Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach

Time-dependent effect of clarithromycin on pro-inflammatory cytokines in CRS

Background: The purpose of this study was to assess the time-effect of clarithromycin on the inflammatory response in chronic rhinosinusitis (CRS), to further explore the use of macrolides in cell culture as a model for CRS, and its action on the immune system. Methodology: The time effect of clarithromycin on several cytokines was examined for IL-1β, IL-4, IL-5, IL-8 and GM-CSF. Samples prior and post-incubation were assessed, as well as samples collected 24h following removal of clarithromycin to determine if any immunomodulatory effect persisted. Cytokines were quantified using ProcartaPlexTM assays. Results: Of the 5 cytokines assessed, only IL-1β and IL-8 production were significantly inhibited at 4h. Increased levels of IL-4 were observed at 72 hours of incubation and returned to near baseline levels after its removal. IL-8 showed the most time-dependent relationship with clarithromycin. No differences between the expression of IL-5 and GM-CSF were found. Conclusions: The present work suggests a specific and dose-dependent impact of clarithromycin on the inflammatory response in CRS. Moreover, the immunomodulatory effects of clarithromycin on the cytokines IL-4 and IL-8 varied depending on length of exposure to clarithromycin. Further studies to further establish the relationship between length of exposure and cytokine expression, and with additional “actors” in CRS pathophysiology should be considered. This may enable us in the future to determine appropriate duration of macrolide therapy in patients with CRS.

Structural and energetic basis for the inhibitory selectivity of both catalytic domains of dimeric HDAC6

HDAC6 is a protein involved in cancer, neurodegenerative disease and inflammatory disorders. To date, the full three-dimensional (3D) structure of human HDAC6 has not been elucidated; however, there are some experimental 3D structural homologs to HDAC6 that can be used as templates. In this work, we utilized molecular modeling procedures to model both of the catalytic domains of HDAC6 connected by the linker region where DMB region is placed. Once the 3D structure of human HDAC6 was obtained, it was structurally evaluated and submitted to docking and molecular dynamic (MD) simulations along with Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method to explore the stability and the binding free energy properties of the HDAC6-ligand complexes. In addition, its structural and energetic behavior was explored with each one of the catalytic domains in the molecular recognition of six selective HDAC6 inhibitors, HPOB, CAY10603, Nexturastat, Rocilinostat, Tubacin and Tubastatin A for DD2, and with the so-called 9-peptide which is DD1-HDAC6 selective substrate. The use of the whole system (DD1-DMB-DD2) showed a tendency toward the ligand affinity of DD2, CAY10603> Tubacin > Rocilinostat > Nexturastat > HPOB > Tubastatin > 9-peptide, which is in line with experimental reports. However, 9-peptide showed a higher affinity for DD1, which agrees with experimental reports elsewhere. Principal component analysis provided important information about the structural changes linked to the molecular recognition process, whereas per-residue decomposition analysis revealed the energetic contribution of the key residues in the molecular binding and structural characteristics that could assist in drug design.