Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine

Abstract

Squalene epoxidase (SE) is a key flavin adenine dinucleotide (FAD)-dependent enzyme of ergosterol and cholesterol biosynthetic pathways and an attractive potential target for drugs used to inhibit the growth of pathogenic fungi or to lower cholesterol level. Although many studies on allylamine drugs activity have been published during the last 30 years, up until now no detailed mechanism of the squalene epoxidase inhibition has been presented. Our study brings such a model at atomic resolution in the case of yeast Saccharomyces cerevisiae . Presented data resulting from modeling studies are in excellent agreement with experimental findings. A fully atomic three-dimensional (3D) model of squalene epoxidase (EC 1.14.99.7) from S. cerevisiae was built with the help of 3D-Jury approach and further screened based on data known from mutation experiments leading to terbinafine resistance. Docking studies followed by molecular dynamics simulations and quantum interaction energy calculations [MP2/6-31G(d)] resulted in the identification of the terbinafine-squalene epoxidase mode of interaction. In the energetically most likely orientation of terbinafine its interaction energy with the protein is ca. 120 kJ/mol. In the favorable position the terbinafine lipophilic moiety is located vertically inside the squalene epoxidase binding pocket with the tert-butyl group oriented toward its center. Such a position results in the SE conformational changes and prevents the natural substrate from being able to bind to the enzyme's active site. That would explain the noncompetitive manner of SE inhibition. We found that the strongest interaction between terbinafine and SE stems from hydrogen bonding between hydrogen-bond donors, hydroxyl group of Tyr90 and amine nitrogen atom of terbinafine. Moreover, strong attractive interactions were recorded for amino acids whose mutations resulted in terbinafine resistance. Our results, elucidating at a molecular level the mode of terbinafine inhibitory activity, can be utilized in designing more potent or selective antifungal drugs or even medicines lowering cholesterol in humans.

Squalene monooxygenase – a target for hypercholesterolemic therapy

“…Tertbutyl substituent of terbinafi ne points toward the center of the enzyme blocking the main (one of two) entrance to the enzyme ' s catalytic site. This sustains the experimental evidence that terbinafi ne inhibits fungi SE in non-competitive manner (Favre and Ryder , 1996 ;Nowosielski et al , 2011 ).…”

“…Based on a molecular docking detailed mechanism of the SE, inhibition by terbinafi ne was proposed. According to that model the inhibitor interacts with amino acids at C-terminus and the central part of the enzyme (Nowosielski et al , 2011 ). The naftalene ring interacts with residues in a small, highly hydrophobic cavity near the entrance to the substate's binding pocket.…”

Terbinafine Resistance of Trichophyton Clinical Isolates Caused by Specific Point Mutations in the Squalene Epoxidase Gene

“…The atomic three-dimensional (3D) modeling of the S. cerevisiae SQLE protein was built based on previously available experimental findings, and, furthermore, it would screen the detailed amino acids critical for binding terbinafine to the enzyme (18). Among the 50 amino acids screened in that study, Phe 402 , Cys 416 , Phe 417 , Phe 420 , Tyr 90 , and Val 92 seem to interact especially strongly with this agent.…”

“…This study was partly supported by the National BioResource Project-Pathogenic Microbes in Japan and the Joint Usage/Research Program of the Medical Mycology Research Center, Chiba University (grant number [16][17][18][19][20][21][22][23][24][25][26].…”

In Silico Analog Design for Terbinafine Against Trichophyton rubrum: A Preliminary Study

“…Moreover, it is evidenced that Squalene epoxidase leads to synthesis of ergosterol following a cascade of biosynthetic pathways which are essential to maintain integrity and functionality of fungal cells. Due to this property, it acts as major target for the drugs which are designed to inhibit dermatophytosis [5]. terbinafine, chemically written as N,6,6-trimethyl-N-(naphthalen-1-ylmethyl)hept-2-en-4-yn-1-amine is commercially used drug for treating dermatophytosis [6].…”