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Medicinal Chemistry > Part 1 > Flashcards

Part 1 Flashcards

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1
Q

Therapeutic Index

A

relative safety of a drug; wider = better

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2
Q

Poison

A

a substance capable of causing an organism harm or death

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3
Q

Drug

A

a compound that interacts with a biological system and causes a biological response

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4
Q

Drug Target

A

the macromolecule that a drug binds to

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5
Q

Binding site

A

usually in a hollow or canyon on the macromolecular target

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6
Q

Binding regions

A

functional groups on the macromolecular target’s binding site that the binding groups on the drug interact with

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7
Q

Binding groups

A

functional groups on the drug that interact with the binding regions on the macromolecular target’s binding site

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8
Q

HBA

A

the group with the electron-rich heteroatom

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9
Q

HBD

A

the group with the electron-deficient H

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10
Q

Pharmacodynamics

A

what does the drug do to the body; target interaction

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11
Q

Pharmacokinetics

A

what the body does to the drug; ADME

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12
Q

ADME

A

how the drug is absorbed, distributed, metabolized, excreted

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13
Q

Toxin

A

poison from a biological source

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14
Q

Medicinal Chemistry

A

study, development, and synthesis of new drugs

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15
Q

What influences how tightly a drug binds?

A

number and type of intermolecular bonds

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16
Q

Pharmacology

A

studies how drugs interact with biological targets to produce effects on living systems.

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17
Q

ionic/electrostatic bonds

A

bonding between groups with opposite charges; strongest of non covalent bonds

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18
Q

hydrogen bonds

A
  • bonding between an electron deficient H and an electron rich heteroatom
  • strength of the H-bond is determined by distance, polarity, and bond angle
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19
Q

Van der Waals

A

-interactions between hydrophobic regions
-requires really close interactions, relatively weak
-induced dipoles
-aka London forces

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20
Q

Dipole-dipole, ion-dipole

A
  • permanent dipole moment leads to partial charges, asymmetrical electron sharing
  • strength is between Van der Waals and Ionic interactions
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21
Q

Desolvation

A

desolvation of binding site and drug are key to drug binding

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22
Q

Primary Protein Structure

A
  • (AKA polypeptide sequence)
  • the amino acid polymer chain (a boring shoestring)
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23
Q

Secondary Protein structure

A
  • higher order structures formed by backbone interactions
    • alpha helices
    • beta sheets
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24
Q

Tertiary Protein Structure:

A

-folded, three-dimensional structure formed from backbone and side chain interactions
- a lot of diverse IMF’s: ionic/electrostatic, polar, hydrogen bonding, hydrophobic forces, covalent bonding
- the shoe string is a complex woven shape

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25
Q

Quaternary protein structure:

A

refers to proteins with multiple chains
- 2+ shoestrings fold then group up

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26
Q

What are the hydrophobic amino acids?

A

ala, val, leu, Ile, pro, phe, gly, met, trp

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27
Q

What are the polar amino acids?

A

ser, thr, tyr, cys, asp, gln

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28
Q

What are the basic/charged amino acids?

A

lys, arg, his

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29
Q

What are the acidic/charged amino acids?

A

glu, asp

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30
Q

What are the names of the beginning and the end of the amino acid sequence of a protein?

A

first: amino terminus/ N-terminus
last: carboxyl terminus/ c-terminus

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31
Q

Subunit

A

in proteins with multiple chains, one folded chain is often called a subunit
- Example: the tetramer of hemoglobin has four individual subunits

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32
Q

Domain

A

domains often refer to an independently folded region of the protein that often have a specific function
- Example: the calmodulin-binding domain

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33
Q

Motif

A

a small, frequently found protein structure
Example: Zinc-finger motif

34
Q

Disordered/ Intrinsically Disordered

A

a section of protein that exists in a disordered, highly-flexible state

35
Q

What are the types of post-translational modification?

A

-Acetylation
-hydroxylation
-carboxylation
- phosphorylation
-glycosylation

36
Q

Amino Acid

A

the basic unit of proteins

37
Q

Polypeptide Chain

A

the amino acid polymer chain

38
Q

What are the common protein functions?

A
  • structural, transport, enzymes, receptors
39
Q

Enzymes

A

a specific type of protein; catalyzes a chemical reaction

40
Q

What’s a catalyst?

A

it makes the reaction easier, faster, and lowers the activation energy
- does not change the free energy/ equilibrium
- it does change the rate of the reaction

41
Q

cofactors

A
  • helper molecules used by enzymes
  • additional chemistries available by recruiting a organic molecule or ion
  • ex: NADH, PLP, Biotin, FAD
42
Q

Active site on an Enzyme

A

a location on the protein that is responsible for binding and catalyzing the reaction
- often a small part of the overall enzyme structure
- active sites can be targets for drugs
- is often more hydrophobic than surface of protein

43
Q

Active site Amino Acids

A
  • amino acids in the active site are conserved and essential for substrate binding, cofactor binding, and/or catalysis
44
Q

Strategies for Enzyme-Catalyzed Reactions

A
  • Metal Assisted
  • Acid Base
  • Covalent Modification
  • Approximation and Orientation
  • Cofactors are often found in the active site
45
Q

Covalent Modification

A

The enzyme may be temporarily (must reset our enzyme) covalently bound to a substrate

46
Q

Approximation and Orientation

A

a bond/group is positioned ideally for reaction

47
Q

Effect of enzymes on reaction rate?

A
  • enzymes can not only speed up the rate but can be a fine tuned way to control/vary the reaction rate
48
Q

How are enzymes regulated?

A
  • Allosteric effectors
  • Post-translational Modification: modifications like phosphorylation can activate or inhibit activity
49
Q

Isozymes

A

enzymes with the same function but different amino acid sequence
- often have tissue/cell specific expression

50
Q

Activation of Ion Channel Receptor

A
  • ion channel is opened when a messenger ligand binds to the receptor binding site.
    -Gate opens and ions flow down concentration and potential gradient
51
Q

Ion channel subunits

A
  • pentameric channel
  • may contain different types of subunits or multiple of the same
  • location of the ligand binding site varies from one receptor to the next
  • each subunit contains 4 transmembrane (TM) regions / helices
52
Q

What determines ion gate channel size?

A

channel size is specific for the size and charge of the ion that is going through

53
Q

What do GPCRs do?

A

-respond to hormones and neurotransmitters
-embedded in the membrane and activation of GPCR’s leads to activation of G-proteins within the cell

54
Q

What does GPCR stand for?

A

G-Protein-coupled Receptors

55
Q

How fast are GPCR’s?

A

slower than ion channels bc the have more complex downstream effects

56
Q

GPCR structure

A

-All GPCR have a similar structure but vary in sequence, ligand binding, and G-protein binding
-consist of single chain, 7 transmembrane regions, extracellular loops, and intracellular loops

57
Q

What is the purpose of GPCR extracellular loops?

A

ligan binding

58
Q

What is the purpose of GPCR intracellular loops?

A

G-protein binding

59
Q

Kinase-linked receptors or Receptor Tyrosine Kinases (RTKs)

A
  • includes and extracellular ligand binding and an intracellular enzyme domain (kinase)
60
Q

What does a kinase do?

A

adds a phosphate

61
Q

Structure of RTKs

A
  • single chains, on transmembrane region
  • N-terminus ligand binding
  • C-terminus kinase domain
  • RTKs can dimerize when a ligand is present
62
Q

Intracellular receptors

A
  • no embedded in the cell membrane
  • often called hormone or steroid receptors
  • hormone receptors act directly as transcription factors
  • c-terminal ligand binding and a DNA binding domain
63
Q

Receptor

A
  • Proteins that receive a signal and communicate to the cell
  • primary targets for drugs
64
Q

Messenger Chemical

A
  • aka receptor ligands
  • comes in many forms
  • simple molecules like amino acids or calcium ions
  • complex molecules like peptides or lipids
65
Q

Ligand

A
  • a molecule that binds to (usually larger) molecules
  • similar to a substrate binding an enzyme but causes no catalysis
66
Q

Neurotransmitter

A

signaling molecule secreted by a neuron to affect another cell across a synapse

67
Q

Signal Transduction

A

the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events

68
Q

Ion Channel Receptors

A
  • five subunits form a hydrophilic tunnel through the membrane
  • closed at rest
69
Q

Transmembrane Region

A
  • made up of alpha helices
  • each subunit contains 4 TM regions
70
Q

Gating

A

TM’s have bent structure that closes gate. When opened, bent part sticks out and opens gate. Channels size is specific for size and charge of ions

71
Q

Zinc Finger Domains

A
  • DNA binding region
  • DNA back bone is negative so it binds to positive zinc finger
72
Q

Substrate

A

bonds with an enzyme active site

73
Q

Michaelis Constant

A

combination of the individual rate constants (k1, k2, k3)/ [substrate] at 1/2 Vmax

74
Q

Lineweaver-Burk Plots

A

double-reciprocal plots 1/[s] and 1/Vo

75
Q

General Features of Receptor Proteins

A
  • mediate cell to cell communication
  • frequently located at/embedded in a cell membrane
  • receive messenger molecules from CNS and endocrine organs
  • to regulate everything
76
Q

Allosteric Effectors

A

small molecules that bind to the enzyme at a location away from the active site, activate or inhibit activity

77
Q

Would you anticipate electrostatic/ionic bonding to be stronger or weaker in the active site of an enzyme?

A

More hydrophobic. The active site of an enzyme is often partially buried (hollow/cleft), is more hydrophobic than surface and has less water around it resulting in stronger electrostatic interactions due to less or no competition with water

78
Q

Km constant

A

can generally tell us how well the enzyme interacts with substrate
- Large Km=weaker substrate interaction

79
Q

If an enzyme active site contains a conserved histidine residue and it is mutated/changed to an alanine, what issues could arise due to this mutation?

A
  • going from a basic charged aa to a small hydrophobic aa
  • could disrupt important intermolecular interactions between histidine and other amino acids or substrate
  • likely would impair/kill enzyme activity
80
Q

alpha helices

A

helixes held together by local hydrogen bonding between amino acids

81
Q

beta sheets

A

strands of the polypeptide chain woven into a sheet, running either parallel or anti-parallel

82
Q
A

Medicinal Chemistry (4 decks)

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