Download Plants Examples with Historical Background in Medicinal Chemistry | CHEM 4000 and more Study notes Chemistry in PDF only on Docsity! CHAPTER 1: HISTORICAL BACKGROUND Plant Examples Ch’ang shang: roots of Dichroa febrifuga…treat fever in China Ma huang: stems of Ephedra sinica…treat cough, asthma in China Squill: bulb of Urginea maritimai…used as diuretic, cardiac tonic in Egypt Autumn crocus: Colchicum autumnale…treat joint pain in Egypt Ourari: vines of Chododendrum tomentosum…used in hunting as paralytic in S. America Coca: leaves of Erythroxylon coca…used as euphoric in Inca Opium poppy: Papaver somniferum…treat pain in Sumer, Egypt, Greece, China White Willow: bark of Salix alba…treat inflammation in Greece, Sumer, Assyria, America Common foxglove: preparation of Digitalis purpurea…”dropsy” taxol: bark of Taxus brevifolia…treats tumors Isolation of Pure Compounds important isolations o 1805: Serturner - morphine from poppy o 1820: Pelletier - colchicines from Autumn crocus o 1839: salicylic acid from White willow o 1855: Gaedcke - cocaine from Coca o 1885: Nagai - ephedrine from Ma huang isolation of an alkaloid o powder the plant, extract w/benzene & Na2CO3 (amine in organic phase) o extract benzene w/dilute HCl (amine in aqueous phase, protonated) o extract aqueous layer w/CHCl3 & K2CO3 (amine in organic phase, free base) o evaporate CHCl3, recrystallize as oxalate salt Semi-Synthesis o common reaction: alcohol to acetate ester morphine heroin (more lipophilic, much more addictive) salicylic acid acetylsalicylic acid (aspirin) (less irritating to stomach) Structure Identification o advances in spectroscopy during 1900s o analog synthesis (advances in synthetic tech) making complex natural products o advances in biochem protein structure, DNA structure, allows for targeting o understanding of specific interaction with macromolecular target (mechanisms) o degradation of natural products into smaller pieces led to structure identification morphine, burning and identifying from elemental analysis, long & tedious! natural products include: codeine & thebaine o modern methods include NMR, IR, MS, x-ray (more efficient) taxol, isolated from Taxus brevifolia Total Synthesis from small, commercially available precursor allows for preparation of analogs from various points in process can be racemic or enantioselective (usually only one enantiomer is active) ephedrine synthesis o Nagai achieved racemic mixture in 3 steps o Hildebrandt achieved enantiopure in 2 steps (enzymatic process!) morphine synthesis is now far more efficient, achieving enantiopurity Mechanism of Action Work Ehrlich introduced “side-chain” theory, explained toxin-antitoxin interactions o concept of “magic bullet” to target specific bacteria led to first synthetic drug! o side-chain theory developed into concept of receptor for poisons or drugs o first synthetic drug: salvarsan (treats syphilis), toxic but has antibacterial properties Langley stated that the drug interacts with a “specific receptive substance” o observed antagonist action of atropine (speeds) and pilocarpine (slows) pilocarpine: derived from Pilocarpus shrubs, muscarinic agonist atropine: derived from Atropa belladonna, muscarinic AchR antagonist Clark quantified drug action (dose response) Ahlquist distinguished between α and β subtypes of adrenoceptor (different receptor types) 1970s: isolation of specific receptors Enzyme History Kuhne proposed “enzyme” term to describe fermentation of sugar to alcohol Buchner named “zymase” to be the enzyme responsible Fischer propsed “lock and key” hypothesis to describe enzyme/substrate interaction Phillips obtained first x-ray of lysozyme o x-ray structure collection is easier to perform on enzymes than receptors due to size Drug Discovery begin with “hit” or “lead” identification early lead sources o natural sources o natural ligands o compound libraries o literature o clinical observations lead modification (to make a drug) o structure-activity relationships (SAR)…Which parts are important for binding? o modify lead to maintain pharmacophore, improve activity, reduce toxicity o increase/decrease side chains, use bioisosteres o modify the core structure drugs from folk medicines o morphine meperidine (Demerol) o cocaine procaine (novocaine) o tubocurarine pancuronium ephedrine modification o analogs include: amphetamine, mathamphetamine, fenfluramine, methylphenidate (Ritalin) o act at adrenoceptor (mimic adrenaline aka epinephrine) CHAPTER 3: DRUG DISCOVERY-LEAD MODIFICATION reasons to perform lead modification improve intrinsic activity o in vitro screening (IC50) tells you binding affinity to substrate (inhibitory concentration) o in vivo screening (ED50) tells you defined activity in animal model (effective dose) improve pharmacokinetics (ADME studies) o absorption o distribution o metabolism o elimination reduce toxicity o LD50 tells you lethal dose in 50% of animals tested o therapeutic index (LD50 / ED50) should be high, toxic only at high concentrations allow for patentability maintain pharmacophore throughout o 3-D arrangement of functional groups required for binding o usually has 3-4 contact points with target o remainder of molecule is “scaffold” o example: somatostatin naturally occurring peptide hormone analog synthesized by Merck pharmacophore elements include: tryptophan (indole) and lysine (alkyl amine) side chains non-peptide analog: substituted β-D-glucose overlap of two essential side chains indicates promising drug potential o example: opioid pharmacophore consists of a ring structure and N with 2 alkyl groups is maintained throughout analogs of morphine drugs include: morphine codeine heroin levorphanol? pentacocine? meperidine (Demerol) Darvon methadone etorphine pharmacophore identification o determine relative importance of different functional groups in one congeneric series o important functional groups H-bond donors (OH, SH, NH) H-bond acceptors (C=O, NR3) ionic groups (CO-2, R4N+) aryl groups alkyl chains o hypothesize on correspondence to other series or compounds or to binding site model o methods include: classical SAR and molecular modeling classical SAR (structure-activity relationships) identify compounds with known activity, compare and identify common structural features, so all new compounds should have those features example: sulfanilamide antibacterials o 1935: discovered from azo dyes, lead: prontosil (red dye) o marketed sulfanilamide as elixir in ethylene glycol (“antifreeze”) o 1938: Food, Drug, and Cosmetic Act passed requiring proof of safety o act was modified in 1962 to include efficacy o pharmacophores include: p-amine-aryl-sulfonamide p-alkyl-aryl-sulfonylurea bicyclic aryl sulfonamide QSAR (quantitative SAR) mathematical relationship between structure and bioactivity biological properties are function of physicochemical parameters o electronic parameter Hammett constant () tells you about e-withdrawing property of substituent H = log (KX/KH), with subst. X and dissociation constant KH higher value indicates greater electron-withdrawal o lipophilicity partition coefficient (P) drug needs to cross cell membrane physical measurement with partition between 1-octanol & H2O P = [drug]oct/[drug]water low value indicates hydrophilicity high value indicates hydrophobicity optimum lipophilicity when C is concentration of dose log (1/C) = -k(logP)2 + k’(logP) + k” lipophilicity contant for substituent (π)) Hansch developed contants for various substituents π = logPX - logPH π) > 0, nonpolar substituent π) < 0, polar substituent o electronic & lipophilicity parameters are additive and constitutive additive means that they accumulate across the structure constitutive means they depend on the overall structure o substituent size (sterics) drug needs to approach target and fit into active or binding site Verloop parameters calculate size of substituent (STERIMOL) L = length along bond axis from parent B1 - B4 = width perpendicular to axis QSAR equations o Hansch analysis linear multiple regression analysis relates biological activity to physicochemical parameters from congeneric series (C=concentration of drug to give specific activity log 1/C = -a π2 + b π + p + Ces + d o Free-Wilson/Additivity Method relates biological activity (BA) to effects of substituents (X) If a substituent is present, X=1; if absent, X=0 a = magnitude of substituent effect, = activity of parent BA = ΣaaiXi + o 3D-QSAR (computer-assisted drug design or CADD) direct CADD usually relies on x-ray crystal structure of drug/analog bound in enzyme co-crystallize drug with target study specific binding interactions and try to improve example: HIV protease inhibitor (ritonavir: Abbott) o function of HIV protease: cleaves Phe-Pro bond o x-ray structure is of aspartic protease homodimer with C2 symmetry o design based on C2 symmetry and known aspartic protease inhibitors o first series: symmetrical diamino alcohols drug fits into flap of drug when bound initial x-ray shows H-bonds to enzyme extension of chain allowed for better H-bonding further changes to improve pharmacokinetics led to ritonavir (1996) indirect CADD develop a model of the pharmacophore need a set of high-affinity ligands select pharmacophore elements model to identify low-energy conformers of ligands superimpose conformers, match elements to give model! example: D1 agonists o dopamine receptor has D1- and D2-like subtypes o goal was to develop low-energy conformers for D1 subtype o overlap of pharmacophore elements m- and p-hydroxyls, N, and β-C accessory ring substituent CoMFA (comparative molecular field analysis) identify set of compounds with common pharmacophore generate low-energy conformers superimpose 3D structures, match elements establish 3D grid around overlaid structures calculate steric and electronic fields for each compound in every grid point generate data table and perform partial least squares o determines minimal set of grid points to explain measured bioactivity generate 3D structure of steric field generate 3D structure of electronic field CHAPTER 4: DRUG DEVELOPMENT Pre-Clinical Development-prior to human testing drug discovery: lead discovery & modification efficacy patenting—concurrent with drug discovery o takes 2-5 years, gives exclusive right to sell drug for specified purpose for 20 years o types of patents: composition of matter: specific compounds needs to be novel, useful can file continuation-in-part by adding new compounds to series process: synthetic procedure covers method of manufacture method of use: can be old compounds with new use example: minoxidil Rogaine process development—large-scale synthesis o prepare kilogram quantities o modify original synthesis efficient (< 10 steps) cost-effective (reagents, intermediates) low toxicity of reagents pilot plant-compatible (avoid chromatography & liquid extraction) government-regulated FDA: follow cGMP protocols o regulates sanitation, storage, and testing of intermediates, packaging & labeling o subject to government inspection toxicology studies o genetic toxicity: check for mutagenicity (ex: Ames test) o acute to chronic in vivo establish safety and dose levels acute single dose: look for signs of toxicity (vomiting, diarrhea, death) range-finding 2-4 weeks of daily dosing to establish dose levels sub-chronic o 1-3 months of daily dosing chronic o 6-12 months of daily dosing long-term dosing (toxicity) o 18-24 months of daily dosing (carcinogenicity) reproductive toxicity (required after thalidomide) segment I: fertility, reproductive performance segment II: teratogenicity, embryo toxicity in early pregnancy segment III: late pregnancy, delivery, and lactation pharmacokinetics: ADME studies o parameters: bioavailability: amount of drug available to act = fraction of drug absorbed intact distribution: location of drug (blood, tissue) clearance: ability of body to eliminate drug through metabolism and elimination o ADME studies are done in several animal models absorption: determines bioavailability, concentration of drug in bloodstream plot time vs. plasma concentration (calculate AUC) oral bioavailability = (AUCoral/AUCIV)x100 half-life: time for half of drug to disappear (duration of action) process of absorption: o stomach (pH = 1-2), approx. 30-60 minutes o small intestine (pH = 5-7), approx. 4-6 hours (most drugs absorbed) o large intestine (pH = 8-8.5) o portal vein liver (first pass)…most metabolism occurs here o general circulation to target organs distribution: location of drug regulated by binding to plasma proteins and transport mechanisms o passive diffusion o active transport o facilitated diffusion metabolism: chemical changes to drug reactions carried out by nonspecific enzymes Phase I: functional group reactions on drug, usually stereospecific o oxidation…cytochrome P-450s o reduction…aldo-keto reductases o hydrolysis of esters & amides…esterases & proteases Phase II: conjugation to endogenous molecules o enzymes are conjugating enzymes or transferases o glucuronidation conjugation of glucuronic acid, nucleopphilic attack onto anomeric carbon of UDP-glucuronic acid o glutathione conjugation nucleophilic endogenous tripeptide o amino acid conjugation usually glutamate or glycine o N-acetylation o methylation elimination: how drug is cleared file IND (investigational new drug) Clinical Development-human testing Phase I: safety o 20-100 healthy volunteers, usually young males o determine safety and dosing levels, human pharmacokinetics Phase II: dosing and efficacy o 500 patients o establish dosing and efficacy double-blind studies (one gets drug, other gets placebo) Phase III: long-term tolerance, verify efficacy o 1000s of patients o verify efficacy o long-term tolerance o interactions with other medicines o effect in children and the elderly file NDA (new drug application) example: development of imatinib (Gleevec) o see powerpoint notes for explanation CHAPTER 5: RECEPTORS receptor = macromolecular complexes that span cell membranes (proteins) exception is for nuclear receptors (intracellular) function: transfer message from outside to inside of cell Receptor Classes: G Protein-Coupled Receptors (GPCRs) nuclear receptors Ligand-Gated Ion Channels (LGICs) Voltage-Gated Ion Channels (VGICs) Receptor Mechanism: ligand carrying message binds causes conformational change in receptor message is transferred inside cell by effector system causes change in second messenger result is activation of enzyme or ion channel to give physiological result Components of Receptor System ligand: endogenous molecule or drug receptor: protein complex effector system: ion channels or G proteins second messengers: ions (Na+, K+, Cl-), cAMP, DAG, IP3 Ligands: natural or drug agonist: binds to receptor, causes some defined response partial agonist: binds to receptor, causes less than full response inverse agonist: binds to receptor, causes of defined response antagonist: binds to receptor, causes no response (blocks others from binding) o competitive antagonist: competes with agonist/ligand for binding (same site) o non-competitive antagonist: independent of agonist/ligand concentration (different site) Two-State Model of Receptor Occupancy o receptor exists in equilibrium between two states: relaxed (ON) and tense (OFF) o agonist binding shifts equilibrium to ON o antagonist binding shifts equilibrium to OFF o partial agonist has partial affinity for both states Receptor-Ligand terms: o affinity: ability of ligand to bind to receptor, proportional to binding constant o intrinsic activity: proportionality constant of ability of agonist to activate receptor in comparison to standard (defined as having maximum activity) o amino-terminal o DNA-binding (Zn finger, fits into major groove of DNA) o carboxy-terminal intracellular: upon binding to ligand domain, complex is transported into nucleus DNA binding results in protein production or suppression drugs: o agonists: estradiol o antagonists: raloxifene…treats breast cancer, osteoporosis tamoxifen…treats breast cancer Androgen Receptors o natural ligand: testosterone 5α-dihydrotestosterone o agonist: stanazolol o antagonist: flutamide o non-selective antagonists: cyproterone, spironolactone Hormone Receptors (tyrosine kinase-linked receptors) 3 domains: o extracellular o transmembrane o intracellular ligand binding causes dimerization and conformational change o intracellular domain autophosphorylates o results in phosphorylation of other proteins ligands: o insulin o growth factors protein tyrosine kinase inhibitors o imatinib (Gleevec)…treats CML (chronic myelogenous leukemia) binds at ATP binding site of bcr-abl kinase stabilizes active conformer CHAPTER 6: ENZYMES Enzymes proteins that recognize a substrate and catalyze a chemical reaction characteristics o substrate specificity (can be broad or specific) o reaction specificity (catalyzes only one type of reaction) o acceleration (rate may be 1010 – 1012 vs. uncatalyzed reaction) binding interactions: o covalent o noncovalent o stereochemistry transition state stabilization o enzyme binds the substrate most tightly at the transition state Enzyme Mechanisms approximation: enzyme is template to bring substrate close to active site covalent catalysis: nucleophilic amino acid side chain forms bond to substrate o serine (OH) o cysteine (SH) o lysine (NH2) general acid-base catalysis: proton transfers to increase nucleophilicity of side chain o aspartic acid o glutamic acid o histidine o serine o lysine electrostatic catalysis/desolvation o desolvation exposes charged groups at active site, stabilize charged transition state strain/distortion: raises ground state energy to lower the activation energy Reasons for Enzyme Inhibition diseases arise from excess or deficiency of enzymatic product o vasoconstriction—excess of angiotensin II (inhibit ACE) o Alzheimer’s disease—deficiency of acetylcholine (inhibit acetycholinesterase) foreign organisms have unique enzymes o HIV virus—HIV protease o bacteria—dehydropteroate synthase (folic acid biosynthesis pathway) Drawbacks to Enzyme Inhibition inhibiting enzymes needed for metabolic pathways o NSAIDS: inhibit cyclooxygenase—prostaglandin biosynthesis desired effect: inhibit inflammation caused by prostaglandins undesired effect: inhibit protection of gastric mucosa by prostaglandins Types of Inhibitors Reversible o competitive: bind at active site o non-competitive: bind at allosteric site reduce substrate binding by conformational change to substrate binding site Irreversible o affinity labeling agents o mechanism-based inactivators (suicide inhibitors) determine reversible/irreversible based on drug kinetics o competitive: Vmax is eventually reached by increasing substrate concentration o non-competitive: Vmax is never reached by increasing substrate concentration Reversible, Competitive Inhibitors sulfanilamide antibacterials o discovered in 1935 from azo dyes o lead: prontosil (red dye) o active against Gram-positive bacteria o bacteriostatic o inhibit dihydropteroate synthase (DHP) o drugs: sulfamethoxazole: inhibit DHP trimethoprim: inhibits dihyrdofolate reductase combined with sulfametoxazole (Bactrim) dapsone: inhibits DHP…treats mycobacteria (M. leprae, M. tuberculosis) ACE inhibitors o inhibit last step in renin-angiotensin cascade cleavage of Phe-His bond in angiotensin I (10 AA) to form angiotensin II (8 AA) o angiotensin II causes vasoconstriction, release of aldosterone, degrades bradykinin o discovery captopril (1981) enalapril [prodrug converted to enaliprat in vivo] lisinopril o design: natural product: peptides from snake venom, have C-terminal proline x-ray was unknown, but it was known to be like carboxypeptidase A known inhibitor was (R)-2-benzylsuccinic acid C-terminal proline Zn binding group (SH or COOH) hydrophobic pockets (methyl and/pr benzyl) CHAPTER 7: DNA AS A DRUG TARGET DNA Function replication: copied to form identical daughters transcription: copied to form RNA (5’ – 3’ direction) translation: decoded on ribosomes to direct protein biosynthesis DNA Structure two strands of nucleotide polymers oriented antiparallel in a double helix A/T (adenine/thymine) form 2 H-bonds C/G (cytosine/guanine) form 3 H-bonds aromatic (planar) bases on inside sugar-phosphate backbone on outside supercoiling occurs o interconversion mediated by topoisomerase Drug Binding Sites A/T or C/G pairs in center sugar-phosphate backbone on outside major and minor grooves nucleophilic sites on base pairs o guanine: N7 < O6 o adenine: N1 < N3 o cytosine: N3 Drugs Directly Interacting with DNA DNA alkylators o nitrogen mustards derived from sulfur mustards drugs: cyclophosphamide o metabolized to form phosphoramide mustard chlorambucil (Leukaran)…treat Hodgkin’s & Non-Hodgkin’s lymphoma, chronic lymphocytic leukemia melphalan (Alkeran)…treats multiple myeloma & ovarian cancer o N-nitrosoureas methylate DNA yields diazonium ion o platins drugs: cisplatin carboplatin oxaliplatin DNA intercalators o planar aromatic compounds o bind by π) stacking between base pairs o secondary H-bonding and electrostatic interactions with backbone o unwinds DNA at binding site, interferes with binding of DNA enzymes o important enzymes: DNA topoisomerase (supercoiling) Topo II involves cleavage and resealing of strands via cleavable complex some drugs bind to DNA-Topo II complex result is lethal double-strand breaks DNA polymerase (elongation of strand) intercalation can block progression along DNA strand some drugs act as antimetabolites and bind to enzyme o drugs: o dactinomycin (actinomycins) binds DNA at transcription initiation complex prevents chain elongation by RNA polymerase o daunomycin, adriamycin (anthracyclines) inhibits topoisomerase o aminophenoxazone (prefers guanines) o cyclic peptides (minor groove), carcinogenic-not widely used o daunorubicin DNA intercalator/strand breakers o structural features: intercalating region, reactive region o cleave backbone via radical mechanism o drugs: bleomycin glycopeptide, couples to copper before being transported into cell exhanges copper for iron bisthiazole region intercalates iron complex binds oxygen, generates radicals at backbone calicheamycin (enediynes) Drugs Interacting with Enzymes DNA Processing Enzymes o DNA/RNA polymerase inhibitors catalyzes formation of phosphodiester bond nucleoside is phosphorylated by kinases at 5’ position drug: Ara-C: mimic nucleoside (arabinose analog of cytidine) o topoisomerase inhibitors forms transient breaks in DNA strand to allow one strand to pass through another binds to DNA, forms covalent bond to 3’-phosphate—forms cleavable complex helix unwinds and 5’ – 3’ bond is re-formed drugs: o Topo I inhibitors: camptothecins camptothecin topotecan irinotecan o Topo poisons etoposide analogs—analogs of podophyllotoxin epimers at 4’ position stabilize Topo II-DNA complex glycoside, C & D rings w/DNA; A, B, &, E rings w/enzyme drugs: etoposide teniposide o methyl transferase inhibitors methylates 5’ position of cytidines (methylation pattern is involved in expression drug: 5-azacytidines DNA Synthesis Enzymes o thymidylate synthase inhibitors converts deoxyuridine to deoxythymidine Cys146 adds to dump, resulting enolate adds to CH2 of N5-N10- methylenetetrahydrofolate, removal of αH inactivates enzyme drugs: 5-fluorouracil prodrugs of 5-fluorouracil: o Tegafur o capecitabine o dihydrofolate reducase inhibitors drugs: methotrexate: analog of folic acid, N-methyl analog of aminopterin o inhibits formation of N5-N10-methylenetetrahydrofolate o treats leukemia raltitrexed (Tomudex)…treats colorectal cancer premetrexed (Alimta)…treats lung cancer Drugs Affecting Microtubules microtubules are components of the cytoskeleton o involved in mitosis o polymers of α- and β-tubulin o dynamic instability assembly and disassembly at ends of microtubules drugs binding to microtubules affect this polymerization/depolymerization process o binding sites: CHAPTER 8: ANTIVIRALS Drugs Affecting Virus Attachment & Budding fusion inhibitors o HIV drugs enfuvirtide (T20) miraviroc (Selzentry) neuraminidase inhibitors o influenza drugs substrate: sialic acid oseltamivir (Tamiflu): orally administered zanamivir (Relenza): nasal spray Drugs Affecting Virus Uncoating disoxaril & analogs o lead: arildone o rimantidine…treats Influenza A o pleconaril…treats enterovirus & rhinovirus o amantidine Drugs Affecting Transcription nucleosides (traditional): prodrugs phosphorylated by viral or cellular kinases; triphosphate acts as anti-metabolite, then drug is incorporated into DNA/RNA o ribavirin (Virazole)…guanine analog w/modified base…treats RSV o acyclovir (Zovirax)…guanine analog w/acyclic deoxyribose…treats HSV & VSV o gancyclovir (Cytovene)…guanine analog w/ acyclic deoxyribose…treats CMV o entecavir o lobucavir…treats HSV, VZV, CMV, HIV (in humans) o abacavir…treats HIV, active against HIV reverse transcriptase non-nucleosides (NNRTIs) o nevirapine o efavirenz HIV Therapy HIV reverse transcriptase inhibitors o nucleosides azidothymidine (AZT) dideoxyinosine (ddI) dideoxycytosine (ddC) lamivudine (3TC) abacavir o non-nucleosides (NNRTIs) nevirapine…originally synthesized as a muscarinic antagonist efavirenz etravirine (Tibotec)…active against resistant strains of HIV-1 HIV protease inhibitors…based on C2 symmetry, peptidomimetics…HIV protease is an aspartic protease, so they also screened library for renin inhibitors o amprenavir (Agenerase) o nelfinavir (Viricept) o lopinavir o ritonavir o DuPont-Merck cyclic ureas HIV integrase inhibitors…cleaves two nucleotides from 3’ end of viral DNA and ligates viral DNA into host chromosomal DNA o raltegravir o elvitegravir o enfurvirtide (mimics as C-terminal segment of gp41 transmembrane segment of glycoprotein)…treats HIV-1 o miraviroc…antagonist for CCR5 CHAPTER 9: CENTRAL NERVOUS SYSTEM DRUGS Drugs for Alzheimer’s Disease (two approaches-cholinergic and amyloid) cholinergic approach-increase cholinergic function in remaining neurons o donepezil (Aricept)…acetylcholinesterase inhibitor o galantamine (Ramanyl)…acetylcholinesterase inhibitor o rivastigmine (Exelon)…acetylcholinesterase inhibitor o tacrine (Cognex)…acetylcholinesterase inhibitor, N-heptyl amide = Cogmine amyloid approach-affect plaques of β-amyloid protein o BACE1 inhibitors CoMentis Sunesis