Date of Completion

2024

Document Type

Thesis

Degree Name

Bachelor of Science in Biochemistry

Keywords

aptamer, in silico, steroid 5a-reductase 2, benign prostatic hyperplasia, androgenic alopecia

Abstract

Aptamers are short single stranded (SS) oligonucleotide structures that have variable shape and high selective affinity for their target compounds. However, the conventional process of producing such aptamers through the systematic evolution of ligands by exponential enrichment (SELEX) requires extensive duration and laborious processes. As such, an in silico approach was used as a screening measure for a potential aptamer inhibitor candidate for S5αR-2 enzyme, which catalyzes the conversion of testosterone to dihydrotestosterone, and is thought as one of the causes of benign prostatic hyperplasia (BPH) and androgenic alopecia (AGA). The initial sequences of the aptamers were based on the selection of tRNA sequences from various species. The secondary structures of these sequences were generated from UNAfold, then rendered into 3D structures through 3dRNA. The docking simulation was predicted using the HDOCK web server. Modifications of the sequences were performed through the BIOVIA Discovery Studio client. Lastly, the intermolecular attractions were analyzed using PLIP web server. Seventeen aptamers were found to preferably bind to the cytosolic portion of the enzyme. Out of those seventeen candidates, six aptamers were chosen for their relative binding scores, ranging from -280 to -340 HDOCK scores. Aptamer HMO-1 had the strongest binding affinity of - 340.8 due to its extensive intermolecular attraction containing 13 H-bonds and 8 salt bridges with the enzyme. Aptamer MJR-1, MJR-2, HMO-2, MJR-3 and HMO-3 had the HDOCK scores of - 305.94, -302.66, -296.91, -287.89 and -282.16 respectively with intermolecular interactions ranging from H-bonds, salt bridges, π-cation and π-stacking. The aptamers undergone modifications by the conversions of all their ribose sugars to locked nucleic acids (LNA). The LNA counterpart of aptamer HMO-1 was shown to have marginal increases in its binding score while still having extensive interactions with the cytosolic loops L1, L3 and L5, while the LNA counterpart of MJR-3 only exhibited the latter. Aptamer MJR-2 and two other aptamers were also subjected to GC content increase as additional modifications, with only one harboring similar binding affinity. The aptamers designed in this study may have the potential to inhibit the activity of the enzyme as it binds to the cytosolic loops L1, L3 and L5, which may increase the barrier of NADP+/NADPH exchange.

First Advisor

Margel C. Bonifacio

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