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==Module 1: drug discovery==
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Small molecules, or ligands, are important research tools used to explore cellular processes and therapeutic targets.  The use of high-throughput and unbiased strategies to identify small molecules that bind specific biomolecules, such as proteins, can provide insight on the structure or function of targets.  Additionally, a small-molecule screen can identify new chemical probes for target proteins of interest. 
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The small-molecule microarray (SMM) is a high-throughput method that enables the detection of protein-ligand binding. Briefly, ligands are 'printed' onto a slide and incubated with purifed protein.  Unbound protein is washed from the slide and bound protein is detected using a tag on the protein of interest.  Because the location of every ligand on the slide is known, the detection of protein indicates that it is bound to the ligand at that location.
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In this module, you will leverage the SMM technology to identify small molecules that putatively bind MAX (myc-associated factor X), our protein target.  The MAX protein contains the basic helix-loop-helix and leucine zipper motifs and functions as a transcription factor in humans.  In this role, it forms homodimers and heterodimers with other transcriptional factors.  Notably MAX dimerizes with Myc, an oncogenic transcription factor.  Because this dimerization is required for Myc to act as a transcription factor, inhibitors of this process are clinically relevant and may lead to the development of a drug therapy to treat cancer.
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<font color=  #015526    >'''Research goal:  Identify small molecules that putatively bind to MAX using SMM technology.'''</font color>
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[[Image:Sp23 M1 overview.png|center|750px|thumb|Image generated using BioRender.]]
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==Lab links: day by day==
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M1D1: [[20.109(S23):M1D1 | Complete in-silico cloning of protein expression plasmid]]<br>
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M1D2: [[20.109(S23):M1D2 |Perform protein purification protocol]] <br>
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M1D3: [[20.109(S23):M1D3 |Assess purity and concentration of purified protein]] <br>
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M1D4: [[20.109(S23):M1D4 |Confirm purified protein using Western blot]] <br>
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M1D5: [[20.109(S23):M1D5 |Image Western blot of purified protein]] <br>
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M1D6: [[20.109(S23):M1D6 |Prepare and scan small molecule microarray (SMM) slides]] <br>
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M1D7: [[20.109(S23):M1D7 |Analyze SMM data to identify putative small molecule binders]] <br>
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M1D8: [[20.109(S23):M1D8 |Organize Data summary figures and results]] <br>
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==Major assignments==
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[[20.109(S23):Research talk |Research talk]] <br>
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[[20.109(S23):Data Summary |Data summary]] <br>
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==References==
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*[[Media:Sp17 M1 reference NatProt.pdf| A method for the covalent capture and screening of diverse small molecules in a microarray format.]] ''Nature Protocols.'' 1:2344-2352.
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*[[Media:Sp17 M1 reference ChemBiol.pdf| Recent discoveries and applications involving small-molecule microarrays.]] ''Chemical Biology.'' 18:21-28.
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==Notes for Instructors==
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[[20.109(S23): Prep notes for M1| Prep notes for M1]]

Latest revision as of 21:13, 5 February 2023

20.109(S23): Laboratory Fundamentals of Biological Engineering

Sp23 banner image v2.png

Spring 2023 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Drug discovery        M2: Protein engineering        M3: Project design       


Module 1: drug discovery

Small molecules, or ligands, are important research tools used to explore cellular processes and therapeutic targets. The use of high-throughput and unbiased strategies to identify small molecules that bind specific biomolecules, such as proteins, can provide insight on the structure or function of targets. Additionally, a small-molecule screen can identify new chemical probes for target proteins of interest.

The small-molecule microarray (SMM) is a high-throughput method that enables the detection of protein-ligand binding. Briefly, ligands are 'printed' onto a slide and incubated with purifed protein. Unbound protein is washed from the slide and bound protein is detected using a tag on the protein of interest. Because the location of every ligand on the slide is known, the detection of protein indicates that it is bound to the ligand at that location.

In this module, you will leverage the SMM technology to identify small molecules that putatively bind MAX (myc-associated factor X), our protein target. The MAX protein contains the basic helix-loop-helix and leucine zipper motifs and functions as a transcription factor in humans. In this role, it forms homodimers and heterodimers with other transcriptional factors. Notably MAX dimerizes with Myc, an oncogenic transcription factor. Because this dimerization is required for Myc to act as a transcription factor, inhibitors of this process are clinically relevant and may lead to the development of a drug therapy to treat cancer.


Research goal: Identify small molecules that putatively bind to MAX using SMM technology.

Image generated using BioRender.



Lab links: day by day

M1D1: Complete in-silico cloning of protein expression plasmid
M1D2: Perform protein purification protocol
M1D3: Assess purity and concentration of purified protein
M1D4: Confirm purified protein using Western blot
M1D5: Image Western blot of purified protein
M1D6: Prepare and scan small molecule microarray (SMM) slides
M1D7: Analyze SMM data to identify putative small molecule binders
M1D8: Organize Data summary figures and results

Major assignments

Research talk
Data summary

References

Notes for Instructors

Prep notes for M1
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