Chemistry Research Projects 2021

Kyle Bledsoe

Advisor: Yan Kung

Mutagenesis of BpHMGR to Explore Cofactor Specificity

The key mevalonate pathway enzyme HMG-CoA reductase (HMGR) prefers to use either NADH or NADPH as a cofactor, depending on the composition of a specific α-helix near the cofactor binding site. In recent work, three newly identified amino acids of this helix were hypothesized to play significant roles in determining cofactor specificity. However, the importance and effect of these three amino acids are still unknown. This summer, I will conduct mutagenesis studies on BpHMGR, which prefers NADH but can also use NADPH, to switch the three newly identified amino acids to those found in DaHMGR, which can only use NADH. After expressing, purifying, and studying the kinetics of these mutants, I expect that BpHMGR will lose its ability to use NADPH. This work will be helpful in furthering our understanding of cofactor specificity in HMGR and the relation between HMGR structure and function.

Hannah Braverman

Advisor: Yan Kung

Studying the role of a “cofactor helix” in conferring NADH or NADPH cofactor specificity in HMGR 

Regions of the mevalonate pathway enzyme HMG-CoA reductase (HMGR) are responsible for controlling specificity for either NADH or NADPH cofactors. In particular, the focus of my research is to investigate the relationship between amino acids of a short helical region we call the “cofactor helix” and HMGR cofactor preference. Here, I will study a modified enzyme in which the “cofactor helix” of EfHMGR, which prefers NADPH, has been switched to that of BpHMGR, which prefers NADH, and determine whether this EfHMGR-BpHelix enzyme will retain its NADPH preference or switch to preferring NADH. In addition, HMGR crystal structures have also suggested that the amino acid at position 484 may also influence cofactor preference. Therefore, I will also explore the cofactor specificity of a mutant EfHMGR-BpHelix-S444C-I484A enzyme. By expressing, purifying, and conducting kinetics experiments on these modified EfHMGR proteins, I will determine whether they will prefer NADPH, NADH, or both. Further, I will try to crystallize these proteins to determine their structures using X-ray crystallography. The results of this research will be important to better understand the relationship between the HMGR structure and cofactor specificity.

Dana Caldwell

Advisor: Bill Malachowski

How the Heck to Enantioselectively Synthesize Quaternary Carbon-Containing Phenanthridinone Derivatives

Many drug candidates that succeed in clinical trials have a higher proportion of sp3 carbons and chiral centers than those that fail. Unfortunately, limitations exist in the efficient synthesis of such candidates, leading to most clinical drug candidates containing a preponderance of planar sp2 carbons and flat, aromatic structures. Molecules with sp3 and chiral carbons have fewer indiscriminate interactions with other bioactive molecules, have better solubility properties, and increased selectivity. Phenanthridinone, a flat, aromatic structure, is found in 3,200 bioactive molecules (PubChem search). Presently, no analogs of phenanthridinone with sp3 and chiral carbons exist. A new enantioselective tool that generates analogs of phenanthridinone could enable the synthesis of drug candidates that maintain the bioactivity of phenanthridinone while increasing therapeutic potency and physiological selectivity. I am developing a new synthetic tool, the Birch-Heck sequence, to generate fused tricyclic ring systems with a chiral quaternary center. First, the Birch reduction-alkylation reaction produces symmetrical 1,4-cyclohexadiene structures. To enable enantioselective control, a desymmetrizing Mizoroki-Heck reaction uses nickel metal with chiral ligands. The versatile structures generated by the Mizoroki-Heck reaction are further derivatized, and the collection of new molecules synthesized will be screened for anti-cancer biological activity with collaborators at Lankenau Institute of Medical Research. Refining the Birch-Heck sequence to generate highly enantioselective analogs of the bioactive molecule phenanthridinone will hopefully lead to more successful clinical trial drug candidates and better therapeutic outcomes.

Saeina Charles

Advisor: Jonas Goldsmith

Synthesis of a bi-metallic molecule composed of a photosynthesizer and an electron relay component for a photocatalytic water reduction system

In the last couple of centuries, the need for renewable sources of energy grew more evident as our planet continues to suffer from human-induced climate change. The overarching goal of this research is to create a photocatalytic water reduction system that will generate cleaner energy. A photocatalyst is a molecule that absorbs light to excite electrons to catalyze reactions; in this lab, the photocatalyst is used to split water to obtain hydrogen atoms. These hydrogen atoms are relevant particularly to this research because they are energy sources. The main components of the photocatalytic system are the following: a photosynthesizer (PS), an electron relay (ER), and a sacrificial reductant (Sac). The photosynthesizer is a molecule with the higher level of stability when excited by light. The electron relay (ER) is an intermediate compound that uses energy from the photosynthesizer to reduce water. The sacrificial reductant is a molecule that reduces the photosynthesizer after it was oxidized. Throughout the summer, my project aims to create a “bi- metallic” molecule that contains a photosynthesizer and an electron relay component. The synthesis of this bi-metallic molecule makes it more efficient to harvest the hydrogen atoms. It is important that the PS and the ER are in close proximity with each other. This allows more efficient redox reactions to occur between them. The more efficient the redox reactions, the more efficient the photosystem will be hence more hydrogen atoms generated. The strategy is to synthesize these two components separately as substituted bipyridines with specific and complementary parts attached to them. Eventually these interdependent molecules will fit perfectly like a “lock and key” coupling process. Although this method appears to be straightforward, the biggest challenge will be to figure out what molecules will combine to create the ligand that connects the bipyridines.

Lynn Chen

Advisor: Bill Malachowski

Screening for Enantioselective Quaternary Carbon Centers

Chiral centers generally increase the specificity of drugs and reduce their side effects. Mal group started a Birch-Heck project to synthesize phenanthridinone and carbazole analogs with chiral centers and sp3 carbons, which are good drug candidates. This summer, I continued my work as part of the project. We hope to develop an efficient and enantioselective synthetic method for making quaternary carbon centers. In the past ten weeks, I worked on the enantioselective Heck reaction to find compounds that have a high enantiomer ratio after going through the Heck reaction. If a compound with such characteristics is found, I would then try to remove the Mom group from the compound and characterize the compound(s) made in the mom-removal reaction.

Rachel Lee D'Emilia

Advisor: Yan Kung

Characterization and Structure Determination of Mevalonate Kinase

The mevalonate pathway is an important metabolic pathway that produces the precursors to isoprenoids, which are a large and diverse class of natural products that include drugs used to treat serious diseases such as cancer and malaria. One key enzyme in the regulation of this pathway is mevalonate kinase (MK), which uses ATP and mevalonate to produce 5-phosphomevalonate. Using X-ray crystallography as well as kinetics and inhibition studies, this research will characterize three MK homologs (MmMK, LmMK, and ScMK) to provide insight into how mevalonate, ATP, and inhibitors bind to MK and the varying potencies of MK inhibition. By studying the structure, kinetics, and inhibition of MK, we hope to better understand this important enzyme, with applications in medical and pharmaceutical fields.

Rubia Fernandes

Advisor: Jonas Goldsmith

Synthesizing Bimetallic Compounds to Optimize Photocatalytic Water Reduction Reactions

Carbon-free sources of hydrogen is a potential decarbonization solution to reaching a greenhouse gas (GHG)-neutral economy. In theory, green hydrogen could fuel long-haul freight vehicles, therefore replacing fossil-based oil, as well as provide a cleaner heat source in heavy industry manufacturing. Transition metal complexes can serve as catalysts and electron shuttles, for producing hydrogen from water and sunlight. In many cases the catalytic process involves electron transfer facilitated by the ability of transition metal complexes to shuttle between multiple redox states. The cycle is dependent on the interaction of photosynthesizers and electron relays in a solution. In theory, combining both molecules into one bimetallic compound will increase the efficiency of this reaction. One proposed method of synthesizing the bimetallic compound is through a peptide synthesis. To determine whether efficiency has increased, time and percent yield will be compared between the proposed and traditional methods.

Catherine Getty

Advisor: Sharon Burgmayer

Investigating the Effect of the Pyranopterin in the Closed Form of the Molybdopterin Dithiolene Complex of the Molybdenum Cofactor

          The molybdenum cofactor (Moco) is an essential part of catalytic reactions in every living organism. This cofactor contains a molybdopterin, which has one or two molybdopterin dithiolene ligands (MPT). These ligands are essential to the catalytic processes of molybdenum-containing enzymes, but their exact purposes are not entirely understood. Through the synthesis of model systems, the pterin dithiolene ligands are researched in the Burgmayer group. Currently, the lab uses the model system [Tp*Mo(O)(S2BMOPP]-, which exists in equilibrium between its open form and closed form via the formation of a pyran ring. Recently, research into this system has shown that protonation of the complex at the N5 position of the pterin ligand locks the complex into its closed form, and the pyranopterin ring creates a delocalization that leads to an intraligand charge transfer (ILCT).  

           The group is focused on studied the importance of the pyranopterin ring through this model complex, by both protonation, when ILCT occurs and also methylation, when it doesn’t. Another aspect of this research is to synthesize the model system with the molecule BDMPP, instead of BMOPP. BDMPP locks the complex in its open form, without the pyranopterin ring, and we hope to study the effects of protonation and methylation of this complex.

          This summer’s research will focus on further investigation into the methylation of the current BMOPP complex. We will work on synthesis of this BDMPP-containing complex and hope to study protonation and methylation of this complex as well. We will also continue to characterize our complexes through NMR.

Karen Guo

Advisor: Jonas Goldsmith

Vinyl Bipyridine Thin Films in Photocatalytic Water Reduction Systems

Hydrogen is a commonly used energy source and with major concerns over global warming and climate change being expressed in recent decades, it is more important than ever to focus on cleaner energy production methods. Photocatalytic water reduction systems, involving a photosensitizer and a quencher, provide a more environmentally friendly alternative to traditional methods of hydrogen production. These systems are able to successfully produce hydrogen through using solar energy to split water without the production of harmful by-products. Traditional photocatalytic water reduction systems have been set up such that the involved species of the cycle exist within the solution surrounding an electrode. To maximize the harvest of solar energy, certain components of the cycle, such as the photosensitizer and the electron relay compounds, can be polymerized into thin films. This will allow for more direct control over the positioning of these components during the cycle, as well as make coupling of the thin-film system with the water oxidation half-reaction of the photocatalytic water reduction cycles easier. The goal of this summer’s research is to successfully synthesize a photosensitizer compound that can be polymerized into stable thin-films through electropolymerization of the monomer species. This particular photosensitizer is aimed to be a ruthenium or iridium based vinyl bipyridine compound, as those particular transition metals have proved to be efficient photosensitizers.

Rania Hammami

Advisor: Patrick Melvin

Fluorine is widely used in the medical and agricultural fields and has been proven to enhance the effectiveness of bioactive molecules. Deoxyfluorination is a common method for fluorine incorporation, wherein an oxygen-containing functional group is substituted for fluorine. To improve on current deoxyfluorination reagents, the following novel sulfonimidinium fluorides were synthesized: [S(VI) Ph Bz Me]OTf, [S(VI) Ph Ph Me]OTf and [S(VI) Ph Py Me]OTf. These reagents were then tested with various deoxyfluorination targets, such as phenols to generate aryl fluorides and carboxylic acids to produce acid fluorides and trifluoromethyl groups.

Erica Ko

Advisor: Patrick Melvin

Design of novel sulfonimidinium fluoride reagents for use in deoxyfluorination

Even though fluorinated organic compounds are rising in demand in agrochemical and pharmaceutical industries, the difficulty of integrating fluorine to organic molecules remains. The focus of my research was to achieve efficient deoxyfluorination, the process of replacing an oxygen-containing functional group in organic molecules with fluorine, by developing novel reagents. The reagents that were synthesized were three variations of sulfonimidinium fluorides with propyl, cyclopropyl, and isopropyl substituents on the nitrogen, respectively. These were then screened in the transformations of alcohols to alkyl fluorides and aldehydes to difluoromethyl moieties.

Karley LaBenne

Advisor: Patrick Melvin

Synthesis of Sulfonimidinium Fluoride Reagents for Deoxyfluorination Reactions

Although fluorinated organic compounds have many biochemical applications, not many methods are currently available to insert fluorine atoms into organic molecules. However, one key method is deoxyfluorination, which can transform oxygen-containing functional groups into fluorine, a process important in the development of fluorine-containing pharmaceuticals and agrochemicals. My summer research focus is on the synthesis and development of sulfonimidinium fluorides, reagents containing fluorine that can be used in deoxyfluorination reactions. The goal of my research is to develop several sulfonimidinium fluoride reagents containing isopropyl, tert-butyl, cyclohexyl, and 2-methylphenyl functional groups. Once these reagents are successfully synthesized, they will be tested for their utility in standard deoxyfluorination reactions.

Darya Ostapenko

Advisor: Sharon Burgmayer

Molybdenum enzymes are known to be a cornerstone of several catalytic reactions in the human body. A Molybdenum cofactor (Moco) is found at the active site of those enzymes. One of the parts comprising Moco is a pyranopterin dithiolene ligand that supposedly plays a role in the enzymatic reactions that involve Moco. Synthetic reactions of pyranopterin dithiolene complexes resembling Moco are multistep processes that can be conducted under different conditions. These reactions are air-sensitive and therefore conducted in Schlenk lines under nitrogen. However, it is not entirely studied whether the presence of water molecules could negatively affect the yield. During this summer science research program, I will be focusing on learning how to work on a Schlenk line, gaining proficiency in conducting synthesis of pyranopterin dithiolene complexes and researching the impact of water on the yield in aforementioned reactions.

Anam Rawoof

Advisor: Jonas Goldsmith

Using Thin Film to Consolidate Photocatalytic Water Reduction System

In this lab we will focus on a photocatalytic water reduction system in the hopes of coming up with a cleaner source of hydrogen. Because hydrogen is commonly used as a source of energy and is currently synthesized in ways that harm the environment, this research could positively impact the environment. This system involves an electrode, a photosynthesizer, which is a molecule that is stable when excited by light, and an electron relay, which promotes the reduction of water and the oxidation of the photosynthesizer. These components of the photocatalytic system need to be in order and need to collide correctly for the system to be successful. To control the order in which the components are used and the position of components, we will be focusing on thin films which will force all components to be close together in a solid state and can consolidate the process because we will be able to control the sequence of the components through the different layers of the film. We hope that this film will also adhere to the electrodes so that all components of the system can be connected. We will focus on the ligand vinyl bipyridine, which has been proven to have the ability to be electropolymerized and will work with this ligand to create a thin film.

Mia Tran

Advisor: Bill Malachowski

Enantioselective synthesis of tricyclic structures with quaternary carbon stereocenters via a Birch-Heck sequence

Phenanthridinones is a flat aromatic structure commonly found in bioactive compounds, which however is not very selective. The new enantioselective synthetic tool being developed in this lab, the five reaction Birch-Heck sequence, will efficiently generate phenanthridinone analogs with chiral sp3 centers, which retain the bioactivity of phenanthridinone and overcome its nonselective reactivity to limit side-effects in drug candiates. The Birch reduction-alkylation is the first step of the chain reaction, and the last step is a desymmetrizing Mizoroki-Heck reaction to produce tricyclic rings with an all-carbon quaternary center.

Kalyn Wiley

Advisor: Bill Malachowski

The Enantioselective Synthesis of Quaternary Carbon Phenanthridinones Using the Birch-Heck Sequence

Through organic synthesis and medicinal chemistry experimentation, a primary goal this summer is the development of new processes and tools that explore unknown areas of the chemical structure space for drug development. My current research seeks to solve challenges in developing successful new therapies through efficiently making drug molecules with quaternary centers. Molecules with quaternary centers benefit from their chirality and their three-dimensional structure because they bind more selectively to proteins and have improved solubility properties; two key considerations in developing successful drugs. The new synthetic chemistry tool that we are using is the Birch-Heck sequence, which combines the steps of the versatile Birch reduction-alkylation reaction with the Mizoroki-Heck reaction. The objective is to generate phenanthridinone analogs with chiral centers and sp3 carbons to make them more selective and active towards biological targets for therapeutic purposes. Phenanthridinone structures are flat, sp2 containing structures with well-documented, but indiscriminate bioactivity. I am working on different drug analogs based on the particular alkylating agent used for the Birch reaction and the different amine used in an amide coupling reaction. These amide products are then subjected to the enantioselective intramolecular desymmetrizing Mizoroki-Heck reaction. Each of the successfully synthesized phenanthridinone analogs created will be sent for screening with the group’s biological collaborators at Lankenau Institute of Medical Research. In particular, the bioactivity analysis will determine if the new molecules have potential anti-cancer activity.