Bioinformatics Module | Bioinformatics and Drug Design

Pharmaceutical Sciences | 7-classes module

Author

Instructor: Isabel Duarte

Published

September 1, 2025

This 7-week module introduces bioinformatics concepts and tools relevant for pharmaceutical sciences. Students will gain hands-on experience with public databases and online tools to retrieve, analyse, and interpret genomic, proteomic, and transcriptomic data.

Format:

Weekly: 1-hour theory class + 1.5-hour practical class (repeated for 2 student groups).
Each week focuses on one theme, covered in both theory and practical sessions.

Target audience: Pharmacy students with basic knowledge in molecular biology and genetics.

Assessment:

Final short video report: characterisation of a gene/protein using bioinformatics tools.
- 2-5 minutes;
- Groups of 2 students;
- Final presentation and discussion of the video report.

Goal

Learn to independently explore and critically interpret bioinformatics resources in order to connect drugs with their molecular targets and understand their pharmacological, mechanistic, and clinical relevance.

Learning outcomes

By the end of the TP practical classes, students should be able to:

Identify the molecular target(s) of a given drug using authoritative online bioinformatics resources.
Retrieve and interpret relevant information on drug classes, mechanisms of action, target function, pathways, and clinical associations.
Integrate data from multiple sources to explain the pharmacological and clinical importance of a drug–target pair.
Demonstrate independent inquiry skills by selecting appropriate databases, justifying search strategies, and reflecting on findings.
Communicate discoveries clearly through concise answers, group discussions, and structured information reporting.

Evaluation

Any student choosing to complete the worksheet and take part in the class discussion, will earn one bonus point toward the final grade for the bioinformatics module evaluation (the video + presentation report).

Their participation in class will be evaluated using these criteria:

Complete answers → Did you cover everything that was asked?
Smart searching → Did you find the info in a clear and simple way?
Double-checking → Did you confirm the info by looking at more than one place?
Sharing → Are you ready to explain to the class how you found your answers?

Activities general overview

Starting from a drug, the students will be guided on the journey to discover its molecular target, priming them to explore online resources in order to uncover information that is central to pharmaceutical sciences students.

Every activity will follow the same conceptual map:

Drug ➝ Target ➝ Mechanism ➝ Structure ➝ Pathway ➝ Clinical impact

The categories of information that students should be able to find online and articulate for each drug–target pair are:

A. Drug Basics
- Therapeutic category
- Mechanism of action
- Therapeutic indications
- Adverse effects
B. Target Identity
- Gene name and synonyms
- Protein function
- Tissue expression
- Pathophysiological relevance
C. Molecular Mechanism
- Binding site
- Structural information
- Known mutations
- Pathway involvement
D. Clinical and Translational Relevance
- Drug resistance mechanisms
- Drug–drug interactions
- Biomarkers of response
- Approved vs experimental uses

Most relevant databases for each category of relevant information to retrieve for each drug-target pair are (as a general rule):

Drug bank, (ChEMBL, PubChem) = drug details
UniProt = protein details
NCBI/Ensembl/UCSC = gene identity & functional details
PDB = structure
ClinVar/OMIM = clinical genetics & variants
KEGG/Reactome = pathways

Resources summary table

Category	What to Find	Top Resource(s)
1. Drug Basics	Therapeutic category (e.g. NSAID, benzodiazepine, kinase inhibitor, etc.)	NCBI, EBI Search, DrugBank, (PubChem, ChEMBL)
	Therapeutic use (major diseases or conditions it treats)	OMIM, (PubChem, ChEMBL)
	Mechanism of action (at a high level: inhibits, activates, modulates…)	UniProt, DrugBank, (PubChem, ChEMBL)
	Common adverse effects (especially those linked to its mechanism)	ClinVar, OMIM
2. Target Identity	Gene name + synonyms (official symbol, aliases)	Ensembl, NCBI Gene
	Protein function (normal biological role)	UniProt
	Tissue expression (where it is most abundant in the body)	UCSC Genome Browser, UniProt, (The Human Protein Atlas)
	Pathophysiological relevance (disease(s) associated with target)	OMIM, ClinVar, (dbSNP)
3. Molecular Mechanism	Drug binding site (active site, allosteric site, receptor domain)	RCSB PDB
	Structural information (are there PDB structures with the drug bound?)	RCSB PDB
	Known variants/mutations (variants that alter drug response)	ClinVar, (dbSNP)
	Pathways (biological processes where the target participates)	KEGG, Reactome
4. Clinical & Translational Relevance	Drug resistance mechanisms (mutations, enzymatic degradation)	OMIM, ClinVar, (dbSNP)
	Drug–drug interactions (e.g. common metabolising enzymes)	DrugBank, (PubChem, ChEMBL)
	Biomarkers of response (genetic or protein markers that predict efficacy/toxicity)	ClinVar, OMIM, (ChEMBL)
	Approved vs experimental/repurposed uses (has it been repurposed, or are there ongoing trials?)	(ClinicalTrials.gov), DrugBank, (PubChem, ChEMBL)

Activities worksheet [template]

Student and Activity Identification

Activity number: ____________________________

Date & TP group: ____________________________

Student(s) name(s): ___________________________

Drug-Molecular Target report

Drug name: ____________________________

Molecular target (gene/protein): ____________________________

1. Drug Basics

Therapeutic category: _____________________________________
Therapeutic use(s): ______________________________
Mechanism of action (summary): ___________________
Common adverse effects (linked to mechanism): ____

2. Target Identity

Official gene name + synonyms: ___________________
Protein function (normal physiology): ______________
Tissue expression (where is it active?): ____________
Pathophysiological relevance ____________________________

3. Molecular Mechanism

Where does the drug bind? ________________________
Is there a known 3D structure with drug bound? (yes/no; PDB ID if found)
Variants or mutations affecting drug response: ______
Pathways involved (KEGG/Reactome): ______________

4. Clinical and Translational Relevance

Known resistance mechanisms: ____________________
Drug–drug interactions (key enzymes, e.g. CYPs): ____
Biomarkers of response (if any): ___________________
Approved vs experimental/repurposed uses: _________

5. Integrated Reflection

Why is this drug–target pair important in pharmacology?
One new/surprising fact I found for this drug-target pair:

Topic 1 | Introduction to Bioinformatics and Biological Databases

Lecture Topics:

Definition and scope of bioinformatics.
Bioinformatics in drug discovery.
Overview of databases per biological data types.
Primary and secondary databases.
Bioinformatics as an experimental science: search, compare, model, and integrate data.

TP Activity 1:

From Data to Databases: Using Dice to Illustrate Principles of Bioinformatics

Topic 2 | Drugs and Molecular Information

Exploring databases: DrugBank, NCBI

Lecture topics
- Retrieving drug and compound information — DrugBank
- Accessing reference sequences and molecular records — NCBI
- Linking chemical and molecular data — DrugBank / NCBI
Learning goals
- Learn how to retrieve drug and target information from online resources.
- Explore NCBI as a central entry point for biological data.
- Connect pharmacological and molecular data sources.
TP Activity 2
- Ibuprofen & Prostaglandin Pathways

Topic 3 | Proteins and Structures

Exploring databases: UniProt, RCSB PDB

Lecture topics
- Accessing protein annotation, domains, and sequence features — UniProt
- Visualising receptor structures — RCSB PDB
- Exploring ligand binding sites in protein complexes — RCSB PDB / UniProt
Learning goals
- Learn to retrieve and interpret protein functional information.
- Explore 3D receptor structures.
- Integrate protein sequence and structural data.
TP Activity 3
- Diazepam & GABA Receptor Structures

Topic 4 | Variants and Diseases

Exploring databases: ClinVar, OMIM

Lecture topics
- Accessing clinical variant data — ClinVar
- Exploring disease associations and inheritance — OMIM
- Understanding how genetic variation is linked to disease — ClinVar / OMIM
Learning goals
- Learn to retrieve disease-related variant information.
- Explore how clinical resources document genetic associations.
- Relate molecular changes to curated disease knowledge.
TP Activity 4
- Imatinib & Chromosomal Fusions

Topic 5 | Genomes and Regulation

Exploring databases: Ensembl

Lecture topics
- Navigating the Ensembl genome browser — Ensembl
- Exploring the Glucagon-like peptide 1 receptor (GLP1R) gene — Ensembl
- Understanding gene structure (exons, introns, UTRs, CDS) — Ensembl
Learning goals
- Learn to locate a gene in a genome browser.
- Retrieve basic genomic information such as chromosomal position and gene structure.
- Interpret visual representations of genes and transcripts.
TP Activity 6
- Exploring the Semaglutide Target - GLP1R in Ensembl

Topic 6 | Pathways and Signalling

Exploring databases: KEGG, Reactome

Lecture topics
- Exploring EGFR signalling pathways — KEGG
- Mapping growth factor–mediated cascades — Reactome
- Comparing complementary pathway visualisations — KEGG / Reactome
Learning goals
- Learn to navigate pathway maps to locate molecular participants in signalling.
- Compare representations of EGFR signalling across pathway databases.
- Connect EGFR pathways to therapeutic strategies such as tyrosine kinase inhibition in cancer treatment.
TP Activity 6
- EGFR Signalling & Targeted Therapies

Final Evaluation | Integrating Bioinformatics information

Presentation and discussion of the video report prepared by each group, followed by a class discussion, to serve as final evaluation of the bioinformatics module.