The crystal structure of human ADAMTS-5 Mp/Dis domains (PDB code 2RJQ)13 complexed with its reference inhibitor is currently the only reported structure of the joint Mp/Dis domains in ADAMTS-5 and was therefore chosen for our in silico studies. This structure was minimized using AMBER16 software and ff14SB force field at 300 K, after removing all hydrogen atoms. The complex was placed in a rectangular parallelepiped water box, an explicit solvent model for water, TIP3P, was used and the complex was solvated with a 10 Å water cap. Sodium ions were added as counter-ions to neutralize the system. Two steps of minimization were then carried out; in the first stage, we kept the protein fixed with a position restraint of 500 kcal/mol Å2 and we solely minimized the positions of the water molecules. In the second stage, we minimized the entire system through 5000 steps of steepest descent followed by conjugate gradient (CG) until a convergence of 0.05 kcal/Å mol. Molecular docking calculations were performed with AUTODOCK 4.2 using the improved force field46,47. Autodock Tools were used to identify the torsion angles in the ligand, add the solvent model and assign the Kollman atomic charges to the protein, while ligand charges were calculated with the Gasteiger method. A grid spacing of 0.375 Å and a distance-dependent function of the dielectric constant were used for the energetic map calculations. Compound 4b was subjected to a robust docking procedure already used in virtual screening and pose prediction studies4851. The docked compound was subjected to 200 runs of the AUTODOCK search using the Lamarckian Genetic Algorithm performing 10,000,000 steps of energy evaluation. The number of individuals in the initial population was set to 500 and a maximum of 10,000,000 generations were simulated during each docking run. All other settings were left as their defaults and the best docked conformation was considered. For the modelling of 4b/GM6001/ADAMTS-5 co-complex, GM6001 was first subjected to the docking procedure as above. The so-obtained ADAMTS-5-GM6001 complex was used for the docking evaluation of compound 4b by using all parameters described above. The results were then clustered by applying a root-mean-square deviation (RMSD) of 6.0 Å. The clusters with a population of at least 40 poses (corresponding to the 20% of the total poses) were considered. The cluster analysis suggested three possible binding orientations for 4b (Supplementary information Fig. S3), which were subjected to MD simulations.

All simulations were performed using AMBER, version 16. MD simulations were carried out using the ff14SB force field at 300 K. The complex was placed in a rectangular parallelepiped water box. An explicit solvent model for water, TIP3P, was used, and the complex was solvated with a 20 Å water cap. Sodium ions were added as counter-ions to neutralize the system. Prior to MD simulations, two steps of minimization were carried out using the same procedure described above. Particle mesh Ewald (PME) electrostatics and periodic boundary conditions were used in the simulation. The MD trajectory was run using the minimized structure as the starting conformation. The time step of the simulations was 2.0 fs with a cut-off of 10 Å for the non-bonded interactions, and SHAKE was employed to keep all bonds involving hydrogen atoms rigid. Constant-volume periodic boundary MD was carried out for 3.0 ns, during which the temperature was raised from 0 to 300 K. Then 100 ns of constant pressure periodic boundary MD was carried out at 300 K by using the Monte Carlo barostat with anisotropic pressure scaling for pressure control. All the α carbons of the protein were blocked with a harmonic force constant of 10 kcal/mol Å2. General Amber force field (GAFF) parameters were assigned to the ligand, while partial charges were calculated using the AM1-BCC method as implemented in the Antechamber suite of AMBER 16. A representative docking pose belonging to each of the three cluster of poses (C1–C3) was subjected to a 103 ns MD simulation with explicit water molecules. By analyzing the RMSD of the position of compound 4b during the simulation with respect to the starting pose, we observed an average RMSD of 6.4 and 7.5 Å for C1 and C3. Considering the high degrees of freedom that characterizes 4b, these two orientations were considered quite stable. On the other hand, the C2 binding mode was highly unstable (average RMSD: 30.4 Å) (Supplementary information Fig. S4) and therefore discarded. The minimized average structure of the ADAMTS-5/GM6001/4b complex was modified and used as a starting point for the construction of the ADAMTS-5/4c complex (Supplementary information Fig. S6). Then a 103 ns MD simulation with explicit water molecules as reported above and analyzed.

Relative binding free energy evaluations were performed using AMBER 16. The trajectories extracted from the last 100 ns of each simulation were used for the calculation, for a total of 100 snapshots (at time intervals of 1 ns). Van der Waals, electrostatic and internal interactions were calculated with the SANDER module of AMBER 16, whereas the Poisson − Boltzmann method was employed to estimate polar energies through the molecular mechanics and Poisson Boltzmann surface area (MM-PBSA) module of AMBER 16 as previously reported51. Gas and water phases were represented using dielectric constants of 1 and 80, respectively, while nonpolar energies were calculated with MOLSURF program. The entropic term was considered as approximately constant in the comparison of the ligand–protein energetic interactions. All three binding modes were further analyzed through MM-PBSA method. This approach averages the contribution of solvation free energy and gas phase energy for snapshots of the ligand–protein complex and the unbound components extracted from MD trajectories. The results of the MM-PBSA analysis suggested pose C1 as the most favorable binding mode, since it showed an interaction energy (ΔPBSA = − 14.7 kcal/mol) that was more than 8 kcal/mol lower than that estimated for the binding mode C2 and C3 (Supplementary information Table S1). The results obtained from these analyses suggested the MD-refined C1 pose as the most reliable binding disposition of 4b within ADAMTS-5.

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