MED ORG LEC - 01 Review of Prerequisites

Target

Biomolecule which is targeted by the ligand

Receptor

Transmits signals through messengers

Transporter

Transports ions (channels, pumps)

Enzyme

Catalyzes reactions

Catalyst

Speeds up reaction

Ligand

Compound which binds to the target

Drug

Approved by the FDA

TRUE

TRUE or FALSE

Not all ligands are drugs, but all drugs are ligands

Drug

Approved by the FDA

Inhibitor

Prevents enzyme breakdown

Chemical Foundations

1. The molecule themselves

   1. Small molecules

   2. Biomolecules

2. Polarity and Ionization

   1. Weak acids and bases

   2. Intermolecular forces (IMF)

3. Isomerism

4. Reactivity

Saturated

Molecule with purely single C-C bonds

Unsaturated

Molecule with at least one C=C or C≡C

Conjugated

Alternating C-C and C=C bonds

ex. benzene

Open-chain

• Has terminal parts

• Not cyclic

ex. linear, branched

Cyclic

• Has no terminal parts

• Forms a ring

ex. clycopentane

Carbocyles

• Phenol

• Aniline

• Toluene

• Catechol

• Resorcinol

• Hydroquinone

• Orthoxylene

• Orthocresol

• Benzaldehyde

• Benzoic Acid

• Salicylic Acid

• Anthralinic Acid

• Naphthalene

• Anthracene

• Phenanthrene

Heterocycles

• Pyrrole

• Furan

• Thiophene

• Imidazole

• Oxazole

• Thiazole

• Pyridine

• Pyrazine

• Piperidine

• Piperazine

• Pyrimidine

• Purine

• Quinoline

• Indole

• Isoquinoline

• Benzimidazole

Small Molecules

• Involve organic or inorganic compounds with a MW not exceeding 500 g/mol

  • Must also have a reasonable polarity, allowing it to be either ionized or not depending on the pH

• May be extracted naturally (pharmacognosy) or produced synthetically (synthetic medicinal chemistry)

  • Many natural product exceed 500 g/mol but are still enough to fit some drug targets

    • ex. digoxin 780 - anti-arrythmic

    • vincristine 824 - for cancer

    • erythromycin 734 - antibiotic

Amino Acids

Building blocks of Proteins

Nucleotides

Building blocks of Nucleic acids

Monosaccharides

Building blocks of Carbohydrates

No Universal Building Block

Universal blocks of Lipids

Nonpolar Amino Acids

1. Glycine (Gly, G)

2. Alanine (Ala, A)

3. Valine (Val, V)

4. Leucine (Leu, L)

5. Isoleucine (Ile, I)

6. Methionine (Met, M)

7. Phenylalanine (Phe, F)

8. Tryptophan (Trp, W)

9. Proline (Pro, P)

Polar Amino Acids

1. Serine (Ser, S)

2. Threonine (Thr, T)

3. Cysteine (Cys, C)

4. Tyrosine (Tyr, Y)

5. Asparagine (Asn, N)

6. Glutamine (Glu, Q)

Electrically-charged Amino Acids

1. Aspartate (Asp, D)

2. Glutamate (Glu, E)

3. Lysine (Lys, K)

4. Arginine (Arg, R)

5. Histidine (His, H)

Fischer Projection

Fischer Project or Haworth Projection

ex. D-Glucose

Haworth Projection

Fischer Project or Haworth Projection

ex. α-D-Glucopyranose

Pyrimidine Bases

• Cytosine (C)

• Uracil (U)

• Thymine (T)

Hint: Py-CUT

Purine Bases

• Guanine (G)

• Adenine (A)

Hint: Pur-GA

Guanosine diphosphate

Name this:

Carboxylic Acids

Organic acids are often _____

Amines

Organic bases are often _____

Unionized

Ionized or Unionized

• Acidic pH

• Weak Acid

Ionized

Ionized or Unionized

• Basic pH

• Weak Acid

Ionized

Ionized or Unionized

• Acidic pH

• Weak Base

Unionized

Ionized or Unionized

• Basic pH

• Weak Base

Aspririn

Name this structure

Unionized

Is Aspirin (acidic) ionized or unionized in the stomach?

Amphetamine

Name this structure

Ionized

Is Amphetamine (basic) ionized or unionized in the stomach?

Intermolecular Forces

The actualization of the binding between target and ligand

Ion-Dipole

IMF Type where:

• One should be: Ion (cation/anion)

• The other: Polar

Hydrogen Bond

IMF Type where:

• One should be: Polar, specifically OH, NH, or FH

• The other: Polar

Dipole-Dipole (Keesom)

IMF Type where:

• One should be: Polar

• The other: Polar

Dipole-Induced Dipole (Debye/Van der Waals)

IMF Type where:

• One should be: Polar

• The other: Polar

Induced Dipole-Induced Dipole (London/Hydrophobic)

IMF Type where:

• One should be: Nonpolar

• The other: Nonpolar

Isomerism

• Same molecular formula having different arrangement

• Allows us to review why some molecules have certain prefixes or suffixes in their name

Skeletal isomerism

• n

• iso

• sec

• tert

Positional Isomerism

• ortho

• meta

• para

Configurational Isomers

• Geometric Isomers

  • cis

  • trans

  • E

  • Z

• Optical Isomers

  • R

  • S

  • Racemic Mixtures

Active Conformation

• Conformational Isomers

Optimal arrangement in the binding site