Spotlights-Research at the CBI

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)

Kat Wardrup

Ovarian cancer continues to be the most lethal gynecological malignancy and the 5th leading cause for cancer associated deaths among women in the United States.  Over 75% of patients are diagnosed at an advanced metastatic stage, at which point extant therapeutic strategies are ineffective. Consequently, the 5-year survival rates for patients with metastatic disease are disappointingly low (<30%). This clinical reality highlights the urgent need to identify new drug targets and more effective therapeutic strategies to treat metastatic ovarian cancer. However, achieving this goal has proved challenging, largely due to the existing knowledge gaps in our understanding of factors that drive metastasis and drug resistance. My thesis work focuses on understanding the role of a transcription factor and novel oncogene, Zinc Finger Protein 217 (ZNF217), in ovarian carcinogenesis. Patients with high levels of ZNF217 display a decrease in overall survival predictions, however the underlying cause for this relationship remains unknown. Further, there are no reports on how ZNF217 is regulated by the cell. My thesis work aims to address these knowledge gaps to better understand ZNF217’s utility as a novel therapeutic target in metastatic ovarian cancer.

Notable publications and presentations:

  1. Wardrup, K. Padmanabhan, A. Characterizing the Role and Regulation of ZNF217 in Ovarian Carcinogenesis. American Association for Cancer Research. Orlando, Florida. April 2023 (Poster).
  2. Wardrup, K. Padmanabhan, A. Characterizing the Role and Regulation of ZNF217 in Ovarian Carcinogenesis. 2022 Graduate Association for Biological Science Research Symposium. University of Maryland Baltimore Country. Baltimore, Maryland. March 2022 (Poster, First Place Award).
  3. Wardrup, K. Padmanabhan, A. Understanding the Regulation of ZNF217 by Metformin in Ovarian Cancer. 2021 Graduate Association for Biological Science Research Symposium. University of Maryland Baltimore Country. Baltimore, Maryland. March 2021 (Poster, First Place Award).

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).

Zach Nichols

Sample preparation is an essential step in nearly every analytical technique and is often the limiting factor in terms of costs and turnaround time. To minimize the time required and simplify the preparation process, many different sample preparation methods have been developed. One method that has been developed by the Geddes Lab is the use of devices called microwave lysing triangles (MLTs) which use thin metal films on a glass substrate to direct radiation from a microwave oven to a small area of high electric field intensity. When a biological sample is placed in this area and irradiated it undergoes rapid heating and the MLTs generate reactive oxygen species (ROS) from oxygen in the atmospheric environment which can inactivate pathogens, extract nucleic acids and proteins from cells, and fragment nucleic acids for downstream analysis or processing. My project focuses on further characterizing how MLTs generate ROS and  expanding their sample throughput via the modification of a common microplate. This is done by creating a periodic array of thin metal films on the bottom of the microplate, called a metasurface. Metasurfaces modulate electromagnetic radiation via the boundary conditions of different materials, in our case a metal and a dielectric, which are modified by changing the spatial arrangement of the materials. I have created and characterized several metasurfaces and microplate prototypes already and am currently working on comparing biological samples prepared with the microplates to those prepared with MLTs. Future work and cross-training will focus on assessing the utility of our microplates and MLTs in preparing samples for genomic sequencing assays as well as probing the ROS generation mechanism with fluorescent sensing probes.

Notable publications and presentations:

  1. Nichols, Z. E.; Saha, L.; Knoblauch, R.; Santaus, T. M.; Geddes, C. D. “Development of a Microplate Platform for High-Throughput Sample Preparation Based on Microwave Metasurfaces”
    IEEE Access. 2021, 9, 37823-37833.
  2. Nichols, Z. E.; Geddes, C. D. “Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review” Molecules. 2021, 26 (18), 5666.
  3. Nichols, Z. E.; Geddes, C.D. Applying Metasurfaces to Biological Sample Preparation and Clinical Diagnosis. 2022 UMBC Graduate Research Conference. University of Maryland, Baltimore County. Baltimore, Maryland. March 2022. (Poster)

 

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. 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. bioRxiv. 2022, DOI: 10.1101/2022.02.26.482101
  2. 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.
  3. Brown JB, Lee MA, Smith AT. Ins and Outs: Recent Advancements in Membrane Protein-Mediated Prokaryotic Ferrous Iron Transport. Biochemistry. 2021 Nov 9;60(44):3277-3291.