pocket, active site, ligand, receptor, and others. For example, aspirin is a
ligand for the molecular target phospholipase A2 (Figure 2B) and
functions by blocking the active site. Interestingly, aspirin also binds
to cyclooxygenase (lesson 2, part 2), which can be mentioned to students as an example of a drug interacting with multiple proteins.
Lesson 2: Drugs Interact with Proteins
Part 1: Introduction to Protein Structure
Figure 3 can be used to explain the hierarchical structure of proteins.
Alternatively, if the Protein Data Bank (PDB; Table 2) has already
been mentioned, students can use a combination of Figure 3 and
their own protein structure images. Concepts that can also be introduced here are native state and protein function dependence on the
correct folding to the native state ( i.e., adopting a unique 3D conformation of the amino acid chain). Students can complete Worksheet 2A
(see Supplemental Material) as part of in-class activity or homework.
Part 2: Exploring Structures of Protein–Drug
Complexes (~30 minutes)
This exercise can be completed in a few different ways depending on
the students’ level of interest and preparation. The easiest way is to use
PDB and its Molecule of the Month library ( http://pdb101.rcsb.org/
motm/motm-by-category). We recommend choosing the “You and
Your Health” or “Drug Action” categories. However, the instructor
or students can choose any other category depending on the overall
context in which this material is taught. Each protein–drug pair in
the Molecule of the Month library is described in the context of dis-
ease symptoms and mechanism of the protein’s native and disease-
causing function, and a URL link (showing as PDB ID) is provided
directly to the protein structure record in the PDB (for an explanation
of PDB ID, see Table 3 footnotes). In this way, students learn the nec-
essary background before accessing the structure file. We typically use
the example of cyclooxygenase from “Drug Action” (http://pdb101.
rcsb.org/motm/17). This particular example is advantageous because
it pertains to a well-known drug (aspirin), allows for an introduction
to pain killers in general, and explains the off-target interactions and
side effects that drugs most often cause. After reading the information
provided, students can follow the link to the structure of the COX-
ligand complex, 4COX, or 1PTH. Figure 4 shows the summary
page of the PDB record for 1PTH, from which students can access
the structure file (via Download tab), literature reference for this
protein structure, and “3D View” programs (“Structure” or “Ligand
Interaction”). “3DView” Structure/Ligand can be used to analyze
the protein’s secondary and tertiary structures as well as the ligand
binding site. The exact location of the ligand binding pocket can be
determined along with the amino acid residues that form the
pocket. More detailed analysis of the structure of the binding
pocket (using “Ligand Interaction”; Figure 5) will help students
understand the mechanism of drug action (blocking the enzyme
active site near the heme group), and identify which amino acids
bind the drug and through what types of interactions (hydrogen
bond, hydrophobic, metal ion). Students learn how the ligand “fits”
the binding pocket in terms of space (ligand size) and interactions
with neighboring amino acids. This knowledge helps inform the
design of an alternative/improved drug. We recommend Work-
sheet 2B (see Supplemental Material) to guide students through
this part of lesson 2 and to help them write meaningful observa-
tions that should be used in lessons 3 and 4.
Alternatively, a more difficult and more advanced form of this
exercise would be to search PDB directly for (1) all available structures of a specific drug target (e.g., adrenergic receptors) to identify
structures that contain a ligand or different ligands, or (2) all available protein structures that are bound to a specific ligand (e.g.,
Figure 2. Examples of proteins bound to drug molecules.
These images (saved from PDB Structure 3D View) illustrate the
protein 3D structure and the concept of ligand binding to a
cavity in the protein surface. (A) Ribbon model of AZT-resistant
HIV reverse transcriptase (PDB ID 1RT3) bound to novel drug
marked by an arrow. (B) Space-filled models of phospholipase
A2 bound to aspirin (PDB ID 1OXR). The ligand is shown in
both A and B as a space-filled model.
Figure 3. The hierarchical nature of protein structure.
(A) Amino acids and peptide bonds form a protein chain.
(B) Backbone folds to form secondary structural elements
(alpha-helices and beta-strands) with side chains “hanging.”
(C) Tertiary structure showing the conformation of the
backbone and secondary elements. (D) Space-filled model of
the tertiary structure illustrating dense packing of atoms.
Images created using VMD (Humphrey et al., 1996) of OXA-24
beta-lactamase (PDB ID 3PAE).