Damanhour University Faculty of Pharmacy

Department of Pharmaceutical Chemistry

Course Name Drug Design

Course Code PC 807

Amino acids

Student Name: Amal Mohammed Walid Mohammed El-Shahawy

Student ID: 19048
Level: four
Under Supervision: Dr. Mahmoud Ragab

Submission: 20/3/2023
 Drug Design (PC807)

Classification of amino acids according to...

Polarity
Polar amino acids:
Arginine (Arg) Asparagine (Asn) Asparate (Asp)
Glutamine (Gln) Glutamate (Glu) Histidine (His)
Lysine (Lys) Serine (Ser) Threonine (Thr)
Tyrosine (Tyr)

Non-polar amino acids:

Alanine (Ala) Glycine (Gly) Isoleucine (Ile)
Leucine (Leu) Methionine (Met) Phenylalanine (Phe)
Proline (Pro) Tryptophan (Trp) Valine (Val)
Cysteine (Cys)

Acidity and basicity

 Acidic amino acids
Aspartate (Asp) - Glutamate (Glu)
 Basic amino acids
Arginine (Arg) - Lysine (Lys) - Histidine (His)
 Neutral amino acids
Serine (Ser) Threonine (Thr) Tyrosine (Tyr)
Alanine (Ala) Glycine (Gly) Isoleucine (Ile)
Leucine (Leu) Methionine (Met) Phenylalanine (Phe)
Proline (Pro) Tryptophan (Trp) Valine (Val)
Cysteine (Cys) Asparagine (Asn) Glutamine (Gln)

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 Drug Design (PC807)

Types of non-covalent interactions can amino acids engage in…

Aspartate
Ionic interaction can occur by the carboxylate group that is formed under
physiological conditions (pH=7.4).

Asparagine
Asparagine has a high propensity to hydrogen bond, since the amide group can
accept two and donate two hydrogen bonds. It is found on the surface as well as
buried within proteins.

Glutamate
Ionic interaction can occur by the carboxylate group that is formed under
physiological conditions (pH=7.4).

Glutamine
It has a high propensity to hydrogen bond, since the amide group can accept two and
donate two hydrogen bonds.

Arginine
It has a high propensity to hydrogen bond, since the amide groups can accept and
donate hydrogen bonds. And It can participate in ionic interaction in the protonated
form
.

Lysine
It can participate in hydrogen bonding, since the amide groups can accept and
donate hydrogen bonds. And It can participate in ionic interaction in the protonated
form.

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 Drug Design (PC807)

Histidine
Four interaction types of histidine, including: (1) Cation-π interactions, in which the
histidine acts as the aromatic π-motif in neutral form (His), or plays the cation role in
protonated form (His+); (2) π-π stacking interactions between histidine and other
aromatic amino acids; (3) Hydrogen-π interactions between histidine and other
aromatic amino acids; (4) Coordinate interactions between histidine and metallic
cations.

Serine
It can participate in hydrogen bonding, since the amide groups can accept and
donate hydrogen bonds.

Threonine
It can participate in hydrogen bonding, since the amide groups can accept and
donate hydrogen bonds.

Tyrosine
It can participate in van der Waals interaction, hydrogen bonding, since the amide
groups can accept and donate hydrogen bonds, and hydrophobic interaction by the
aromatic ring.

Glycine
It can participate in charge-induced dipole interaction, hydrophobic interaction
and hydrogen bonding, since the amide groups can accept and donate hydrogen
bonds.

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 Drug Design (PC807)

Isoleucine
It can participate in hydrophobic interaction by the side chain.

Leucine
It can participate in hydrophobic interaction by the side chain.

Methionine
The methionine side chain is found to fold locally, forming a hydrogen bond with
the neighboring amide groups. It also can participate in hydrophobic interaction. It
cannot form disulfide bond because it lacks a functional S-H site.

Phenylalanine
It can participate in van der Waals interaction, charge-induced dipole interaction
and hydrophobic interaction by the side chain, and has a high propensity to it
because of the aromatic ring.

Tryptophan
It can participate in van der Waals interaction, charge-induced dipole interaction,
hydrogen bonding, since the amide groups can accept and donate hydrogen bonds,
and hydrophobic interaction by the aromatic ring.

Valine
It can participate in hydrophobic interaction by the side chain.

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 Drug Design (PC807)

Alanine
It can participate in hydrophobic interaction by the side chain.

Cysteine
The sulfhydryl group allows the formation of disulfide bonds (however, this is a
covalent bond). It can also participate in weak hydrogen bonding with strong donor
groups.

Proline
It can participate in van der Waals interaction.