Myrnel A. Fortuna

I am an MS Chemistry student at the University of the Philippines Diliman, College of Science, Institute of Chemistry. I work under the supervision of Dr. Ricky B. Nellas. I obtained my undergraduate degree in Industrial Pharmacy at the University of the Philippines Manila. My training focused on medicinal chemistry, drug design, and drug formulation. My undergraduate thesis investigated the effects of varying temperatures and relative humidities of the Philippines on amoxicillin tablets, frequently misused and improperly stored drugs in the country. After obtaining my pharmacy license, I worked in the industry for almost two years before deciding to pursue a Master’s degree and transition into research.

I initially joined Dr. Aaron Villaraza’s peptide synthesis lab but transitioned to Computational Chemistry after a short internship offered by Dr. Ricky. I joined his laboratory in Q1 2021, studying cancer pathways, specifically the MAPK pathway, to identify new drugs for the NRAS GTPase.

I worked as a research assistant under the Department of Science and Technology – Philippine Council for Health Research and Development (DOST-PCHRD), as part of the Discovery and Development of Health Products (DDHP) program under Project 6: Computer-Aided Drug Design of Natural Products-Based, and Synthetic Antidiabetic, Antifungal, and Anticancer Lead Compounds and Derivatives. My work involved computer-aided drug design (CADD) for anticancer lead compounds. I collaborated with organic chemists from Dr. Monissa Paderes’ group on lead compounds and conducted novel binding site searches using MD simulations for cancer targets, such as HSP90, the androgen receptor, and the estrogen receptor. I also introduced network pharmacology to the lab, presenting findings through posters and oral presentations at the Philippine Chemistry Congress. This project provided extensive experience in computational drug repurposing.

After the DDHP program ended, I joined the DOST Technical Battle Against COVID-19, where I conducted CADD studies on different SARS-CoV-2 variants. I collaborated with experimentalists to verify the binding affinities of synthesized compounds and used CGMD, molecular docking, and MM-GBSA to calculate binding free energies of top compounds identified through bioassays. Additionally, I helped develop an in-house chemical library to expand the chemical space of potential COVID-19 inhibitors. This work is part of a research paper currently being drafted in collaboration with the Molecular Endocrinology Laboratory of the National Institute of Molecular Biology and Biotechnology (NIMBB).

Additional work for the COVID-19 project included biophysical analyses of the spike protein to identify the effects of glycosylation on its dynamics. A research paper which I co-authored from this study was recently accepted in Scientific Reports and is due to be released. I also designed the supplementary journal cover of a published paper under the program.

My latest research experience was at the UST Research Center for the Natural Sciences and Applied Sciences (RCNAS), where I worked under Assistant Professor Leonardo A. Guevarra. My work involved peptide modeling for spider venom sequences from Philippine spider species and studying their binding to ion channels. Currently, I apply steered MD simulations to understand the behavior of spider venom peptides in crossing lipid membranes and their dynamics upon binding to ion channels.

Side Projects
In 2023, I took over our lab’s protein engineering project, training two undergraduate interns. I co-authored a paper on the reverse engineering of bacterial PAL lipase.

Research Interests

• Computer-Aided Drug Design
• Computational Biophysical Analysis
• Protein Engineering of Industrial Enzymes
• Peptide Folding and Ion Channels

Relevant Courses Taken

• Chem 359 (Institute of Chemistry, UPD): Biophysical Analysis under Dr. Ricky B. Nellas.
• Math 236 (Institute of Math, UPD): Chemical Reaction Networks under Dr. Byran Hernandez.
• MBB 390 (NIMBB, UPD): Systems Biology and Bioinformatics under Dr. Isaiah Lee (paper draft in progress).

Relevant Trainings and Workshops

• 10th Annual CCPBioSim & MGMS Conference, February 2024: Molecular Modelling in Structure-Based Drug Design
• Hybrid Hünfeld Workshop, 2024: Computer Simulation and Theory of Macromolecules, Max Planck Institute for Multidisciplinary Sciences
• EU-ASEAN HPC School, 2023: BRIN, Bogor, Indonesia
• UNHAN Quantum and Qiskit Workshop, 2023: Jakarta, Indonesia
• Hybrid Hünfeld Workshop, 2022: Computer Simulation and Theory of Macromolecules, Max Planck Institute for Multidisciplinary Sciences

Misc Lab Activities
I enjoy automating analysis using shell and Python scripts, optimizing terminal navigation with aliases, and creating high-quality graphs using Mathematica. I use Blender for visualizations in posters and presentations. I also co-developed our lab website and introduced the lab to the FAIR principles. Currently, I manage our lab’s GitHub account.