Introduction to Chemical Thinking: Through the Lens of Antimalarial Drug Design
Ellis Bell, University of San Diego
Dawn Marin, Gaston Community College, NC
David Hecht, Southwestern Community College, CA
Location: California
Abstract
An Introduction to Chemical Thinking: Through the Lens of Antimalarial Drug Design
This CURE is taught in a standard 3-4 hour lab taught once a week throughout the semester. Each class during the semester has components focused on a) the project and b) foundational concepts of introductory chemistry that they see in the separate lecture sections. The project was designed to satisfy the standard Chemistry Lab Learning Goals that all sections of General Chemistry Lab address. The CURE project, threaded throughout the semester, features all the standard elements of a CURE, Relevance, Scientific Background, Hypothesis Development, A Proposal, Experiments & Teamwork, Data Collection and Reproducibility, Data Analysis and evidence based conclusions, and a formal presentation of the overall project.
In this CURE section students gain both technical expertise & research experience through the lens of Antimalarial Drug Design. During the semester they develop and present a research project proposal including relevance, scientific background, and hypothesis development. They design and perform experiments using a variety of classic chemistry techniques (quantitative reagent preparation including buffers, titration, kinetics, spectroscopy, molecular modeling) in the context of experiments to explore structure function relationships of potential antimalarial drugs targeted towards a specific enzyme, Malate Dehydrogenase. Students will develop and test research ideas related to novel approaches to target the parasite but not the human host. Based on appropriate data analysis (including statistical analysis and appropriate graphical representation) they select key experiments to repeat to establish reproducibility, allowing them to draw evidence based conclusions. At the end of the semester they present all aspects of their project in a final presentation. Each of the three presentations in the course includes peer review and revision and students are provided with extensive rubrics for each presentation.
Student Goals
- Students will appreciate what a good research project entails and will develop approaches to develop a novel hypothesis that makes predictions that can be tested experimentally, and present a proposal for their project
- Students will learn how to design and execute experiments to test their hypothesis, will learn appropriate data analysis approaches and will appreciate the importance of accurate documentation of their work and reproducibility of their experiments.
- To develop a description of their research project in written, poster or a slide presentation suitable for verbal presentation
Research Goals
- To develop ideas for potential lead compounds that can distinguish between pathogen and host homologs of a potential drug target
- To understand the target structure-function relationships that underpin orthosteric or allosteric inhibitors of the target.
- To initiate potential approaches for optimizing the potential of such lead compounds to increase their suitability as candidates for potential future drug design
Context
This CURE was designed for introductory chemistry students in a lab class of 18-24 students at three different institutions, University of San Diego, Southwestern Community College and Gaston Community College. The CURE can be taught as either a full semester CURE or as a 4-6 week modular CURE within a standard laboratory class. It is suitable for students in an introductory level chemistry class and requires no specialized knowledge. This CURE is readily adaptable to any disease or potential drug target as well as other aspects of drug discovery and optimization.
CURE Design
The research theme at the heart of this CURE is a perennial problem facing drug development- how can you achieve specificity for a pathogen target when host homologs exist. The CURE starts with discussions of the target enzyme, Malate Dehydrogenase and what it does in both pathogen and host and introduces some basic ideas of both orthosteric and allosteric drugs. Students then decide which approach they want to pursue, do background reading into Malaria, start to pose questions of what they need to know or be able to do to uniquely target the pathogen MDH. They start some bioinformatics and protein visualization approaches and develop ideas for compounds they would like to screen (including high throughput screening, screening extracts of natural products eg herbal extracts etc), making a hypothesis and developing their research proposal. They screen potential "drug-like" molecules based on known or potential orthosteric ligands using enzyme inhibition kinetics, and explore potential cryptic allosteric sites computationally all the time using pathogen target and human homologs. They explore Lipinsky rule of 5 properties both experimentally, determining logP, or structure-activity relationship properties computationally. As part of their experiments they learn and apply appropriate data analysis and display approaches, and accurate recording of experimental details and data archiving before selecting, based on their hypothesis and actual data they collected which experiments need repeating to validate their evidence based conclusion. In each stage the course uses peer review of presentations on critical elements of the research enterprise and students have the chance to revise based on feedback prior to grading
Depending on the approach they chose to use there are a variety of potential stake holders, and students are encouraged to think about the relevance of their project proposal and communicate as appropriate their plans early in the course and research products at the end of the course, explaining why there is a continual need for new antimalarial drugs and what approach they have chosen to pursue.
Tasks that Align Student and Research Goals
Student Goals ↓
Students use computational docking of ligands (using freely available SwissDock) to target and explore specificity and affinity and structure-activity relationships-for potential binding sites. Students are encouraged to use structure activity relationships to attempt to design new ligands and maximize specificity and affinity. They are provided with a template to record their thinking and approach and results.
Commercially available software such as OpenEye Scientific Cadence Molecular Sciences, or MOE can also be used for ligand based or structure based drug design.
Students determine LogP determinations using phase separation of specific compounds and use MolView to explore Lipinsky Rule of 5 properties of compounds
There are three student "presentations" during the course-1) a formal research proposal, 2) a Data Presentation and 3) a final presentation of the whole project and its outcomes. At each presentation we use a peer review system and the students get a chance to revise prior to grading.
Instructional Materials
Syllabi (Acrobat (PDF) 385kB Jun2 23)
Assessment
Combined CURE Essentials Rubrics (Acrobat (PDF) 268kB Jun2 23)
Experimental Design and Execution Rubric (Acrobat (PDF) 186kB Jun2 23)
Instructional Staffing
The class at USD (PUI) runs with the help of a student teaching assistant who helps with assisting students and helping to trouble shoot problems as necessary. The TA is usually a student who has taken the course previously. Department prep staff are responsible for making sure appropriate chemicals are available and setting up necessary equipment (pH meter, balances, spectrophotometers). We incorporate collaboration in two ways, using an external faculty collaborator, and using student to student collaboration where the collaborating students are in a different CURE studying the same basic problem.
The class at GCC uses an instructor and department prep staff to run and prep the lab, help students trouble shoot and assist with data analysis.
The class at SWCC has one instructor to run the lab and supervise students and had department prep staff to prep common reagents and ensure appropriate materials were available.
Students in the class were responsible for setting up and calibrating their pH meters and spectrophotometers. Students also design and prep their own buffers and necessary reagents
Author Experience
Ellis Bell, University of San Diego
This CURE, "Introduction to Chemical Thinking: Through the Lens of Antimalarial Drug Design" was developed developed and implemented to provide undergraduates in first year chemistry with exposure to a research area that required an interdisciplinary approach to a problem of global relevance that would provide insight into how not only chemists but also biologists can collaborate, and that is easily adaptable to both the Community College setting and the 4 year College setting.
Dawn Marin, Gaston Community College
Dawn Marin developed a modular CURE on drug design for the human mitochondrial version of MDH as a way to get students involved in undergraduate research with the SPARC program at Gaston College, and to give students an authentic experience of what a medicinal chemist could do as a potential career choice. In addition, molecular modeling and docking are valuable tools to help students to visualize chemistry and understand how molecules interact..
David Hecht, Southwestern Community College
At Southwestern Community College, this CURE introduced students to how biotech and pharmaceutical companies actually conduct new leads discovery utilizing the tools and techniques that are typically introduced at the general chemistry level. Care was taken to ensure that the activities matched the learning objectives for the course.
Advice for Implementation
This CURE is readily adaptable to other pathogen based diseases since a major question is based on how a potential drug might distinguish pathogen from host target. It is also a CURE where a wide variety of computational approaches can be incorporated which helps to maintain low costs without diminishing the incorporation of the CURE elements since most of the computational approaches are available free on servers around the world or use free downloadable software.
Iteration
Students learn first to identify that they have a problem- for example in measuring enzyme kinetics their first trouble shooting experience comes in deciding how much enzyme to add to the assay using a "TOTALS" approach where they learn to Try something, Observe the outcome, Think about their observation, Adjust the amount of enzyme they add based upon what they observed and repeat until they get what they know is required for them to get an accurate initial rate at which point they can leave Lab Smiling knowing that they have learned how to trouble shoot an experiment so they get good reproducible data. Later in the course they have to identify key experimental observations that lead to important conclusions and repeat the whole experiment to confirm their findings.
Using CURE Data
Students learn how to keep accurate records of experimental details and how to appropriately archive both primary and meta-data. The final presentations are shared with stakeholders. Important results are repeated and built upon in subsequent classes and often confirmed in non CURE research activities by individual students or collaborators.
Early in the course the ultimate goal of publishing the project in the peer reviewed scientific literature is discussed and students made aware of the importance of thoroughly documenting their ideas and hypothesis and experimental work emphasized. Authorship is attributed based upon who contributed authenticated data, figures, ideas etc to a final manuscript. Where important data is authenticated both the original creator of the data and the authenticator of the data are eligible for authorship. All authors are required to read any manuscript and approve prior to submission.
Resources
- Teaching Virtual Protein-Centric CUREs and UREs Using Computational Tools, Bell, Jr., A, Christian, L, Hecht, D, Huisinga, K, Rakus J, and Bell,E. Biochem Mol Biol Educ. 2020 Nov;48(6):646-647. doi: 10.1002/bmb.21454. Epub 2020 Sep 12
- Using research to teach an "introduction to biological thinking". Bell E., Biochem Mol Biol Educ. 2011 Jan-Feb;39(1):10-6. doi: 10.1002/bmb.20441.
- *Allosteric Proteins & Drug Discovery" by J.Ellis Bell & Jessica K. Bell. Burger's Medicinal Chemistry, Drug Discovery & Development, 8th Edition, Abraham, D.J. Ed., Vol. 2, 2021, John Wiley and Sons, Inc: New York City.
- *Lunev S, Butzloff S, Romero AR, Linzke M, Batista FA, Meissner KA, Müller IB, Adawy A, Wrenger C, Groves MR. Oligomeric interfaces as a tool in drug discovery: Specific interference with activity of malate dehydrogenase of Plasmodium falciparum in vitro. PLoS One. 2018 Apr 25;13(4):e0195011. doi: 10.1371/journal.pone.0195011. PMID: 29694407; PMCID: PMC5919072.
- Karami TK, Hailu S, Feng S, Graham R, Gukasyan HJ. Eyes on Lipinski's Rule of Five: A New "Rule of Thumb" for Physicochemical Design Space of Ophthalmic Drugs. J Ocul Pharmacol Ther. 2022 Jan-Feb;38(1):43-55. doi: 10.1089/jop.2021.0069. Epub 2021 Dec 14. PMID: 34905402; PMCID: PMC8817695.
- Duchowicz PR, Talevi A, Bellera C, Bruno-Blanch LE, Castro EA. Application of descriptors based on Lipinski's rules in the QSPR study of aqueous solubilities. Bioorg Med Chem. 2007 Jun 1;15(11):3711-9. doi: 10.1016/j.bmc.2007.03.044. Epub 2007 Mar 18. PMID: 17418580.
- *Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 2001 Mar 1;46(1-3):3-26. doi: 10.1016/s0169-409x(00)00129-0. PMID: 11259830.
* indicates papers students should read/be guided through. Students also are led through how to find appropriate literature and how to read a paper as a critical part of the CURE
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