20.109(F20):Module 2

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20.109(F20): Laboratory Fundamentals of Biological Engineering

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Fall 2020 schedule        FYI        Assignments        Homework        Communication |        Accessibility

       M1: Genomic instability        M2: Drug discovery        M3: Metabolic engineering       

Module 2

Lecturer: Jacquin Niles
Instructors: Noreen Lyell, Leslie McClain, and Becky Meyer


Malaria is a mosquito-borne disease caused by Plasmodium parasites. This life-threatening disease is estimated to be responsible for over 400,000 deaths with 228 million cases worldwide per year. The impact of malaria is disproportionately represented in Africa where 93% of malaria cases and 94% of malaria deaths occurred in 2018 (World Health Organization).

In this module, you will explore drug discovery by focusing on a specific infectious disease, malaria, as an example of how small molecules can be used in therapeutics. The process by which new therapeutics are tested to ensure safety and effectiveness often requires years or decades. Here we will focus on the front-end of this process by considering what makes a good therapeutic. The basis for making this decision is often rooted in knowledge regarding the fundamental biology of the organism / disease. Sometimes little is known about what is occurring at the molecular level and therefore it is difficult to design a therapeutic.

Small molecule screens can be useful in drug discovery when a targeted approach is not feasible. For your project you will use a small-molecule microarray (SMM) to identify molecules that putatively bind a protein target in Plasmodium falciparum. The Niles Laboratory has been working to identify small, essential proteins of unknown functions from P. falciparum for drug discovery attempts. In this, multiple genes of interest have been cloned and knocked down in the parasite and if found to be essential the targets were used for drug screening by SMM.

The protein that you will study this semester is a protein that was identified using this process. Thought the structure of the protein was solved, the literature is not rich for this gene. This is one of the troublesome features of working with uncharacterized proteins but they can be good drug targets because, most likely, these genes do not have a human orthologue. Therefore, drug selectivity can be achieved.

Research goal: Identify small molecules that bind to the PF3D7_1351100 protein in Plasmodium falciparum using small-molecule microarray

Image generated using BioRender.

Lab links: day by day

M2D1: Complete in silico cloning of protein expression plasmid
M2D2: Perform protein purification protocol
M2D3: Assess purity and concentration of purified protein
M2D4: Prepare small molecule microarray (SMM) slides with purified protein
M2D5: Scan SMM slides to identify putative small molecule binders
M2D6: Analyze SMM data to confirm putative small molecule binders
M2D7: Examine putative small molecule binders for common features

Major assignments

Journal club presentation
Research article


A method for the covalent capture and screening of diverse small molecules in a microarray format. Nature Protocols. (2006) 1:2344-2352.

Recent discoveries and applications involving small-molecule microarrays. Chemical Biology. (2014) 18:21-28.

PF3D7_1351100 genetic validation image Image Reference linked here: [1]

Brief description of the plot: ranked order plot of all Plasmodium falciparum genes ranked from most essential (left) to dispensable (right) along the x-axis. A piggyBAC insertion mutagenesis screen (mobile element that inserts into genes to disrupt production of their encoded protein) was used to generate the data included in the plot.

Notes for teaching faculty

Prep notes for M2