Advanced Medicinal Chemistry Lecture 2: Finding a Lead PDF

Advanced Medicinal Chemistry Lecture 2: Finding a Lead Dr Shaymaa Alnaqib  The Drug Discovery Process Target 3 months to Identification 2 years! HTS 3-4 months Active-to-Hit...

Advanced Medicinal Chemistry Lecture 2: Finding a Lead Dr Shaymaa Alnaqib  The Drug Discovery Process Target 3 months to Identification 2 years! HTS 3-4 months Active-to-Hit (AtH) 3 months Hit-to-Lead (HtL) 6-9 months New Lead Optimisation 2 years Projects (LO) Candidate Drug (CD)  Lead Compounds from a Variety of Sources R H N 1. Chance Discovery O N S penicillins O OH O O O 2. Natural Products NH O O O OH HO O OH H O O O taxol O O 3. Clinical Observation O HN N O O N 4. Natural Ligands N S N Viagra N O 5. Existing Drugs 6. High Throughput Screening (HTS)  Natural Ligands OH HO H N R=H adrenaline R HO R=Me noradrenaline Formoterol Salbutamol AstraZeneca GlaxoSmithKline OH H O H OH N H HO HN N HO HO O Catechol Increased size bioisostere (selectivity and duration) (toxicity) Catechol bioisostere Increased size (toxicity) (selectivity and duration)  Existing Drugs Also known as the “Me-Too” or “Me-Better” Approach Pfizer O Issues: short duration N O O HN N Multiple side effects and N S N Viagra incompatibility with other drugs N O BEWARE: Patent Issues!! Eli Lilly O N Bayer N N Cialis O H O O O HN N N S N N Levitra O N O O 36h duration (“the weekend pill”) Fewer side effects and incompatibility with other drugs  High Throughput Screening (HTS) “An industrialised process which brings together validated, tractable targets and chemical diversity to rapidly identify novel lead compounds for early phase drug discovery” 50-70% of new drug projects originate from a HTS How? validated, tractable targets target selection for HTS industrialised process HTS assay technologies and automation chemical diversity sample selection for HTS  Establishing a HTS validated/ tractable targets HT Screen target Development ID O human & pathogen O genomes Cl N chemical OH space compound selection compound collection Microtitre Plates – the HTS test tube For 200K data points: 96 384well plates 125 x 1536 300-100l 100-25l 9mm pitch 4.5mm pitch 384LV 1536 25-5l 10-1l 500 x 384 well plates 4.5mm pitch 2.25mm pitch 9mm 2000 x 96 well plates  Charnwood HTS Technologies; 1995-2001 SPA FLIPR Filter 30% 1% Fluorescence 4% Reporter 2% Yeast TR-FRET 1% 16% Alphascreen FP Screening can utilise numerous 19% 3% technologies e.g radioactivity, fluorescence, luminescence 24% None are universally applicable, each with advantages and disadvantages  High throughput radioligand binding assays Scintillation Proximity Assay – the first true homogeneous HTS screening technology Molecule too far away to activate bead Bound molecule I125 Nothing bound bead activated Molecule binds bead not activated, I 125 no light light produced Antibody/receptor I125 Molecule cannot bind I125 Suitable for I125, 3H, 33P  SPA (Scintillation Proximity Assay) First true homogeneous HTS technology Allows throughput of ~30K compounds/day in 384 format Easy to automate, no significant volume of aqueous waste BUT: Radioactive (safety headaches) Long read times (>30min/plate) Susceptible to quench artefacts Not applicable to all targets  FLIPR – a high throughput fluorimeter Fluorescent Imaging Plate Reader Real-time simultaneous imaging of 96- & 384-well plates Used for HTS Ca2+ flux assays and ion channel screening  FLIPR – how it works PC Cells loaded with fluorescent dye 96/384-Tip Pipettor sensitive to Ca2+ (fluo-3) CCD camera images base of Drawer Holding microtitre plate 5 Microplates Addition of receptor agonist stimulates Ca2+ release, resulting 6 W Argon Ion Laser in fluorescence increase Cooled CCD Camera Whole plate is read simultaneously, allowing kinetic analysis ‘Functional’ screen (i.e.whole cell) – greater relevance than simpler screening methods Throughput is 1000x greater than cuvette-based fluorimeter assay  Establishing a HTS validated/ tractable targets HT Screen target Development ID O human & pathogen O genomes Cl N chemical OH space compound selection compound collection  The AstraZeneca Compound Collection 1994 ASTRA ARCUS ASTRA PAIN CONTROL 1993 1999 Ca 9% compound overlap Not a recipe for an optimal screening bank  Compound Collection Enhancement AZ global initiative to boost screening collection – Target: ensure viable Hits from 75% of AZ HTS Five-year initial lifespan. Two concurrent themes… Acquisition Synthesis 300K from 107 available Nominal 500K over 5 years Target-class focus Stringent filters Aligned to Research Areas Big Medchem input Early Bioscience input Accept IP risks  CCE Structure HTS HTS Charnwood GPCR Kinase AP Charnwood Alderley Park ~60 Scientists Central Bioscience Med Chem Cheminformatics Bioscience Comp Chem Informatics Protease Channel Mölndal Compound Södertälje HTS Management HTS Mölndal AP US Chemistry deliberately embedded in Research Areas – Not centralised – Benefit of Project exposure – Feeds parallel synthesis skill back into projects  CCE – Library Chemistry Types of reactions amide coupling sulphonamide formation reductive amination 3 most commonly used reactions- aminopyrazoles Boronic acid coupling Amide coupling Multicomponent reaction (3 variants so far) imidazopyridines imidazothiazoles Sulphonamide arylation imidazopyrimidines Ester hydrolysis Reductive amination aminothiazoles Acyl sulphonamide formation aminooxadiazoles Urea formation Sulphonamide formation triazolopyrimidines Epoxide opening aminotriazoles Anhydride opening aminobenzimidazoles Condensation to form benzamidazoles triazolopyridines Mitsunobu pyrazolopyrimidine 3-aminoquinolines N-, O- and S-Alkylation triazolopyridazines Sulfonylurea formation triazolopyrazines benzoxazinone formation thiazolidin-4-one Pyridone formation 3-amino-1,2,4-triazoles tetrazole formation pyrimidin-2-ones Boc or t-butyl deprotection triazolo[1,5-c]quinazoline cyclization to heterocycles (21 types - see list) imidazolidin-2-one Nucleophilic aromatic substitutions (2 types) quinazolinone 1,2,4-oxadiazole  CCE – Common Combinatorial Reactions Amide Coupling O N PF6- 1 O HATU, Et 3N 1 N R H R 3 N + 3 N R N N N + 2 HO R 2 O R NMP R HATU N Sulphonamide Formation Et 3N O O O O R 1 H 1 R S 3 N NMP N S N R 2 + Cl R 3 2 O R NMP R Reductive Amination O Na(AcO)3BH 1 1 R H R 3 N 3 N R 2 + H R 2 R AcOH, NMP R  PF6- Mechanism PF - 6 + N + N O N O O Amide N N N O +H+ 3 +H+ R 1 3 HO R 3 N O R N R Coupling N -H+ -H+ R 2 1 R H N 2 R O O S O O 3 -H+ Sulphonamide Cl R 1 R S 1 N 3 R + N + R H H Cl 2 R Formation N 2 R + Na O O O O B O Reductive + H + H H O Amination -H+ OH -H2O O R 1 1 R 1 R 3 N + R 3 R 3 3 N N R H R R 2 R 2 2 1 R R H N 2 R