Pharmacology Is the Study of Drugs and Their Action on the Body. a Drug Can Be Broadly Defined As Any Man-Made, Natural, Or Endo

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Pharmacology is the study of drugs and their action on the body. A drug can be broadly defined as any man-made, natural, or endogenous molecule which exerts a biochemical and/or physiological effect on the cell, tissue, organ, or organism. It is the study of the interactions that occur between a living organism and chemicals that affect normal or abnormal biochemical function. Any substance that has medicinal properties, is considered a pharmaceutical. Pharmacology encompasses drug composition and properties, synthesis and drug design, molecular and cellular mechanisms, organ/systems mechanisms, signal transduction/cellular communication, molecular diagnostics, interactions, toxicology, chemical biology, therapy, and medical applications and antipathogenic capabilities. 1

Medicinal chemistry encompasses synthetic organic chemistry and aspects of natural products and computational chemistry in close combination with chemical biology, enzymology and structural biology, together aiming at the discovery and development of new therapeutic agents. It involves chemical aspects of identification, and then systematic, thorough synthetic alteration of new chemical entities to make them suitable for therapeutic use. It includes understanding their structure-activity relationships (SAR). Pharmaceutical chemistry is focused on quality aspects of medicines and aims to assure fitness for purpose of medicinal products.

Medicinal chemistry interfaces biology and chemistry and is a highly interdisciplinary. It places organic, physical, and computational chemistry alongside biochemistry, molecular biology, pharmacognosy and pharmacology, toxicology and veterinary and human medicine. It also requires business aspects, including project management, statistics, and pharmaceutical business practices, systematically oversee altering identified chemical agents such that after pharmaceutical formulation, they are safe and efficacious, and therefore suitable for use in treatment of disease.

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Some of the things the body can do to a drug.

The two main areas of pharmacology are pharmacodynamics and pharmacokinetics.

Pharmacodynamics studyies the effects of the drug on biological systems. Pharmacodynamics examines the interactions of the chemicals with the biological receptors,

Pharmacokinetics studies the effects of biological systems on the drug. Pharmacokinetics examines the absorption, distribution, metabolism, and excretion (ADME) of chemicals from the biological systems.

Pharmacology is not synonymous with pharmacy.

Pharmacology, a biomedical science, deals with the research, discovery, and characterization of chemicals which show biological effects and the elucidation of cellular and organismal function in relation to these chemicals.

Pharmacy is a health services profession concerned with application of the principles learned from pharmacology in its clinical settings; whether it be in a dispensing or clinical care role. 3

Metabolism is a constant battle of life and death. Metabolism (Greek: "change") is the set of life‐ sustaining chemical transformations within the cells of living organisms. Three main purposes of metabolism are:

1. the conversion of food/fuel to energy to run cellular processes, 2. the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates, and 3. the elimination of nitrogenous wastes.

These enzyme‐catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells.

Metabolism is usually divided into two categories:

1. catabolism, the breaking down of organic matter, for example, by cellular respiration, and 2. anabolism, the building up of components of cells such as proteins, lipids, carbohydrates and nucleic acids. Usually, breaking down releases energy and building up consumes energy. 4

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http://www.nature.com/nrc/journal/v16/n10/full/nrc.2016.77.html

Reprogramming glucose metabolism in cancer: can it be exploited for cancer therapy? Nature Reviews Cancer Volume: 16, Pages:635–649 Year published:(2016) DOI:doi:10.1038/nrc.2016.77 Published online 16 September 2016

Chapter 1 - Drugs and drug targets: an overview Drug (Medicine) - a natural or artificial substance given to treat or prevent disease or to lessen pain, a substance other than food (?) that causes a physiological change in the body, use can be short term (acute problems) or regular (chronic problems) Drugs are classified in various ways. All drugs have some side effects and can possibly lead to addiction. Examples of various types of medicines Almost any chemical can 1 For the gastrointestinal tract (digestive system) affect a living organism. 2 For the cardiovascular system Any chemical that can 3 For the central nervous system affect the body is, in a 4 For pain and consciousness (analgesic drugs) sense, a "lead" compound. 5 For musculo-skeletal disorders The more we know how a 6 For the eye drug works (its mechanism 7 For the ear, nose and oropharynx of interaction) the better 8 For the respiratory system we can direct its usefulness 9 For endocrine problems and control its side effects. 10 For the reproductive system or urinary system 11 For contraception These are our 12 For obstetrics and gynecology biological 13 For the skin components. 14 For infections and infestations Each is incredibly 15 For the immune system complicated, 16 For allergic disorders separately and 17 For nutrition together (blood, 18 For neoplastic disorders (tumors, benign or malignant) nerves, lymph, 19 For diagnostics immunity, etc.) 20 For anesthesia 21 For euthanasia 6

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Anatomical Therapeutic Chemical Classification System (ATC) - assigns ATC code = an alphanumeric code that assigns a drug to a specific class. Code = jargon, language of experts, not a common language of everyday people. First level The first level of the code indicates the anatomical main group and consists of one letter. There are 14 main groups: A Alimentary tract and metabolism B Blood and blood forming organs O C03CA01 C Cardiovascular system HO D Dermatologicals G Genito-urinary system and sex hormones O H Systemic hormonal preparations, excluding sex hormones and insulins HN S NH J Antiinfectives for systemic use 2 L Antineoplastic and immunomodulating agents O M Musculo-skeletal system O N Nervous system Cl P Antiparasitic products, insecticides and repellents Furosemide (Lasix) used to treat fluid build- R Respiratory system up due to heart failure, liver scarring, or S Sensory organs kidney disease. It may also be used for the V Various treatment of high blood pressure. It has also Example: C Cardiovascular system been used to prevent and treat race horses for exercise-induced pulmonary hemorrhage. Second level The second level of the code indicates the therapeutic main group and consists of two digits. Example: C03 Diuretics Third level The third level of the code indicates the therapeutic/pharmacological subgroup and consists of one letter. Example: C03C High-ceiling diuretics Fourth level The fourth level of the code indicates the chemical/therapeutic/pharmacological subgroup and consists of one letter. Example: C03CA Sulfonamides Fifth level The fifth level of the code indicates the chemical substance and consists of two digits. Example: C03CA01 Furosemide 7

A: alimentary tract and metabolism We are like a big stack of donuts.

How can Food and something on Beverages go in the inside at the top and... really be something on the outside. Surface area outside = 20 m2, inside = 400 m2.

intestines

nutrients bacteria viruses fungi parasites

The intestinal epithelium is the layer of cells that forms the luminal surface or lining of both the small and large intestine (colon) of the gastrointestinal tract. It is composed of simple ...waste columnar epithelium. It has two important functions: absorbing products helpful substances and providing a barrier against harmful come out at substances. Our gut has trillions of bacteria (and other the end. microorganisms). 8

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C: cardiovascular system

Drugs can be differentiated by:

How they are administered - consumed (liquid or solid by stomach or intestines), dissolved under tongue or in eyes, injected, inhaled, absorbed (patch, cream or ointment), insufflation (snorted), rectally (as a suppository), vaginally

Sources – plants, whole or parts (herbs and spices from stems, leaves, flowers, roots) or extracted substances (about 70% of pharmaceutical drugs come from natural products), organic synthesis (vast topic), synthesis by microorganisms (alcohol by yeast, penicillins, cephlosporins, cyphamycins, cyclosporins by fungi = yeast/molds, etc.), toxins (snakes, spiders, frogs, insects, puffer fish, algae red tides, etc.), genetically modified bacteria or yeast (to synthesize human insulin), animals (bovine or porcine insulin, Premarin as Hormone Replacement Therapy from horse urine, blood thinning drug called ATryn, is made in the milk of genetically altered goats).

Often regulated into 3 categories:: over the counter (OTC) available in supermarkets without any restrictions, behind the counter (BTC) can be dispensed by a pharmacist without doctor's prescription prescription only medicine (POM) prescribed by licensed pharmacist (a doctor)

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Types of Shapes O C O carbon dioxide linear Shape and polarity control almost everything in chemistry F It can be simple and it can be complex BFboron trifluoride F trigonal planar O Simple shapes: sp, sp2, sp3 (C, N, O, S, P, etc.) P phosphate O O tetrahedral Simple polarity: ionic , polar (and H bonds) , dispersion O F (sugars, amino acids, fatty acids, nucleic acids) F F phosphorous P pentafluoride Complex shapes: infinite variety (molecules, polymers) F trigonal bipyramidal F Complex polarity: infinite variety F F F (carbohydrates, proteins, lipids, DNA & RNA) sulfur S hexafluoride F F octahedral F

H H H H H Types of Polarity C C O O H2 C H H H C H C C H3C O O H C C +2 -2 Na Cl Ba O H H H H3C H H H H3C H ionic ionic hydrogen bonding hydrogen bonding dispersion dispersion dispersion dipoles dipoles ethanol sodium chloride barium oxide methanal ethanal water forces forces forces methane ethene propene o o o o o o bp = 1413 C bp = 1923 C bp = -19 C bp = +20 C bp = +78 C bp = +100 C bp = -161oC bp = -104oC bp = -48oC o o o o o o mp = 801 C mp = 2000 C mp = -92 C mp = -123 C mp = -114 C mp = 0 C mp = -182oC mp = -169oC mp = -185oC  = ?  = ?  = 2.3 D  = 2.7 D  = 1.7 D  = 1.8 D  = 0 D  = 0 D  = 0.4 D 11

The acceptor binding region of vertebrate UGT proteins. Shown is an alignment of the acceptor binding region of the human UGT1 and UGT2 proteins. Comparisons were made among human, chimpanzee, rhesus monkey, baboon, dog, mouse, rat, chicken, and zebrafish.

Complex shapes: infinite variety (molecules, polymers)

Complex polarity: infinite variety (carbohydrates, proteins, lipids, DNA & RNA) (ionic, dipoles, H bonds, dispersion forces)

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Review Topics: Polarity and Shape control the chemistry. Full shells (or subshells) This is the goal.

n = 1 H Atomic attraction for electrons He (Where does polarity come from?) +1 +2 valence electrons = bonding electrons (attracted by Zeffective) core electrons = full inner shells that shield Ztotal Ztotal = 1 Ztotal = 2 shielding = 0 Attractions are stronger across a row because the effective nuclear charge is larger. shielding = 0 Zeffective = 1 Zeffective = 2 radius = 52 pm radius = 31 pm n = 2 Li Be B C N O F Ne

+3 +4 +5 +6 +7 +8 +9 +10

Z = 7 Z = 9 Z = 10 Ztotal = 3 Ztotal = 4 Ztotal = 5 Ztotal = 6 total Ztotal = 8 total total shielding = -2 shielding = -2 shielding = -2 shielding = -2 shielding = -2 shielding = -2 shielding = -2 shielding = -2 Z = 5 Z = 7 Z = 8 Zeffective = 1 Zeffective = 2 Zeffective = 3 Zeffective = 4 effective Zeffective = 6 effective effective radius = 167 pm radius = 112 pm radius = 87 pm radius = 67 pm radius = 56 pm radius = 48 pm radius = 42 pm radius = 38 pm n = 3 Na Cl Ar

Attractions arestronger up a column because the valence electrons +11 are closer to the same +17 +18 effective nuclear charge.

Ztotal = 11 Ztotal = 17 Ztotal = 18 shielding = -10 shielding = -10 shielding = -10 Zeffective = 1 Zeffective = 7 Zeffective = 8 radius = 190 pm radius = 79 pm radius = 71 pm K (243 pm) other Br (94 pm) Kr (88 pm) Cs (298 pm) radii other radii I (115 pm) Xe (108 pm) 13

nucleus Volume of electron cloud compared to volume of nucleus electron clouds 3 V re e 4 3 15 determine the ecore e = = (1.33)(3.14)(100,000) = 4 x 10 valence Vn 3 rn overall volume of atoms

p,n mass protons mp protons and neutrons = = 1800 mass electrons me 1 determine an atom's mass

p = protons = constant # that defines the element 1 n = neutrons = varies = defines the isotope e = electrons = varies, depending on bonding patterns associated term 100,000 if electrons = protons (same # of e's and p's) atom 5 feet if electrons < protons (deficiency of e's) cation vs. if electrons > protons (excess of e's) anion 100 miles

(eval) = valence electrons = The outermost layer of electrons, which determines the bonding patterns. The usual goal is to attain a noble gas configuration. This is accomplished by losing e's (forming cations) or gaining e's (forming anions) or sharing e's (covalent bonds)

(ecore) = core electrons = The innermost layer(s) of electrons (usually full shells or subshells). These e's are held too tightly for bonding (sharing) and not usually considered in the bonding picture. These e's cancel a portion of the nuclear charge (called shielding) so that the valence e's only see part of the nuclear charge, called Zeffective.

Zeffective = (# protons) - (core e's) = the effective nuclear charge. This is the net positive charge felt by the valence e's (bonding and lone pairs). Zeffective = same # as the column of the main group elements. 14

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Atoms (valence shell, Ztotal, core electrions = shielding, Zeffective)

H He shell = 1 1 Ztotal = +1 +2 core e- = 0 0 Zeffective = +1 +2

C N O F Ne

shell = 2 2 2 2 2 +9 +10 Ztotal = +6 +7 +8 core e- = 2 2 2 2 2 Zeffective = +4 +5 +6 +7 +8

Si P S Cl Ne

shell = 3 3 3 3 3 +17 +18 Ztotal = +14 +15 +16 core e- = 10 10 10 10 10 +8 Zeffective = +4 +5 +6 +7

Electronegativity,  (chi), is the property that indicates an atoms attraction for electrons in chemical bonds with other atoms. Approximate electronegativity values for some main group elements. (atoms in red have some biological significance) Group 1A Group 2A Group 3A Group 4A Group 5A Group 6A Group 7A Group 8A Z = +3 Zeff = +1 Zeff = +2 eff Zeff = +4 Zeff = +5 Zeff = +6 Zeff = +7 Zeff = +8 H = 2.2 V Cr Mn Fe He = none Li = 1.0 Be = 1.5 Co Ni Cu Zn B = 2.0 C = 2.5 N = 3.0 O = 3.5 F = 4.0 Ne = none Na = 0.9 Mg = 1.2 1 . 6 5 - 1 . 9 0 Al = 1.5 Si = 1.9 P = 2.2 S = 2.6 Cl = 3.2 Ar = none K = 0.8 Ca = 1.0 3d elements Ga = 1.6 Ge = 2.0 As = 2.2 Se = 2.5 Br = 3.0 Kr = 3.0 Rb = 0.8 Sr = 0.9 4d elements In = 1.8 Sn = 2.0 Sb = 2.0 Te = 2.1 I = 2.7 Xe = 2.6 Simplistic estimate of bond polarities using differences in electronegativity between two bonded atoms.

A B bond polarity based on  = A B   0.4 considered to be a pure covalent bond (non-polar) 0.4 <  < (1.4 - 2.0) considered to be a polar covalent bond (permanent charge imbalance) (1.4 - 2.0) <  considered to be an ionic bond (cations and anions)

Br Mg Br H F

 =    = H  Mg Br Rules can be F ambiguous.  =   = 1.8  =   = 1.8 o o TBP = 711 C TBP = 20 C (ionic salt) (molecular) o o CuI (TBP = 1290 C NH3 (TBP = -33 C 16

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1. Dispersion forces / van der Waals interactions / London forces (nonpolar attractions)

Dispersion forces are temporary fluctuations of negative electron clouds from one direction to another, relative to the less mobile and more massive positive nuclear charge. These fluctuations of electron density induce fleeting, weak dipole moments. Polarizability is the property that indicates how well this fluctuation of electron density can occur about an atom. In a nonpolar molecule the and are centered, on average. This would seem to indicate that in nonpolar molecules there is no polarity or attraction between molecules. So Dispersion Forces why do such substances and are not centered liquify and solidify? Why creating tempory polarity. aren't they always gases? Fast moving electrons shift position relative to slow moving nuclei, creating a + - + - temporary imbalance of charge, +Z +Z +Z +Z which induces a similar distortion of the electron clouds in neighbor structures +Z = nuclear protons Weak, fluctuating polar forces and a weak attraction for of attraction between molecules. = electron cloud neighbor molecules.

Periodic trends in polarizability, .

C NOF

Zeff = +4 Zeff = +5 Zeff = +6 Zeff = +7 F is like a marble.

Polarizability is larger with smaller Zeff Cl because the electrons are not held as Polarizability is tightly, so they are more easily greater because distortable. Zeff = +7 there is a weaker hold on the electrons because they are Features that increase polarizability: farther away from Br the same effective 1. smaller Zeff, favors C > N > O > F nuclear charge, so they aremore easily 2. valence electrons farther from the Zeff =+7 distortable. nucleus when Zeff is similar I > Br > Cl > F. I I is like a cotton ball.

Zeff = +7 18

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The halogen molecules are similar in shape and Phase at room temperature nonpolar. There is a smooth, increasing trend in both melting and boiling points. This is suggestive F2 = gas He = gas 250 of some factor increasing the forces of attraction Cl2 = gas Ne = gas between molecles of the halogen family as they get Br2 = liquid Ar = gas larger. The smooth trend in melting point is not 200 bp I2 = solid Kr = gas I2 typical, because it can vary so much with differences in shapes. The even change in melting points is 150 observed here because the halogen molecules all have a simililar, rigid shape. mp 100 X X Br2 A AA Temp.50 room temp  25oC (oC) A AA 0 1 atom vs. 2 atoms Cl2 -50 The Noble gas molecules are similar in shape and nonpolar. There is a smooth, increasing trend in -100 bp both melting and boiling points. This is suggestive mp of some factor increasing the forces of attraction -150 Xe between molecles of the halogen family as they get F Kr larger. The smooth trend in melting point is not 2 typical, because it can vary so much with differences -200 Ar in shapes. The even change in melting points is H2 observed here because the halogen molecules all -250 Ne have a similar, spherical shape. He -273 absolute zero = 0 K

Dispersion forces are cumulative, so when the contact surface area is larger, the interactions are stronger (because there are more of them). Higher molecular weight alkanes have more carbon atoms to interact than lower molecular weight alkanes (even though only similar weak dispersion forces are present in both).

Alkane boiling point Alkane boiling point From the examples above, you can see that even the weak methane, CH -162  tridecane, C H 235 dispersion forces of attraction become significant when a 4 13 28 large number of them are present. ethane, C2H6 -89 73 tetradecane, C14H30 254 propane, C3H8 -42 47 pentadecane, C15H32 271 butane, C4H10 0 42 hexadecane, C16H34 287 CH4 CH4 (x1) Larger molecules have more contact surface area pentane, C5H12 36 36 heptadecane, C17H36 302 hexane, C H 69 33 octadecane, C H 316 with neighbor molecules. 6 14 18 38 CH3CH2CH2CH2CH2CH3 Greater dispersion forces heptane, C H 98 29 7 16 nonadecane, C19H40 330 mean a higher boiling point. octane, C8H18 126 28 icosane, C20H42 343 CH3CH2CH2CH2CH2CH3 (x6) nonane, C9H20 151 25 henicosane, C21H44 356 decane, C10H22 174 23 doicosane, C22H46 369 CH CH CH CH CH CH CH CH CH CH CH CH undecane, C11H24 196 22 tricosane, C23H48 380 3 2 2 2 2 2 2 2 2 2 2 3 dodecane, C12H26 216 20 triacotane, C30H62 450 (x12) CH CH CH CH CH CH CH CH CH CH CH CH tetracotane, C40H82 563 3 2 2 2 2 2 2 2 2 2 2 3 350 Boiling Point o 300 Temp ( C) 250 Easy to compare 200 because they are all linear. 150 100 bp of water 50 0 mp of water -50 -100 -150

C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 Straight chain alkanes 20

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In alkane isomers (having the same number of atoms, CnH2n+2), more branching reduces contact with neighbor molecules and weakens the intermolecular forces of attraction. Linear alkanes have stronger forces of attraction than their branched isomers because they have a greater contact surface area with their neighbor molecules. Branches tend to push neighbor molecules away. The strength of these interactions falls off as the 6th power of distance. A structure twice as far away will only have 1/64 the attraction for its neighbor. CH H2 H2 H2 H H 3 6 2 2 reference H3C C CH3 H3C C C CH3 H C C C CH 1 = 1 3 3 1 distance bp = -42oC H3C C CH3 bp = -0.5oC o H 6 bp = -0.5 C 1 bp = -12oC = 1 2 64 More atoms increase the contact Less branching increases contact surface area with neighbor surface area with neighbor molecules (not isomers). molecules in these isomers.

150oC Stronger dispersion forces because of greater surface contact area in linear chain bp = +126 (higher bp). More efficient packing in lattice structure due to compact rigid shape bp = +106 100oC 100oC boiling point = closer contact mp = +101 (higher mp). Temp (oC) hot dog? T = 75oC your finger? 50oC

25oC room temp water

0oC 0oC freezing point boiling melting point far apart point larger ( no interaction) smaller energy -50oC energy mp = -57 solid lattice, fixed, liquid, mobile, gas, mobile, close positions close positions separated, PV=nRT 21

Hybridization explains the shapes we observe in organic and biochemistry. 3 2 sp sp sp sp2 sp sp2 H H H H H H H C C CC H C C H Ca Cb Ca H H H H H H H allene ethane ethene trigonal planar carbon atoms tetrahedral carbon atoms trigonal planar carbon atoms ethyne linear carbon atoms at the ends and a linear carbon atom in the middle HCH bond angles  109o HCH bond angles  120o (116o) o o o HCC bond angles = 180o HCC bond angles  109 CCH bond angles  120 (122 ) o HCaH bond angles  120 o HCaCb bond angles  120 o CaCbCa bond angles = 180

Lone pairs can occupy a similar space to a bonded atom. (Zeff(C) = +4, Zeff(N) = +5, Zeff(O) = +6) H H H H C N H H H H CN H C N Ca Cb N H H hydrogen cyanide H methanamine methanimine ethenimine

H H H C O CO C O H O C O H H methanol methanal carbon monoxide carbon dioxide Which electrons are held tighter, lone pair electrons or bonded electrons? 22

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Resonance occurs through parallel p orbitals and stabilizes positive charge, negative charge, free radicals and neutral conjugated pi systems. allylic carbocation enolate anion (2D and 3D structures) (2D and 3D structures) H H H H

H2C C CH CH H C C O 2 H2C C 2 2 H2C C O

H H H H H H H H CC CC CC CC H C H H C H H O H O H H

allylic free radical bezene resonance (2D and 3D structures) (2D and 3D structures) H H equivalent structures H2C C CH 2 H2C C CH2

H H H H H H H H CC CC C C C C H C H H C H H C C H H C C H H H CC CC

H H H H 23

2a. Dipole-dipole interactions (in between polarity) - Dipole moments are less than full charges and the bonds are very directional (not "omni"), so attractions for neighbor molecules are weaker than is found in ionic salts. However, polar molecules usually have stronger attractions than nonpolar molecules of similar size and shape. Boiling points are a better indication of the strength of attractions among neighbor molecules than melting points (when other factors are similar). A higher boiling point indicates stronger attractions. Molecular dipole moments are indicators of charge imbalance due to a difference in electronegativity , bond length and molecular shape.

nonpolar polar more polar H H H H C O O C electron proton o resonance Tbp = 84 C 0.208A C C C C H H H H H H H H versus  = 0.0 D  = 2.3 D = 1.0 Debye o bp = -104oC bp = -20 C  = (q)x(d) = dipole moment O o mp = -169oC mp = -92 C q = charge H O sol. = 400g/L d = distance C H2O sol. = 2.9mg/L 2 H H pK = NA pKa = 44 a bond CH3-X (D) d(pm) energy nonpolar H polar more polar CH3-F 1.85 138.5 461 H C N N CH -Cl 1.87 178.4 356 C C resonance 3 C C CH -Br 1.81 192.9 297 C H 3 H H H CH3-I 1.62 213.9 239  = 0.0 D versus o T = 107oC  = 2.98 D bp = -81 C bp o o bp = +26 C N mp = -84 C o C mp = -13 C H2O sol. = insoluble H H2O sol. = miscible pKa = 25 pKa = 9.2

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What is the effect of "R" groups? Do they make the molecule more polar, less polar or no different? Electron donation or electron withdrawal through sigma bonds is called an inductive effect.

N nonpolar H polar more polar C N C N H3C C resonance C C H C H C 3 versus 3 H3C H  = 0.78 D  = 3.92 D C o o o bp = -23 C Tbp = 104 C bp = +81 C C mp = -102oC mp=-46oC H3C H2O sol. = insoluble H2O sol. = miscible

O polar O polar O polar O O O resonance resonance resonance C C C C C C H3C H H C H H C CH H H H H 3 3 3 H3C CH3  = 2.3 D  = 2.68 D  = 2.91 D o bp = -20 C bp = +20oC bp = +56oC o mp = -92 C mp=-123oC mp = -94oC H2O sol. = 400g/L H2O sol. = very sol. H2O sol. = very sol.

Is the conclusion above consitent with the following observations? H H H CH H H C H C 3 H3C 3 3 H C H C C H3C C H C C 3 3 CO CO CO CO CH H H H H 3 CH3 H H3C H H H3C H3C kcal kcal kcal kcal G = 315 G = 270 G = 250 G = 230 pK = 17.1 mole mole mole mole pKa = 15.5 pKa = 15.9 a pKa = 19.2 25

2b. Hydrogen bonds - Hydrogen bonds represent a very special dipole-dipole interaction. Molecules that have this feature have even stronger attractions for neighbor molecules than normal polar bonds would suggest. Solvents that have an O-H or an N-H bond are called "protic solvents" and can both donate and accept hydrogen bonds (because they also have lone pairs of electrons). They generally have higher boiling points than similar sized structures without any "polarized hydrogen atoms". We call such interactions "hydrogen bonds". A molecule that has such a polarized hydrogen is classified as a hydrogen bond donor. A molecule that has a partial negatively charged region that can associate with such a hydrogen is classified as a hydrogen bond acceptor.

H accepts Hydrogen bonding holds the molecules more tightly O hydrogen to one another. This can be seen in higher boiling H bond points among similar structures where hydrogen H donates O H bonding is possible versus not possible. Many examples hydrogen below show this property. bond H O donates H hydrogen H H Cl donates O bond accepts hydrogen accepts hydrogen hydrogen H bond donates H accepts bond bond hydrogen hydrogen O H O bond bond H O H3C H3C C CCH3 C C C H H O H O H3C CH3 three hydrogen bonds in G-C base pair H two hydrogen bonds in A-T base pair H N O H N N N H O N N H N N DNA N H N N N DNA N N H O DNA N guanine adenine H cytosine thymine O DNA Which base pair binds more tightly, GC, AT or are they about the same? 26

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Provide an explanation for the different boiling points in each column. 4B 5B 6B 7B 8B o 100 H2O boiling points ( C) CH4 NH3 H2O HF He o bp = -164oC bp = -33oC bp = +100oC bp = +20oC bp = -269 C o 50 mp = -182oC mp = -78oC mp = 0oC mp = -84oC mp = -272 C Temp HF  = 0.0 D  = 1.42 D  = 1.80 D  = 1.86 D  = 0.0 D o ( C) H Te  = 0.3  = 0.8  = 1.2  = 1.8  = NA 0 2 SbH3 PH NH H2Se SiH4 3 H2S HCl Ne 3 HI o o o o bp = -112oC bp = -88 C bp = -60 C bp = -85 C bp = -246 C -50 o H S AsH3 o mp = -132oC o mp = -114 C mp = -249oC 2 SnH4 mp = -185 C mp = -82 C HCl HBr  = 0.0 D  = 1.0 D  = 1.0 D  = 0.0 D PH  = 0.0 D -100 3 GeH4  = 0.0  = 0.4  = 1.0  = NA  = 0.3 SiH AsH Ar 4 GeH4 3 H2Se HBr o o -150 bp = -88oC bp = -62oC bp = -41oC bp = -67 C bp = -185 C o CH Kr mp = -165oC mp = -111oC mp = -66oC mp = -87oC mp = -189 C 4 Ar  = 0.0 D  = 0.0 D  = ? D  = 0.8 D  = 0.0 D -200  = 0.2  = 0.0  = 0.4  = 0.8  = NA

SnH4 SbH3 H2Te HI Kr -250 Ne o o bp = -52oC bp = -17oC bp = -2oC bp=-35 C bp=-153 C He o o o mp = -51oC mp = -157oC mp = -146 C mp = -88 C mp = -49 C -300  = 0.0 D  = ? D  = 0.4 D  = 0.0 D  = 0.0 D row row  = 0.5  = NA row row  = 0.2  = 0.2  = 0.1 2 3 4 5

Column shifted down one row.

Offer explanations for the following observations.

H 2 H2 C O C H H C CH H3C CH3 3 3 H3C O  = 0.08 D  = 1.30 D  = 1.69 D o  = 20oC o o bp = -42 C bp = -22 C  = 100 C bp =+78oC o o mp = -188 C mp = -141 C mp = -114oC H2O sol. = 0.004 mg/L H O sol. = 71g/L 2 H2O sol. = miscible

H H2 2 H3C O CH3 H3C C O H3C C CH3 C C C C C C H H2 H2 H2 H2 H2 H2  = ? D  = 1.15 D  = 1.66 D o o o bp = +36 C  = -1oC bp =+35C  = 83oC bp =+118C mp = -130oC mp = -116oC mp = -90oC H2O sol.  0 mg/L H2O sol. = 69 g/L H2O sol. = 73 g/L

Perhaps, polarity is buried inside nonpolar covering. Holds back dispersion forces with neighbor molecules. 28

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The types of interactions between molecules depends on functional groups and solvation. Organic functional groups are mostly similar to biochemical functional groups.

O O O O O O

C H C C C R C R C R O R O R R O R S R Cl carboxylic acids anhydrides esters thioesters acid chlorides

O O O R C N C H H R N C C R H R R R O H nitriles aldehydes ketones alcohols amides (1o, 2o, 3o)

H R R R X N H R N R O R S X = F, Cl, Br, I R O R S H o o o thioethers halogen thiols amines (1 , 2 , 3 ) ethers sulfides compounds nitroso compounds

O H H There is chemical logic N for all of these functional C C R C C H groups. You have to N understand how they react R O R H to plan strategies in drug nitro compounds alkenes alkynes aromatic heteroaromatic design. 29

H H N O S N O S heterocycles are common in biochemistry and aziridine oxirane thiirane azetizine oxetane ethylene oxide episulfide thietane medicinal chemistry

H H H N O S N O S N O O N

N N pyrrolidine tetrahydrofurane tetrahydrothiophene pyrrole furane thiophene imidazole oxazole isoxazole (THF) H N N O O S S

piperidine pyridine tetrahydropyrane pyrane thiane thiopyrane H H 3 3 7 N N O O N N N N 4 4 2 2 8 5 N 1 N 1 N O O N 5 H O N 9 H 6 6 piperazine morpholine dioxane dioxane pyrazine pyrimidine purine

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Biochem structures are more like names of your classmates. Every one has to be learned individually. (* = chiral center). Stereochemistry is critical part of each structure. HO HO HO HO OH * * O * O * O HO O * * * * HO OH HO O OH * * * * * * * * * hemi-acetal * * HO OH HO OH HO OH HO OH aldose 4 acetal 2 stereoisomers pyranose 10 5 2 stereoisomers and 2 stereoisomers OH HO multiple ways to attach hemi-ketal * OH HO ketal OH O OH * O HO OH * O * * * OH O OH * * * HO * * * HO O * * HO OH * OH ketonse furanose * HO OH 3 4 2 stereoisomers 2 stereoisomers HO glycosides H H H 29 stereoisomers and 3 3 3 H N 4 multiple ways to attach N 4 9 N 9 H2N N 4 9 N 2 N N 1 2 2 5 8 8 8 2 N 1 N 1 HN 1 N N N 4 N steriods 5 6 5 7 5 6 7 6 7 3 hormones purine NH imidazole proteins 2 adenine O guanine fatty acids glycerides NH O 2 O R H neurotransmitters 4 and on and on... 3 5 C O N HN N HN H2N S C

2 6 OH N O O O N 1 N N amino acids H H H (20 essential, pyrimidine cytosine thymine uracil there are 100s of others) 31

aldehyde carbohydrates (3C, 4C, 5C, 6C, more?)

O O O H H H When the second to the last "OH" C C C R top is on the right side, biochemists CO2H achiral R refer to it as a "D" carbohydrate. H OH H OH HO H H OH Most carbohydrates in nature are H2N H D "D". Most amino acids, on the L H CH OH CH OH 2 CH2OH 2 other hand are "L" with a "NH " R glycoaldehyde 2 D-glyceraldehyde L-glyceraldehyde generic carbohydrate on the left side. generic amino acid O O O O H H H H C C C C Biochem names are all different. Organic names are easier. All of these are 2,3,4-trihydroxybutanal. R H OH HO H HO H H OH 1 = (2R,3R)-2,3,4-trihydroxybutanal R H OH HO H H OH HO H 2 = (2S,3S)-2,3,4-trihydroxybutanal 3 = (2S,3R)-2,3,4-trihydroxybutanal CH OH 2 CH2OH CH2OH CH2OH 4 = (2R,3S)-2,3,4-trihydroxybutanal D-erythrose L-erythrose D-threose L-threose O O O O O O O O H H H H H H H H C C C C C C C C R H OH HO H HO H H OH H OH HO H HO H H OH R H OH HO H H OH HO H HO H H OH HO H H OH R H OH HO H H OH HO H H OH HO H H OH HO H

CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH CH2OH D-ribose L-riboseD-arabinose L-arabinose D-xylose L-xylose D-lyxose L-lyxose

O O O O O O O O H H H H H H H H C C C C C C C C R H OH HO H HO H H OH H OH HO H H OH HO H R H OH HO H H OH HO H HO H H OH H OH HO H R H OH HO H H OH HO H H OH HO H HO H H OH R H OH HO H H OH HO H H OH HO H H OH HO H

CH OH CH OH CH OH CH OH 2 2 2 2 CH2OH CH2OH CH2OH CH2OH D-allose L-allose D-altrose L-altrose D-glucoseL-glucose D-gluose L-gluose

O O O O O O O O H H H H H H H H C C C C C C C C

HO H H OH H OH HO H HO H H OH HO H H OH

HO H H OH HO H H OH H OH HO H HO H H OH

H OH HO H HO H H OH HO H H OH HO H H OH

H OH HO H H OH HO H H OH HO H H OH HO H

CH OH CH OH CH OH CH OH 2 2 2 2 CH2OH CH2OH CH2OH CH2OH D-mannose L-mannose D-galactose L-galactose D-idoseL-idose D-talose L-talose 32

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Famous Drugs Psychoactive drugs - chemical substances that affect the function of the central nervous system, altering perception, mood or consciousness: ethanol (depressant: wine beer, hard liquor, chough medicines, etc.), nicotine (stimulant: cigarettes, cigars, pipes, patches, drops, etc.) and caffeine (stimulant, estimated used by 90% of the population: coffee, tea, chocolate, etc.) are the most widely consumed psychoactive drugs used worldwide and are also considered recreational drugs since they are used for other than medicinal purposes O CH3 H H 2 H3C N C N N H3C OH CH3 ethanol O N N N caffeine nicotine CH3

Other recreational drugs: hallucinogens (LSD), opiates (morphine, heroin) and amphetamines (phenethylamine has been used to treat ADHD, narcolepsy and obesity, methamphetamines), also use can be spiritual or religious (mescaline from peyote used by indigenous peoples for about 6,000 years, cannabis (THC = tetrahydrocanabinol) used for spiritual purposes for about 4,000 years) Lysergic acid diethylamide morphine phenethylamines mescaline (LSD) (and heroine) O NH HO (huge variety) 2 R2 R N O H R3 N O H * * RN * O H O * *  * R H * R4 R6 One Hundred Years of Solitude (1967) N N 7 generations of Buendia family in Columbia * * CH3 CH3 R5 features mescaline and ghosts H HO Gabriel García Márquez

Epinephrine, also known as adrenalin Methylphenidate HN * = chiral center OH (ritalin) H O O HO * N tetrahydrocanabinol * CH3 OH THC H CH N H 3 * * * HO * H H N O CH * 3 methamphetamine (racemic, free base) levomethamphetamine (weaker) and CH3 dextromethamphetamine (stronger)

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Therapeutic Index = toxic dose (50% of subjects) / effective dose (50% of subjects), a safe drug has a high number and a dangerous drug has a low number. Or, some define it as the safe amount of drug in the blood. Digoxin cardiac glycoside from foxglove plant: 0.8 to 2.0 ng/mL. Mainly used for atrial O fibrillation, atrial flutter, and heart failure, taken by mouth or by injection into a vein.[ O HO -9 C38H58O14 therapeutic amount = 2 x 10 g / mL = 3 x 10-12 moles / mL H Mol. Wt.: 738.86 = 8 x 10-5g / 40L

O O H OH complicated O medicine HO O O O H

HO HO HO -5 23 17 molecules (8x10 g / 40L)(1 mol/800g)(10 molecules/mol) = 1x10 molecules 1x103 molecules cell =  100,000,000,000,000 cells cell lithium citrate - used to treat bipolar depression O OH O Li lithium: 0.8 to 1.2 meq/L (toxic over 1.5 meq/L) C6H5O7Li3 Li -3 therapeutic amount = 1 x 10 meq Li / L Mol. Wt.: 201 O O = 0.33 x 10-3 mmoles salt / L O O = 2 g salt / 40L simple Li medicine older method

LD50 = lethal dose, 50% of subjects ED50 effective dose, 50% of subjects (2g / 40L)(1 mol/200g)(6x1023 molecules/mol)(3 Li/molec.) = 18x1021 molecules 2x107 Li+ Li+ =  cell 14 cell 100,000,000,000,000 cells ( 10 cells) 35

Water distribution in people is estimated to be 48 ±6% for females and 58 ±8% water for males (averages). Water constitutes as much as 73% of the body weight of a newborn infant. Body water and salt is regulated by hormones (anti‐diuretic hormone = ADH = vasopressin), aldosterone and atrila natriuretic peptide.

Body water can be broken down into the following compartments:

Intracellular fluid (about 2/3 of body water). Per Guyton: in a body containing 40 liters of fluid, about 25 liters is intracellular, which amounts to 62.5% (5/8), close to the 2/3 rule of thumb ( 6 gallons)

Extracellular fluid (1/3 of body water). Per Guyton: in a body containing 40 liters of fluid, about 15 liters is extracellular, which amounts to 37.5%, close to the 1/3 rule of thumb. ( 4 gallons, donate a pint in blood donation  1/32  3%)

Plasma (1/5 of extracellular fluid). Per Guyton: of the 15 liters of extracellular fluid, plasma volume averages 3 liters. Interstitial fluid (4/5 of extracellular fluid), transcellular fluid (a.k.a. "third space," normally ignored in calculations), inside organs, gastrointestinal, cerebrospinal, peritoneal and ocular fluids.

Estimates are for about 6 quarts of blood flow per minute, 83 gallons per hour and 2,000 gallons per day. Blood circulates through the body in about 1 minute. Video of blood flow: http://www.brainstuffshow.com/blog/how‐fast‐does‐blood‐flow‐ throughout‐the‐human‐body/ 36

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Pain relivers = analgesia, relief from pain. (many possibilities)

HO O H OH O

O O ibuprofen (MW = 206) Aspirin (MW = 180) (Advil, Motrin)

H OH N

O O O HO naproxen (MW = 230) acetaminophen (MW = 151) (Aleve, Naprosyn) (Tylenol)

Tylenol or paracetamol or acetaminophen or APAP - most commonly used medication for pain and fever H The good: It is used to treat pain and fever and appears to act centrally in the brain, rather than peripherally in nerve endings. It is often sold in N combination with other drugs (cold medications and opioid pain medications for cancer or after surgery). Its mechanism of action is not well understood. It is thought to inhibit COX enzymes (cyclooxygenase O 1 (has isoleucine at position 523 in active site) and cyclooxygenase 2 HO (has smaller Val523 there), 65% homologous and very similar active Tylenol (MW = 151) sites),which prevents metabolism of arachidonicacid to 'unstable' protaglandin H2, which is converted to pro-inflamatory compounds. It Toxic metabolite also may inhibit the uptake of anandamide, increasing concentrations of H endogenous cannabinoids, modulating pain pathways and lowering body temperature. It may also block synthesis of nitric oxide. The half N life in adults is about 3 hours, but is longer in infants, so the dose gets progressively lower the younger the patient.

Typical dose = 2 tablets = 625 mg = 0.625 g = 0.0041 mole = valine isoleucine 2.5 x 1021 molecules x 5 times/day = 1022 molec/day 22 14 H N H N CO # molecules/cell = 10 molec/10 cells = 100,000,000 molecs/cell 3 CO2 3 2 H H COX 2 COX 1

19 4/3/2017

Tylenol or paracetamol or acetaminophen or APAP - most commonly used medication for pain and fever H The good: It is used to treat pain and fever and appears to act centrally in the brain, rather than peripherally in nerve endings. It is often sold in N combination with other drugs (cold medications and opioid pain medications for cancer or after surgery). Its mechanism of action is not well understood. It is thought to inhibit COX enzymes (cyclooxygenase O 1 (has isoleucine at position 523 in active site) and cyclooxygenase 2 HO (has smaller Val523 there), 65% homologous and very similar active Tylenol (MW = 151) sites), which prevents metabolism of arachidonic acid to 'unstable' protaglandin H2, which is converted to pro-inflamatory compounds. It Toxic metabolite also may inhiinhibit the uptake of anandamide, inincreasining concentrations of H endogenous cannabinoids, modulating pain pathways and lowering body temperature. It may also block synthesis of nitric oxide. The half N life in adults is about 3 hours, but is longer in infants, so the dose gets progressively lower the younger the patient.

O The bad: Use at high dosages can cause liver failure. It is the most O common cause of liver failure in the US and UK. Damage to the liver, or hepatotoxicity, results not from acetaminophen itself, but from one N-acetyl-p-benzoquinoneimine of its metabolites, N-acetyl-p-benzoquinoneimine (NAPQI). which (NAPQI) depletes the liver's natural antioxidant glutathione and directly damages cells in the liver, leading to liver failure. COX 2 COX 1 valine-523 isoleucine-523 protein H N protein H N N C protein N C protein H H H H O O Typical dose = 2 tablets = 625 mg = 0.625 g = 0.0041 mole = 2.5 x 1021 molecules x 5 times/day = 1022 molec/day # molecules/cell = 1022 molec/1014 cells = 100,000,000 molecs/cell 39

We need this from our diet. 2 4 6 2 HO 4 6 O 1 3 5 HO 1 3 5 7 7

8 8 enzyme HO 1 3 5 O O 2 4 linoleic acid (LA) 9 enzyme reactions 6 reactions 9 (add 2 carbons) 18:2n-6 -linolenic acid (LA) dihomo--linolenic acid (LA) 7 (add a 20:3n-6 10 double bond) 18:3n-6 10 8 18 11 18 19 17 9 17 17 11 20 18 16 10 16 12 12 14 16 15 13 11 15 13 14 14 15 13 Our bodies 12 Linoleic acid is an essential, can do this as polyunsaturated fatty acid used in the enzyme part of our reactions biosynthesis of arachidonic acid (AA) O fatty acid O (add a and thus some prostaglandins, metabolism. double bond) leukotrienes (LTA, LTB, LTC), and HO N 1 3 5 thromboxane (TXA). It is found in the H 2 4 6 HO 1 3 5 lipids of cell membranes. It is 2 4 6 7 enzyme abundant in many nuts, fatty seeds and reactions arachidonic acid (AA) 7 8 their derived vegetable oils. It 20:4n-6 8 comprises over half (by weight) of 19 17 9 20 18 19 17 9 poppy seed, safflower, sunflower, 16 10 20 18 16 10 corn, and soybean oils. It must be 15 13 11 consumed for proper health. A diet 14 12 15 13 11 only deficient in linoleate (the salt 14 12 form of the acid) causes skin scaling, anandamide - fatty acid neurotransmitter and found hair loss, and poor wound healing in 9 enzyme as the natural receptor for  -THC compounds in O reactions rats cannabis (tetrahydrocannabinol in marijuana). R HO 1 3 5 8 2 4 6 oxygen R 9 R 9 O or 8 8 7 9 O O prostaglandin H2 9 P-450 O O 10 10 (blood clotting, immune response) 8 10 10 O O O R 11 12 12 20 12 R 11 R 11 18 16 14 11 19 17 15 13 12 prostaglandin H2 OH 40

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O https://en.wikipedia.org/wiki/Prostaglandin_H2

OH (prostaglandins are 20 carbon compounds that do many things, stop bleeding, part of immune PGJ2 response, cause inflammation, temperature control, etc.)

O OH

O O O

O OH OH OH HO HO HO

PGF2 6-keto-PGF12 PGD2

HO O HO OH OH OH

PGD synthase PGE 9-ketoreductase O O O

OH OH HO O

Prostaglandin H PGE Prostacyclin O 2 PGE2 O synthase PGI2 Synthase O

HO OH OH

HO OH Thromboxane O Synthase O O

OH OH OH O O

TXA 2 PGB2 PGA2 O

OH OH OH 41

How does acetaminophen cause liver damage? We need to look at some related biomolecules. You are not responsible for these mechanisms.

FAD / FADH2 - Flavin adenine dinucleotide (oxidation - reduction) - used to deliver hydride to C=C or take hydride from CH-CH (fatty acid metabolism, TCA cycle and electron transport chain in mitochondria) simplified structures for FAD and FADH2 H B R R R R

FAD - flavin dinucleotide H B R C C R (a hydride acceptor) C C N O H R R H H Hydride transfer hydride transfer N reduces FAD to N O O from FADH2. N FADH2. reduces C=C, R H makes FAD R R N N R C C R C C B H H R B R R FADH2 - flavin dinucleotide (a hydride donor) O O FAD - flavin dinucleotide O P O P O N (a hydride acceptor) O NH2 O O N HO actual OH structure N HO N OH OH R R N N O N N O N N O NH N NH resonance NH atypical nitrogen N N (electron poor) O O O only 6 e- 42

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Aldopentoses - 5 carbon aldehyde carbohydrates, naturally occuring carbohydrates tend to be D, 3 chiral centers leads to 23 = 8 possible stereoisomers (naturally occurring aminoacids tend to be L with "S" chirality) OH OH OH OH

* * * HO * O HO * * * * * * * O HO O HO * O OH OH OH OH OH OH OH OH D-arabinose D-lyxose D-ribose D-xylose O H O O H H O H S HO H S R R HO H H OH H OH R H OH S R S HO H H OH HO OH R R H OH R R H OH H OH H OH H C 2 H2C H C OH 2 H2C OH OH OH enantiomer enantiomer enantiomer enantiomer Ketopentoses - 5 carbon ketone carbohydrates, naturally occuring carbohydrates tend to be D, 2 chiral centers leads to 4 possible stereoisomers (naturally occurring aminoacids tend to be L with "S" chirality) OH OH NH2 * * * HO OH HO * OH 5-phosphate N N O OH O OH O D-ribulose D-xylulose O P O N N OH OH 5 adenosine O O can 4 1 rotate O O H H ribose here R S H 3 2 H H OH HO H OH OH R R adenosine monophosphate (AMP) H OH H OH

H C 2 H2C OH OH enantiomer enantiomer 43

Keto / Enol tautomerization is a common transformation, happens twice in glycolysis. * = chiral center D-glucose epimeric center ( / ) OH HO R S S R R S R S HO OH R S R S * OH S R R S * O R S R S R S S R * O HO R S R R HO * * * O HO OH S S R S HO OH HO OH * * * * * R S S R R S S R * * * * D-mannose R S S R S R R S D-glucose OH D-galactose OH R S R S S R S R S R R S R S R S 25 = 32 possible stereoisomers for cyclic aldohexoses H B D-mannose D-galactose H B H H HO O OH OH HO O OH HO O

enzyme enzyme H * * * * H H H OH O OH H O -2 B O OH O OH O -2H -2 O3P O P O P D-glucose-6-phosphate 3 B 3 endiol D-fructose-6-phosphate 24 = 16 possible stereoisomers

O O H B O

O P H B O P H P H O O O O O O O O O O enzyme enzyme H H H H H OH O O H B B D-glyceraldehyde-3-phosphate endiol dihydroxyacetonephosphate Most of life makes D carbohydrates, though some bacteria can make both kinds (self defense). 44

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NAD+ and NADP+ - nicotinamide adenine dinucleotide (hydride acceptor)

4 CONH2 NH2 5 3 Why is C N 4 N similar role in electrophilic? O O 6 = organic chem: 2 Jones, PCC, N 1 N H2C O P O P O CH2 N Swern oxidation O N OH R HO O O H H O simplified H H structure actual OH OH NADP+ has a structure phosphate here.

NADH and NADHP - nicotinamide adenine dinucleotide (hydride donor) H H4b H4a CONH2 NH2 H N similar role in N organic chem: Why is H4 = O O nucleophilic? NaBH4, LiAlH4 N H2C O P O P O CH2 N N O N OH HO O O H H R O H H OH OH NADPH has a phosphate here.

H B H B H B N O N O N O Transfers 2e-s and 2H, possibly as hydride and a NADH NADH N proton or in free NAD+ N radical transfers. reverse H FAD N FAD (simplified) H R N FADH2 (simplified) oxidized R N H R N oxidized H H (simplified) reduced H

O H B fatty acid catabolism - most reactions in biochemistry are under enzyme control H FAD O H B B fatty acid chain N BH O O H R acyl-CoA O mixed anhydride enzyme O high energy thioester N O R O ester O O hydrolysis H O H O R P ENZ-1 O O S O O O O R R H R H H OP OP OPO B triglyceride - fatty acid BH S ENZ-1 N ATP chains are often 16-18 O O O H carbons long B

acyl CoA N (2 carbons shorter, B cycle repeats) -ketothioester -hydroxythioester H FADH2 O B ,-unsaturated thioester BH ENZ-2 H O S H O O ENZ-1 R O O H ENZ-1 S ENZ-1 S NAD+ R BH S R H R O H H H H H H N R BH O ENZ-1 B S H NADH S ENZ-2 B H H CoA S N R B H H All of this is "Co-A" O O O O O HS O P O P O N CoA N N O NH S ENZ-1 S H H 2 O O N acetyl CoA - involved H OH in many biochemical Thiol esters form here. This is an acetyl group N cycles in the body actual N repeat O HO HS Co-A structure OH simplified Acetyl Co-A = modify DNA, histones: effects structure S CoA gene expression, glycolysis, TCA cycle, fat metabolism, many things. 46

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fatty acid structures saturated fatty acid chain (no C=C bonds) O O  12 10 8 6 4 2 O 11 9 7 5 3 1 1 R HO 3 5 7 9 11 Lauric acid, C12 O  4 6 8 10 12 dodecanoic acid O O

O R HO 1 3 5 7 Myristic acid, C O 9 11 13 14  4 6 8 10 12 14 tetradecanoic acid O R triglyceride - triester of glycerol HO 1 3 5 7 9 11 13 15 Palmitic acid, C16 O  4 6 8 10 12 14 16 hexadecanoic acid O O R Stearic acid, C O HO 1 3 5 7 9 11 13 15 17 18  4 6 8 10 12 14 16 18 octadecanoic acid O O  O  = D = double bond R 9 5 3 1 7 2 8 6 4 cis-9-Octadecenoic acid O P CH3 1 3 HO 5 7 9 10 12 14 16 18 Oleic acid, 18:1 cis-9  4 6 8 11 13 15 17 O CH  HO N 3 O  CH3 9 7 6 4 2 8 5 3 1 diglyceride - phosphatidyl choline HO 1 3 5 7 9 10 17 Linoleic acid, 18:2n-6  12 13 15 4 6 8 11 14 16 18 18:2 cis,cis-9,12  2 4 6 O 9 10 HO 1 3 5 oleic acid (LA) 7 18:1n-9 7 8 11 12 8 HO 1 3 5 O 6 2 4 6 5 13 14 linoleic acid (LA) 9 18:2n-6 arachidonic acid (AA) 7 4 15 20:4n-6 3 16 10 8 O 19 17 2 18 9 1 What came first in life? 17 18 17 11 20 18 amino acids proteins, 16 10 16 12 HO nuclotide bases RNA DNA, 14 15 13 11 fats & lipids membranes, 15 13 14 12 carbohydrates structure, energy, ...or some combination of all of these 47

Example of cytochrom P-450 oxidative enzymes, common in the liver, protoporphyrin, the iron sits in the middle of a complicated heme molecule. There are over 21,000 distinct P-450 enzymes known.

N +3 N Fe simplified structure, N +3 N N binds to enzyme N through a sulfur Fe enzyme, cysteine +3 N N Fe

S anchored to enzyme, All extraneous parts are left out to show only the iron HO2C hemoglobin uses Enz imidazole of histidine atom in an oxidized state. S CO2H H ready for oxidation reactions shown below Enz B (symbolic cytochrom P-450 enzymess)

The proteins are complicated and can hold iron‐heme complexes.

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Steps shown below in cytochrome P-450 oxidations (and next slide) 1. Ferric iron ion abstracts an electron from flavin mononucleotide (FADH2), an enzyme co-factor, and is reduced from +3 to +2. 2. Iron gives up an electron to make a bond with oxygen. (+2 to +3). Possible radical reactions with oxygen. 3. Oxygen atom abstracts an electron from flavin mononucleotide (FADH FAD), an enzyme co-factor. 4. FAD gets reduced by NADH (hydride donor) and picks up a proton to reform FADH2 5. The basic oxygen anion picks up a proton (or two?) from an acidic enzyme site. 6. A weak O-O bond breaks homolytically (hydroxyl radical) or heterolytically, and releases water. 7. An electron is supplied from iron to stabilize the oxidized oxygen atom. +3 to +4, which is now ready to oxidize bio-molecules. 1e- O O 1e- FADH O BH +3 2 O O Fe 1 O FADH possible +2 2 +3 3 Fe Fe +3 O Fe O +H+ 8, 9, 10 superoxide (see next) NAD+ NADH 5 4 FAD H O H 2 H BH heterolytic H O O O O reactive +3 8, 9, 10 O peroxide Fe (see next) +4 7 6 +3 Fe +3 Fe homolytic Fe Possible leakage of hydroxyl Every step represents a protein target for a radicals (extremely dangerous in the body), but also part of body's H medicine. Side effects occur when other O biochemical reactions are also affected. immune defense in all out warfare, collateral damage possible. 49

8. The free radical-like oxygen atom converts a C-H bond to an C-OH bond via free radical chemistry 9. The free radical-like oxygen atom converts a C=C bond to an epoxide via free radical chemistry Nature's magic tricks. 10. The free radical-like oxygen atom converts a N or S lone pair to an N-O or S-O bond. The iron is reduced back at Fe+3 to begin the process all over again.

8 sp3 C-H bonds alcohols

H C H O H C O O C hydrophobic hydrophilic becomes.... Fe +3 Fe Fe +4 +4 The free radical-like oxygen atom abstracts a hydrogen The carbon free radical abstracts hydroxyl(OH)from iron, atom from a C-H bond in the enzyme cavity, forming an making an C-OH bond where a C-H bond had been. The iron is O-H bond and a carbon free radical. reduced back at Fe+3 to begin the process all over again. R H hydrophilic 9 R B R R R OH R R O H R C R C C C R C CC C R R HO R O O O R R R Diols are much more alkenes or aromatics BH +3 water soluble, can be Fe +4 hydrophobic Fe +4 epoxides Fe eliminated from the body. becomes.... The free radical-like oxygen atom adds to a C=C The carbon free radical abstracts the oxygen atom from the iron, making an bond (alkene or aromatic) in the enzymecavity, epoxide ring.Theiron is reduced back at Fe+3 to begin the process all over forming a O-C bond and a carbon free radical. again. Reactive epoxides can be opened up to diols (more water soluble).

10 S O R S R O R O R N O sulfur +3 R/H substrate Fe S sulfur R R (1e-) R substrate R Fe +4 Fe +4 sulfoxides, further oxidation is N-oxides, further oxidation is (nitrogen too) -2 -1 possible, all the way to sulfate, SO4 possible, all the way to nitrate, NO3

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Toxicity of acetaminophen N-hydroxylation by cytochrome P-450 (too much acetaminophen uses up all the capacity of the enzyme to oxidize target molecules) H H H Fe +3 H O N O N O O H N O ( 20%) Fe +4 O Fe +4 HO HO acetaminophen O HO gluconidation sulfonation H conjugation conjugation ( 30%) ( 50%) H N Too much acetaminophen uses up the P-4450 oxidizing power BH N O of the liver. Other compounds H that need oxidation are not O O O oxidized and can build up to HO N O toxic levels. O S O O OH O HO H O makes these B O more water soluble OH Conjugation joins xenomolecules with biomolecules, usually helps to eliminate them from the body in the urine (kidneys) or feces (intestines). N Toxic metabolite (see next slide) Furanocoumarins are found in O citrus fruits and can cause O similar problems when taking N-acetyl-p-benzoquinoneimine (NAPQI) O O O certain medicines. Psoralen is a mutagen found in grapefruit, and is used for this purpose in molecular biology research. Psoralen intercalates into the DNA and, on exposure to ultraviolet (UVA) radiation and can form monoadducts and covalent interstrand cross-links (ICL) with thymines preferentially at 5'-TpA sites in the genome, inducing apoptosis (cell death). 51

Tylenol  100,000,000 molecs/cell (that doesn't mean they all getting into the cell) glutathione (5mM in cells) (about 300,000,000 / cell) HS Glutathione is an important reducing agent in body (can -13 provide electrons from sulfur). Vol  10 L O H O Glutathione also protects against toxicity by O2C conjugating with N  S N O R H metabolites, making them water soluble and H N glutathione excreting them. The 3 glutamic acid H O (tripeptide) cysteine glycine bodies store of (backwards) glutathione is used up reacting with NAPQI. glutathione conjugation with NAPQI The sulfur atom can also H B H quench free radicals. B S N R H N R S glutathione O O HO O Other important anti-oxidants found in the body: glutathione, vitamin C and vitamin E. All protect against free radical damage in the body. Food can be medicine too, and food can be toxic!

HO O O vitamin E (-tocopherol) electron rich anti-oxidant HO HO fat soluble (in membranes) there are several variations OH HO vitamin C (ascorbic acid) O electron rich anti-oxidant water soluble (blood and cytosol) 52

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Possible membrane damage from free radicals and possible protection from vitamins E and C.

HO O The damage O OH saturated fatty acid chain saturated fatty acid chain

dangerous O O HO O uncontained O free radical O O diglycerides in cell membranes Free radicals reacting with unsaturated fatty acid pi bonds unsaturated cis fatty acid can possibly cross link fatty chains in cell membrane acid chains, making cell membranes more rigid and less functional over time, leading to cell death. HO O O OH saturated fatty acid chain saturated fatty acid chain

O O OH O O

O O

continued unsaturated cis fatty acid damage chains in cell membrane

hydroxyl free radical = danger The protection HO resonance and inductive effects stabilize radical so it does not do damage O H O O H H

O R resonance O R O R

vitamin E located HO HO H O in cell membranes hydroxide is quenches radicals HB neutralized by O vitamin C reduces body's buffer H O vitamin E back to system normal and ultimately HO O O O washes out of the body, H O R vitamin C is 4 steps away from glucose. O O O H O H O H O O B resonance H O R H O R H O R B protects a O R second time O vitamin E is recharged O and still in cell membrane O oxidized vitamin C form washes out of the body

O R

HO O O HO vitamin E (-tocopherol) vitamin C electron rich anti-oxidant HO water soluble fat soluble (membranes) (blood and cytosol) OH O HO 54

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O 1. hydration 2. oxidation (NAD+) O H O esterification H O H H H O H O OH O H OH enzyme x enzyme y OH OH HO OH H HO OH H HO H OH Could also form OH aldohexoses, hemiacetal first and glucose in some animals then oxidize to ester. OH We lost oxidation enzyme z mannose and galactose in plants functionality (NAD+) of this enzyme. O O H O H O O tautomers H O

OH OH H O O vitamin C OH OH Dogs and cats can make their own vit. C, but humans cannot. We lost the oxidizing enzyme of the last step. Some speculate that because H2O2 was also produced maybe there was some advantage in not making that. Another theory is that because vit. C regulates a stress related transcription factor that regulates 100s of stress related enzymes, we can better control the amount of vit. C by using our dietary intake. No one knows exactly why we lost this ability. 55

= diglycerides, helps compartmentalize aqueous regions in the body, cell membranes, mitochondria, vacules, nucleus, etc. cell membrane (lipid bilayer) OH exocytosis - cell transports proteins to outside cholesterol - endocytosis - cell transports proteins to inside helps stabilize membrane proteins cell membrane and source of all other body steroids. OH endocellular protein HO golgi apparatus + processes proteins Na mitochondria ion channels

ribosomes HO nucleus G7 coupled protein complex, 1/3 of all medicines act on G7 proteins. OH NH3 endoplasmic reticulum DNA O2C exocellular histones ribosomes protein rough - protein synthesis smooth - lipid synthesis chromosomes chromatin transscription RNA lysosome +2 Ca OH HO ribosomes +2 Ca+2 Ca translation proteins Ca+2 + K carbohydrates Ca+2 ion channels fats, lipids, other mitochondria vacule ion channels biochemicals

cell membrane Biomolecules: proteins (aminoacids), carbohydrates (sugars), lipids (cholesterol) and fats (diglycerids, triglycerids), DNA and RNA, vitamins, co-factors, minerals, combinations of all of the above, etc.

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signal Can be the key that turns on the amplification of signal enzyme engine. Can amplify 100s to 1000s of cycles. allosteric activator allosteric alloster. activator allosteric binding at allosteric alloster. enzyme site allosteric site enzyme site active enzyme turns on enzyme active enzyme site catalyst site catalyst A

substrate allosteric substrate binds activator at catalyticsite allosteric alloster. enzyme site A active enzyme reacts site again substrate catalyst reacts substrate

allosteric allosteric activator activator allosteric alloster. product allosteric alloster. enzyme site releases enzyme site active active site enzyme B enzyme catalyst site catalyst product Every step is a potential attack site for a medicine. B Usually, earlier is better.

reaction 1 reaction 2 reaction 3 A enzyme a B enzyme b C enzyme c D (x 100) (x 100) (x 100) 1A 100 B 10,000 C 1,000,000 D possible amplification of signal

possible feedback inhibition

Problem - The terms "hydrophilic" and "hydrophobic" are frequently used to describe structures that mix well or poorly with water, respectively. Biological molecules are often classified in a similar vein as water soluble (hydrophilic) or fat soluble hydrophobic). The following list of well known biomolecules are often classified as fat soluble or water soluble. Examine each structure and place it in one of these two categories. Explain you reasoning. R O H N H2N a b O

Ar Ar OH O P HO Ar O changes with its biochemistry, O serves many roles in body vitamin A OH

c O

N HO O d vitamin B6 (pyridoxine) HO H

HO OH

vitamin C OH (ascorbic acid) vitamin E (-tocopherol)

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Problem - Bile salts are released from your gall bladder when hydrophobic fats are eaten to allow your body to solubilize the fats, so that they can be absorbed and transported in the aqueous blood. The major bile salt glycolate, shown below, is synthesized from cholesterol. Explain the features of glycolate that makes it a good compromise structure that can mix with both the fat and aqueous blood. Use the 'rough' 3D drawings below to help your reasoning, or better yet, build models to see the structures for yourself (though it's a lot of work).

OH O

H H H N synthesized in many, H H many steps in the body H H cholesterol O HO HO OH glycolate O 1. source for steroids and bile acids syntheses in the body H (bilesalt) 2. important constituent of cell membranes 2. transported in blood to delivery sites via VLDL LDL HDL All polar groups are on the same face. Which side VLDL = very low density lipoprotein, has high cholesterol concentration faces water and which side faces fat molecules? LDL = low density lipoprotein, has medium cholesterol concentration (See structures below.) HDL = high density lipoprotein, has low cholesterol contcentration

CO2 OH representation of cholesterol OH representation of bile acid (glycolate) as as a long flat shape a long bent shape havingtwo different faces, one polar and one nonpolar HO OH

H2O blood HO H2O Glycolate has a nonpolar, hydrophobic OH blood blood face that can cover the inside of a fat ball HO H O and ahydorphilic face that can point H2O OH 2 HO outward toward the aqueous blood, which OH allows fats to be transported throughout O2C CO2 the body to reach fat storage cells and blood nonpolar fats blood other essential locations. There is a whole and cholesterol family of bile acids that are produced from inside H O cholesterol. The body produces about 1 2 gram of cholesterol each day and about H2O O2C half of that is converted into bile acids that HO CO2 are released into the intestine to help H2O OH absorb fats. About 12-18 grams of bile HO blood acids are released each day and most of blood OH H2O that is reabsorbed and recirculated (95%). HO The rest is lost in the feces. The body's H2O OH blood blood store of bile acids is about 4-6 grams. H2O 59

= water molecule G = H - TS Water molecules rigidly order nonpolar themselves around a nonpolar molecule. This is an entropy expense (S is lower) and increases free energy, G (less favorable). nonpolar Weak dispersion forces. Nonpolar molecules associate hydrophobic effect together, separate from water. The water molecules are less structured, nonpolar more disordered this way. This is an entropy gain (S is higher) and nonpolar free energy, G is more negative (favorable). Nonpolar molecules are said to be hydrophobic. The nonpolar compounds float or sink based on relative density. compound density dipole moment water 1.0 g/cm3 1.8 D octane 0.8 g/cm3 0 D carbon tetrachloride 1.6 g/cm3 0 D

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Biopharmaceutics Classification System - classifies drugs according to their solubility and permeabilty or absorption properties. This system restricts the prediction using the parameters solubility and intestinal permeability. The solubility classification is based on a United States Pharmacopoeia (USP) aperture. The intestinal permeability classification is based on a comparison to the intravenous injection. All those factors are highly important because 85% of the most sold drugs in the United States and Europe are orally administered.

According to the Biopharmaceutics Classification System, drug substances are classified as follows:

Class I - high permeability, high solubility. Compounds that are well absorbed and their absorption rate is usually higher than excretion. Example: metoprolol

Class II - high permeability, low solubility. The bioavailability of these products is limited by their solubility. A correlation between the in vivo bioavailability and the in vitro solubility can be found. Examples: glibenclamide, bicalutamide, ezetimibe, phenytoin

Class III - low permeability, high solubility. The absorption is limited by the permeation rate but the drug is solvated very fast. If the formulation does not change the permeability or gastrointestinal duration time, then class I criteria can be applied. Example: cimetidine

Class IV - low permeability, low solubility. These compounds have a poor bioavailability. Usually they are not well absorbed over the intestinal mucosa and a high variability is expected. Example: hydrochlorothiazide, Bifonazole •A drug substance is considered HIGHLY SOLUBLE when the highest dose strength is soluble in < 250 ml water over a pH range of 1 to 7.5.

•A drug substance is considered HIGHLY PERMEABLE when the extent of absorption in humans is determined to be > 90% of an administered dose in comparison to an intravenous reference dose.

•A drug product is considered to be RAPIDLY DISSOLVING when > 85% of the labeled amount of drug substance dissolves within 30 minutes in a volume of < 900 ml buffer solutions. 61

Class I - high permeability, high solubility Metoprolol, (tradename Lopressor) is used to treat high OH blood pressure, various heart problems and migraine H headaches. It may be combined with the diuretic O N hydrochlorothiazide. Metoprolol was first made in 1969. It is available as a generic drug. In 2013, it was the 19th most prescribed medication in the United States. O Class II - high permeability, low solubility O O O S O O N N H H

N Glibenclamide is an antidiabetic drug in a H class of medications known as sulfonylureas, closely related to sulfonamide antibiotics. It was developed in 1966.

Cl Class III - low permeability, high solubility H N Cimetidine (Tagamet) is a histamine H2 receptor N antagonist that inhibits stomach acid production. It is N mostly used in the treatment of heartburn and peptic N S C ulcers. It was discovered in 1971 and marketed in N N 1976. H H Class IV - low permeability, low solubility N

N Bifonazole is an imidazole antifungal drug. Bifonazole is marketed under the trade mark Canespor in ointment form.

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Pharmacokinetics - what the body does to the drug (the fate of the drug in the body)

Pharmacodynamics - what the drug does to the body (mechanism of drug action on the target site)

A common descriptor describing the fates of drugs inside the body is ADME

Absorption - the process of a substance entering the blood circulation.

Distribution - the dispersion or dissemination of substances throughout the fluids and tissues of the body.

Metabolization (or biotransformation, or inactivation) – the recognition by the organism that a foreign substance is present and the irreversible transformation of parent compounds into secondary metabolites.

Excretion - the removal of the substances from the body. In rare cases, some drugs irreversibly accumulate in body tissue.

The two phases of metabolism and excretion can also be grouped together under the title elimination. The study of these distinct phases involves the use and manipulation of basic chemical concepts in order to understand the process dynamics. For this reason in order to comprehend the kinetics of a drug it is necessary to have detailed knowledge of a number of factors such as: the properties of the substances that act as excipients (substances added to stabilize the drug), the characteristics of the appropriate biological membranes and the way that substances can cross them, or the characteristics of the enzyme reactions that inactivate the drug.

Pharmacokinetics blood brain barrier? brain Pharmacodynamics drug mouth stomach intestines blood liver kidneys urine interaction target feces various interstitial lymphatic tissues tissues system 63

Naming systems Letters and numbers are used for drugs in early research (lead compounds). Letters are specific to the research company undertaking the research and numbers are for the specific compound being studied. There may be 100s to 1000s of derivatives made.

Book examples of anti-HIV drugs. ABT-538 MK-639 Ro31-8959 early research (Roche) (Abbott) (Merck) saquinavir ritonavir indinavir names in testing

Fortovase Norvir Crixivan Trade names

Fortovase 200 mg of saquinavir in a gel-filled beige-colored capsule. different formulations Invirase 200 mg of saquinavir as the mesylate salt in a brown/green capsule Generic drugs are not allowed to use the trade name used by the originator of the drug.

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saquinavir ritonavir N indinavir H2N O S N OH H N N S N O O O HN HN O OH N HN O N OH N H OH HN O N H N O N O H O H NH

Saquinavir is an antiretroviral drug used Ritonavir is an antiretroviral medication used Indinavir is a protease inhibitor used together with other medications to treat along with other medications to treat as a component of highly active or prevent HIV/AIDS. Typically it is HIV/AIDS. The combination treatment is antiretroviral therapy to treat taken orally with ritonavir or known as highly active antiretroviral therapy HIV/AIDS. Unfortunately, indinavir lopinavir/ritonavir. It is in the protease (HAART). It is taken by mouth and used to wears off quickly after dosing, so inhibitor class and works by blocking inhibit the enzyme that metabolizes other protease inhibitors. leading to higher requires very precise dosing every 8 the HIV protease. Saquinavir was first concentrations of those other medications. It hours to thwart HIV from forming sold in 1995. As of 2015 it was not first came intousein 1996 and costs between drug-resistant mutations. Pills cost available as a generic medication and $10 and $55 per day, depending on the dose about $1.50/pill. Also, many drug wholesale cost is about $4.50 per day ( $11,000/year). interactions are possible. ( $1500/year).

Scanning electron micrograph of HIV-1 budding (in green) from cultured lymphocyte. Color enhanced.

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Design of indinavir (Crixivan®) - HIV medicine (human immunodeficiency virus) The development of indinavir started from renin inhibitors (for high blood pressure) previously made by Merck that showed inhibition of HIV protease enzymes. Renin (angotensinogenase) helps to regulate extracellular fluid and arterial vasoconstriction by inhibiting the conversion of angiotensinogen (from the liver) to angiotensin I, which is converted by angiotensin converting enzyme (ACE) to angiotensin II, which is the most vasoactive peptide. It narrows the blood vessels, retains sodium ions in the kidneys and acts on the CNS to stimulate thirst to retain water and reduces urine loss and causes the post pituitary gland to release vasopressin. All of this helps to regulate blood pressure in a very complicated sequence of steps and illustrates the incredibly complex network of interactions that must be considered when designing a drug. The best compound from the renin inhibitors for HIV inhibition was called L 364505. This was the starting point for indinavir. P = left half of molecule P' = right half of molecule L364,505 was a potent inhibitor of HIV protease. However, Ph its antiviral activity was low due to poor pharmacokinetics O (vulnerable to degradative enzymes, rapid biliary clearance (gall blader) and poor oral absorption). Several smaller BocPhePhe molecules were made in hopes to find one with similar activity. N LeuPheNH 2 Phe = phenylalanine and Leu = leucine amino acids H OH removed Ph IC50 = is the amount of an inhibitor to decrease a biological L364,505 (IC = 1 nM) process by half. It is a measure of the effectiveness of a 50 substance in inhibiting a specific biological or biochemical function. Ph O O

O N The left two "Phe" amino acids could be removed without LeuPheNH2 loss of activity (from the P side) against HIV protease. It lacked any activity against renin (that's a good thing). (Boc) H OH Ph removed L682,679 (IC50 = 0.6 nM)

next slide 67

P = left half of molecule P' = right half of molecule Ph O O

The right two amino acids (Phe and Leu) could be O N N removed and replaced with a benzyl group H (compound II). A drop in activity occurred, but it H OH did not dissappear, which meant they could keep Ph trying to make improvements. compound II (IC50 = 111 nM)

more rigid Ph O O It was thought that greater rigidity would help fit better in the binding pocket, so an indan O N N derivative was made (compound III). Five fold improvement in the IC50 was observed, but III had H OH H poor oral bioavailability and poor water solubility. Ph It was thought that introducing a polar substituent compound III (IC50 = 21 nM) would help.

Ph O O An "OH" was added and antiviral activity increased 70 fold, but there was still poor oral bioavailability O N N and poor water solubility. H H OH OH

L 685,434 (IC50 = 21 nM) greater polarity

H 68

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P = left half of molecule P' = right half of molecule A nitrogen atom was introduced to the right side (P') of the molecule to help oral bioavailability and water solubility. A molecular modeling exercise was carried out (in silico) and showed that the aromatic rings were pointing away from the active Ph O side and faced out towards the enzyme surface. It was felt that it O should be possible to add substituents "para" on the aromatics which could increase water solubility, but not interfere with the active site, leading to L 689,502. The morpholine group is know O N N H to increase water solubility and was connected with a hydroxyethylene spacer. H OH OH Therewasaslight drop inactivity, but the O L 689,502 (IC50 = 0.45 nM) antiviral activity went up as a result of improved penetration of the cell. Oral N bioavailability also improved to 5%. O Unfortunately, animal studies showed liver toxicity.

O H H O N H N N H N N It was known that the HIV active site was H symmetrical, so a decision was made to H H OH combine two different features that were both H O effective on the different sides of the molecule. Roche already had an anti-HIV drug on the H NH market, called saquinavire (Ro-8959/003). O 2 Merck decided to join the two together. saquinavire (Ro-8959/003), Roche saquinavire combined with compound III on next slide

P = left half of molecule P' = right half of molecule L 704,486 was less active as an inhibitor of the HIV enzyme, but the decahydroisoquinoline ring provided O greater water solubility and greater bioavailability H O (15%). Anti-viral activity was still weak. It was decided to switch in a piperizine ring. This would N allow functionalization on the #4 nitrogen atom to help with binding in the S3 subsite. (It could be H N N H H made hydrophobic or hydrophilic.) The additional OH amine would also increase water solubility and OH bioavailability. H

comes from L 689,502 L 704,486 (IC50 = 7.6 nM) switched out for S2' piperazine ring S2 S# = subpockets of L 732,747 had improved inhibitor activity H active site on the enzyme and better anti-viral activity in cell bases assays. It was co-crystallized N O piperazine with the enzyme and an X-ray structure ring O determined. This revealed that the S2 and S3 S2' pockets were filled and the benzoyl 2 1 group on the piperazine fitted in the 3 N N lipophilic S3 binding pocket. There was H still problems with crossing the cell 4 O N OH OH membrane. High activity means nothing if the drug cannot get inside the cell. Many derivatives were made and it was found O that replacing the phenyl ring with a S1 piperidine ring, which was weakly basic S1' and improved water solubility. L 732,747 (IC50 = 0.5 nM)

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P = left half of molecule P' = right half of molecule S2' S2

N O O S3

N N H O N OH OH

O S1 S1' L 732,747 (IC50 = 0.5 nM)

S2 S2'

N O This is indinavir.It was O introduced in 1996 and is still S3 used today. It has negligible inhibition of mamalian proteases, N N H yet is active against both HIV-1 and HIV-2 proteases. It has N O N OH OH better oral bioavailability than saquinavir and is less bound by plasma proteins (only 60%). O S1 S1' Indinavir (MK 639, L 735,524) (IC = 0.56 nM) 50 71