Date of Publication

2023

Document Type

Master's Thesis

Degree Name

Master of Science in Chemistry

Subject Categories

Chemistry

College

College of Science

Department/Unit

Chemistry

Thesis Advisor

Stephani Joy Y. Macalino

Defense Panel Chair

Rodolfo E. Sumayao, Jr

Defense Panel Member

Faith Marie G. Lagua
Junie B. Billones

Abstract/Summary

Vitamin K epoxide reductase (VKOR) is an enzyme that contributes to the synthesis of several clotting factors and its inhibition is a well-known mechanism of anticoagulant action. Though the VKOR inhibitor warfarin remains essential and popular today, its adverse effects still make it a high-risk medication. This study intends to identify novel compounds with predicted VKOR inhibition and pharmacokinetic stability as well as explain the mechanistic basis of their action.

A combination of pharmacophore modelling, druglikeness prediction, and molecular docking techniques was employed to find hits from existing compound libraries. Cell-based VKOR inhibition using the FIXgla-PC chimera reporter protein was then done to validate the in silico hits and determine the most potent hits. Fourteen hits showed suitable in vitro activity at the micromolar level, led by compound A116 (IC50 = 6.6 µM). The docked protein-ligand complexes of the in vitro hits were then subjected to molecular dynamics simulations to obtain atomic-level interaction information between the target and hits. High hydrogen bonding occupancies with Asn80, Cys135, and Tyr139 were noted for the top compounds, and ligand binding free energies were most significant at residues Phe55 to Phe63, Phe83, Leu120 to Leu128, and Cys135. Root-mean-square deviation (RMSD) measures suggest that VKOR inhibitors stabilize the luminal loop while root-mean-square fluctuation (RMSF) measures and network analyses add that inhibitors also reduce loop flexibility and residue communications.

The combined in silico and in vitro data suggest that VKOR inhibitors must have a bicyclic nucleus that can elicit hydrophobic forces with luminal residues 55 to 63 and TM3 residues 120 and 128, as well as extensively hydrogen bond to Asn80 and Tyr139 or Cys135. Additionally, shorter side chains interact primarily with Phe83 while longer side chains interact with residues from Phe83 to Phe87. An extra side chain, like warfarin’s alkyl ketone, may not be essential. This proposed structure-activity relationship can serve as a useful guide for designing improved and novel vitamin K antagonists in the future.

Abstract Format

html

Language

English

Format

Electronic

Physical Description

xvi, 132 leaves

Keywords

Vitamin K; Enzymes

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Embargo Period

8-12-2025

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Available for download on Tuesday, August 12, 2025

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