Current Fellow Spotlights: Research at the Chemistry-Biology Interface

Current CBI Fellows:

Ally Smith

When used in isolation, neither in silico nor in vitro biophysical methods provide a complete understanding of protein structure and dynamics. Integrative approaches, which attempt to overcome the shortcomings of individual techniques, are thus gaining increasing popularity amongst computational and experimental biophysicists alike. By providing unique insights into biomolecular structure and dynamics, allostery, and ligand binding, this framework serves to aid downstream efforts in materials science, disease pathophysiology, and structure-based drug design. My research focuses on the development of computational tools and methods for integrating solution-phase HDX-MS data with molecular dynamics (MD) simulations in order to model native-state protein conformational ensembles with atomistic resolution. I designed an experimentally directed adaptive sampling algorithm called “HDX-AS” to drive MD simulations towards a target HDX-MS dataset. In practice, this involves running several independent replicas in parallel, scoring them based on their similarity to the target experimental dataset, and propagating multiple walkers from the top-ranking simulations. Moreover, differential HDX-MS data between two distinct states (e.g., ligand-bound vs. unbound) may be leveraged to improve protein structure prediction accuracy. Future work and cross-training efforts will therefore center on building a supervised machine learning model to identify protein-small-molecule docking poses with the correct binding interface.

Notable publications and presentations:

  1. Kihn, K. C.; Wilson, T.; Smith, A. K.; Bradshaw, R. T.; Wintrode, P. L.; Forrest, L. R.; Wilks, A.; Deredge, D. J. Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting. Biophys. J. 2021, 120(23), 5141-5157.
  2. Lee, P. S.; Bradshaw, R.; Marinelli, F.; Kihn, K.; Smith, A.; Wintrode, P. L.; Deredge, D. J.; Faraldo-Gómez, J. D.; Forrest, L. R. Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. LiveCoMS. 2022, 3(1), 1521.
  3. Smith, A. K.; Deredge, D. J. Generating In Silico
    Protein Structural Ensembles that Agree with Solution-based Experiments: An HDX-MS-steered Adaptive Sampling Approach for Molecular Dynamics. 68th
    Biophysical Society Annual Meeting. February 2024. (Poster, 2nd Place Award)

Sean O’Sullivan

Electronic cigarette (e-cigarette) usage has risen dramatically over the past few decades, with more than 2.5 million adolescents using them in 2022. Data suggests that e-cigarette usage is linked to increased depression, anxiety, and worsening cognitive capabilities. E-cigarette vapors contain a mixture of harmful chemicals including propylene glycol, formaldehyde, glycerin, flavorants, nicotine and heavy metals. The strong sensation of pleasure from e-cigarettes is derived from  flavors in the vapor, which are detected by gustatory and olfactory neurons in the tongue and nose, respectively. E-cigarette exposure on the main olfactory epithelium (MOE) is of particular concern because of the potential to transfer harmful chemicals into the olfactory bulb (OB), whose connections to the MOE traverse without the blood-brain barrier. In the case of e-cigarette derived heavy metals which are produced from repeated use of the heating coils, this allows a potential pathway for metals to traffick their way through olfactory sensory neurons (OSNs) into the MOE, OB, and higher order regions of the brain. The olfactory system and connected regions like the hippocampus, amygdala, and anterior olfactory cortex are some of the first brain regions to show signs of neurodegeneration, and loss of smell is a highly reported prodromal symptom of mental illness and neurodegenerative diseases. My thesis work aims to discover the mechanism of e-cigarette derived heavy metal uptake through the MOE, and to identify the downstream consequences of exposure on cellular/tissue functions and various olfactory and cognitive-guided behaviors using mice as a model system.

Notable publications and presentations:

  1. O’Sullivan, S.M; Lin, W. The Impacts of E-Cigarettes on Mitochondrial Health in Olfactory Epithelial Cells. Greater Baltimore Society for Neuroscience Annual Meeting (September 2022). (Poster)
  2. O’Sullivan, S.M; Lin, W. Effects of Heavy Metals on Mitochondria and Intracellular Calcium in Mouse Olfactory Neurons. UMBC Graduate Association of Biological Sciences Symposium (March
    2023) at the 14th Frontiers in Chemistry and Biology Symposium (May 2023). (Poster)

Michael Marciniak

Delivery of chemotherapeutic agents via systemic administration is a routine treatment option for malignancies.  The cytotoxic efficacy of these agents corresponds to low therapeutic indices, where off-target interactions with healthy cells result in negative side effects and a decrease in patient’s quality of life.  Circumventing off-targeting during chemotherapy treatment is possible through the design of multifunctional drug delivery systems that incorporate controlled drug release, active tumor targeting, and diagnostic capabilities all-in-one.  Dendronized gold nanoparticles (gold nanoparticles with highly-branched polymer surface coatings) offer a modular platform that can be decorated to include therapy, targeting, and diagnostic functionalities.  My research involves the design and synthesis of dendronized gold nanoparticles that deliver a combined payload of chemotherapeutics (doxorubicin and docetaxel) to metastatic prostate cancer cells in vitro. These cytotoxic drugs are tethered to dendronized gold nanoparticles using acid-labile chemical bonding that limits their premature release during transport to tumor sites.  Additionally, these dendronized gold nanoparticles host fragment antibodies that are specific for actively targeting metastatic prostate cells as well as gadolinium-based MRI contrast agents for diagnostic functionality. The resulting delivery system is intended to improve the systemic administration of docetaxel and doxorubicin by increasing therapeutic activities and decreasing off-target adverse effects through active tumor targeting and controlled drug release, with additional diagnostic functionality that enhances delivery monitoring.

Notable publications and presentations:

  1. Marciniak, M.; Daniel, M-C. Synthesis of Gadolinium(III) Bearing Dendron and Development of an MRI Contrast Agent Nanoplatform. 2023 UMBC Graduate Research Day. University of Maryland, Baltimore County. Baltimore, MD. March 2023. [Poster, Awarded Outstanding Graduate Research Award (Pre-Candidacy)].
  2. Marciniak, M.; Khanal, N.; Banerjee, R.; Daniel, M-C. Gold nanoparticles for diagnostic and targeted HIFU treatment. 21st International Nanomedicine and Drug Delivery Symposium. Massachusetts Institute of Technology. Cambridge, MA. September 2023. (Poster).
  3. Marciniak, M.; Daniel, M-C. Synthesis of Dendronized Gold Nanoparticles Bearing Docetaxel and an Antibody Fragment for Targeted Chemotherapy of Metastatic Prostate Cancer. Frontiers at the Chemistry-Biology Interface Symposium. University of Maryland, Baltimore County. Baltimore, MD. May 2024. (Poster).
  4. Khanal, N; Marciniak, M.; Daniel, M-C.; Zhu, L.; Lanier, M.; Dumoulin, C.; Banerjee, R. Functionalized Nanoparticles Mediated High Intensity Focused Ultrasound (HIFU) Ablation in Mice. Summer Biomechanics, Bioengineering and Biotransport Conference. Lake Geneva, WI. June 2024. (Conference Paper).

Christopher Goodis

The growth of tumor cells has been heavily linked to the hijacking of intrinsic apoptotic pathways. This involves the upregulation of several proteins to circumvent programmed cell death. The Bcl-2 family of proteins are instrumental in the apoptotic pathway found within cell mitochondria. Cancer cells can upregulate Bcl-2 anti-apoptotic proteins to sequester pro-apoptotic proteins which promotes tumor growth. Bcl-2, Bcl-xL, and Mcl-1 are all examples of these upregulated proteins. Most studies focused on the discovery of inhibitors to these proteins utilize the alpha-helical pro-apoptotic proteins as a starting point. While there have been extensive studies on these proteins, anti-apoptotic protein BFL-1 has received less attention despite evidence showing that certain cancers such as melanomas, leukemias, and lymphomas are dependent on BFL-1 upregulation. Most inhibitors target the binding groove found within the anti-apoptotic proteins which comes with it a unique set of challenges. To accelerate the design of a potent BFL-1 inhibitor, we will also be utilizing the unique Cys55 found within the binding grove of BFL-1 by incorporating a covalent warhead to increase affinity of our compound. Utilizing the findings of previously validated BH3 mimetics, computer-aided drug design (CADD), and virtual high-throughput fragment screening, my research aims to modify these mimetics to further selectivity towards BFL-1 as well as deliberately position warheads to react with Cys55. Utilizing cell data, molecular modeling, and mass spec analysis, we will undergo an iterative approach with our compounds to optimize their ability to inhibit BFL-1.

Notable publications and presentations:

  1. Goodis, C.C., Chan, A., Pommier, E., Fletcher, S. Recent Application of Covalent Chemistries in Protein-Protein Interaction Inhibitors. RSC Medicinal Chemistry, 2022, 13, 921-928. (*co-first authors)
  2. Goodis, C.C., Drennen, B., Bowen, N., Yu, W., Vickers, G., Wilder, P., Mackerell, A.D., Fletcher, S. Scaffold Hopping from Indoles to Indazoles Yields Dual MCL-1 / BCL-2 Inhibitors from MCL-1 Selective Leads. RSC Medicinal Chemistry, 2022, 13, 963-969. (*co-first authors)
  3. Truong, N., Goodis, C.C., Cottingham, A.L., Shaw, J.R., Fletcher, S., Pearson, R.M. Modified Suberoylanilide Hydroxamic Acid Reduced Drug Associated Immune Cell Death and Organ Damage under Lipopolysaccharide Inflammatory Challenge. ACS Pharmacol. Transl. Sci., 2022, 5, 11, 1128–1141.
  4. Goodis, C.C., Wenbo, Y., Lowe, B.D., MacKerell, A.D., Fletcher, S. Discovery of Novel BFL-1 Inhibitors by CADD and Screening an In-House Library of Synthetic BH3 Mimetics. Graduate Research Conference, Oral Presentation. University of Maryland, Baltimore, Baltimore, MD; March 2023.
  5. Goodis, C.C., Wenbo, Y., Lowe, B.D., MacKerell, A.D., Fletcher, S. Discovery of Novel BFL-1 Inhibitors by Computer-Aided Drug Design and Screening an In-House Library of Synthetic Alpha-Helix Mimetics. ACS Spring 2023: Crossroads of Chemistry, Poster Presentation. Indianapolis Convention Center, Indianapolis, IN; March 2023.

 

Mark Lee

Across all bacteria, the ferrous iron (Fe2+) uptake (Feo) system is the most prevalent and the most well-distributed system dedicated to the acquisition of Fe2+. However, despite Feo’s nearly ubiquitous presence across the prokaryotic domain, this system remains poorly understood. The Feo system consists canonically of three proteins: FeoA, FeoB, and FeoC. FeoB is a complex, transmembrane G protein and is arguably the most important component of the Feo system. The function of FeoB is to transport iron across a lipid bilayer to within the cytosol, but the structural and mechanistic details of this process are lacking. My research focuses on the incorporation of FeoB into lipid-protein and copolymer nanodiscs for functional and structural characterizations of FeoB. In addition, recent studies have suggested that not all FeoBs are GTP-specific, but rather may be NTPases. To probe this hypothesis, I am working to determine the structure of the N-terminal domain of FeoB (NFeoB) in the presence of adenosine nucleotides. Finally, recent bioinformatics data from my lab have identified genes encoding a small transmembrane protein (designated FeoD) of unknown function adjacent to FeoB in the feo operon. This protein is predicted to bear a single transmembrane helix with a C-terminal cysteine-rich tail. Because FeoD is present in many bacterial genomes that lack FeoC (a soluble, [Fe-S] cluster-binding protein) I predict that FeoD may function similarly. Thus, I am also working to clone, to express, to purify, and to characterize (structurally and functionally) the newly-discovered FeoD protein. Combined, this work helps elucidate the mechanistic details of this essential iron acquisition pathway.

Notable publications and presentations:

  1. Lee, M.; Magante, K.; Gómez-Garzón, C.; Payne, S. M.; and Smith, A. T. Structural determinants of Vibrio cholerae FeoB nucleotide promiscuity. 2024 bioRxiv. DOI: 10.1101/2024.05.22.595361
  2. Brown, J. B.; Lee, M. A.; and Smith, A. T. The structure of Vibrio cholerae FeoC reveals conservation of the helix-turn-helix motif but not the cluster-binding domain. J. Biol. Inorg. Chem. 2022, 27, 485-495
  3. Sestok, A. E.; Lee, M. A.; and Smith, A. T. Prokaryotic ferrous iron uptake: exploiting pools of reduced iron across multiple microbial environments. In: Hurst, C.J. (eds) Microbial Metabolism of Metals and Metalloids. Advances in Environmental Microbiology,2022, 10, 299-357. Springer, Cham.
  4. Brown JB, Lee MA, Smith AT. Ins and Outs: Recent Advancements in Membrane Protein-Mediated Prokaryotic Ferrous Iron Transport. Biochemistry. 2021 , 60, 3277-3291.