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PHRM 100 – IMC > IMC 02: Understanding Functional Groups in Medicinal Chemistry > Flashcards

IMC 02: Understanding Functional Groups in Medicinal Chemistry Flashcards

1
Q

What are the most common functional groups in drug-like molecules and proteins?

A
  • carboxylic acid
  • amine
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2
Q

What results in interesting chemical and biological properties?

A

presence of pi bonds or other non-carbon or hydrogen atoms (heteroatoms)

  • while sp3 to sp3 carbon-carbon bonds, and sp3 to s carbon-hydrogen bonds are found in nearly all organic compounds and drug molecules, these bonds do not generally play a major role in chemical reactions or have particularly strong roles in interactions between drug molecules and their molecular targets
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3
Q

What is a functional group?

A

can consist of several atoms that may change the chemical or biological properties at a particular site of a molecule

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4
Q

Alkanes

A
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5
Q

Alkenes and Alkynes

A
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6
Q

Aromatics (Benzene, Naphthalene)

A
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7
Q

Alkyl and Aryl Halides (F, Cl, Br, I)

A
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8
Q

Alcohols (1º, 2º, and 3º)

A
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9
Q

Esters (cyclic esters = lactones)

A
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10
Q

Ethers (and cyclic ethers)

A
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11
Q

Aldehydes and Ketones

A
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12
Q

Amides (cyclic amide = lactam)

A
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13
Q

Carboxylic Acids (aliphatic and aromatic)

A
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14
Q

Phenol

A
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15
Q

Sulphonamides

A
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16
Q

Thiol Amines (1º, 2º, and 3º, piperidine, piperazine)

A
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17
Q

Pyridine

A
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18
Q

Purine, Adenine, Guanidine

A
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19
Q

Pyrimidines (cytosine, thymine, uracil)

A
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20
Q

What is an L-a-Amino acid?

A

molecule containing single sp3-hybridized carbon between amino group and carboxylate group

  • categorized based on their side chains (R groups) – 20 natural variations
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21
Q

What are the 20 amino acids?

A
  • alanine (ALA)
  • glycine (GLY)
  • isoleucine (ILE)
  • leucine (LEU)
  • proline (PRO)
  • valine (VAL)
  • phenylalanine (PHE)
  • tryptophan (TRP)
  • tyrosine (TYR)
  • aspartic acid (ASP)
  • glutamic acid (GLU)
  • arginine (ARG)
  • histidine (HIS)
  • lysine (LYS)
  • serine (SER)
  • threonine (THR)
  • cysteine (CYS)
  • methionine (MET)
  • asparagine (ASN)
  • glutamine (GLN)
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22
Q

Alanine

A

ALA
aliphatic

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23
Q

Glycine

A

GLY
aliphatic

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24
Q

Isoleucine

A

ILE
aliphatic

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25
Q

Leucine

A

LEU
aliphatic

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26
Q

Proline

A

PRO
aliphatic

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27
Q

Valine

A

VAL
aliphatic

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28
Q

Phenylalanine

A

PHE
aromatic

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29
Q

Tryptophan

A

TRP
aromatic

30
Q

Tyrosine

A

TYR
aromatic

31
Q

Aspartic Acid

A

ASP
acidic

32
Q

Glutamic Acid

A

GLU
acidic

33
Q

Arginine

A

ARG
basic

34
Q

Histidine

A

HIS
basic

35
Q

Lysine

A

LYS
basic

36
Q

Serine

A

SER
has alcohol

37
Q

Threonine

A

THR
has alcohol

38
Q

Cysteine

A

CYS
has sulfur

39
Q

Methionine

A

MET
has sulfur

40
Q

Asparagine

A

ASN
has amide

41
Q

Glutamine

A

GLN
has amide

42
Q

What does aliphatic mean?

A

include the alkanes, alkenes, and alkynes and substances derived from them

43
Q

What are the aliphatic amino acids? (6)

A
  • alanine (ALA)
  • glycine (GLY)
  • isoleucine (ILE)
  • leucine (LEU)
  • proline (PRO)
  • valine (VAL)
44
Q

What are the aromatic amino acids? (3)

A
  • phenylalanine (PHE)
  • tryptophan (TRP)
  • tyrosine (TYR)
45
Q

What are the acidic amino acids?

A
  • aspartic acid (ASP)
  • glutamic acid (GLU)
46
Q

What are the basic amino acids? (3)

A
  • arginine (ARG)
  • histidine (HIS)
  • lysine (LYS)
47
Q

What are the amino acids that have alcohol?

A
  • serine (SER)
  • threonine (THR)
48
Q

What are the amino acids that have sulfur?

A
  • cysteine (CYS)
  • methionine (MET)
49
Q

What are the amino acids that have amide?

A
  • asparagine (ASN)
  • glutamine (GLN)
50
Q

Alkanes, Alkenes, Alkynes, Aromatics

What are the key properties?

A
  • hydrophobic
  • mostly scaffolding for appending functional groups
  • aromatics can participate in cation-pi and pi-pi stacking interactions
51
Q

An alkane as a functional group is referred to as ________.

A

alkyl group

  • note: it is NOT an alkyne
52
Q

Alkanes vs. Alkenes vs. Alkynes

A
  • alkanes: single bonds
  • alkenes: double bond
  • alkynes: triple bond
  • aromatics: cyclic
53
Q

What are the 3 types of branched hyrdocarbons?

A

(pentane C5H12)

  • normal-butyl (n-butyl)
  • iso-butyl (i-butyl)
  • tert-butyl (t-butyl)
54
Q

What are the 3 types of aromatic hydrocarbons?

A
  • ortho: CH3 at 1,2 positions
  • meta: CH3 at 1,3 positions
  • para: CH3 at 1,4 positions
55
Q

What are properties of alcohols, ethers, and carbonyls?

A
  • polar covalent bonds
  • lone pairs on oxygen and nitrogen atoms
  • alcohols and esters may have poor pharmacokinetic properties due to oxidation or hydrolysis (respectively)
56
Q

What are alcohols classified based on?

A

number of carbons that are attached to the carbon that the alcohol is attached to

  • special (0º) – ie. water
  • primary (1º) – ie. ethanol, methanol
  • secondary (2º) – ie. 2-propanol
  • tertiary (3º) – ie. t-butanol
57
Q

What are amines classified based on?

A

number of carbons attached to nitrogen atom

  • special (0º) – ie. ammonia
  • primary (1º) – ie. methylamine
  • secondary (2º) – ie. dimethylamine
  • tertiary (3º) – ie. trimethylamine
  • quaternary (4º) – ie. tetramethylamine
58
Q

What are lactones?

A

cyclic esters

59
Q

What are lactams?

A

amides in ring

60
Q

What are the key properties of halogenated alkanes and aromatics?

A
  • can improve aqueous or lipid solubility (depending on which halogens are used)
  • can be chemically inert or highly reactive
  • introduces polar covalent bonds and can change electron density in aromatic rings
61
Q

What are ionizable groups?

A

functional groups that carry + or - charge under physiological conditions

62
Q

What are the general properties of weak acids?

A
  • H-bond donors
  • can be metabolically labile
  • may lose proton to form anions
63
Q

Weak Acids

What are the key properties of carboxylic acids (and benzoic acids)?

A
  • good water solubility
  • acidic, negatively charged at pH 7.4
  • conjugate base is resonance stabilized
  • pKa range 2-6 (depends on R)
  • make ionic interactions and hydrogen bonds with biological targets
64
Q

Weak Acids

Why is carboxylic acid so acidic?

A

because of the stability of the conjugate base it forms

  • lose proton
  • negative charge is delocalized between two oxygens
65
Q

Weak Acids

What are the key properties of phenols?

A
  • conjugate base is resonance stabilized
  • good solubility – has dipole
  • pKa around 10 (depends on R)
66
Q

What is piperidine?

A
  • cyclic amine
  • weak base
67
Q

What is piperazine?

A
  • cyclic amine
  • weak base
68
Q

Are anilines charged (protonated) at physiologic pH?

A

NO

69
Q

Are pyridines charged (protonated) at physiologic pH?

A

NO

70
Q

Are imidazoles charged (protonated) at physiologic pH?

A

yes if pKa is around 7.5

71
Q

Describe pyridines.

A
  • looks like benzene, but with a nitrogen atom in the ring
  • has permanent dipole – contributes to solubility

PHRM 100 – IMC (11 decks)

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