Methylations Rerick Final GM - Baran Lab

Baran Group Meeting1/09/2020The Magic Methyl: Methylations in Drug DiscoveryAlex RerickMethylated DrugsOf the top 200 pharmaceutical products by retail sales in 2018, over 73% ofthe small-molecule drugs contain at least one methyl group,“The methyl group, so often considered as chemically inert, isable to alter deeply the pharmacological properties of amolecule.”-Camille WermuthMe2NThe earliest recorded use of methanol is from the ancient Egyptians whoused it in their embalming processMe Ambien (zolpidem)insomnia treatmentONIn 1661, Robert Boyle isolated and described methanol, distilling it fromthe bark of Boxwood treesH 2NMeNNJean-Baptiste Dumas and Eugene Peligot determined the chemicalstructure of methanol in 1834MeNDumas and Peligot formed the word “methylene” during their attempt todescribe methanol.Methylene came from the Greek methy (wine) and hȳlē (wood) to mean“alcohol from wood” but they misused the term hȳlē which translatesmore closesly to “forest.” The proper term would have been xylo.Nonetheless, in the 1840s, the word “methyl” was derived from their term“methylene”NH2OHMeSOHpenicilin VSheehan, 1957 isOOMe OHOHNH2MeOHvitamin B1Cline 1936MeOHOthienamycinMerck, 1980MeMeHHHHOHOtestosteroneJohnson, 1955OOOOcarpanoneChapman, 1971NNSHZyprexa (olanzapine)antipsychotic medicationNH2MeNHMeMeL-methanphetaminenasal decongestantMeMeNamenda (memantine)dementia treamentOverviewDisclaimer: This is certianly not a comprehensive review ofmethylative methods.Topics Not Covered- N-, S-, or O-methylations- Methylations from activated C-X bonds, including cross-couplings- Installation of “hidden” methyl groupsMethyl effects are not: homologation or esterification / etherificationNNOSMeMeOHOHAdderall (amphetamine)ADHD and narcolepsy treatment1. Methyl Effects on Drug Efficacy2. Hot Spots for Methyl Effects2. Biological Methylation3. Synthetic Methods: sp2, sp3, and sp C-H Methylations4. Late Stage MethylationsMethylated Natural ProductsHNMeORelevant LiteratureMethyl Effects in Med Chem: Chem. Rev. 2011, 111, 5215; Angew. Chem.Int. Ed. 2013, 52, 12256Methyl Effects on Protein-Ligand Binding: J. Med. Chem. 2012, 55, 4489Transition [M]-catalyzed Methylations: Adv. Synth. Catal. 2015, 357, 1333Peroxides as Methylating Reagents: Synthesis 2016, 48, 329Radical SAM-mediated Methylations: J. Bio. Chem. 2015, 290, 7, 3995Late Stage Functionalization: Chem. Soc. Rev., 2016, 45, 546Removal/Modification of Directing Groups in C-H FunctionalizationChemistry: Org. Biomol. Chem. 2021, Advance ArticleBorrowing Hydrogen Catalysis: Chem. Rev. 2018, 118, 14101

Baran Group Meeting1/09/2020The Magic Methyl: Methylations in Drug DiscoveryAlex RerickA single methyl can impart dramatic effects on biological activityMeOOFClFNN 200-fold increasein efficacyNO2NNNMeHNMeMeHNMeNNNNOMeClOClMe 480-fold increasein efficacy 150-fold increasein efficacy590-fold increasein efficacy(compared to des-methyl drug targets)Ligand-Lipophilicity Efficiency (LLE) can be incredibly favorable for methyl, as it adds little lipophilicity while (potentially) having profound effects onpotencyCompare to CF3, which may increase potency, but deleteriously affects lipophilicity and therefore impacts a drug candidate’s ADME (absorption, distribution,metabolism, and excretion) while methyl is less likely to negatively impact ADME factors- This dramamtic effect is extremely rare, but it can be so profoundly impactful that it is often worth testing potential methyl “hot spots” on the molecule,especially if the analogues are easily accesibleAngew. Chem. Int. Ed. 2013, 52, 12256ONHNHOMeMeMeNHNHDNA and RNA bases onlydiffer by one methyl impacting transcriptionand replication due toDNA conformationMeAmino acids differing by one MeNH2OValineMeMeMeHONH2OLeucineCommon methylation tactic to increase efficacyof prostagladinsOOHONH2ROIsoleucineHOHOMeR CH2CH2CH3OONH2Prostaglandin endoperoxide synthases (PGHS) convert arachadonic acidSCysZnto prostagladinsSNThis difference in hinderance allows for the development of selectiveNNAD NSAIDsCysHOPGHS-2PGHS-1ONInhibition of PGHS-2 is primarilyHHNNresponsible for the analgesicProstaglandinMeMeHOeffect of NSAIDs, as thesedehydrogenases oxidize thereceptors synthesizeC-16 alcoholOOOprostaglandins responsible forhydrophobicTyr385mediating pain, fever, andpocket is nowOpocketinflammationOMeMe sterically hinderedBlocking PGHS-1 causesMeHO MeMeMeunwanted gastrointestinalmisoprostolside effectsinhibits gastric secretionMeHOHOHONH2Celebrex (celecoxib) is a PGHS-2NH2selective NSAID, brought to theMethylation at C-16 blocks hydride transfer leading to [O] and thusOOmarket in 1999increases the drug’s half-life and reduces side effectsIle5232Val523

Baran Group Meeting1/09/2020The Magic Methyl: Methylations in Drug DiscoveryAlex RerickThe Methyl Behind the CurtainMethyl induces high energy barrier between atropisomersIt’s Not Magic, It’s Just .MeChange in Desolvation EnergyDiazepamNDue to its slight increase in lipophilicity (ΔclogP 0.55 per methyl),methylation lowers the free energy of solvation in hexadecaneWhen transferring a solvent exposed drug to a hydrophobic proteinpocket, there is an energy benefit, measured as ΔGtransHONHNClMeOHN17.6 kcal/mol ClHactive conformerrecognized bybenzodiazepam receptorsProton to methyl replacement has a benefit of ΔΔGtrans 0.7 kcal/molinactive drugMethylene hydrogens have a coupling constant of 14.0 Hzchromone12Antagonist of Adenosine A2a ReceptorMeO33-fold better binding affinity thandesmethylated drug leadThe methyl displaces a high energywater molecule from the active siteDesdimethyldiazepam has a low barrier of rotation(methylene hydrogens are present as a singlet in 1H NMR)OOEffect on Drug MetabolismNMeMeOSOcocaineMeOMeMeNNHIn Silico Pharmacol. 2013, 1, 23Me Xylocaine (lidocaine)Productive Change in ConformationLidocaine, an antiarrhythmic drug and anesthetic, was iteratively designedLock molecule into conformation that more closely resembles itsfrom cocaineconformation when bound to a protein, lowering the reorganization energyProcainamide, an earlier derivative, is active but metabolized quickly in vivoMethyls on lidocaine twist arene out of plane and this increased steric bulkFprevents it from binding to plasmatic amidases which hydrolyze amideMebondsMeClNN(No magic methyl effect)NOFFNNFFOOONNN NN NFFNFRMeMeCelebra (celecoxib)H 2NH 2NR H 9 nM0.2 nMSSMeSC-236R Me 96 nMantiinflammatory drugMeO OO ONotably, cis orientation of the substituents has deleterious effect onSC-236 has a half life of 117 h as the chlorine protected metabolism byefficacy compared to desmethylated drug leadP450sChemMedChem 2012, 7, 415A methyl group provided the needed lipophilicity in the C-4 position on theJ. Med. Chem. 2012, 55, 44893Bioorg. Med. Chem. Lett. 2009, 19, 2997 arene for proper selectivity while, reducing the half-life to 17 hNNHprocainamideMeMe

Hot Spots for Magic Methyl EffectsVeliparib9-fold increase in potencyMethyl group thought to impart favorableMepharmacokineticsAbbVie is developing as an anti-cancer drugwhich prevents cancer cells from repairing byNNHinhibiting polymerasesHNH2O1. Ortho to Large substituentsHNNGleevec (imatinib)4-fold increase in potencyMeTreatment for chronic myeloid leukemiaNNHNNNMethyl group increased binding in theAbl1 kinase pocketMeCrystallographicdatashows that imatinib more closeslyOresembles the conformation of the bound drug than thedes-methyl derivativeOα-p38 MAP kinase inhibitor 200-fold increase in efficacyBlocks pathways to inflammatory responsesMeNHMe 595-fold increase in potencyMeDisplays anti-cancer activity byinhibiting isoprenylcysteinecarboxyl methyltransferase (ICMT)3. Between Freely Rotating BondsHO2. On Substitued RingsOF3CAnacetrapibChloesteryl ester transfer protein inhibitor toreduce HDL cholesterol levels6-fold increase in efficacyF CCompound displayed favorable ADME 3parametersAdvanced to phase 3 clinical trials at Merck,but failed in 2017J. Med. Chem. 2011, 54, 4880N MeMeOOMeMeNHOMeZocor (simvastatin)desmethyl: lovastatinSimvastatin is one of the most prescribeddrugs in the world, used to treat highcholesterol 2.5-fold increase in potencyMethyl thought to fill lipophilic pocket inactive site and potentially slow hydrolysis ofester, increasing half-lifeMeMeH 2NTreatment of coronary artery disease byinhibiting secreted phospholipase A2Des-methyl drug lead had negative drug-druginteractions when administered with statinsSteric bulk reduced off-target binding andyielded a 70-fold increase in efficacyCurrently being developed by AstraZenecaMeF3COMeMeOMeNOMe MeNCF3MeOOONHOJ. Med. Chem. 2011, 54, 5031Ortho methylation changes the dihedral angle of the biphenylsystem, lowering the preorganization energyThe methyl group also fills a lipophilic pocket in the binding siteF3COBaran Group Meeting1/09/2020The Magic Methyl: Methylations in Drug DiscoveryAlex RerickNOMeCO2HAZD2716PhACS Med. Chem. Lett. 2016, 7, 884NHMeCO2HMeibufenac, the desmethyl derivative, was also marketed asOHOHMean NSAID but was taken off the market in 1967 forWay-260022hepatotoxicity (damage to liver cells)Orginal drug target was metabolized to free amine and had low efficacyIbuprofenThe methyl on Ibuprofen slows the metabolism of theDimethylation increased metabolic stabilitydrug, increasing its half-life from 1.1 h to 4 hPfizer is developing as treatment for regulation of blood vessel constriction and4as a norepinephrine reputake inhibitorBioorg. Med. Chem. Lett. 2018, 28, 3283

Primary Methyl Donors in Biological SystemsS-Adenosylmethionine“A Natural Methyl Iodide”5-methyltertrahydrofolateH 2ONH3SAHhydrolaseOOCSSAM is a cofactor in the C-H methylation of many sp3 and sp2 bonds,including the bleomycin family of antiobiotics, thiostrepton, and nosiheptideamong other antiobiotics, as well as uctetrahydrofolateOOCNH3S-adenosyl nineNH3MeNNCysRS MeHRNMe SAHMeO3 equivalents of SAM are used toproduce caffeine from adenine,the 3 methyl groups make it aparticularly strong CNS stimulantFeOCysSFeFe SFeSSFeH2NOadenineOO MeOHOHMeCys5′-dA Cys5′-dA will then act as a hydrogen abstractor on the substrate to be methylatedThe second equivalent of SAM will then be attacked by the newly formed radical,homolytically cleaving the Me-S bondChem. Rev. 2014, 114, 8, 4229Acc. Chem. Res. 2012, 45, 4, 555hopane methylation requiring two equivalents of SAMSAM is vital to the biosynthesis ofethylene in plants, a crucial signalingmoleculeSAM methylates cytosine to 5-methylcytosine in DNA methylationSAM is implicated in cyclopropanations, including in jawsaymicin biosynthesisChem. Rev. 2011, 111, 5215FEBS Lett. 2001, 499, 50FeOFe SFeSS2 CysSN MeNNCysMe SH2N1 RNOHOHMe SRO MeNadenineOATP, H2OHOH OHS-Adenosylmethionine(SAM)NMeThe first equivalent of SAM undergoes a redox event using radical SAM (RS)enzymes, where redox active 4Fe/4S1 clusters cleave SAM to 5′-deoxyadenosyl5′-radical (5′-dA )NH2ROHOThese C-H methylations consume two equivalents of SAMSPi, PPiRBaran Group Meeting1/09/2020The Magic Methyl: Methylations in Drug DiscoveryAlex RerickPNAS 2010, 107, 19, 8537J. Biol. Chem. 2015, 290, 7, 3995HHMeMeHHMeHR SAMSAMMeMeMeHMe MePNAS 2010, 107, 19, 8537MeHmethionine5′-dAHSAHHRMeMeHMe Me5