in valine. • Add valine to the three retained dipeptide mixtures. • Active component narrowed down to one of three possible tripeptides. • Synthesize each tripeptide and test. 2- Tagging  Method of identifying the structure present on a bead.  Tagging molecule is constructed on the same bead as the target molecule.  Use amino acids or nucleotides to construct the tagging molecule.  Each amino acid or nucleotide is used to indicate a specific reagent or reactant used at each step.  An amino acid or nucleotide is added after each step in the reaction sequence.  Peptide tag is identified using automatated peptide sequencing.  Oligonucleotide sequence is identified using DNA sequencing.  Require a linker with two functional groups (e.g. Safety- Catch- Acid- Labile SCAL linker). One example of a multiple linker is called the safety catch acid-labile linker ( SCAL ) ( Fig. 16.30 ), which includes lysine and tryptophan. Both these amino acids have a free amino group. The target structure is constructed on the amino group of the tryptophan moiety and, after each stage of the synthesis, a tagging amino acid is built on to the amino groups of the lysine moiety. Figure 16.31 illustrates the procedure for a synthesis involving three reagents, so that by the end of the process there is a tripeptide tag where each amino acid defines the identity of the variable groups R, R′, and R″ in the target structure. The non-peptide target structure can be cleaved by reducing the two sulphoxide groups in the safety catch linker, then treating with acid. Under these conditions, the tripeptide sequence remains attached to the bead and can be sequenced on the bead to identify the structure of the compound that was released. Example of Tagging 3- Bar coding • More Efficient method of tagging. • Use a bar coding or encryption method employing a triplet code. • For example, it is possible to identify which one of seven possible reagents has been used in the first stage of a synthesis with the use of only three molecular labels (A–C). This achieved by adding different combinations of the three tags to set up a triplet code on the bead. Thus, adding just one of the tags (A, B, or C) will allow the identification of three of the reagents. Adding two of the tags at the same time allows the identification of another three reagents and adding all three tags at the same time allows the identification of a seventh reagent. • Three different molecular tags (D-F) can be used for up to seven reagents used in the second stage of the synthesis. • Tags D-F are chosen to have a longer retention time on a gas chromatograph compared to tags A-C. • The bar code is then read from the chromatograph, not only identifying the reagents used, but the order in which they were used. •Tags are linked to bead by a photo cleavable bond. •Irradiation removes all the tags at the same time. •Mixture is passed through a gas chromatograph. •Tags are identified by their retention time. • Absence or presence of tags identifies reagents used at different stages of the synthesis. •Identifies the product (assuming reaction goes as predicted). AIM Planning and designing a compound library To generate a large number of compounds. To generate a diverse range of compounds. To increase the chances of finding a lead compound that will bind to a binding site. 1- Synthesis of scaffolds Scaffold: A term describing the core structure of a compound or series. The ideal scaffold should be: Small in order to allow a wide variation of substituents. It should also have its substituents widely dispersed around its structure (spider-like) rather than restricted to one part of the structure ( tadpole-like ). Finally, the synthesis should allow each of the substituents to be varied independently of each other. 1- Synthesis of scaffolds "Spider' scaffolds  In general, it is best to synthesize ‘spider-like’ molecules ( spider scaffolds ), socalled because they consist of a central body (called the centroid or scaffold ) from which various ‘arms’ (substituents) radiate ( Fig. 16.11 ). 1- Synthesis of scaffolds "Spider' scaffolds These arms contain different functional groups which are used to probe a binding site for binding regions once the spider-like molecule has entered ( Fig. 16.12 ). The chances of success are greater if the ‘arms’ are evenly spread around the scaffold, as this allows the exploration of the three-dimensional space ( conformational space ) around the molecule. The molecules made in the synthesis must contain different functional groups on their arms, placed at different distances from the central scaffold to increase the chance of having good pharmacological effect. 1- Synthesis of scaffolds Tadpole scaffolds • Variation restricted to a specific region round the molecule . • Less chance of favorable interactions with a binding site. 1- Synthesis of scaffolds "Spider' scaffolds Examples : 2- Designing ‘drug-like’ molecules The ‘spider-like’ approach increases the chances of finding a lead compound which will interact with a target binding site, but it is also worth remembering that compounds with good binding interactions do not necessarily make good medicines. There are also the pharmacokinetic issues to be taken into account, and so it is worthwhile introducing certain restrictions to the types of molecule that will be produced in order to increase the chances that the lead compound will be orally active. In general, the chances of oral activity are increased if the structure obeys Lipinski's rule of five . Target molecules should obey Lipinski's 'Rule of Five' for oral activity: Examp le : (Lipinski's 'Rule of Five for aspirin)