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Biopharmaceuticals. > Module #2 - Biotargets of Drugs > Flashcards

Module #2 - Biotargets of Drugs Flashcards

1
Q

4 main types of biological moleules

A

proteins, nucleic acids, polysaccharides, and lipids

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2
Q

proteins

A

linear chain of amino acids connected by amide (peptide) bonds

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3
Q

nucleic acids

A

linear chain of nucleotides connected by phosphate esters

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4
Q

polysaccharides

A

linear chain of sugars connected by acetals

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5
Q

lipids

A

linear chains of acetate or propionate connected by reduced aldol

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6
Q

importance of modular characteristic of biological molecules

A

allow for complex structures to easily be assembled and disassembled

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7
Q

what “machine” puts together proteins

A

ribosomes

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8
Q

what “machine” takes apart proteins

A

proteasomes

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9
Q

what is the typical process of drugs in the body

A

drug attaches to biological target of a biological molecule (usually a protein) –> results in a biological change (usually a change in shape on protein) –> results in a biological response (ex. lower blood pressure)

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10
Q

importance of 3d properties of biomolecules

A

allows for biomolecules to bind and be recognized

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11
Q

how many amino acids

A

20

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12
Q

general composition of an amino acid

A

amine, acid group, and carbon side chain of some sort

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13
Q

what is the stereochemistry of the side chain of an amino acid

A

always at the back

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14
Q

primary structure of proteins

A

a linear chain of amino acids

listed in order from N-terminus to C-terminus

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15
Q

what is the n-terminus of an amino acid

A

the amine portion

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16
Q

what is the c-terminus of an amino acid

A

the acid portion

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17
Q

what connects for proteins to form

A

the n terminus (amine portion) connects to the c terminus (the acid) of another amino acid

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18
Q

secondary structure of proteins

A

the regular, local structure of the protein backbone

a-helix, beta sheet, loop, turn

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19
Q

why do secondary structures form

A

due to restrictions in protein chains specifically:
- conformational restrictions in amide bonds

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20
Q

what are two main characteristics of amide bond:

A

sp2 hybridization due to blend of resonance forms, so the structure is flat

can either get a sigma trans or a sigma cis conformations

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21
Q

what happens if you get a sigma-trans conformation of an amide bond

A

large groups are away from each other and don’t interact

amide bonds will always choose this option if possible because more stable

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22
Q

what happens if you get a sigma-cis conformation of an amide bond

A

large groups are close to each other and interact

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23
Q

characteristics of side groups of amide bonds

A

can be +, -, or nothing (only H)

negative charges attract positive charges

H bonding occurs between size chains and backbones

non-polar size chains interact with other non-polar chains

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24
Q

what is a localized structure

A

the sum of all the effects of side chain interactions on a protein chain adding together

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25
Q

characteristics of alpha helix structure

A

spiral shape
represented by ribbon diagrams

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26
Q

characteristics of beta strand

A

everything is in same plane

flat in nature

side chains stick out

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27
Q

characteristics of beta sheet

A

formed by several beta strand associating together

can be parallel or antiparallel

held together by hydrogen bonds

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28
Q

parallel beta sheet

A

both sheet go in same direction (n-c, n-c, etc.)

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29
Q

antiparallel beta sheet

A

sheets go in opposite directions (n-c, c-n, etc)

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30
Q

characteristics of beta barrel

A

large beta sheets curling around themselves to form a cylinder

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31
Q

characteristics of loops

A

area with no defined secondary structure

looks like spaghetti

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32
Q

tertiary structure of proteins

A

combination of all secondary structures added together

result of interactions between non-adjacent regions

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33
Q

tertiary structure of proteins

A

combination of all secondary structures added together

result of interactions between non-adjacent regions

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34
Q

what do secondary structures result from?

A

side chains interacting with each other (adjacent regions interacting)

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35
Q

what type of bonding exists in tertiary structures

A

lots of noncovalent

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36
Q

what are the four attractive forces in tertiary structures (strongest to weakest

A

disulphide
ionic bonding
hydrogen bonding
van der waal

37
Q

disulphide bonding

A

strongest covalent bond
involves formation of disulphide bond

38
Q

ionic bonding

A

involves a complete positive and complete negative charge being attracted to each other

39
Q

hydrogen bonding

A

involves hydrogen being attracted to a pair of electrons on an atom

40
Q

van der waal

A

involves greasy side chains interacting with greasy side chains (non-polar + non-polar interactions)

41
Q

why are van Der Waals so important

A

because allow for inside of protein to be non-polar and outside to be polar which allows for a strong structure

42
Q

polar + polar

A

weakened bonds

43
Q

polar + nonpolar

A

strengthened bonds

44
Q

quaternary structures

A

combination of two+ tertiary structures binding together

45
Q

two ways that quaternary structures can form

A

either proteins can be the same or different

46
Q

what type of interactions occur in quarternary structures

A

protein protein interactions

47
Q

why are protein protein interactions so strong

A

lots of surface contact area

lots of chemical interactions

exclusion of water from space between

proteins stick together tightly

48
Q

how are quaternary structures formed

A

proteins have big surface areas which allows them to come together easily and have a strong interaction

water squeezes out from in between, and the proteins stick together

49
Q

is most of a protein functional?

A

no, most if scaffold - only very small part is the active site

50
Q

what are the four types of protein targets for drugs

A

enzymes

receptors

ion channel

structural proteins

51
Q

how does a drug work if it has an enzyme as target

A

it functions to stop the enzyme from working

most drugs are enzyme inhibitors

52
Q

how does a drug work if it has a receptor as a target

A

drug activates (agonist) or deactivates (antagonist) the receptor

some drugs do both

53
Q

how does a drug work if it has an ion channel as target

A

drug works to open or close the channel

some drugs do both

54
Q

how does a drug work if it has a structural protein as target

A

can interfere with assembly or disassembly of certain protein structures

55
Q

what is an enzyme

A

special group of proteins that catalyze reactions

create custom perfect environment for reaction to occur

lowers the energy of transition state so the reaction will go faster

56
Q

what is the active site of an enzyme

A

where the chemical reaction takes place

very small

57
Q

chemical environment characteristics for an effective enzyme

A

complementarity of chemical properties important (must be positive and negative charges)

typically an acid base mechanism occurring when active site of enzyme touches substrate

58
Q

general steps of enzyme catalyzed reactions

A

enzyme binds to substrate forming enzyme substrate complex

enzyme typically changes shape to accommodate substrate + substrate also changes shape and joins active site of enzyme

substrate converted into product in active site of enzyme

equilibrium creates between product and enzyme, and product diffuses away

59
Q

what are two theories of enzymatic conformational change

A

lock and key

induced fit

60
Q

lock and key theory

A

states that enzyme is the exact shape necessary for substrate to fit into

substrate and enzyme don’t change shape for each other

61
Q

induced fit theory

A

states that the binding of a substrate and other molecule with an enzyme changes the shape of that enzyme

conformational change in shape activates or deactivates the enzyme

more realistic than lock and key

62
Q

what is involves in michaelis-menten kinetics

A

used to describe enzyme efficiency

states that enzyme and substrate come together to form enzyme substrate complex

shows kinetics behind enzyme catalyzed reactions

63
Q

what is a Michaelis menton plot

A

tracks how an enzyme produces product over time

64
Q

what are the three main types of enzyme inhibition that drugs can perform as

A

competitive inhibition

noncompetitive inhibition

uncompetitive inhibition

65
Q

competitive inhibition

A

drug (inhibitor molecule) competes with substrate for active site

binding occurs within the active site of enzyme

inhibitor binds to active site, eating the substrate cannot bind, and preventing the product from being produced

66
Q

noncompetitive inhibition

A

drug (inhibitor molecule) bind to enzyme, but not in the active site, and changes the shape of enzyme

the substrate binds to active site inside

drug is not necessarily competing with substrate - they both bind to respective locations

67
Q

uncompetitive inhibition

A

drug (inhibitor molecule) binds to enzyme-substrate complex

binding destroys the catalytic ability of the enzyme substrate complex

substate binds first, changes the shape, and then the drug can attach (to the enzyme/substrate complex)

68
Q

how do competitive inhibitors change plots

A

kinetics are changed, max is not

y-intercept stays same, slope does not

69
Q

example of competitive inhibitor

A

disulfiram

drug for alcoholics

blocks the chemical that stops your body from getting sick due to hangover

70
Q

how do non competitive inhibitors change plots

A

changes both slope and y-intercept

km is unaltered - meaning substrate can still bind to free enzyme

vmax reduced - meaning inhibitor changes the enzyme substrate complex

71
Q

example of noncompetitive inhibitor

A

fluconazole

side effect of interfering with enzymes in liver and prevents them from working

72
Q

what is a fourth type of enzyme inhibition (unofficial)

A

irreversible inhibitor (covalent/suicide inhibitors)

bond covalently to enzyme, and inhibit by altering conformations/disabling functionalgroups

block function of enzyme by forming a covalent bond between themselves and the enzyme

73
Q

example of uncompetitive inhibitor

A

lithium

exact mechanism is unknown

74
Q

example of irreversible inhibitor

A

penicillin

75
Q

what is a receptor

A

a molecule that moves information from one place to another (usually from inside to outside of cell, or vice versa)

specialized proteins embedded in cell membrane

76
Q

what changes the shape of a receptor

A

interactions between messenger and the receptor

77
Q

how do receptors work?

A

receptor and messenger come together

shape changes upon interaction

something becomes activated on the other side of membrane that allows information to be carried

once information has been transmitted, the receptor spits out the messenger and starts the process thin

78
Q

what are the five types of drug classes

A

agonists, antagonists, partial agonists, inverse agonists, and allosteric agonists

79
Q

what is an agonist

A

essentially replaces the messenger

transmits information/amplifys signals without messenger present

creates a shape change that is same/similar to regular messenger

80
Q

what is an allosteric modulator

A

works with ion channels

bonds to channel, just not in same location as regular messenger

this changes the shape/sensitivity towards normal messengers –> alters the way the receptor will act with messenger going forward

81
Q

what is an antagonist

A

induces abnormal shape change of receptor so that it is not accessible by regular messenger molecule + there is no signal transmission (no transmission of information)

may bind at active site, or other locations (like allosteric sites)

82
Q

what is an allosteric antagonist

A

basically binds in some location on receptor molecule, and alters the actual messenger binding site so that the messenger can no longer bind

83
Q

what is a partial agonist

A

similar to agonists, but not as strong - are more weak

binds to receptor, and produces a non-ideal conformational change allowing for a weak signal to be sent

can either bind in an agonism way, or in an antagonism way

84
Q

what is an inverse agonist

A

essentially seem to give a reverse reaction

drugs are inverse agonists depending on interactions with receptor, not drug itself

wipe out any weak background signals on receptor (instead of amplifying it - like other drug classes do)

85
Q

what is the biological effect of an agonist

A

as you increase concentration, biological response increases

ex. blood pressure increases

86
Q

what is the biological effect of a partial agonist

A

as you increase concentration, the biological response increases (just not to the same degree as a full agonist)

ex. blood pressure increases, just not as much as a full agonist

87
Q

what is the biological effect of an antagonist

A

blocks the action of the receptor + results in no response

prevents signals from being transmitted

concentration doesn’t appear to have an effect on level of biological response - there will always be no activity no matter the dosage

ex. blood pressure remains the same

88
Q

what is the biological effect of an inverse agonist

A

reverse reaction occurs

goes in opposite direction

ex. blood pressure decreases

89
Q

types of biological assays

A

high throughput screening

routine SAR work

kinetics or special studies

Biopharmaceuticals. (5 decks)

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