After taking organic chemistry, I had an opportunity to synthesize compounds with my professor, Dr. Oyinda Oyelaran. The research question we developed was to understand the effect of human host blood type on malaria susceptibility. To answer this, we set out developing an anti-malarial lead compound, which the Walter Reed Army Institute agreed to assay for us. With their feedback, we optimized the compounds to achieve better IC values, lower cross reactivity, and improved solubility. Using the Tres Cantos Anti-Malarial Set from GlaxoSmithKline, my professor and I chose a class of compounds with low IC50 values for malaria, high EC50 values for receptors like 5-HT2B, and a high degree of modularity. Beginning in June 2012 with a lead compound, we mapped out a retrosynthesis and began the synthesis.
Early on, I searched for SciFinder literature to help me choose reaction conditions. I encountered problems soon because the literature was not often reproducible. More importantly, the lab was not set up when I started. There was a constant shortage of basic equipment like a refrigerator, oven, rotavapor, glassware, and reagents. To address these issues, I borrowed space in an oven and fridge from nearby labs and coordinated when I could access the rotavapor. As a result, I had refrigerated reagents, dry glassware, and time on a rotavapor at key times of the day. The lab itself was small, so I made sure to keep equipment clean and arranged every day. The result was that I had glassware and syringes when needed. Due to reagent shortages, I was frequently delayed in moving the synthesis forward. Instead, I chose to stockpile the product from the previous step. This worked well because I would have enough starting materials to troubleshoot the next reaction under varying conditions. Monitoring reactions was difficult and I did not find literature for the exact compounds I was making. Moreover, I was limited to TLC and occasionally NMR. Faced by these challenges, I tried several different solvent combinations for TLC mobile phases. I also read through an NMR manual to learn the software and my preparation resulted in more efficient use of NMR time.
In October, I completed the synthesis I started in June and recently reached out to a post-doctorate fellow who helped me characterize my final product with LC-MS and HPLC. As he was unfamiliar with my compound, working with him has taught me a lot about faithful record-keeping and having diverse sources of data. I consistently documented the masses of all my compounds to help assess the purity of my products. I also drew information from UV activity on TLC and from TLC staining. I obtained NMR spectra of all starting materials, crude products, and purified products to show changes in the compound from start to finish. When presenting my sample, it is helpful that I can explain its solubility, molar mass, staining, structure by NMR, and any possible byproducts that may be present with the desired compound.
Overall, I contributed a majority of the progress to solve my research problem. Since no one else worked in my lab to move the research forward, I tried taking advice from graduate students and fellows in other labs and learned from their experience. When waiting to collaborate with the post-doc I contacted, I spent my time reading about different purification techniques besides chromatography, including extraction, precipitation, recrystallization, and distillation.
Carrying this research forward has helped me build the skills to design and carry out my own research question. Characterizing my compounds using different data sources – mass, UV, TLC staining, and NMR spectroscopy – has helped me think analytically and has shown me the importance of controls in an experiment. I am already applying the derivatization and analytical skills I have developed in my method development project at my co-op with the Ensemble Discovery group.
Faraz Arastu, Chemistry