Synthesis and In Silico Evaluation of Nucleoside Analogues as Potential Pancreatic Cancer Therapeutics

Alina Aguilar-Gonzalez, Karlitha Leonard, & Dr. Ahmed Awad

Detecting Pancreatic Ductal Adenocarcinoma in its early stages poses a significant challenge, while treating it effectively remains difficult due to chemoresistance and the inability to operate on metastases. Although current chemotherapy agents can shrink tumors and deter reoccurrence, the one-year survival rate stands at a mere eighteen percent. Gemcitabine, the standard FDA-approved chemotherapy for cancers like PDAC, targets ribonucleotide reductase (RNR). However, controversies surround Gemcitabine, including cytotoxicity, poor cellular penetration, and high rates of chemoresistance.
Ribonucleotide reductase (RNR) is a critical enzyme catalyzing the conversion of ribonucleotides to deoxyribonucleotides, vital for DNA synthesis and repair. By inhibiting RNR, which plays a pivotal role in de novo deoxynucleotide triphosphate (dNTP) synthesis, tumor cell growth can be impeded as cancer cells heavily rely on DNA synthesis for replication.
In this study, we synthesized four aryl sulfonamide nucleoside analogues resembling Gemcitabine, each modified at the C-2’ region with benzene sulfonamide derivatives featuring electron-withdrawing groups like fluorine and chlorine. These modifications were hypothesized to enhance binding affinity towards RNR. Computational analyses were conducted on these compounds to assess their interactions with the large M1 subunit of Ribonucleotide Reductase (HRMM1), including amino acid residues, hydrophobic/hydrophilic interactions, and RMSD values.
Biological activity and drug-likeness of the aryl sulfonamide compounds were evaluated through PASS and SwissADMET analysis, identifying three top compounds: 2-chloro-4-fluoro-5-sulfamoylbenzoic acid (Compound A), 4-fluorobenzoic acid (Compound B), and 3-fluoro-4(trifluoromethyl)phenylacetic acid (Compound C). PASS prediction analysis indicated a higher Pa value compared to Pi value for each compound, suggesting a greater likelihood of biological activity. Compounds A, B, and C yielded Pa > Pi values of 0.198 > 0.011, 0.107 > 0.029, and  0.078 > 0.051, respectively. Compounds A, B, and C also demonstrated binding affinities to the active site of RNR, with average Edoc scores of -27.65, -27.54, and -29.28 kJ/mol, respectively. The promising results from molecular docking, pharmacological profile analysis, and biological  activity suggest that these aryl compounds are potential RNR inhibitors for pancreatic cancer.

Poster Presentation

Session 2

1:00pm – 2:15pm
Grand Salon

Chemistry

Synthesis of Conformationally Constrained di Amino L-Proline Analogues: Potential Central CNS Drug Pharmacophores

Heather Torgerson, & Dr. Thomas Schulze

Neurosciences (Central Nervous System, CNS) Research & Development (R&D) is a modern field of study with pivotal implications in the pursuit of novel pharmacological studies. Currently available anti-psychotic drugs (aka: Risperidone, Paliperidone) contain 6-Membered Piperidine & Piperazine ring systems which are well-established central pharmacophore systems likely responsible for biological action. Their highly unfavorable side-effect profile is mainly attributed to an enormous amount of Off-Target biological actions, here hypothesized by very high degree of conformational freedoms exerted my 6-Membered Ring Systems. It is hypothesized that conformationally flexible substituted 6-Membered Piperidine ring systems may potentially be responsible for Off-Target biological activity. The research objective is to synthesize conformationally constrained 5- Membered Proline-Based Diamine Analogues. By using Trans-Hydroxy-4-L-Proline as the starting molecule, the diamine analogue is planned to be synthesized in 6 steps. The first 2 synthetic steps have been completed, using small quantities initially and then repeating at larger multi-gram scale. The diamine synthesis is planned to be governed by Lipinski’s Rule-of-Five considerations.

Poster Presentation

Session 1

9:15am – 10:30am
Grand Salon

Chemistry

Connecting with Science: An Evaluation of the Types of Real-World Chemistry Applications Identified by General Chemistry I Students and the Connection to Course Material

Natalie Leon, & Dr. Ariel Vaughn

Science is often perceived as difficult and abstract due to the disconnect between real-world applications and scientific concepts taught in the classroom. In General Chemistry courses, it has been observed that the disconnect with science contributes to high failure and withdrawal (DFW) rates, as well as students feeling that they cannot be successful in STEM. Finding ways to make science more accessible, engaging, and inclusive for students is essential in addressing the disconnect between applications and science. During this fifteen week study, forty-four General Chemistry I students from California State University Channel Islands were asked to provide a weekly short answer response to the question, “How have you observed chemistry outside of class this week?” Using NVivo 14, the responses were qualitatively evaluated for the real-world chemistry applications observed by students. The results showed that 86% of students identified 5 or more different types of real-world chemistry applications, with 55% of students identifying 7 or more examples. Moreover, it was observed that students primarily observed chemistry in cooking/food-related situations and beverages, aside from examples observed in the lecture and laboratory course. The analysis also included an evaluation of how the examples related to course concepts taught during the semester. For example, students related cooking/food-related examples to 11 different course concepts. Overall, the study suggested that student-oriented homework assignments helped increase student understanding of chemistry and connection with science, which may be a contributing factor to the decreased DFW rate observed in General Chemistry I.

Poster Presentation

Session 1

9:15am – 10:30am
Grand Salon

Chemistry

Going the Extra Mile: Analyzing Student Responses in General Chemistry I Homework Assignments

Noleen Kirya, & Dr. Ariel Vaughn

General Chemistry I has a reputation for being difficult. This leads to a large number of students failing the course, causing students to have less confidence in their abilities as scientists. This is an issue for diverse students in particular, because many do not see role model scientists that look like them. If students can observe that chemistry is everywhere in their surroundings, this may help cultivate a sense of scientific identity, allowing them to envision themselves as scientists. Homework assignments is one way to do this. In this study, we analyze the responses of 173 students in General Chemistry I from the Keck Science Department at the Claremont Colleges over the course of 14 weeks. The students were asked, “How have you observed chemistry outside of class this week?”. The responses underwent qualitative coding using NVivo 14. Students were not specifically prompted to provide detailed descriptions of the chemistry involved, yet we observed that many responses included supplementary explanations, diving further into the chemistry within their examples. This indicates students exceed the requirements of this assignment. Data is still being analyzed. Preliminary results from Weeks 1-4 show students are providing more explanations as the semester progresses. Through offering supplementary explanations, students recognized the presence of chemistry in their surroundings, demonstrating involvement with the assignment. This level of involvement could suggest that students have developed a scientific identity, which assists them in envisioning themselves as scientists.

Poster Presentation

Session 1

9:15am – 10:30am
Grand Salon

Chemistry

Students are Scientists Too: Students’ Use of Scientific Language in a General Chemistry Weekly Homework Assignment

Isabella Jackson, & Dr. Ariel Vaughn

Many students find General Chemistry to be very difficult because it is a fast paced and algebra intensive course. This causes many students in General Chemistry to receive D’s, F’s, or withdraw (W’s) from the course. This leads to students, especially students from historically underrepresented groups, not seeing themselves as scientists. Homework assignments are one tool to alleviate this problem that students face and may change students’ perceptions of chemistry. In this study, each week students at the Keck Science Department at Scripps, Claremont McKenna, and Pitzer Colleges were asked the simple question, “How have you observed chemistry outside of the classroom this week?”. Responses to the question were analyzed for the use of scientific language. The responses were coded into categories including: No Scientific Language, Some Scientific Language, and Clearly Scientific Language. Responses categorized as No Scientific Language were when no scientific terms were used. Responses labeled Clearly Scientific Language contain either three or more scientific terms or forty percent of the sentence consists of scientific terms. Some Scientific Language is any response between Clearly and No Scientific Language. Qualitative analysis is currently underway in NVivo 14. We anticipate that students will use more scientific language as they become more comfortable with scientific terms, resulting in a trend as the semester progresses. As students use scientific language more comfortably, students will feel more confident communicating in scientific spaces. This new level of comfort will hopefully empower students to see themselves as scientists.

Poster Presentation

Session 1

9:15am – 10:30am
Grand Salon

Chemistry

The Impact of Polychlorinated Biphenyls on S. Cerevisiae’s Proteome

Andrew Hale, Matthew Dutzi, & Dr. William Munroe

Polychlorinated-Biphenyls (PCB) are a category of persistent chemicals. PCBs are slightly soluble in water and endure in the environment for long periods, leading to water supply contamination and PCBs status as a forever chemical. PCBs are known to induce oxidative stress on cancer cell lines, oxidative stress is a phenomenon where reactive oxygen species are increased. These molecules easily degrade DNA leading to its infamous status as a cancer causing chemical. S. cerevisiae is a unicellular eukaryotic yeast that share several very similar pathways with H. sapiens; S. cerevisiae is frequently used to study the anti-cancer BCL-2 pathway which is a combination of proteins that induces cell death in cells that have genomic damage. S. cerevisiae has several proteins that contain BH3 domains, a structural motif that a induces cell death when activated. S. cerevisiae and H. sapiens both have proteins that have BH3 domains to induce apoptosis and prevent DNA damage. This project aims to induce a proteomic change in S. cerevisiae via treatments with a common PCB, Aroclor-1254, to determine the change in S. cerevisiae’s proteome. A microtiter plate assay was developed to determine the effect Aroclor-1254 had on S. cerevisiae’s growth rate. Next, two-dimensional gel electrophoresis was performed to identify the isoelectric points, molecular weights, and relative concentration of individual proteins in S. cerevisiae’s proteome. Upon adding Aroclor-1254, there was a xxx(+/-xxx)% reduction in cell growth rate. A protein of interest was identified via the analyses of two-dimensional gels. The protein of interest has an approximate isoelectric point of xxx and molecular weight of xxxkDa. Further work aims to confirm the identity of this protein through mass spectral analyses.

Poster Presentation

Session 1

9:15am – 10:30am
Grand Salon

Chemistry

Reactivity-informed Pharmacophore Editing and Biological Evaluation of Andrographolide and its Analogs

Carina Zhou, Sanghyuk Ko, Tiffany Gu, & Dr. Edward Njoo

Natural products and their analogs have long served as inspiration for the exploration and development of small molecules with therapeutic significance. One such compound is andrographolide, a labdane diterpenoid extracted from the plant Andrographis paniculata, which has been extensively studied as an anti-cancer therapeutic. It is known to function putatively through covalent inhibition of Nf-kB, a transcription factor that modulates tumor survival and metastasis. Remarkably, functionalization of the C-19 hydroxyl and C-17 alkene putatively alters the primary mode of action from inhibition of Nf-kB to the modulation of the Wnt/𝜷-catenin signaling pathway. To interrogate the structure-activity relationship of these two positions, we synthesized a library of andrographolide analogs by protecting the C-19 hydroxyl with large, hydrophobic silyl and trityl ethers and epoxidizing C-17. We also optimized the facio-selective installation of the epoxide on the C-8/17 exo-olefin. MTT assays revealed that all of our C-19 analogs in HCT-116 colorectal cancer cells showed greater anti-proliferation compared to that of andrographolide but had relatively similar IC50 values in MDA-MB-231 metastatic breast cancer cells. Additionally, previous studies show that the installation of a TBDPS protecting group at C-19 and epoxidation of C-17 led to modulation of the Wnt/𝜷-catenin signaling pathway through GSK3𝜷 inhibition. To further investigate the mechanism of action of these analogs, we performed western blots to assess the relative levels of active 𝜷-catenin compared to phosphorylated 𝜷-catenin. Finally, we describe progress towards the first chemical synthesis of an andrographolide A-ring oxetane analog, which is a co-isolated naturally-occurring metabolite of Andrographis paniculata, whose biological activity and synthetic preparation have not been previously described.

Oral Presentation

10:45am – 12:15pm
Del Norte 2550

Chemistry

Discovery, Synthesis, and Optimization of 5-phenylisoxazole Based Covalent Inhibitors Targeting G12C Mutant KRAS for the Treatment of Cancer

Arshia Desarkar, & Dr. Edward Njoo

Oncogenic mutations in the GTPase protein KRAS are implicated in approximately 25% of human cancers. Specifically, the G12C mutation, a common mutation found in KRAS-related pathology, is found in 12% of non-small cell lung cancers and 3% of colorectal and other solid tumors. This single residue substitution causes irreversible binding of GTP/GDP to the catalytic site, thereby forcing the protein into a permanent, activated state. While KRAS has been previously considered an undruggable chemotherapeutic target, the discovery of acrylate-based covalent inhibitors of G12C KRAS has led to the development of two FDA-approved drugs: Sotorasib (AMG-510) and Adagrasib (MRTX849) which inspired our own pharmacophore model, and our library of isoxazole-based covalent inhibitors of G12C KRAS. En route, we optimized a previously reported amide coupling in which our library of analogs exhibited a comparatively higher yield of 98%. This transformation tolerates air with a trivial loss of yield and has been applied to 12 different examples of arylmethyl isoxazole acids and alkyl substituted piperazines including in the synthesis of Nucleozin. In vitro potency was then evaluated through MTT assays against Calu-1 cancer cell lines, and to test the selectivity, against HCT-116 cancer cell lines. Our S-methyl compounds were shown to be selective in targeting mutant G12C, as they were ineffective in HCT-116 colon cells, and our lead compound in specificity amongst these contains a 2,6-dichloroaryl ring.

Oral Presentation

10:45am – 12:15pm
Del Norte 2550

Chemistry

Designing and Synthesizing Novel Nucleoside Analogs as Potential Pancreatic Pancreatic Cancer Chemotherapeutics

Delyar Khosroabadi, & Dr. Amed Awad

Pancreatic ductal adenocarcinoma (PDAC), the most prevalent type of pancreatic cancer with a high mortality rate due to a lack of early detection techniques leading to diagnosis at a terminal stage which limits treatment options. The current standard chemotherapeutic for pancreatic cancer is a drug called Gemcitabine. The diphosphorylated form of this prodrug covalently binds within the catalytic site and inhibits the activity of ribonucleotide reductase (RNR), while the triphosphorylated form of the drug gets directly incorporated into the DNA sequence, inhibiting DNA polymerase. The problem with gemcitabine is that it faces drug resistance which hinders its chemotherapeutic potential. This is mainly due to the presence of cytidine deaminase in cells which inactivates most of the drug upon entry. Gemcitabine is also commonly administered alongside other medications possessing iron or zinc chelating properties, resulting in additional side effects. Our goal is to modify the chemical structure of gemcitabine to increase its chemotherapeutic potential. Our proposed nucleosides feature an OH group on the 4’ nitrogen of the base of the nucleoside, inhibiting cytidine deaminase from inactivating the drug which increases its bioavailability. Another modification that we are introducing is the addition of a zinc and iron chelator at the 2’ carbon of the ribose sugar. To achieve these objectives, we use multi-step organic synthesis under inert conditions. Some of the named reactions we use include the Mitsunobu reaction and Yamaguchi esterification reaction. Our computational studies of the analogs include molecular docking, SWISSADME, and PASS prediction. The molecular docking studies are performed using internal coordinate mechanics algorithm (ICM) which allows analysis of the edock score, root mean square deviation (RMSD), and H-bonding formation of the analogs in the catalytic site of RNR. The results of these computational studies support the potential of these compounds as RNR inhibitors.

Oral Presentation

10:45am – 12:15pm
Del Norte 2530

Chemistry