Undergraduate Research in Chemistry

Hands-on lab research is an important part of being a chemistry major at Pomona College. Students have the opportunity to use modern instrumentation, computational facilities and sophisticated software in the classroom and on independent research projects as early as their first year. Below are some recent summer research projects conducted by chemistry students.

Hydrophobicity and Drug Delivery: A QSAR Approach

Jacob Al-Husseini ’22; Advisor: Malkiat Johal​

In this work, Dual Polarization Interferometry (DPI) and Quartz Crystal Microgravimetry with Dissipation Monitoring (QCM-D) were used to examine the binding characteristics and structure-activity relationships of 12 common drugs on a model bovine serum albumin (BSA) film. By taking advantage of the different hydration sensitivities of DPI and QCM-D we were able to quantify changes in the solvent state upon drug binding to BSA. Quantifying the changes in water mass within binding pockets and upon drug-protein binding allows for a more complete understanding of binding phenomena between drug molecules and serum proteins. For the drugs tested, a quantitative structure-activity relationship (QSAR) was used to establish a correlation between drug binding (KD) and hydrophobicity (ClogP), with the latter being related to the drug’s ability to desolvate the BSA upon binding. In summary, the QSAR analysis shows that both the strength of binding and the loss of water due to binding increase with drug hydrophobicity. It is not surprising that more hydrophobic drugs lead to greater water loss from the BSA, but the corresponding increase in binding strength is noteworthy. This study underscores the importance of hydrophobicity to drug binding kinetics and may be used to further understand and improve drug design and delivery protocols.

Identification of Odor Blend Used by Caenorhabditis elegans for Recognition of Evolved Bacteria

Emily Rainge ’22; Advisor: Charles Taylor

Caenorhabditis elegans (C. elegans) are worms that inhabit bacteria-rich environments such as rotting fruit and plant matter. They use their sense of smell to make choices about what bacterial species they can consume without succumbing to disease (Shtonda and Avery 2006). The goal of this project is to investigate what blends of chemical cues C.elegans olfactory systems use to distinguish among different bacteria. To accomplish this, we have used Gas Chromatography-Mass Spectrometry to analyze volatile organic chemicals present in the air above samples of two strains of E. coli: OP50 and HB101 (a food source that is more nutritious to C.elegans than OP50). Our preliminary results show that the volatile chemicals emitted from OP50 and HB101 differ; OP50 headspace contained dimethyl disulfide, while HB101 headspace contained 1-Butanol and 2,4-Di-tert-butylphenol. Both OP50 and HB101 emitted isobutyric acid,2-(hydroxymethyl)-1-propylbutyl ester and butyl butanoate into their headspaces. Now, we want to test whether worms can tell the difference between the odors of OP50 and HB101 using bacterial choice assays.

Characterizing the Regulatory Function of Novel Riboswitches Genetically Engineered in Escherichia Coli.

Chanha Kim ’22; Advisor: Jane Liu

Riboswitches are sequences in messenger RNAs (mRNAs) that can regulate expression, either positively or negatively, by binding small molecules, and they have numerous applications, such as synthetic biology, biosensor development and virus control. We aimed to characterize the regulatory function of novel theophylline-binding riboswitches that were previously engineered in the lab. Specifically, we investigated whether riboswitch 3-5 regulates expression at the transcriptional or translational level. We used in vitro protein synthesis and western blotting to determine how riboswitch 3-5 regulates protein synthesis in response to theophylline. We also performed northern blot analyses to probe whether or not riboswitch 3-5 regulates expression transcriptionally in response to theophylline. Western blot analysis suggests that riboswitch 3-5 regulates protein synthesis in response to theophylline, and northern blot analysis suggests this to be, at least in part, occurring at the level of transcription or mRNA stability. Both analyses, however, suggest that further optimization of these experiments or transitioning to other in vitro methods are necessary to determine more precisely how riboswitch 3-5 regulates expression in response to theophylline. Doing so will contribute to the greater understanding of how novel riboswitches function and may aid future researchers in innovating riboswitch applications.

Chemical Analysis of Traditional Vietnamese Medicinal Herbs

Rachel Hall ’22; Advisor: Chemical Analysis of Traditional Vietnamese Medicinal Herbs

Bear Bile Farming (BBF) began as a practice in Vietnam in the 1990s in response to consumer demand for bear bile and traditional medicines that contain it. Although BBF was outlawed in Vietnam in 2005, bear owners were allowed to keep their bears after certifying that they would not be harvesting bile from them. The compound found in bear bile known to have medicinal value (ursodeoxycholic acid) is now commercially available. This work focuses on the chemical analysis of herbs used in preparing traditional medicines that have the same uses as bear bile.

Our goal was to determine if any compounds extracted from these herbs have been used to treat similar ailments. Our approach has been to 1) determine which compounds are extracted from these herbs and 2) identify which of these compounds could be responsible for particular medicinal properties. Using GCMS and LCMS we found volatile and non-volatile chemical constituents of these herbs. We were then able to gather more information related to the medicinal properties of each compound using databases such as SciFinder and PubChem. Another aspect we wanted to look at was which compounds can be found in more than one herb. We have identified six compounds that were common to three or more of the herbs, all with known medicinal properties.