Research day Abstracts

Department of Chemistry and Biochemistry, 12 May 2021 spring semester Bebbington Lab

Cyclic sulfones by double conjugate addition of Rongalite Melina Goga, Hao Zong, Jazmin Prana, Rudolph Michel, Antonia Muro and Dr. Magnus Bebbington Department of Chemistry and Biochemistry, Montclair State University

Fig. 1 Structure of Rongalite Sulfonyl derivatives are a major class of structural motifs in pharmaceuticals.1 Rongalite is a widely used bleaching agent prepared by electrochemical reduction of sulfur dioxide in the 2- presence of formaldehyde and sodium hydroxide. It behaves as an equivalent for the unstable SO2 anion, and was used in conjugate addition reactions as early as the 1970s.2 Since that time, potential uses of the reagent have been underexplored, but have undergone a resurgence in recent years. By comparison with most sulfur compounds, Rongalite is low odor, and is also very cheap ($23/500g).

Fig. 2 Addition of Rongalite to dibenzalacetone We have recently discovered that Rongalite will undergo double conjugate addition to dibenzalacetone and other dienones under practically straightforward, open flask conditions in good yields. The diastereoselectivity, for the 3,5-trans isomer of the cyclic ketosulfone product, is believed to be specific to cyclizations of related sulfur nucleophiles and we are currently examining this through a collaboration with the computational chemistry group of Dr. H. Eshuis, also at Montclair State.

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1. E. A. Ilardi, E. Vitaku, J, Njardarson, J. Med. Chem. 2014, 57, 2832. 2. S. Kotha, P. Khedkar, Chem. Rev. 2012, 112, 1650.

Catalano Lab

The role of residue M305 in Mammalian Cytochrome P450 2S1 Kenneth Mosquera-Reinoso, Natalia Reis, Jaclyn Catalano, Department of Chemistry and Biochemistry, Montclair State University Cytochrome P450 (CYP) is an essential enzyme present in all living organisms and is in charge of breaking down xenobiotics, metabolizing drugs, and takes part in steroid and vitamin synthesis. Cytochrome P450 2S1 (CYP2S1) is an unusual cytochrome because it only catalyzes the reduction of substrates under low concentrations of oxygen and has not conclusively shown to oxidize substrates. It is important because it is overexpressed in oxygen-deficient areas such as cancerous areas related to colorectal, metastatic ovarian, and carcinomas. CYP2S1 is being investigated as a prodrug target for cancer therapies. Prodrugs are inactive (nontoxic) until they become activated (toxic) by an enzyme such as CYP2S1. CYP2S1 has been shown to breakdown and reduce anticancer prodrug, AQ4N. However, the basic biochemistry of CYP2S1 and why this enzyme’s chemistry is different from other CYPs has not been investigated. Our hypothesis is M305 in CYP2S1 is responsible for preventing oxidation of substrates. Current research involves mutants to a model enzyme to determine the importance and role of M305 in the CYP2S1 structure. We have utilized N-palmitoglycine as a substrate to test the efficiency and rate of the mutants that are tested. Using UV-Vis Spectroscopy we were able to record absorbance at 418nm to determine the concentration and monitor the decrease in NADPH (340 nm) absorbance while the reaction is happening. In P450 BM-3 (a model enzyme) the glutamic acid has been replaced using site-directed mutagenesis to a Methionine E267M, Valine E267V, Lysine E267K, and Serine E267S to be analyzed and determine the catalytic efficiency. In conclusion, two of the mutations, E267V and E267K, have a higher catalytic efficiency than the wild type BM-3 and two of the mutations have no activity E267M and E267S. Data collection for WT will be repeated with a new batch of protein and substrate to come to final conclusions.

References: 1. Furuya, H., Shimizu, T., Hirano, K., Hatano, M., Fujii-Kuriyama, Y., Raag, R., and Poulos, T. L. (1989), Biochemistry 28, 6848-6857. 2. Imai, M., Shimada, H., Watanabe, Y., Matsushima-Hibiya, Y., Makino, R., Koga, H., Horiuchi, T., and Ishimura, Y. (1989), Proc Natl Acad Sci U S A 86, 7823-7827.

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3. Coon, M. J., Vaz, A. D., McGinnity, D. F., and Peng, H. M. (1998), Drug Metab Dispos 26, 1190-1193. 4. Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Gallo Cassarino, T., Bertoni, M., Bordoli, L., and Schwede, T. (2014), Nucleic Acids Res 42, W252-258. 5. Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J., and Schwede, T. (2009), Nat Protoc 4, 1-13. 6.. Xiao, Y., Shinkyo, R., and Guengerich, F. P. (2011), Drug Metab Dispos 39, 944-946.

Desilva Lab

SYNTHESIS AND STUDY OF A NEW FLUORESCENT SENSOR FOR PROTONS

John Eakley

The design of new molecules that function as fluorescent sensors for cations is an area of current interest. Some of these sensors are based on a chromophore-spacer-receptor design and use photoinduced electron transfer (PET) to generate or quench a fluorescence signal. Anthracene and pyrazoline chromophores are widely used in the design of fluorescent PET sensors. We are interested in developing a new fluorescent sensor for protons (5) based on a conjugated pyrazoline-anthracene chromophore.

Our progress in the synthesis of this new sensor will be presented.

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Eshuis Lab

Exploration of the Geometric Isomers of Cyclic Sulfones Scott Piotrowsky Rongalite is a useful reagent for making sulfones and is used in Dr. Bebbington's group to synthesize cyclic substituted sulfones. It is observed that the major product is the trans configuration instead of the cis configuration which is expected to be thermodynamically more stable. In this work, we use computational methods to elucidate the pathway leading to each product in an attempt to understand why the trans product is the kinetically favored. Internal reaction coordinate techniques are used to compute reaction pathways and to find transition states. Here, we present relative energies of the structures and optimized reaction paths for ring closures. The work is in progress and so far definite conclusions cannot be given.

Computational studies of the reaction mechanism of trifluoromethylation of boronic acids Olivia Schmidt The mechanism of the photo-catalyzed trifluoromethylation of boronic acids in the presence of a copper co-catalyst is investigated using computational methods. The focus of this work is on the copper-catalyzed part of the process. Density functional methods and internal reaction coordinate schemes are used to find optimized structures and energies of reactants, products, intermediates, and transition states. Results for three steps are presented. Preliminary results indicate that the copper-coordinated dissociation of the boronic acid is the rate-limiting step.

Gao Lab

Glycan Characterization via Free Radical-Activated Glycan Sequencing (FRAGS) Reductive Amination Conjugation, Mass Spectrometry, and Sodium Adducts Ray Murtada Abstract: The elucidation of glycans via tandem mass spectrometry and free radical chemistry is a progressing field for analytical research. Using the second generation free-radical activated glycan sequencing reagent (FRAGS II), glycans can be characterized. This is primarily achieved by coupling the reagent with a glycan by reductive amination reaction. The purpose of reductive amination is to favor the formation of just one of the three glycan isomers within the isomeric interconversion, allowing for greater feasibility in characterizing glycans. Different disaccharides provide unique structural fragmentation patterns that can be used to distinguish the glycans. With

- 4 - this prospective preliminary data, this approach seeks the potential for application onto larger glycans.

Gindt Lab

Ahmad Daghestani Stabilization of proteins in solution can be achieved with the use of osmolytes, small soluble compounds such as sugars that can be found in nature. This study explores the physical-chemical properties in protein stabilization in the presence of osmolytes and incubation time. The stability of thermophile DNA photolyase, Sulfolobus sulfataricus, is analyzed using buffer with 0.55 M trehalose and 0.20 M β-glycerol phosphate and in the presence of 2.0 M guanidinium hydrochloride as a denaturing agent. The incubation temperature is set at 50o C and for the control, the sample is incubated at 4o C and the half-lives of the proteins were quantified. The incubation time of the thermophile prior to the denaturation was crucial to the stability of the protein.

Jessica Vasquez DNA photolyase uses the absorption of blue light to repair cyclopyrimidine dimers, a UV-light induced damage, on DNA. We are interested in the enzyme (SsPL) from the thermophilic organism, Sulfolobus solfataricus. In the course of our studies, we found that the absorption spectrum of the active site flavin adenine dinucleotide (FAD) cofactor shifts upon heating of the protein, showing a structural change in the FAD binding pocket. This shift may indicate that the thermophilic SsPL produced via overexpression by mesophilic E. coli is be trapped in a metastable state when overexpressed 30oC. We have developed a procedure to measure the enzyme repair before and after heat treatment. We will report our results of the activity studies.

Goodey Lab

Role of E168 in M. tuberculosis indole-3-glycerol phosphate synthase catalysis Huma Booter, Sarah Cho, Joseph LaCap, Paige Fadden, David Konas, and Nina M. Goodey Mycobacterium tuberculosis is a bacterium that affects the lungs and causes tuberculosis, affecting over 10 million people worldwide each year. Due to the organism’s evolving drug resistance, many older drugs can no longer combat the disease and the need to learn more about

- 5 - new drug targets and inhibitors has never been greater. Previous findings suggest that the enzyme indole-3-glycerol phosphate synthase (IGPS) in Mycobacterium tuberculosis (MtIGPS) may be a target in the treatment of tuberculosis as MtIGPS catalyzes the fourth step in the biosynthesis of the amino acid tryptophan, which is essential for survival in bacteria. We investigated the role of residue E168 in the MtIGPS active site. We purified the E168D mutant of MtIGPS and determined the kcat to be 0.0004 ± 0.0001 s-1 and Km to be 11.8 ± 5.08 µM. In comparison, the kcat of the wildtype MtIGPS was determined to be 0.4332 ± 0.0162 s-1 and the Km was determined to be 5.0 ± 1.4 µM. The decreased activity of the E168D mutant suggests that E168 plays an important role in either the catalysis or stability of MtIGPS. The crystal structure of MtIGPS in complex with the product showed that this residue is located close to a positive charge that is predicted to form briefly as part of the catalytic mechanism. Our hypothesis is that the negative charge of E168 stabilizes the positive charge that forms during the mechanism and that when E was replaced by D, the shorter side chain no longer reached the positively charged nitrogen in the intermediate, increasing the energy of the intermediate and resulting in a slower reaction. We also determined kinetic isotope effects, pH profiles, and viscosity effects for the E168D mutant and compared these to the wildtype enzyme. Increased understanding of ligand binding and catalysis in the MtIGPS active site will help the design of inhibitors for MtIGPS.

Identifying single stranded DNA aptamers that bind Ranavirus, a frog pathogen

Maria Fahmy, Stephanie Zapata, Evelyn Visan, Lisa Hazard, Ueli Gubler, Kirsten Monsen, and Nina M. Goodey

Disease outbreaks, such as COVID-19, have called for accurate and rapid pathogen detection methods. Antibody probes are unstable and not ideal for use in field conditions where they On the other hand, aptamers are short, single stranded DNA molecules that form unique three dimensional structures that bind to specific viral targets tightly and selectively. Aptamers can be used in virus sensing because they are inexpensive to produce and stable. The overall goal of the work described here is to develop the first stable, aptamer-based field assay against the emerging pathogen Ranavirus. Ranavirus is a pathogen that kills frogs and other amphibians, causing local extinctions and affecting commercial fishing. Previous work enriched aptamer libraries with aptamers that are predicted to bind Ranavirus. We used computational approaches to identify patterns in these sequences and RNA fold to predict the 2D structures of the aptamers. We have expressed and purified the major capsid protein (MCP), which is displayed on the surface of Ranavirus. We have shown, using SDS-PAGE electrophoresis, that the expression of MCP was successful and that it binds to the GST-tagged protein extraction matrix. The next steps are to find conditions to elute MCP from the GST-tagged matrix and use it in gel shift assays to

- 6 - determine whether the 20 predicted Ranavirus binding aptamers actually bind to the Ranavirus MCP.

Investigating the effects of the E219D mutation on indole-3-glycerol phosphate synthase activity Ashley Peralta, Cinthya Moran, Thomas Oshane, Huma Booter, Sarah Cho, Katherine Leon H., and Nina M. Goodey Abstract: Indole-3-glycerol phosphate synthase (IGPS) plays a major role in the survival of Mycobacterium tuberculosis. It is the bacterium responsible for tuberculosis, an infectious disease that drastically affects the upper respiratory tract. In particular, the tryptophan biosynthetic pathway is involved in the survival of Mycobacterium tuberculosis and IGPS is responsible for catalyzing one of the steps of this pathway. Additionally, mutations made to IGPS, such as E219D, can help us understand the role of the individual amino acids that function within this enzyme. We expressed and purified the E219D mutant and the wildtype IGPS enzymes. Next we will determine the Michaelis Menten constants for the substrate CdRP and learn whether the mutation impacts catalytic activity or substrate binding. Most importantly, since humans do not have an IGPS enzyme and must obtain tryptophan from their diet, this enzyme could be a potential target for antibiotic agents in the treatment of TB.

Figure 1. Cartoon of interactions between E219 and the substrate (predicted via Autodock Vina; left) and product (PDB #3T44; right). These structures led to our hypothesis that E219 may play a role in orienting K119, a proposed catalytic acid in the IGPS catalytic mechanism.

Degradation of polycyclic aromatic hydrocarbons in a barren brownfield soil

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Bhagyashree P. Vaidya1, Sarah Krisak3, Kevin Olsen3, Jennifer A. Krumins2, and Nina M. Goodey3 Department of Earth and Environmental Studies1, Department of Biology2, Department of Chemistry and Biochemistry3, Montclair State University, Montclair, New Jersey 07043. Brownfield sites are areas that were contaminated through industrial activities and dumping. The enzyme catalyzed processes occurring in such extreme soils are unique and not well understood. Our study site, an abandoned rail yard, is classified as a brownfield site and located within Liberty State Park in Jersey City, New Jersey. For 70 years, the polluted section of the park has been closed off and left undisturbed. Previous studies have reported polycyclic aromatic hydrocarbons (PAHs) and inorganic contaminants at the site. Interestingly, ligninolytic enzymes have been reported to play a role in both lignin degradation and the biodegradation of PAHs. We have adapted published protocols to measure the activities of ligninolytic enzymes in soils collected from this brownfield, including lignin peroxidase, laccase, and manganese peroxidase activities. Using chromogenic substrates and a plate reader, we detected the soil enzyme catalyzed conversion of substrate to product. To capture the reactions at maximum velocities, we explored different substrate concentrations in the assay. To attain a reasonable signal, we optimized enzyme concentration by varying the amount of soil that was added to the experimental wells. We compared the ligninolytic enzyme activities in our brownfield soils and uncontaminated control soils to literature values. Our future work will address the hypothesis that lignin peroxidase, laccase, and manganese peroxidase activities are higher in vegetated and in PAH contaminated soils compared to barren and uncontaminated soils, respectively. The results from this study may be relevant for the development of “green” remediation strategies to clean up brownfield sites.

Konas Lab

M. tuberculosis IGP synthase: Preparation, purification, and characterization of the substrate CdRP.

Joseph Lacap, Paige McFadden, Savannah Van Den Berg, Nina Goodey, and David Konas

Indole-3-glycerol phosphate synthase (IGPS) catalyzes the indole-forming reaction in the bacterial tryptophan biosynthetic pathway. This pathway appears to be necessary for bacterial growth and may be a target for potential new anti-infective agents. In order to enable our biochemical studies utilizing the wild-type and mutant IGPS enzymes, a supply of purified and well-characterized enzyme substrate (CdRP) is required. This poster will summarize our current results with respect to the synthesis, purification, and characterization of CdRP.

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Lee Lab

Examining lipid- protein domain phase-separation and behavior at the inter-membrane junction

Ashlynn Knight

Cell membranes are a vital part of all cells, the semipermeable lipid bilayer structure providing a key defense for its cell against the environment, while also responsible for signaling responses, cell-cell interactions, and transportation. Our immune system relies on the membrane’s identification tags to recognize our cells and avoid attacking them. In addition, many viruses take advantage of the receptor molecules that sit on the cell's surface by binding to it with their fusion proteins to induce fusion between the two membranes. Interactions facilitated by the inherent fluidity of the heterogenous mixture lipid membranes, phase separation promoting large scale rearrangements based on small environmental stimuli changes. By using a simple model system to artificially mirror the way lipids and proteins organize under different conditions, we are able to study the complex spatial organization and molecular composition between these molecules at the inter-membrane junction. Our model proteins used in this research are SUMO10-His domains and SIM10MBPHis-Fluo domains, incubated with SLB (Supported Lipid Bilayer) and Giant Unicellular Vesicles (GUVs) and explored under Fluorescence Imaging. So far, observations report a tendency for the model proteins to highly concentrate evenly on the interface, and this behavior appears to affect the lipid composition separation of the vesicles, forming heterogeneous phase separated domains.

Lipid-Protein phase separation in giant unilamellar vesicles.

Juan Urena

The cell membrane is the biological barrier that surrounds the cell and protects it from the outside environment; it is mainly composed of macromolecules that assemble and organize within itself. It has a well-documented property of demixing into composition domains. This phenomenon is known as lipid raft, in which lipids and protein organize within the cell membrane creating well-defined domains. Additionally, some multivalent binding proteins are known to form protein phase droplets or protein liquid condensates at a high enough concentration. Given that, this work intends to study the way in which proteins anchored on the

- 9 - membrane organize themselves when lipid raft and protein domain coexist. For this purpose, we created giant unilamellar vesicles (GUVs) with various compositions to simulate the behavior of a typical cell membrane. We observed that homogeneous GUVs with 5% or lower Ni-DGS in their composition went from homogeneous to phase separation after being exposed to SUMO3- GFP, SUMO10His, and SIM10Cut proteins. Meanwhile, phase-separated GUVs with 10% or higher Ni-DGS in their composition went from phase separation to homogeneous under the same conditions. These results suggest cooperative phase separation and that the opposite driving force of protein crowding is competing with each other. These findings are certainly remarkable and may open the door to better understand the mechanisms in which biological macromolecules compartmentalize into microdomains in the cell membrane.

O’Neal Lab

Enock Arthur

There are many analytical devices designed to selectively identify and quantify the amount of analyte in a sample solution. Techniques like absorption spectrophotometry, chromatography, mass spectrometry, and many others are all used for quantitative analysis. Recently, scientists have been shifting their focus to electrochemical devices, because these devices are cheap, easy to make, portable and have high sensitivity. The goal of our research is to use a 3D printer to design sensors that can be distributed world-wide and made at the point-of-use. In this work, we are aiming to produce sensors to selectively measure Pb in tab water. This experiment is motivated by the vast number of cases of Pb in water that exceed the recommended CDC level of Pb in water (15 ppb). This widespread occurrence of lead in tap water has led to no or limited available drinking water in different parts of the US, such as Flint, MI and Newark, NJ. However, although 3D printed devices are used among different research groups, a variety of filaments are available which have drastically different electrochemical properties. Here, we investigated three filaments (Blackmagic 3D, Amolen, ProtoPasta) and three different pretreatment methods (polishing, AuNP deposition, and NaOH electrolysis) to optimize the electrochemical performance of the sensors for trace level measurements of Pb. We compared the solvent window and capacitance of each filament and pretreated. We found that protopasta NaOH pretreated gave the widest solvent window which will allow to measure Pb in larger potential range and also has the smallest capacitance which will allow us in future experiments to measure tiny traces of Pb. We then incorporate this new finding to make functional Pb sensors by investigating the detection limit and sensitivity of the electrode.

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Sarkar lab

Polymers for Sustainable Energy & Economic Development

Onurcan Buken, Kayla Mancini, Amrita Sarkar

Department of Chemistry & Biochemistry, Montclair State University, NJ 07043 Market for electric vehicles (EVs) has dramatically expanded in the past several years in a collective effort to combat greenhouse gas emissions associated with climate change. By 2040, we expect to see 500 million passenger EVs on roads, all of which will be powered by lithium- ion batteries (LIBs). However, we will face an unprecedented amount of waste due to use of such enormous LIBs. Accumulation of these large amount of wastes without a proper waste- management strategy enables waste of valuable resources. Thus, recycling efforts focused on mitigating the environmental impact and hazards as well as improving the re-use of battery materials for subsequent applications are critical. Likewise, improving the energy efficiency of the manufacturing process and choosing environment-friendly organic components must need to design to reduce the environmental effects of rechargeable batteries. Our group aims to address these challenges by (i) developing a green-solvent based recycling approach and (ii) designing a bio-inspired protein-like polymer for LIBs. We will present some preliminary findings in this event.

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Schelvis Lab

Using Spectroscopy to Investigate Photoprotection Mechanism between MTHF and FAD in DNA Photolyase

Authors: Warner Carnero, Johannes Schelvis Presenter: Warner Carnero

Abstract: The photochemistry in photolyase DNA repair involves a flavin adenine dinucleotide (FAD) and 5,10-methenyltetrahydrofolate polyglutamate (MTHF), where MTHF is believed to harvest and transfer light energy to FAD. We have a new hypothesis that MTHF provides photoprotection to FAD from photodamage due to formation of triplet states under continuous light-induced stress. The goals of our research include testing a protective interaction between MTHF and FAD in solution and characterizing the FAD and MTHF triplet states. To test our hypothesis, we focus on long time-scale absorption experiments in solution to investigate whether there is a concentration dependence between MTHF and the rate of flavin degradation kinetics. The results indicate that the presence of MTHF influences the rate of degradation of FAD at low concentrations. Additional kinetic photodegradation studies with potassium bromide – a singlet excited state quencher – show that FAD stability is improved by the presence of Br-. Furthermore, purging the FAD solution to remove O2, a triplet state quencher, accelerates the FAD photodegradation. Our current results in solution support the hypothesis that MTHF may have a photoprotective role in DNA photolyase and that the triplet states play a role in the photoprotection of FAD by MTHF.

Secondary Structure of Glucose Oxidase and DNA Photolyase in Solution Detected by ATR-FTIR Spectroscopy Presenter: Uchechi Desouza Authors: Uchechi Desouza, Johannes Schelvis

Abstract: In this project, the goal is to monitor the change in secondary structure of DNA photolyase upon heat treatment of a thermophilic enzyme. We first use glucose oxidase (GO) as a model system, because it binds a flavin adenine dinucleotide (FAD) cofactor and has α-helix and β-sheet secondary structures just like photolyase. We used attenuated total reflectance (ATR)-FTIR spectroscopy to monitor the change in secondary structure of GO due to a change in pH and to heating. In protein IR spectra, the amide I band (1600 - 1700 cm-1) is sensitive to secondary structure because of the C=O stretching vibration of the amide linkage. The ATR-FTIR spectrum of FAD in solution was identical to literature data and detectable down to 1 mM. The

- 12 - amide I band of GO was successfully measured at various pH values in H2O and D2O buffer solutions as well as after heat denaturation at pH 7. The results on both FAD and GO and preliminary results on DNA photolyase support the idea that ATR-FTIR can be successfully used to study changes in the secondary structure of photolyase in solution and potentially in changes to individual amino acids after heat treatment of the thermophilic enzyme.

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