Drug development coursework
You and your three colleagues have founded a start-up company using limited funds obtained
from family and friends. You are considering developing a drug candidate based on a natural
product identified from one of the four different plants that you and your team members have
previously worked on as part of the TPODD-1 labs. During initial discussions of the board meeting,
it was concluded that the available funds would be sufficient for in-silico work. Therefore, it was
agreed to:
1. Conduct preliminary studies as a basis for the selection of the most promising compound that
can be taken for lead optimization (50% of marks – individual mark)
a. Select a bioactive molecule found in the extract from a plant from the mini-project,
justify selection (10 %);
b. Assess the ADME and drug-likeness (identify 3 favourable properties and 3 properties
that could be improved via drug optimization) (10%);
c. Identify potential drug target for this compound and PDB ID for a selected target
(10%);
d. Identify the therapeutic area/disease to be targeted (5%);
e. Explore the patient base and the market size (15%).
2. Develop a drug candidate and validate its drug-like properties (40% of marks – team mark)
a. Select one candidate out of four proposed molecules and justify your selection (5%);
b. Each team member suggests one chemical modification that could improve the drug_xfffe_like properties of the candidate (10%);
c. For all four analogues predict ADMET properties and binding affinities to a relevant
protein (15%);
d. Provide a justification for a selection of an analogue with optimal properties that can
be submitted to CRO for synthesis and experimental evaluation (10%).
3. Propose a funding strategy to experimentally confirm the drug candidate′s suitability for
further development (10% marks; team mark)
You must produce a joint report that will be evaluated by business angels. The report must be
submitted by 5pm on 13th February 2023 via Moodle.
Coursework requirements and document formatting.
Every member of the team should be submitting an identical copy of the report prepared by the
team. The report must be in a PDF format and named as:
Team_name.pdf
(Team_name should be replaced by the name that you chose). Your identity (your name or student
number) should not be revealed anywhere in the file or file name.
The file should contain:
– Title page
– A brief introduction to the project stating the background, plants and aims (max 100 words –
not marked, but the lack of the paragraph or poorly presented information will result in a mark
reduction of up to 10%).
– For task 1: four tables, one table per team member and each table on a separate page.
(individually marked):
o A full table caption that explains the content of the table. The table caption must
contain the team name and number of the team member according to the list of
members in the submitted excel file (the student name or number should not
feature in the document).
Plant name: Insert name here Insert latin name here (in
italics)
Selected molecule: Insert name Insert SMILES string
Justify selection: Max 100 words
Drug like property 1: Insert name Insert value
Drug like property 2: Insert name Insert value
Drug like property 3: Insert name Insert value
Property to be improved 1: Insert name Insert value
Property to be improved 2: Insert name Insert value
Property to be improved 3: Insert name Insert value
Predicted drug target and
PDB ID
Insert full drug target name Insert PDB ID
Therapeutic area/disease One sentence justification
Market size Max 200 words.
– For task 2: one table (marked as a team)
o A full table caption that must contain the information on the selected plant and
molecule name – lack of the information will result in zero marksfor this contribution.
a. State the selected candidate for further development and justification for the
selection (50 words). Provide SMILES string and 2D structure as a separate figure
with the figure caption.
b. Include a figure with 2D structures of four analogues. This can be shown as a table
Candidate number 1 – Analogue 1 Candidate number 2 – Analogue 2
Candidate number 3 – Analogue 3 Candidate number 4 – Analogue 4
c. Include a table with selected ADMET parameters and binding affinities against
selected target.
Molecule Original Analogue 1 Analogue 2 Analogue 3 Analogue 4
ADMET name 1
ADMET name 2
ADMET name 3
ADMET name 4
ADMET name 5
ADMET name 6
Binding affinity
or docking score
(include units)
*
replace with the name of the selected property
d. Justify your selection (max 200 words).
– For task 3: concluding paragraph that states the funding strategy (marked as a team – max
300 words).
– References in Vancouver style
All figures and tables should have captions. Formatting issues will result in a reduction of marks
(up to 10%).
Suggested resources but not limited to:
– Literature review to select the most promising compound for your plant and suggest a
therapeutic area (based on your mini project)
– Target prediction (ligand-based and structure-based approaches)
o SwissTargetPrediction (http://www.swisstargetprediction.ch/)
o SuperPred (http://prediction.charite.de)
o LigTMap (https://cbbio.online/LigTMap/)
– ADME and ADMET properties.
o http://www.swissadme.ch/
o Resources discussed in preclinical toxicology lectures
– Lead optimization (previously taught course material).
– Docking
o https://dockthor.lncc.br/v2/
o https://proteins.plus/
o http://dxulab.pharmacy.isu.edu/curry/ezCADD/main.html
o https://durrantlab.pitt.edu/webina/
Prof. Zloh
17.01.2023.
