The Binding Site and Protein-Ligand Docking

Slide Presentation — Lecture 3

The interactive slides for Lecture 3 are embedded below. Use the arrow keys or the on-screen controls to navigate. Press S to open speaker notes (teaching cues and analogies). Press F to go full screen.

Can’t see the slides? All slide content is written out in full below.

Lecture Notes

Slide 1 — The Binding Site and Protein-Ligand Docking

Lecture 3 — Shape, Chemistry and Binding Energy

Opening question:

“Ibuprofen is a non-polar molecule with a large hydrophobic region. The COX-2 binding site is also largely hydrophobic. Why does this chemical match matter? What would happen if you tried to fit a highly charged, polar drug into a hydrophobic pocket?”

Correct idea: a polar drug in a hydrophobic pocket would be energetically unfavourable — like trying to dissolve oil in water.

Slide 2 — The binding site is where the drug physically docks

A binding site (also called an active site or binding pocket) is a cavity or groove on the protein surface where a small molecule can settle and interact with surrounding amino acids. The drug does not interact with the whole protein — only with the 10–20 amino acids that line this pocket.

Three things must all match for binding to occur:

1. Shape — the drug must fit the pocket geometry
2. Size — not too large, not too small
3. Chemistry — matching polarity and charge between drug and pocket

In Project 4 you will identify every amino acid within 5 Å of Ibuprofen inside COX-2 — these residues form the binding site.

Slide 3 — Rule 1: the drug must fit the shape of the pocket

Shape complementarity — the drug must physically fit the pocket geometry.

Induced fit: A real binding site is not a rigid lock — the protein can flex slightly to accommodate a drug that is close to the right shape.

Concrete numbers: The COX-2 binding channel is 6–8 Å wide at its narrowest point. Ibuprofen is approximately 8 Å across its longest axis — a near-perfect fit. Celecoxib is larger and requires a slightly different part of the channel.

Slide 4 — Rule 2: the drug’s chemistry must match the pocket

Chemical complementarity — the chemistry of the drug must match the chemistry of the pocket.

Analogy: Shape complementarity is like finding a key that fits the lock. Chemical complementarity is like making sure the key is made of the right material. A key made of butter might fit the lock perfectly in shape — but it will fail to turn it.

In Project 4 you will classify every binding site residue as hydrophobic, polar, positively or negatively charged. The chemical profile you produce tells you exactly what kind of drug fits best.

Slide 5 — COX-2: a real binding site example

COX-2 (Cyclooxygenase-2) converts arachidonic acid into prostaglandins, which cause pain and inflammation. Blocking its active site prevents this — the mechanism of action of NSAIDs (non-steroidal anti-inflammatory drugs).

The COX-2 active site is a long, narrow hydrophobic channel lined predominantly with non-polar residues. One key polar residue — Serine 530 — is the site where Aspirin covalently bonds (a different mechanism from non-covalent NSAIDs).

The three drugs you will compare in Project 3:

All three are approved COX-2 inhibitors — they all bind and they all work. But they bind with different strengths, making different contacts. Project 3 will quantify those differences.

Slide 6 — Protein-ligand docking: predicting how a drug fits

Protein-ligand docking is a computational technique that predicts how a small molecule (the ligand) will fit into a protein’s binding site, and how strongly it will bind.

Docking predicts two things:

1. Pose — the orientation and position of the drug inside the binding site
2. Binding energy — how tightly the drug binds

What we do in Projects 3 and 4: The drug is already inside the protein — co-crystallised in the PDB structure. We are scoring a known, experimentally confirmed pose, not predicting a new one. This is simpler and more reliable than full de novo docking.

Real-world power: Screen thousands of candidates digitally in hours. Only synthesise and test the top scorers in the lab. Dramatically reduces the >90% failure rate of untargeted drug development.

Slide 7 — Binding energy: the number that ranks drugs

The subtraction method:

Binding Energy = Complex Score − (Protein Score + Ligand Score)

More negative binding energy = tighter binding = better drug candidate.

Worked example with Ibuprofen:

That −27 REU is the energy gained by bringing the drug and protein together — all the van der Waals contacts, hydrogen bonds, and hydrophobic interactions that form when Ibuprofen settles into the COX-2 pocket.

Slide 8 — Interpreting binding energy values

Negative binding energy (e.g. −27 REU): The drug genuinely binds. Energy is released when the complex forms. The more negative, the tighter the binding. This is what you want for a drug candidate.

Near-zero binding energy (e.g. −2 REU): The drug barely binds. Almost no energy is gained. Unlikely to be therapeutically useful at normal doses.

Positive binding energy (e.g. +8 REU): Binding is energetically unfavourable — the complex is less stable than the separated components. This molecule does not bind under physiological conditions.

Important: Binding energy is one factor, not the only factor. A drug also needs bioavailability (reaching its target in the body), selectivity (avoiding side effects), and chemical stability. Docking tells you about binding — the rest requires lab and clinical testing.

Slide 9 — Structure quality affects every docking result

If the binding site geometry in your crystal structure is wrong by even 0.3 Å, your calculated binding energy will be wrong too.

Why Project 2 comes before Project 3: In Project 2 you rank five Lysozyme structures by quality. In real drug discovery, choosing the highest-quality starting structure always happens before any docking. Garbage in, garbage out — the best scoring function cannot compensate for a poor starting structure.

Slide 10 — The contact shell: which residues touch the drug?

A contact residue is any amino acid with at least one atom within 5.0 Å of any atom of the drug — these are the residues physically touching the drug and contributing to its binding energy.

A binding site may have 200 residues nearby, but only 12–15 are actually touching the drug. Those are the ones that matter for binding energy, drug design, and resistance mutations — and the target of Project 4.

Preview of Project 5: Once you know which residues touch the drug, the natural next question is: which of those residues are most important? That is exactly what Project 5 — alanine scanning — will answer.

Slide 11 — Summary and Preparation

Key takeaways from Lecture 3:

• A binding site is a cavity on the protein surface — shape and chemistry both determine whether binding occurs
• Shape complementarity — the drug must physically fit the pocket geometry
• Chemical complementarity — hydrophobic drug regions face hydrophobic residues; polar faces polar; charged faces oppositely charged
• Binding energy = Complex score − (Protein score + Ligand score). More negative = tighter binding
• Structure quality matters — a poor crystal structure gives unreliable docking results
• Contact residues are within 5.0 Å of the drug — typically 12–15 residues form the functional binding site

Preparation for Lecture 4:

“In Project 5 we will mutate every binding site residue to Alanine and measure how much each mutation weakens drug binding. Think about this: if you removed the side chain of a hydrophobic residue lining the binding site, what would happen to the drug’s binding energy? Why?”

Key Vocabulary

Schedule