Theses (MSc in Analytical and Pharmaceutical Chemistry)

Labdane diterpenoids are phytochemicals which have been reported effectively against acetylcholinesterase inhibition. Butyrylcholinesterase is another enzyme involved in hydrolysis of acetylcholine in the brain. Both enzymes are regarded as important therapeutic target for Alzheimer’s disease. Nonetheless, study on the effect of labdane diterpenoids towards butyrylcholinesterase inhibition is scarce. This project aimed to study the pharmacokinetic profiles of labdane diterpenoids of Alpinia genus via in silico methods and to evaluate their binding interactions in the active site of butyrylcholinesterase through molecular docking. A series of thirty labdane diterpenoids from Alpinia genus were investigated for their physicochemical properties using Molinspiration server and the pharmacokinetics profiles using pkCSM. Docking systems consisting of butyrylcholinesterase protein (PDB ID: 4BDS) and labdane diterpenoids were subjected to docking studies using AutoDockTools. Protein-Ligand Interaction Profiler was used to analyse the docking outputs; LigPlot Plus was used to illustrate the binding interactions between butyrylcholinesterase protein and labdane diterpenoids. A total of twenty labdane diterpenoids met the requirement of Lipinski’s rule and complied to Veber rule. Several labdane diterpenoids in the present study have exhibited drug likeness, good oral bioavailability as well as considerable drug distribution and blood-brain-barrier penetration based on in silico prediction. All compounds were shown to have relatively good binding within the binding site of butyrylcholinesterase from the docking studies in comparison to the co-crystallised ligand, tacrine based on the binding energy; their binding energies ranged from -17.70 kcal/mol to -7.3 kcal/mol versus that of tacrine with binding energy of -7.71 kcal/mol. Hydrogen bonding and hydrophobic interactions were found as the main binding interactions between the binding site residues and labdane diterpenoids. Amongst the compounds, ligand no. 1 showed the highest binding energy of -16.00 kcal/mol and the lowest estimated Ki of 1.86 pM. In conclusion, several labdane diterpenoids in the present study have demonstrated good pharmacokinetic profiles based on the in silico prediction. These compounds were also shown to have relatively good binding within the binding site of butyrylcholinesterase based on the molecular docking studies. Keywords: Labdane diterpenoids, butyrylcholinesterase, Alzheimer’s disease, pharmacokinetics, molecular docking

Porphyromonas gingivalis (P. gingivalis) is a Gram-negative, anaerobic rod-shaped bacterium that has been implicated as a keystone pathogen in chronic periodontitis. Such disease is characterized by inflammation and affects the individual’s gums, which eventually leads to tissue destruction and tooth loss. There is an increasing number of evidences on the role of P. gingivalis in Alzheimer’s disease pathogenesis. Inhibition of gingipain K, one of the virulence factors of P. gingivalis, has been considered as an effective strategy for treating Alzheimer’s disease, especially for individuals with concomitant chronic periodontitis. The objectives of this project are to evaluate the binding interactions of a set of FDA-approved drugs in the active site of P. gingivalis gingipain K and to determine their inhibitory activity against the gingipain K. Structure-based virtual screening on gingipain K was performed through molecular docking simulation of 300 FDA-approved drugs obtained from the ZINC 15 database. The top ten compounds (fludarabine, phenylephrine, levetiracetam, midodrine, formoterol, lamivudine, olsalazine, benazepril, ketorolac and diltiazem) with relatively high docking scores were selected for subsequent biological screening. Through gingipain K enzymatic assay, the gingipain K activity was determined by measuring the absorbance at 405 nm over 15 minutes. Results from the molecular docking studies showed that the compounds engaged primarily in hydrogen bonding, π-π stacking, salt bridge and pi-cation interaction with the surrounding residues, namely Trp391, Thr442, Ala443, His444, Gly445, Asn475, Cys477, Ser511, Tyr512, Trp513, Asp516 and His575. The presence of functional groups in the ligands, such as carbonyl groups, amino groups, amido groups, hydroxyl groups as well as aromatic rings was considered important for the binding interaction between ligands and gingipain K. Olsalazine (% gingipain K inhibition = 32.43% at 50 μM and IC50 = 93.44 ± 1.89 μM) was identified as the top hit compound among the ten compounds from the biological evaluation. It is considered as a promising compound for further development as a therapeutic agent for the treatment of AD. Keywords: Porphyromonas gingivalis gingipain K, Alzheimer’s disease, drug repositioning, in silico study, biological evaluation