Patho final exam review (Module 1-Medicinal Chemistry)

Question 1

define pharmacophore

Answer 1

drugs that bind to the same target share a similar structural motif-this motif is necessary for binding to the receptor

Question 2

define the structure-activity relationship

Answer 2

properties of a drug depend on the chemical constituents of the molecule–by modifying the structure one can change the drug properties

Question 3

list chemical properties of drugs that can be deduced from the structure and ones that affect their biological activities, ones that are affected by the change in pH

Answer 3

-pH affects ionization
structure [size, ionization, solubility, hydrophobicity, stereochemistry]
activity [membrane permeability, target binding, metabolism, excretion]

Question 4

identify ionizable groups in drug structures

Answer 4

weak acids and bases pka less than or higher than 7
-rings, carboxyls, phenol, guanidine, alkyl amines

Question 5

estimate the degree of drug ionization at a given pH using Henderson-Hasselbalch equation

Answer 5

pH<pKa is more acidic and more in acid form; protonated
pH>pKa is more basic and more in basic form; deprotonated

Question 6

Predict the range of pH where a drug would be more soluble in water

Answer 6

water is polar
-make more acidic to improve solubility

Question 7

At pH 6.4, what is the ration of this drug in the acid form (neutral) to that in the base form (negatively-charged)? ibuprofen pKa 4.4
A. 100:1
B. 10:1
C. 1:1
D. 1:10
E. 1:100

Answer 7

E. 1:100

Question 8

What are the different modes of permeation into the body?

Answer 8

Intercellular junctions, Lipid cell membranes, Transporters, Endocytosis and exocytosis

Question 9

identify hydrophobic and hydrophilic groups in a drug structure

Answer 9

hydrophobic- methyl, chloro, phenyl, hexyl, cyclohexyl
hydrophillic- alcohol, carboxylic acid, amine, ketone, amide, ester

Question 10

identify hydrogen bond donors and acceptors in a drug structure

Answer 10

donors- OH,NH
acceptors- O,N

Question 11

explain how logP values affect the ability of drugs to reach target sites

Answer 11

-orally active drugs are relatively small and moderately lipophilic; hydrophobic drugs are sticky and bind to its drug better to target
-logP values are usually between -1 and 4
logP < 0
logP = 0 equal distribution
logP > 0 drug factors octanol

Question 12

explain why the relationship of drug effectiveness versus logP is parabolic

Answer 12

the relationship is parabolic because too hydrophobic or not being hydrophobic both can inhibit drug activity the same amount

Question 13

calculate logP of a drug molecule from the pi value of its constituent groups

Answer 13

ClogP
-hydrophobic groups increase LogP (+)
-hydrophilic groups decrease LogP (-)

Question 14

estimate logD using logP an pKa at a given pH

Answer 14

Drug HA is acidic with logP= 2 and pKa=4
-at pH=1 D~P
-at pH=7 D«P
Drug B is a basic drug with logP= 2 and pKa=7
-at pH= 10 D~P
-at pH= D«P

Question 15

Predict the efficiency of passive diffusion of a drug with a known pKa at a given pH

Answer 15

more neutral the compound is, the more can participate in passive diffusion
ratio of 1000:1 means 99.9% is neutral and can penetrate quicker/faster
equal concentration can cross at slower rate because only 0.1% is truly neutral

Question 16

predict where a drug will be absorbed in the digestive system based on the drug’s pKa value

Answer 16

drugs are absorbed in jejunum when pH is between 5-7
acidic drugs are absorbed in stomach where pH is 1-3

Question 17

Define Hammett’s sigma values and estimate the electronic effects of substituent groups on drug ionization using hammett’s sigma values, also electron withdrawing and electron-donating groups

Answer 17

hammett’s sigma defines electronic effects on a functional group
positive sigma value- electron-withdrawing group (more acidic & lower pKa)
negative sigma value- electron-donating group (less acidic & higher pKa)

Question 18

what is the difference between inductive effect and resonance effect

Answer 18

withdrawing effect- negative charges can be stabilized and make molecule more acidic; effect becomes weaker by going through multiple bonds
(inductive effect)
resonance effect- observed with pi bonds, electronegative atoms with withdrawing effects, only occurs in ortho and para positions

Question 19

how do electronic effects of substituent groups affect ionization, acidity and basicity

Answer 19

basic- electron-donating groups make the molecule more basic; electron-withdrawing make the molecule less basic

Question 20

determine R/S and E/Z notations for drugs from their structures

Answer 20

cis- Z (same side)
trans- E (against/across from eachother)

Question 21

what are the differences between R/S, d/l, and D/L nomenclature systems

Answer 21

R/S -by absolute configuration, primary method for drugs. R (clockwise; right) S (counterclockwise; left)
d/l or +/- system- by optical rotation, experimentally determined, depends on solution condition
D/L- by relative configuration to glyceraldehyde; obsolete and only used for amino acids and sugars

Question 22

list factors other than receptor binding that result in different biological properties of drug enantiomers

Answer 22

-permeation by transporters
-nonspecific binding to serum proteins
-metabolism

Question 23

when a pair of stereoisomers are given, determine whether they are enantiomers, diastereomers, or geometric isomers

Answer 23

enantiomers- (1R, 2S) and (1S, 2R); (1R,2R) and (1S,2S)
diastereomers- (1R,2S) and (1R,2R); (1S,2R) and (1S,2S)

Question 24

What is the KD value from a binding isotherm

Answer 24

KD- dissociation equilibrium constant
smaller the KD, the stronger the binding is
KD= (D)(R)/(DR)
When [D]=KD 50% of all receptors are occupied
When [D] &laquo_space;KD ~ 0
When [D]&raquo_space; KD ~ 1

Question 25

calculate delta G(D) from KD & vice versa

Answer 25

DeltaG ~ -1.4 x LogKD (kcal/mol) 10^-6 (KD) = 8.4 (DG) 10^-7 (KD) = 9.8 (DG) 10^-8 (KD) = 11.2 (DG)

Question 26

explain characteristics of type of interactions between drugs and receptors & types of interactions between drugs and receptors from a given structure

Answer 26

Hydrophobic interactions- attraction between nonpolar groups in water; most common type of interactions in protein-ligand complexes; surface area of nonpolar surface is reduced electrostatic interactions- attraction between +/- charges; water is a dipole, loves ions & dipoles can also be in proteins (backbone amide, a-helix) Hydrogen bonds- O and N;ionic H-bonds are stronger than neutral H-bonds aromatic rings- attractions are between electron-rich and electron-deficient regions (can be affected by EWG and EDGs) pi stacking- parallel stacking of aromatic rings T stacking- edge to face Cation-pi interaction- Interaction between a positive charge and an aromatic ring

Question 27

explain the concept of QSARS (quantitative structure-activity relationships)

Answer 27

if you change structure you change the activity; uses mathematics to describe structure activity relationships and can tell roughly if new drug is better or not

Question 28

antimetabolities, structure-based drug design, High-throughput screen, Isosteric replacement, Prodrugs

Answer 28

antimetabolites- analogs of endogenous metabolites (can act as inhibitors). will compete with a metabolite in reactions structure-based drug design- drug designed based on 3-D structure of a target protein Isosteric replacement- improves pharmacokinetics, improve selectivity, reduce side effects, simplify the synthesis process, avoid patent issues (groups not in pharmacophore are replaced with bioisostere) Prodrug- inactive or carrier form of a drug that is transformed in vivo (enzymatically) to the active drug form (prolong/shorten duration of drug, localize drug to a specific target site, advantage of active transport process, formulation problem, decrease toxicity, side effects)

Question 29

bioisoteres explain their uses

Answer 29

functional groups/atoms with similar steric and electronic properties with similar effects too

Question 30

pharmacology, pharmacodynamics & pharmacokinetics

Answer 30

Pharmacology- science of interactions of chemical compounds with biological systems Pharmacodynamics- the study of the biochemical and physiological effects of drugs and the mechanisms of their actions Pharmacokinetics- the study of absorption, distribution, biotransformation, and elimination of xenobiotics

Question 31

identify the sites of drug actions (including receptors)

Answer 31

types of drug interactions- Orthosteric: agonist, antagonist, partial agonist, inverse agonist allosteric- PAMs,NAMs -extracellular, intracellular, on the cell surface

Question 32

law of mass action & receptor occupancy

Answer 32

-law of mass action defines drug-receptor interaction -effect of a drug is directly proportional to the amount of drug-receptor complex formed rate of association =Kon [D][R] rate of dissociation =Koff [DR] KD (dissociation constant) -the LOWER the KD the HIGHER the affinity -KD is the concentration of ligand that will bind half the receptors at steady state

Question 33

outline components in a receptor binding assay

Answer 33

receptor + radio-labeled ligand then filtered -non-specific line on binding analysis radio-labeled ligand competes for same sight as normal ligand

Question 34

principles of receptor binding to measure affinity

Answer 34

how tightly it binds -sometimes 100% binding is not best option -can use data to get IC50 and then use cheng-prusoff to get Ki

Question 35

graphical data for pharmacological profiling

Answer 35

can test several unlabeled compounds to compute Ki for each compound -can calculate rank affinity CHENG-PRUSOFF: Ki=IC50/[1+L/KD]

Question 36

apply receptor affinity to receptor selectivity

Answer 36

affinity can be used to show selectivity but best affinity for something does not mean best selectivity -determined by ratio -higher number means higher selectivity

Question 37

describe the relevance of Bmax to drug action

Answer 37

Bmax is an estimated number of receptors in a given tissue -values are determined through saturation binding studies -are independent of the ligand -can influence downstream signaling events

Question 38

Identify and differentiate between the five classes of receptors

Answer 38

intracellular receptor transmembrane receptor RTKs; cytokine receptors Ion channel GPCRs

Question 39

describe the effects of allosteric modulators on ion channels and GPCRs

Answer 39

lots of allosteric binding sites on these molecules to allow for changes to the receptor and its binding (can have inhibitory effect)

Question 40

describe the features for G protein activation

Answer 40

-extracellular ligand is detected by the cell-surface receptor (R) -receptor triggers activation of G protein (G) -activate G protein changes activity of the effector (E) can be enzyme or ion channel

Question 41

effects of subtypes of G proteins

Answer 41

Ga(stimulatory)-activates adenylyl cyclases, inhibits Src family tyrosine kinases Ga(inhibitory)-inhibits adenylyl cyclases, activates phosphodiesterases Ga(q/11)- activates Phospholipase C Ga(12/13)- recruits Rho guanine exchange factors(RhoGEFs) Gby- inhibits adenylyl cyclase, recruits GRK2&3, activates PI3Ky, ion channels (Ca and K)

Question 42

compare signaling of the second messengers and arrestin

Answer 42

Second Messengers: cAMP (adenylyl cyclase effector enzyme) Phospholipase C (PLC) results in release of phosphoinositides and diacylglycerol cGMP effector enzyme is guanyl cyclase B arrestins serve as an adaptor protein to link activated GPCRs to MAP kinase pathway B-arrestin can uncouple receptor from G protein (desensitization) also endocytosis (recycling, lysosomal degradation) and signaling

Question 43

describe the mechanism and consequence of receptor desensitization

Answer 43

Heterologous desensitization involves the activation of one GPCR can result in the inhibition of another (Gi-linked) Homologous desensitization involves only the activated GPCRs are "turned off" or desensitized

Question 44

assess ligand-receptor concentration response curves for functional selectivity

Answer 44

functional selectivity requires that the receptor couple to multiple signal transduction pathways (G protein & B arrestin) *Prefers one pathway heavily over others but can do multiple pathways (biased)

Question 45

use of the concept of functional selectivity to design better drugs

Answer 45

can be used to avoid a certain pathways and its negative effects with the drug

Question 46

What is the difference between agonist and antagonist binding

Answer 46

-binding of agonist results in induced fit that activates the receptor -binding of an antagonist results in a different induced fit that does not activate the receptor

Question 47

identify and compare dose response curves for each type of ligand in the "ligand spectrum"

Answer 47

full inverse agonist -100% silent antagonist- 0% full agonist- 100% super agonist- 100+%

Question 48

use graphical data to compare potency and efficacy for active ligands

Answer 48

potency- dose of a drug required to produce a particular effect of given intensity efficacy- biological response resulting from the drug-receptor interaction is termed efficacy strong agonist has high affinity and high efficacy

Question 49

describe the concept of a partial agonist

Answer 49

produces a reduced response even at full receptor occupancy, will not produce same maximal effect as a full agonist regardless of concentration

Question 50

apply the concept of partial agonist theory to managing drug therapy

Answer 50

as more partial agonists are added to the mixture, full agonists are being displaced which can help in drug therapy to give appropriate response

Question 51

describe the features of an inverse agonist

Answer 51

-produces opposite response of an agonist -full and partial inverse agonists both exist -stabilizes inactive form of the receptor

Question 52

compare reversible competitive and irreversible, non-competitive inhibition

Answer 52

competitive (REVERSIBLE) -antagonist combines with the same site on the receptor as the agonist; antagonism can be reversed by increasing the dose of the agonist noncompetitive (partially reversible) -antagonist produces its effect at a site of the receptor other than the site used by the agonist; agonist and noncompetitive antagonist do NOT compete with eachother for single binding site IRREVERSIBLE antagonist- will usually bind to the same site as the agonist, will not be readily displaced-generally caused by covalent reaction between antagonist and receptor

Question 53

use the concept of spare receptor to explain drug action

Answer 53

-maximal response is achieved without 100% occupancy of available receptors -important in action of irreversible antagonists (heart, brain, etc.) -system/tissue dependent; cells can have lots of reserve or none

Question 54

describe functional and chemical antagonism

Answer 54

-functional antagonism: two drugs influence a physiological system but in opposite directions; both drugs can elicit response at same time -chemical antagonism: chemical reaction occurs between an agonist and an antagonist to form an inactive product; agonist is inactivated proportionally to the extent of the chemical reaction with the antagonist

Question 55

describe the mechanisms of allosteric modulators and their potential benefit in drug therapy

Answer 55

-bind at sites unique from the agonist/antagonist -PAMs can increase potency, efficacy -NAMs can decrease potency, efficacy

Question 56

define the key means by which drug effect is quantified and compared (onset, intensity, duration)

Answer 56

onset- when the drug starts its effects (MEC) duration of action- how long the drug is active Intensity- peak effect

Question 57

know the differences between a quantal vs graded drug response

Answer 57

quantal response- all-or-none dose-response relationships (anaphylaxis or not; sedated or not) graded drug response- depends on dose and shows progressively increasing effects with increasing concentrations of the drug

Question 58

calculate and compare the therapeutic index between drugs

Answer 58

Therapeutic index= TD50/ED50 TD50 is toxic side effect ED50 is therapeutic effect

Question 59

describe the factors that modify the effects of drugs

Answer 59

-Drug tolerance (occurs by either drug disposition/metabolic tolerance or cellular/pharmacologic tolerance)

Question 60

compare and contrast drug disposition tolerance and pharmacologic tolerance

Answer 60

pharmacologic tolerance affects the normal reactivity of the receptor; downregulation of receptors; change in receptor affinity, etc. drug disposition tolerance affects effectiveness of drug

Question 61

apply cross-tolerance to disease management

Answer 61

tolerance develops to one drug and is seen with drugs belonging to the same class; not always complete (basis for opioid rotation)

Question 62

understand the bases for on-target and off-target adverse effects