Combinatorial Chemistry PDF

Combinatorial Chemistry  Introduction: Combinatorial Chemistry is a new method developed by academics and researchers to reduce the time and cost of producing effective, marketable and competitive new drugs. Scientists use Combinatorial Chemistry to create large numbers of molecules that can be...

Combinatorial Chemistry  Introduction: Combinatorial Chemistry is a new method developed by academics and researchers to reduce the time and cost of producing effective, marketable and competitive new drugs. Scientists use Combinatorial Chemistry to create large numbers of molecules that can be detected efficiently. This technique has captured the attention of many areas such as Pharmaceutical chemistry, Biotechnology and Agro chemistry. Application: Applications of combinatorial chemistry are very wide Scientists use combinatorial chemistry to create large populations of molecules that can be screened efficiently. By producing larger, more diverse compound libraries, companies increase the probability that they will find novel compounds of significant therapeutic and commercial value. Advantages: Fast Combinatorial approach can give rise to million of compound in same time as it will take to produce one compound by traditional method of synthesis. Economical A negative result of mixture saves the effort of synthesis, purification & identification of each compound Easy Isolation purification & identification of active molecule from combinatorial library is relatively easy. Drug Discovery Mixed Combinatorial synthesis produces chemical pool. Probability of finding a molecule in a random screening process is proportional to the number of molecules subjected to the screening process Drug Optimization Parallel synthesis produces analogues with slight differences which is required for lead optimization Combinatorial Chemistry within drug design ( Impact at lead discovery traditionally lead drugs were found from natural products synthetic custom crafted organic molecules made in small numbers analogues of known actives (analogue me-toos) High Throughput screening (HTS) requires large numbers of compounds to fuel the discovery process As an alternative to traditional synthesis many compounds rapidly constructed was needed Tools: 1.Solid Phase Techniques 2.Parallel Synthesis 3.Mixed Combinatorial Synthesis 4.Solution phase synthesis 1. SOLID PHASE TECHNIQUES Reactants are bound to a polymeric surface and modified whilst still attached. Final product is released at the end of the synthesis solid-phase synthesis is a method in which molecules are covalently bound on a solid support material and synthesised step-by-step in a single reaction vessel utilising selective protecting group chemistry. 1. SOLID PHASE TECHNIQUES Requirements A resin bead or a functionalised surface to act as a solid support(made of polymer like polystyrene ) An anchor or linker A bond linking the substrate to the linker. The bond must be stable to the reaction conditions used in the synthesis A means of cleaving the product from the linker at the end Protecting groups for functional groups not involved in the synthesis 1. SOLID PHASE TECHNIQUES Beads must be able to swell in the solvent used, and remain stable Most reactions occur in the bead interior Swelling Starting material, Resin bead reagents and solvent Linkers 1. SOLID PHASE TECHNIQUES Anchor or linker A molecular moiety which is covalently attached to the solid support, and which contains a reactive functional group Allows attachment of the first reactant The link must be stable to the reaction conditions in the synthesis but easily cleaved to release the final compound Different linkers are available depending on the functional group to be attached and the desired functional group on the product Resins are named to define the linker e.g. Merrifield, Wang, Rink Solid phase synthesis: protecting groups ▪ A few protecting groups used in solid phase synthesis. ▪ Foramines. Boc ( t-butoxycarbonyl ) Fmoc (9-fluorenylmetoxy carbonyl) Tmsec (2 [ trimethylsilyl ] ethoxycarbonyl) ▪ For carboxylic acids. TertBu ester(t-butyl ester) Fm ester(9-fluronyl methyl ester) Tmse ester(2 [trimethylsilyl] ethyl) 21 21 Merrifield resin for peptide synthesis (chloromethyl group) = resin bead Cl HO2C NHBoc O Deprotection + O R H NHBoc Linker R H HO2C NHBoc O O R2 H O O O NH2 coupling NH NHBoc R H R H H R2 O HF O Release from OH aa1aa2aa3 aan NH2 solid support HO2C aa1aa2aa3 aan NH2 Peptide equipment for Solid Phase Peptide Synthesis 2. Parallel Synthesis Aims: To use a standard synthetic route to produce a range of analogues, with a different analogue in each reaction vessel, tube or well The identity of each structure is known Useful for producing a range of analogues for SAR or drug optimisation 2. Parallel Synthesis 2.1 Houghton’s Tea Bag Procedure 22 Each tea bag contains beads and is labelled Separate reactions are carried out on each tea bag Combine tea bags for common reactions or work up procedures A single product is synthesised within each teabag Different products are formed in different teabags Economy of effort - e.g. combining tea bags for workups Cheap and possible for any lab Manual procedure and is not suitable for producing large quantities of different products 2. Parallel Synthesis Automated parallel synthesis Wells Automated synthesis are available with 42, 96 or 144 reaction vessels or wells Use beads or pins for solid phase support Reactions and work ups are carried out automatically Same synthetic route used for each vessel, but different reagents Different product obtained per vessel 3. Parallel Synthesis Automated parallel synthesis of all 27 tri peptides from 3 amino acids ETC 2. Parallel Synthesis Automated parallel synthesis of all 27 tripeptides from 3 amino acids 27 TRIPEPTIDES 27 VIALS 2. Parallel Synthesis 2.2 Automated parallel synthesis AUTOMATED SYNTHETIC MACHINES 3. Mixed Combinatorial Synthesis Aims To use a standard synthetic route to produce a large variety of different analogues where each reaction vessel or tube contains a mixture of products The identities of the structures in each vessel are not known with certainty Useful for finding a lead compound Capable of synthesising large numbers of compounds quickly Each mixture is tested for activity as the mixture Inactive mixtures are stored in combinatorial libraries Active mixtures are studied further to identify active component 3. Mixed Combinatorial Synthesis The Mix and Split Method Example - Synthesis of all possible dipeptides using 5 amino acids Standard methods would involve 25 separate syntheses Glycine (Gly) 25 separate Gly-Gly Ala-Gly Phe-Gly Val-Gly Ser-Gly Alanine (Ala) experiments Gly-Ala Ala-Ala Phe-Ala Val-Ala Ser-Ala Phenylalanine (Phe) Gly-Phe Ala-Phe Phe-Phe Val-Phe Ser-Phe Valine (Val) Gly-Val Ala-Val Phe-Val Val-Val Ser-Val Serine (Ser) Gly-Ser Ala-Ser Phe-Ser Val-Ser Ser-Ser Combinatorial procedure involves five separate syntheses using a mix and split strategy  + Gly Gly + Ala Ala Ala Phe + Phe Phe combine Val + Val Val Ser + Ser Ser Gly Split Ala Ala Ala Ala Ala Phe Phe Phe Phe Phe Val Val Val Val Val Ser Ser Ser Ser Ser Gly Gly Gly Gly Gly Gly Ala Phe Val Ser Ala Gly Ala Ala Ala Phe Ala Val Ala Ser Phe Gly Phe Ala Phe Phe Phe Val Phe Ser Val Gly Val Ala Val Phe Val Val Val Ser Ser Gly Ser Ala Ser Phe Ser Val Ser Ser Gly Gly Gly Ala Gly Phe Gly Val Gly Ser 3. Mixed Combinatorial Synthesis The Mix and Split Method Synthesis of all possible tri peptides using 3 amino acids 3. Mixed Combinatorial Synthesis The Mix and Split Method 3. Mixed Combinatorial Synthesis The Mix and Split Method 3. Mixed Combinatorial Synthesis The Mix and Split Method MIX 3. Mixed Combinatorial Synthesis The Mix and Split Method SPLIT 3. Mixed Combinatorial Synthesis The Mix and Split Method 3. Mixed Combinatorial Synthesis The Mix and Split Method 3. Mixed Combinatorial Synthesis The Mix and Split Method 3. Mixed Combinatorial Synthesis The Mix and Split Method MIX 3. Mixed Combinatorial Synthesis The Mix and Split Method SPLIT 3. Mixed Combinatorial Synthesis The Mix and Split Method 3. Mixed Combinatorial Synthesis The Mix and Split Method 3. Mixed Combinatorial Synthesis The Mix and Split Method  3. Mixed Combinatorial Synthesis The Mix and Split Method No. of 9 9 9 Tripeptides  3. Mixed Combinatorial Synthesis The Mix and Split Method No. of 9 9 9 Tripeptides 27 Tripeptides 3 Vials 3. Mixed Combinatorial Synthesis The Mix and Split Method TEST MIXTURES FOR ACTIVITY 3. Mixed Combinatorial Synthesis The Mix and Split Method Synthesise each tripeptide and test 3. Mixed Combinatorial Synthesis The Mix and Split Method 20 AMINO ACIDS HEXAPEPTIDES etc. 34 MILLION PRODUCTS (1,889,568 hexapeptides / vial) Equipment for mixed combinatorial synthesis: 4.Solution phase synthesis solution phase synthesis is the synthesis of molecules primarily in solution (i.e., neither molecule is attached to a solid support during the reaction step) 5. Identification of structures from mixed combinatorial synthesis 5.1 Recursive Deconvolution: Method of identifying the active component in a mixture Quicker than separately synthesising all possible components Need to retain samples before each mix and split stage Example: Consider all 27 tripeptides synthesised by the mix and split strategy from glycine, alanine and valine  Gly Gly Ala Ala Val Val Mix and Split Gly Val Gly Val Gly Val Ala Ala Ala Gly Ala Val Gly Gly Gly Ala Gly Val Ala Gly Ala Ala Ala Val Val Gly Val Val Val Ala All possible di peptides in three vessels Retain a sample from each vessel  Gly Gly Gly Gly Gly Gly Gly Gly Ala Gly Ala Gly Ala Gly Ala Gly Val Gly Val Gly Val Gly Val Gly Gly Ala Gly Ala Gly Ala Gly Ala Ala Ala Ala Ala Ala Ala Ala Ala Val Ala Val Ala Val Ala Val Ala Gly Val Gly Val Gly Val Gly Val Ala Val Ala Val Ala Val Ala Val Val Val Val Val Val Val Val Val Mix and Gly Ala Val Split Gly Gly Gly Gly Gly Ala Gly Gly Val Ala Gly Gly Ala Gly Ala Ala Gly Val Val Gly Gly Val Gly Ala Val Gly Val Gly Ala Gly Gly Ala Ala Gly Ala Val Ala Ala Gly Ala Ala Ala Ala Ala Val Val Ala Gly Val Ala Ala Val Ala Val Gly Val Gly Gly Val Ala Gly Val Val Ala Val Gly Ala Val Ala Ala Val Val Val Val Gly Val Val Ala Val Val Val All possible tripeptides in three vessels 5. Identification of structures from mixed combinatorial synthesis 5.1 Recursive Deconvolution Gly Gly Gly Gly Gly Ala Gly Gly Val Ala Gly Gly Ala Gly Ala Ala Gly Val Val Gly Gly Val Gly Ala Val Gly Val Gly Ala Gly Gly Ala Ala Gly Ala Val Ala Ala Gly Ala Ala Ala Ala Ala Val Val Ala Gly Val Ala Ala Val Ala Val Gly Val Gly Gly Val Ala Gly Val Val Ala Val Gly Ala Val Ala Ala Val Val Val Val Gly Val Val Ala Val Val Val Mixture Mixture Mixture Inactive Inactive Active 9 Possible tripeptides in active mixture All end in valine Add valine to the three retained dipeptide mixtures 5. Identification of structures from mixed combinatorial synthesis 5.1 Recursive Deconvolution Gly Gly Gly Ala Gly Val Ala Gly Ala Ala Ala Val Val Gly Val Val Val Ala Val Val Val Gly Gly Val Gly Ala Val Gly Val Val Ala Gly Val Ala Ala Val Ala Val Val Val Gly Val Val Val Val Val Ala Val Active Active component narrowed down to one of three possible tripeptides Synthesise each tripeptide and test 5. Identification of structures from mixed combinatorial synthesis 5.2 Tagging: SCAL = Safety CAtch Linker H N H2N H O NH2 HN MeOS O NH H O Tryptophan SOMe HN O Lysine NH2 NH2 5.2 Tagging Example NH2 NH2 NH2 aa1 RCHBrCO2H amino acid(aa 1) R'NH2 NH2 NH R HN Step 1 Tag 1 NH R Step 2 O Br O Br NH2 NH2 NH2 aa2 aa2 aa1 aa1 aa1 HN HN HN amino acid(aa 2) R"COCl NH R NH R NH R Tag 2 Step 3 O NHR' O NHR' O NR'COR" aa3 NH2 aa2 amino acid(aa 3) aa1 HN Tag 3 NH R O NR'COR" 6. Identification of structures from combinatorial LIGHT synthesis LIGHT 6.2 Photolithography - example NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX MASK 1 Mask NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NH2 NH2 NH2 NHX NHX Deprotection CO2H NHX NH2 NH2 NHX NHX NHX NHX NHX NHX NHX coupling NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX NHX 6. Identification of structures from combinatorial synthesis 6.2 Photolithography - example Y Y Y Y repeat O O OMe Y fluorescent tag O 2N OMe Target receptor amino acids X= Nitroveratryloxycarbonyl 7. Planning a Combinatorial Synthesis 7.1 Aims To generate a large number of compounds To generate a diverse range of compounds Increase chances of finding a lead compound to fit a binding site Synthesis based on producing a molecular core or scaffold with functionality attached Centroid or scaffold Substituent 'arms' Binding groups 7. Planning a Combinatorial Syntheses 7.1 Aims Target molecules should obey Lipinski’s ‘Rule of Five’ for oral activity a molecular weight less than 500 a calculated log P value less than +5 no more than 5 H-bond donating groups no more than 10 H-bond accepting groups 7. Planning a Combinatorial Syntheses 7.2 Scaffolds ‘Spider’ scaffolds preferable for exploring conformational space Allows variation of functional groups around whole molecule to increase chances of finding suitable binding interactions Binding regions Screen compound library RECEPTOR BINDING SITE Molecular weight of scaffold should be low to allow variation of functionality, without getting products with a MWt > 500 7. Planning a Combinatorial Syntheses 7.2 Scaffolds Tadpole scaffolds - variation restricted to a specific region round the molecule - less chance of favourable interactions with a binding site 'Spider' Scaffold with 'Tadpole' scaffold with 'dispersed' substituents 'restricted' substituents Privileged scaffolds - scaffolds which are common in medicinal chemistry and which are associated with a diverse range of activities - benzodiazepines, hydantoins, benzenesulphonamide etc 7. Planning a Combinatorial Syntheses 7.2 Scaffolds - examples R" R O Me O N R4 O R2 R3 HO2C N R1 R4 R' R2 O N N N N X Ar R1 R2 O R5 R3 R3 R Benzodiazepines Hydantoins b-Lactams Pyridines R3 R4 O R5 Good scaffolds C N R1 O C N R6 Spider like O Low molecular weight R2 Variety of synthetic routes available Dipeptides 7. Planning a Combinatorial Syntheses 7.2 Scaffolds - poor examples OR5 Spider like and small molecular weight - good O R4O OR1 points R3O OR2 But multiple OH groups Glucose Difficult to vary R1-R5 independently Me Me M.Wt. relatively high Restricts no. of functional groups to keep MWt.< R1CO 500 R2 Relatively few positions where substituents Steroid easily added O R3 Tadpole like scaffold H2N R2 Restricted region of N R variability Indole