Lovastatin

The data set was prepared based on an extensive literature survey taking IC₅₀ values of in-vitro enzyme inhibition assays against XO and HMGR by various secondary metabolites. Based on IC₅₀ values, sixteen plant- and fungus-based secondary metabolites (Tables 1 and 2) were chosen for the ligand-protein docking study. The docking study was performed against commercial drugs such as atorvastatin, simvastatin, lovastatin, and pravastatin for HMGR. On the other hand, commercial drugs such as allopurinol, febuxostat, topiroxostat, and probenecid were used for molecular docking studies with XO. The structures of the ligand molecules and the control drugs of both enzymes were retrieved from the PubChem database [38 (link)] and verified from SciFinder. The structures were retrieved in SDF format and were converted to PDB and MOL2 format using Discovery Studio Visualizer 4.0 software. The structure and complete chemical properties, torsional energy, van der Waals potential energy, electrostatic energy, weight, log P, total polar surface area (TPSA), donor atoms, and acceptor atoms of the ligands were listed (Supplementary Table 4S) by the help of MOE Module [39 (link)].

Myobundles were formed by modifying our previously published methods for engineered rodent muscle tissues (Hinds et al., 2011 (link); Juhas et al., 2014 (link)) (Figure 1—figure supplement 2). Expanded myogenic cells were dissociated in 0.025% trypsin-EDTA to a single cell suspension and encapsulated in a fibrinogen (Akron, Boca Raton, FL) and matrigel solution on laser cut Cerex frames (9.2 × 9.5 mm outer dimensions, 6.8 × 8.3 mm inner dimensions) within PDMS molds (cast from Teflon masters and pretreated with pluronic) at 15 × 10⁶ cells/ml (7.5 × 10⁵ cells per myobundle). Specifically, a cell solution (7.5 × 10⁵ cells in 17.2 µl media per bundle + 2 µl of 50 unit/ml thrombin in 0.1% BSA in PBS [Sigma, St. Louis, MO]) and a gelling solution (11 µl media + 10 µl Matrigel + 10 µl of 20 mg/ml Fibrinogen in DMEM) were prepared in separate vials on ice for up to six myobundles per vial. Gelling solution was added to the cell solution and mixed thoroughly then each bundle was individual pipetted within the PDMS mold and onto the frame. The cell/hydrogel mixture was polymerized for 30 min at 37°C followed by incubation in growth media containing 1.5 mg/ml 6-aminocaproic acid (ACA, Sigma). Myobundles were kept in growth media during gel compaction (3–5 days) and then switched to low glucose DMEM with 2% horse serum (Hyclone, Logan, UT), 2 mg/ml ACA and 10 µg/ml insulin (Sigma). Frames were removed from molds at the time of switch to low serum medium and cultured dynamically in suspension for an additional 1–4 weeks. Starting from a 50 mg donor biopsy, typical cell expansion for 5 passages can allow generation of at least 1000 myobundles with a total mass of >5 g, representing a >100-fold amplification of muscle mass when going from native to engineered tissue system.
All drugs were purchased from Sigma. Clenbuterol hydrochloride, chloroquine phosphate, and cerivastatin sodium salt hydrate were prepared at 1000× stock solutions in PBS (control) and sterile-filtered for use. Lovastatin was prepared as a 10,000× stock solution in DMSO in which case DMSO was used as vehicle control. Drugs studies in myobundles or 2D cultures were initiated after 1 week of differentiation. Myobundles were replenished with fresh media and drug each day to maintain drug concentration.