Elucidating the Inhibitory Effect of Resveratrol and Its Structural Analogs on Selected Nucleotide-Related Enzymes

Abstract

Resveratrol, the most widely studied natural phytochemical, has been shown to interact with different target proteins. Previous studies show that resveratrol binds and inhibits DNA polymerases and some other enzymes; however, the binding and functioning mechanisms remain unknown. The elucidated knowledge of inhibitory mechanisms of resveratrol will assist us in new drug discovery. We utilized molecular docking and molecular dynamics (MD) simulation to reveal how resveratrol and structurally similar compounds bind to various nucleotide-dependent enzymes, specifically, DNA polymerases, HIV-1 reverse transcriptase, and ribonucleotide reductase. The results show that resveratrol and its analogs exert their inhibitory effects by competing with the substrate dNTPs in these enzymes and blocking elongation of chain polymerization. In addition, the results imply that resveratrol binds to a variety of other ATP-/NTP-binding proteins.

Keywords: inhibition mechanism; molecular docking; molecular dynamics simulation; nucleotide-related enzymes; resveratrol.

Figure 1

Superposition of two docking poses of trans-resveratrol (purple) and dCTP (green) on DNA polymerase $\alpha$ (PDB ID: 4Q5V).

Figure 2

2-D Protein-ligand interaction diagrams of 4Q5V and four ligands: dCTP (A), trans-resveratrol (B), miquelianin (C), and myricetin (D). The purple arrow indicates the hydrogen bond; the green line represents $\pi$-$\pi$ stacking.

Figure 3

Minimum distance between hydrogen bond donors and acceptors on 4Q5V-ligand complex during MD simulation. The red line indicates the distance between 3${}^{\prime }$-OH of dCTP and Ash1004; the green line indicates the distance between 3${}^{\prime }$-OH of dCTP and Leu864; the blue line indicates the distance between 4${}^{\prime }$-OH of resveratrol and Ash1004; the pink line indicates the distance between 4${}^{\prime }$-OH of resveratrol and Leu864.

Figure 4

(A): Effects of increasing concentrations of resveratrol and its selected analogs on DNA oligo extension by human DNA polymerase $\delta$. The first lane is the 25 mer primer, and the second and third lanes are the controls of the polymerase $\delta$ extension assay without addition of analogs. The inhibitors tested were compound-1, compound-2, compound-3, cis-resveratrol, trans-resveratrol, myricetin, and pterostilbene. The concentrations tested for each inhibitor were 2, 5, 10, 20, and 30 $\mathsf{\mu }$M; (B) Bar chart of intensity of the full-length 40 mer products (as shown in A) by increasing concentrations of resveratrol and its selected analogs.

Figure 5

Superposition of two docking poses of trans-resveratrol (purple) and dATP (green) on HIV-1 reverse transcriptase (PDB ID: 5TXM).

Figure 6

Superposition of the docking poses of trans-resveratrol (purple) and substrates (green) on ribonucleotide reductase (PDB ID: 5TUS). The blue surface refers to the S site, and the substrate inside is TTP; the red surface refers to the C site, and the substrate inside is GDP; the green surface refers to the A site, and the substrate inside is ATP.