My main project was centered on the use of benchtop nuclear magnetic resonance (NMR) spectroscopy to figure out how the addition of a fluorine in the structure of one of the three reagents would influence the mechanism of the Biginelli cyclocondensation (which has three possible mechanisms) to achieve the synthesis of novel trifluorinated pyrimidine compounds.
During her time in the Njoo group at ASDRP, Alice was a part of the chemical neuroscience subgroup where she helped synthesize and test the activity of analogs of rivastigmine, a drug used to treat neurodegenerative diseases. This work was published in the Journal of Emerging Investigators (https://emerginginvestigators.org/articles/modular-mimics-of-neuroactive-alkaloids-design-synthesis-and-cholinesterase-inhibitory-activity-of-rivastigmine-analogs). Alice was also in the NNRTI subgroup, where she worked on optimizing the Buchwald-Hartwig cross-coupling reaction to synthesize and screen a library of N,N-diaryl pyrimidine-2,4-diamines with the goal of terminating viral HIV reproduction.
Robert Benjamin DeMartino
Black holes are the ultimate force in our universe. Nothing, not even light, can escape their grasp once entered. Yet finding them remains incredibly difficult, and we may be missing countless relatively small black holes in our searches. The goal of the mini-Black Hole research group of ASDRP (Aspiring Scholars Directed Research Program) is to identify some of these smaller black holes. My role in this research is to aid in the creation of Python programs to scour publicly available databases for clues (specifically ones regarding stellar radius and radial velocity) as to where these black holes may be hiding. Writing code, documenting it, and collaboration is essential in this area of research. Comfortably Confront
I worked on the CovidVacNet project where we created a digital, interactive map of the world to help plot the network of COVID-19 spread across the globe. We also used machine learning to help predict the risk of an outbreak occurring in the future. I also worked on the NeuroTDA project where we used a technique called topological data analysis to study the shape of various neurodegenerative genes to find similarities between them. This project was recently accepted at the Organization for Human Brain Mapping (OHBM) international conference taking place in Montreal, Canada during July of 2023!
I did Marine Biology research on ocean acidification with Mr. Benson for one semester. Then, I rejoined ASDRP last summer as part of Mr. Chen’s andrographolide group and have been doing HPLC work since. I am currently working on the andrographolide project under Mr. Yamamoto.
I am a part of Jahanikia NeuroLab working in the SynapticYoga EEG Project where I use electroencephalography (EEG) and MATLAB data preprocessing to study the effects of meditation practices on brain activity! With continuing data analysis through EEGLab, we hope to find the direct effects of meditation and how it may benefit cognition, perception, and emotional processing.
With the EEG team we have held colloquia presentations, worked on our expo poster presentation, led virtual blitz talks, and are in process of submitting our abstract to SFN!
As a research intern at ASDRP, I explored the viability of silicon anodes by analyzing the performance of different shapes and compositions of micro and nanosilicon with new doping materials.
The aim of our research was to understand, contextualize, and analyze the environmental impacts of the five leading candidates for anode materials in lithium-ion rechargeable batteries: graphite, silicon, lithium, zinc, and aluminum. Using a novel metric, the Environmental Impact Score (EIS), we measured each material’s environmental impact by calculating a weighted sum of a dozen distinct environmental impacts, ranging from CO2 emissions to groundwater contamination. Each material was carefully researched for every environmental impact and given a score on a scale of 1-3 (low impact to large impact) for each cell.
I utilize the computational algorithm DeepCDR to conduct Drug Target Interaction screening and predict IC50 values (toxicity indicators to determine which novel cancer drugs, potentially, have the ability to inhibit the progression of colon cancer.
Presented research findings at the Fall (2021) and Summer(2022) ASDRP Symposium. Presented at the American Chemical Society’s Western Conference in Las Vegas on October 21st, 2022.
Xina Wang started her research career at ASDRP in the lab of Prabhjeet Kaur where she examined and identified mutualistic fungal species in Northern California to help farmers determine which species to cultivate in their soils. After her work in environmental microbiology, she transitioned into Edward Njoo’s group where she worked on several projects.
She led a project involving the synthesis of carmofur and novel 5-fluorouracil-related analogs to combat SARS-CoV-2. Carmofur is an anticancer drug that was found to have therapeutic potential against COVID-19, however, its synthesis has historically been challenging due to long reaction times, low yields, and the use of toxic chemicals. Fortunately, carmofur has a fluorine molecule that can be used to monitor its synthesis by benchtop 19F nuclear magnetic resonance (NMR) spectroscopy. Her work has involved using benchtop 19F NMR to optimize carmofur’s synthetic conditions and quantitatively and efficiently monitor the synthesis of a variety of more potent carmofur analogs that can possibly have more efficacious biological activity against cancer and SARS-CoV-2. To read more: https://doi.org/10.1139/cjc-2022-0266
She also worked on the chemical synthesis of 2,4-dihydropyrimidinones via Biginelli multicomponent reactions as potential leads in anti-cancer therapeutics. Benchtop 19F NMR was used to monitor the synthesis of novel trifluorinated analogs of monastrol, a dihydropyrimidinone anticancer agent. Additionally, it was used to better understand the mechanism of the multicomponent reaction used to synthesize monastrol– the Biginelli cyclocondensation. She assisted in developing a reaction monitoring workflow of the Biginelli reaction with benchtop 19F NMR and extended this workflow to synthesize analogs with various aryl aldehyde substituents that would elucidate the effects of para and meta-substituted aryl aldehydes on reaction rate and mechanism. To read more: https://doi.org/10.1021/acsomega.3c00290
Finally, she worked on developing photoreleasable chemotherapeutic prodrugs of podophyllotoxin and antibody-drug conjugates (ADCs). Besides assisting in synthesis and development, using homology modeling and molecular docking, she assisted in finding the binding affinities of the prodrugs to its cancer protein target.
Currently, she continues her work developing novel carmofur analogs in the hopes of conducting computational studies and biological testing on them to determine their anticancer and antiviral activity.
I have worked on the computational side of Group 3 of the Cunha Lab. Along with others, I have worked on various computational tools to identify potential inhibitors for the BET proteins, a class of proteins involved in cell cycle regulation overexpressed in types of colorectal cancer.
The first project that Sarah worked on was on berberine, a bioactive isoquinoline alkaloid small molecule isolated from a plant whose therapeutic use in treating human disease dates back several centuries in ancient southeast Asia. A few years ago, we and others reported could act as a photosensitizer to excite ground state triplet oxygen into excited state triplet oxygen, thereby acting as photosensitizer for light-induced biological activity, and Sarah has published on this extensively [Photochemical analog (Sun, et al. JEI 2021); Initial antibacterial SAR (Sun, et al. JEI 2020)]. Specifically, Sarah led our first efforts on non-canonical uses of benchtop NMR spectroscopy to use benchtop NMR to quantify 1O2 by trapping it with a cyclic 1,3-diene to form [2.2.2]bicyclo endoperoxides, and we now have two publications on this, along with an application note co-developed with Nanalysis [App Note, Interview Video]. In parallel, Sarah has also grown a great deal of expertise in using computer modeling for understanding reactive intermediates and small molecule drug candidates (Link to Sarah's Ted Talk here), first in our use of DFT, TD-DFT, and MD in our computational SAR of berberine analogs as DNA-Gquad stabilizing agents (Sun/Ashok, et. al., JEI 2020), later in our SARS-CoV-2 Mpro inhibitors project (Sun, et al., J. Res. HS 2020). When we transitioned the project to work on carmofur, a small molecule originally developed for colorectal cancer but later repurposed for SARS-CoV-2, Sarah was involved in a high throughput analog screen of novel carmofur analogs against wild type and mutant variants of SARS-CoV-2 (Luk, et al., manuscript accepted, 2022). Late in 2022, Sarah was part of a team that worked on our group’s flagship paper of the year, using 19F NMR spectroscopy for monitoring (Chen, et al. ChemRXiv 2022), specifically for tracking the reactive intermediates present in complex multicomponent reactions. This project was shared at STEM Week at Los Altos High School (Link to talk: https://www.youtube.com/watch?v=vIJ-C1tVUbA) and is now under peer review for publication! Currently, Sarah works on several projects in the interface of chemical synthesis, chemical biology, catalysis, and small molecule drug discovery, including our development of difluorocyclopropanation catalyst strategies as well as using stereo- and regio-controlled inverse demand Diels Alder cycloadditions for construction of the tricyclic core of forskolin, a bioactive diterpenoid with therapeutic value in aging research.
First involved in the synthesis of N,N-diaryl pyrimidine-2,4-diamines to create structural analogs of the NNRTI, rilpivirine, using the Buchwald-Hartwig cross coupling reaction, I have since conducted a high throughput virtual screening and homology modeling of analogs of another NNRTI, efavirenz. In addition, I employed similar computational modeling efforts toward common tetracyclines to investigate their antibacterial properties and structure activity relationships. Finally, I’ve also been involved in the synthesis and biological testing of berberine analogs as a natural product pharmaceutical agent.
I joined ASDRP in the summer of 2021 and began research in the Njoo lab. The first project I worked on was the synthesis of rivastigmine, an FDA-approved drug for treating Alzheimer's Disease. Working with my fellow researchers, we identified several alternative conditions that avoided the use of pyrophoric materials. Additionally, we synthesized analogs of rivastigmine, compounds that are structurally similar to the drug but may have different biological capabilities. We did computational modeling and ran enzyme assays on all compounds, the results of which are reported in our paper: https://emerginginvestigators.org/articles/modular-mimics-of-neuroactive-alkaloids-design-synthesis-and-cholinesterase-inhibitory-activity-of-rivastigmine-analogs. Currently, I am utilizing NMR spectroscopy to study cholinesterase enzyme behavior, enzymes of interest for Alzheimer's, to help us better understand the results of our previous study.
When I first started in the group, I was working on a computational chemistry project related to the efficacy of natural small molecules on amyloid-beta peptides involved in Alzheimer's. Eventually, I shifted focus to synthetic work and worked on the semi-synthesis of various small molecules in different subgroups, mostly pertaining to developing anti-cancerous analogs of existing natural products. However, in the past year, I've found my interest lies in in biology and neurology. I've been involved in cell work for a variety of projects in Edward's group, maintaining cell lines and performing biological assays. Additionally, more recently, I started participating in a collaboration to develop spectroscopy methods to quantify neurotransmitters in brain tissue samples in order to analytically identify Parkinson's disease.
Highlights regarding conference proceedings and publications:
Poster at ACS: "Reactivity informed design, synthesis, and targeted delivery of andrographolide and analogs, Nf-kB regulated natural products for cancer treatment and degenerative diseases"
Publication in JEI: Mechanistic Deconvolution of Autoreduction in Tetrazolium-based Cell Viability Assays, manuscript in review, Journal of Emerging Investigators
During my time at ASDRP, I worked on antibody-drug conjugates (ADCs) which are an emerging class of cancer therapeutics that involve three main components: a monoclonal antibody, a selectively-degradable linker, and a cytotoxic payload. ADCs are advantageous compared to traditional therapeutics as they can selectively deliver cytotoxic payloads to cancer cells with minimal effects on healthy cells. I mainly focused on the biochemical aspect of our projects, such as culturing cells or performing cell viability assays. Additionally, I worked on the evaluation of the interference of various reductants on tetrazolium-based in-vitro assays, such as the MTT Assay.
As more small-molecule anticancer drugs are developed, a major obstacle to overcome is their limited selectivity and cytotoxicity to healthy cells, causing side effects such as hair loss, anemia, and weakened immune systems, therefore lowering its overall therapeutic efficacy despite their high potencies.
In my time at ASDRP, my group and I explored a novel class of immunotherapeutics and other prodrugging strategies to mitigate the onset of issues stemming from traditional small molecule chemotherapies. In collaboration with a local biotech company, our research group developed novel linkers to conjugate cytotoxic payloads to their antibodies. In addition, our group explored a photocaging strategy to release cytotoxic payloads at will.
I spent the majority of time at ASDRP within the marine biology group where I studied the California mussels' capability to filter microplastics. Although we encountered a host of challenges, ranging from lack of equipment to mussel die-offs, we persevered and are on the verge of finally publishing a methods paper!
Kara M Tran
Started off in the Kruger lab working on DNA fish labeling, worked on the first tissue cell cultures at ASDRP in the Tallapaka group, then joined the Njoo group, where I worked on many different projects from berberine, the COVID-19 computational work, andrographolide and more! I especially contributed to the tissue culture lab, in which I primarily cultured our cell lines, worked on troubleshooting the MTT assay, and trialed bioassays on our molecules.
Covid Vac Net maps the vaccination candidate connectome on an interactive digital world map using R & Java Script as well as Gephi. We pulled data from verified sources, such as the CDC and New York Times, and through exploratory data analysis, we shaped our data to fit our models. Then, we developed an algorithm using R to calculate vaccination percentages for individual countries as well as the significance of a stringency index on a country’s ability to institute regulations. After the numbers were crunched, we used machine learning to predict the risk of infection among vaccinated candidates on a global scale. With a neural network through an 80-20 split of data, we received accuracies in the range of 93% to 99%, depending on the vaccine candidate.
At ASDRP, I performed research on human epigenetic inhibitors, specifically DNA methyltransferases. I studied the impact of drugs like decitabine and RG108 on the cell viability of HCT116 colorectal cancer cells. I also presented this work at the American Chemical Society conference.
Amulya Bhargava Harish
Started research at ASDRP in the summer of 2020 under Carly Truong. Worked on project to use curcumin to inhibit the formation of alpha-synuclein plaques in E. Coli and C. Elegans. Transferred to the Jahanikia Neuro Lab in the fall of 2021. Worked on project to study the impact of the COVID-19 Pandemic on the cognitive dissonance of adolescence. Helped produced a manuscript that is currently being sent to journals and submitted a research abstract to the Japanese Neuroscience Society’s 2023 conference with the Jahanikia Neuro Lab.
For the past 2 years, I have worked on the CognoTrain and CovidFatigue projects in the Jahanikia Neuro Lab. Before the CognoTrain project separated from ASDRP, I worked on frontend and backend components of the computer based cognitive training software that we had designed. Since then, I have led the CovidFatigue Project, overseeing the creation of our surveying workflow (symptom screening questionnaire, participant outreach, data scoring) to quantify the severity and timeline of COVID-19 after-effects. We have now moved into data collection and analysis, which is an exciting milestone as I end my time at ASDRP. I am eager to see the upcoming literature and conference presentations that will be based on this analyzed data!
I started my research at ASDRP in a psychology group where we performed a meta-analysis on different treatments for adolescents with depression. I then transferred to a biology group where we analyzed the DNA of the sucrose synthase enzyme in genetically modified and heirloom peas. After joining Edward’s group the following semester, I started by researching the effects of polyphenols for neurodegenerative diseases via in-silico testing as well as focusing on an in-silico study of kinesin-like proteins in model organisms. Later that year, I joined several other groups where we investigated the effects of synthetic plant hormones on plant metabolites and worked on an in-silico study of a library of carmofur analogs as potential inhibitors of the SARS-CoV-2 main protease. Then I started primarily working within the chemical neuroscience subgroup, where we explored the synthesis and biological activity of novel neuroactive alkaloids. Throughout my time in Edward’s group, I have been able to co-author several papers and present at conferences such as CSUCI, SCCUR, and ACS.
Performed research in the Machine Learning for Drug Discovery (MLDD) Cheminformatics, Biologics/Bioinformatics, and Pharmacokinetics projects. Applied computational and machine-learning-based techniques to chemistry and biology in order to advance research in the screening of chemical compounds, molecular modeling and classification, and drug development.