Refinement of a Low-resolution Crystal Structure to Better Understand Erythromycin Interactions on Large Ribosomal Subunit

Abstract

Macrolides are a group of diverse class of naturally occurring and synthetic antibiotics made of macrocyclic-lactone ring carrying one or more sugar moieties linked to various atoms of the lactone ring. These macrolides selectively bind to a single high affinity site on the prokaryotic 50S ribosomal subunit, making them highly effective towards a wide range of bacterial pathogens. The understanding of binding between macrolides and ribosome serves a good basis in elucidating how they work at the molecular level and these findings would be important in rational drug design. Here, we report refinement of reconstructed PDB structure of erythromycin-ribosome system using molecular dynamics (MD) simulation. Interesting findings were observed in this refinement stage that could improve the understanding of the binding of erythromycin A (ERYA) onto the 50S subunit. The results showed ERYA was highly hydrated and water molecules were found to be important in bridging hydrogen bond at the binding pocket during the simulation time. ERYA binding to ribosome was also strengthened by hydrogen bond network and hydrophobic interactions between the antibiotic and the ribosome. Our MD simulation also demonstrated direct interaction of ERYA with Domains II, V and with C1773 (U1782EC), a residue in Domain IV that has yet been described of its role in ERYA binding. It is hoped that this refinement will serve as a starting model for a further enhancement of our understanding towards the binding of ERYA to ribosome.

Aldgamycins J–O, 16-Membered Macrolides with a Branched Octose Unit from Streptomycetes sp. and Their Antibacterial Activities

“…Most macrolide antibiotics are typically characterized by a lactone ring and one or more sugar moieties. 6 The absolute configurations of macrolides are difficult to determine, as they contain several stereocenters. The genes and enzymes relevant to the macrolide biosynthesis have been widely investigated by molecular biologists.…”

“…Several well-known macrolides, such as erythromycin, tylosin, leucomycin, avermectins, and milbemycins, have been widely used for many years as important medicines in humans or animals. Most macrolide antibiotics are typically characterized by a lactone ring and one or more sugar moieties . The absolute configurations of macrolides are difficult to determine, as they contain several stereocenters.…”

Molecular Insights into 14-Membered Macrolides Using the MM-PBSA Method

“…Domain IV was discussed before to have exerted direct interaction with the binding of ERYA on the 50S ribosomal subunit. 13 Besides that, the quinolyallyl group of ketolide ABT-773 was shown to have hydrophobic interaction to C1773 in the crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with azithromycin and ketolide ABT-773. 57 In our study, C1773 has the most favorable Coulombic contribution to ERYA with the value of -1.99 kcal/mol, and it has also a favorable van der Waals energy term of -0.98 kcal/mol.…”

“…Both minimizations and MD simulations were executed using the SANDER module of AMBER 8. A detailed procedure of minimization and MD simulation used in this study is described in ref 13. A total of 15,000 steps of minimizations were done using the Steepest Descent and Conjugate Gradient algorithms before proceeding to the heating and equilibration stages of MD simulations.…”

“…6,[8][9][10][11][12] Besides that, our previous MD studies also demonstrated a possible interaction with the Domain IV. 13 These macrolides showed high drug affinity and specificity to the ribosome with K d in the nanomolar range as measured by equilibrium dialysis, 14 footprinting protection experiments, 6,9,15 and binding kinetics 16,17 studies. The actual inhibition mode of ERYA and ROX to the bioactivity of ribosome is so far understood to the most general idea only.…”