An Introduction to Chemical Thinking: Through the Lens of Antimalarial Drug Design:
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Research project this CURE supports: DRUG DESIGN
A brief Introduction to Malate Dehydrogenase
Science/background for this CURE:
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 (Human) homologs exist. Malaria, caused by the pathogen Plasmodium falciparum (Pfalciparum) is an excellent example. Both pathogen and host depend on Malate Dehydrogenase as a key part of their energy metabolism. Pfalciparum Malate Dehydrogenase is tetrameric while the human homologs are dimeric- do the oligomeric differences allow specific targeting of inhibitors to preferentially inhibit the Pfalciparum enzyme. Although Malate Dehydrogenases in general show overall tertiary structure similarities there are some regions of sequence difference between Pfalciparum and Human forms of mDH that, as we have shown, may lead to the existence of unique cryptic allosteric sites that could be targeted for allosteric drug design. Similarly, subtle differences in the active site regions (which bind substrates and orthosteres -orthosteric ligands interacts with the same binding site as the natural endogenous ligand ), while an allosteric ligand binds to another separate site (or sites) on the receptor ) could be exploited for orthosteric drug design. In addition to ligand specificity, bioavailability issues involving exploring the Physicochemical Design Space of potential “lead” compounds for future drug design are also incorporated.
Relevant Literature that support this science:
“Allosterism and Drug Discovery” Bell, E & Bell J., Burger’s Medicinal Chemistry, Drug Discovery and Development, Eighth Edition. Volume 2, pages 163-240, 2021. Publisher- Wiley
The existence of a Cryptic Allosteric Site on Plasmodium falciparum Malate Dehydrogenase, Natalie Botros, Ellis Bell, Jessica Bell, First published: 18 April 2020, https://doi.org/10.1096/fasebj.2020.34.s1.05326
Potential Drug Design for Plasmodium falciparum Malate Dehydrogenase Targeting the Cryptic Allosteric Site, Natalie Botros, Ellis Bell, Jessica Bell First published: 14 May 2021, https://doi.org/10.1096/fasebj.2021.35.S1.02936
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity. Reyes Romero A, Lunev S, Popowicz GM, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak TA, Dömling ASS, Groves MR.Commun Biol. 2021 Aug 10;4(1):949. doi: 10.1038/s42003-021-02442-1.
Oligomeric interfaces as a tool in drug discovery: Specific interference with activity of malate dehydrogenase of Plasmodium falciparum in vitro, Sergey Lunev 1, Sabine Butzloff 2, Atilio R Romero 1, Marleen Linzke 3, Fernando A Batista 1, Kamila A Meissner 3, Ingrid B Müller 2, Alaa Adawy 1, Carsten Wrenger 3, Matthew R Groves 1, PLoS One, 2018 Apr 25;13(4):e0195011., doi: 10.1371/journal.pone.0195011. eCollection 2018.
Exploring the role of the dimer interface in Plasmodium falciparum malate dehydrogenase: The impact of Q11I, I15Q, L19N and L22N mutations on quaternary structure and enzymatic properties. Daniel Armendariz, Diego Hernandez, Megan Keene, Jessica Bell & Ellis Bell, Journal of Biological Chemistry (2023) Vol. 299Issue 3SupplementPublished in issue: 2023
Using enzyme kinetics and computational docking studies to understand substrate and inhibitor interactions with human mitochondrial, human cytosolic, watermelon glyoxysomal and Plasmodium falciparum malate dehydrogenases. Diego Hernandez, Jessica Bell & Ellis Bell , Journal of Biological Chemistry (2023), Volume 299, Issue 3, 103638
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Christopher A. Lipinski”, Franc0 I,ombardo, Beryl W. Dominy, Paul J. Feeney, Advanced Drug Delivery Reviews 23 (1997) 3-25, doi: 10.1016/s0169-409x(00)00129-0. PMID: 11259830
3-5 Learning goals for this CURE:
1. Students will appreciate that a good research project entails nine essential elements of research and will develop a novel hypothesis that makes predictions that can be tested experimentally, and present a proposal for their project. Rubric 1
2. 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. Rubric 2
3. Students will learn to develop a description of their research project in written, poster or a slide presentation suitable for verbal presentation. Rubric 3
Research question for this CURE:
1. Can you develop ideas for potential lead compounds that can distinguish between pathogen and host homologs of a potential drug target?
2. Can you understand the target structure-function relationships that underpin orthosteric or allosteric inhibitors of the target?
3. Can you propose and initiate potential strategies for optimizing the potential of such lead compounds to increase their suitability as candidates for potential future drug design?
2-3 Sample hypotheses students could come up with for this CURE:
Introductory lectures have defined types of approaches to drug development and can be broken down to two basic approaches: structure based drug design or a screening potential candidates approach. Students can select one of these approaches or the approach can be set by the instructor.
Students are led through Hypothesis and Proposal Preparation using the rule of threes approach:
Typically student hypotheses hone in on some unique aspect of theP falci MDH protein structure (established by Clustal Analysis and computational analysis), or some unique aspect of an actual or a potential ligand depending on the overall approach they choose to take (structure based ligand design or screening approach)
What Experimental Approaches can be Incorporated?
Wet Lab Techniques: Link to theory and practical descriptions of wet lab techniques
Computational Techniques
CURE format: modular, semester, Either
Week by week lab activities for a modular version (6 weeks) and/or semester long version of this CURE :
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 (may include aspects of 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.
Ideal group size for this CURE: Groups of 2-3 students
Ideal course/level for this CURE (chem, bio, biochem, interdisciplinary; first year, middle years, capstone): (list as many as are possibilities)
First Year Chemistry or Biology,
middle years,
upper level
Teaching Resources Available:
Powerpoints to Introduce Each Weeks Lab Session
Generic Customizable Templates for student activities for each of the 9 essential elements of research incorporated into the CURE
T4: Proposal
T5: Experimental Design & Execution
T6: Reproducibility
T7: Data Analysis & Conclusions
Rubrics to Guide & Assess Student Performance
Mol and Mol2 files of 3,4, 5 and 6 carbon ligand analogs for use in Computational Experiments
Pdb files of Human Cytosolic MDH Dimer, Human Mitochondrial MDH-Dimer and Plasmodium falciparum MDH Tetramer suitable for computational experiments (Linked to Clone Data Sheets below)
Instrumentation/equipment/key reagents needed for this CURE
Uv-vis Spectrophotometer, Equipment for acid-base titrations, pH Meter, Balance, Water Bath, Stir Plate
Protein (WT and/or specific mutant), organism:
Plasmids needed can be obtained from Addgene:
Plasmodium falciparum, Human Mitochondrial, Human Cytosolic
Clone Data Sheets for this Project Area:
MW(subunit/biological)/pI/ e280 , extinction coefficient (280 nm: calculated using ProtParam.) of protein (WT and/or specific mutant):
Plasmodium falciparum: MWt: 35,715/142,860, pI(theoretical): 6.89 e280 0.375 mL.mg-1.cm-1
Human Mitochondrial: MWt: 34,806/69612, pI(theoretical): 8.33 e280 0.257 mL.mg-1.cm-1
Human Cytosolic:MWt: 39,749/79,498, pI(theoretical): 7.14 e280 0.853 mL.mg-1.cm-1
PDB ID for the WT version of these protein :
Plasmodium falciparum: 5.nfr.pdb
Human Cytosolic: 7rm9.pdb
Human Mitochondrial: 2dfd.pdb
Available Resources for structural analysis and computational approaches: Biologically relevant pdb files
Plasmodium falciparum Tetramer
Human Cytosolic Dimer
Human Mitochondrial Dimer
Landmarked .pse files for use with the project - see clone datasheets for descriptions