Additional file 1 of Inhibition of herpes simplex virus-1 infection by MBZM-N-IBT: in silico and in vitro studies
Creators: name: Kumar, Abhishek
name: De, Saikat
name: Moharana, Alok Kumar
name: Nayak, Tapas Kumar
name: Saswat, Tanuja
name: Datey, Ankita
name: Mamidi, Prabhudutta
name: Mishra, Priyadarsee
name: Subudhi, Bharat Bhusan
name: Chattopadhyay, Soma
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 1.Figure 1: Interaction of penciclovir with HSV thymidine kinase: The ligand and target structures were minimized using the ArgusLab program. Penciclovir was docked against HSV thymidine kinase structure (PDB ID: 1KI3) which was experimentally co-crystallized with penciclovir using the AutoDockVina program. The most stable binding mode visualized by the PyMol software was similar to the experimentally determined mode of interaction.Figure 2: Dose response curve of MBZM-N-IBT: Vero cells were infected with HSV-1 and MBZM-N-IBT was added with different concentrations (2.5µM, 5µM, 10.0µM, 25.0µM, 50.0µM, 100.0µM, 150.0µM and 200.0µM, 250 µM). DMSO was used as a negative control. The infected and drug treated cells supernatant were collected after 24 hpi and virus titer was determined by plaque assay. Representation of HSV-1 inhibition curve, where the x-axis depicts the logarithmic value of the concentration of MBZM-N-IBT and y-axis depicted the percent of PFU/mL.Figure 3: Interaction of MBZM-N-IBTwith (A) gC and (B) ICP8: The ligand and target structures were minimized using the ArgusLab program . MBZM-N-IBT was docked against homologous model of gC and ICP8 of HSV by the AutoDockVina program. The binding affinities were -6.2Kcal/mole and -9.8Kcal/mole for (A) gC and (B) ICP8. Figure 4: Interaction of MBZM-N-IBT with HSV targets: The ligand and target structures were minimized using the ArgusLab program .MBZM-N-IBT was docked against HSV targets involved in multiple stages of its lifecycle using the AutoDockVina program. The binding mode shown by the PyMol software reveals the conformation of the most stable complex with (A) the C-terminal domain of ICP27 protein from HSV-1 (PDB ID : 5BQK), (B) DNA polymerase (UL42) (PDB ID: 2GV9), (C) UL25 DNA packaging protein (PDB ID : 2F5U), (D) DNA-packaging motor pUL15 C-terminal nuclease domain (PDB ID : 4IOX) and (E) extracellular domain of glycoprotein B (PDB ID: 2GUM) respectively. The most stable binding mode of the complex are shown using the PyMol software.Figure 5: Interaction of MBZM-N-IBT with HSV-2 surface envelope glycoprotein D The ligand and target structures were minimized using the ArgusLab program MBZM-N-IBT was docked against glycoprotein D (PDB ID: 4MYV) using the AutoDockVina program. The binding mode shown by the PyMol software reveals the conformation of the most stable complex. Figure 6: Inhibition of HSV-1 by MBZM-N-IBT in Raw 264.7 and BHK cells: Raw264.7 and BHK cells were infected with HSV-1 (MOI 1) and MBZM-N-IBT was added with different concentrations (50 µM and 100 µM). DMSO was used as a negative control. The infected and drug treated cells and supernatants were collected at 24 hpi and virus titer was determined by plaque assay. A and C. represents the percent of PFU/mL of the virus after treatment with different concentrations of MBZM-N-IBT in Raw 264.7 cells and BHK cells respectively. B, D depicts the fold changes of gC and UL9 genes in their RNA levels in HSV-1 infected Raw264.7 and BHK cells respectively. Data represent the mean ± SEM from three independent experiments using the one way Anova, Dunnett’s multiple comparison tests.. p≤ 0.05 was considered be to statistically significant.Table 1 Primers used in RT-PCR