2.2. Virtual Screening and Molecular Docking

The three-dimensional structures of two related target proteins, DHODH protein and UMPS protein, were acquired from the Protein Data Bank (PDB). The crystal structure of human DHODH (PDB: 6QU7) was complex with BAY 2402234 with cogent resolution (1.53 Å), and the crystal structure of human UMPS (PDB: 3L0K) was complex with 6-acetyl-UMP with 1.34 Å resolution. We used the BIOVIA Discovery Studio 2017 R2 Client software (created for Windows by Dassault Systèmes in Paris, France) in this part. Before carrying out the docking protocol, we used the “Remove Cell” protocol to remove all top-level cells while keeping their constituent contents intact. Then the “Prepare Protein” protocol was employed to prepare the protein, performing tasks such as inserting missing atoms in incomplete residues, removing crystal waters, and standardizing atom names. After that, the “Define and Edit Binding Site (Advanced) tools” protocol was used to calculate a binding site of DHODH from a selected ligand and display the receptor sphere; the selected ligand was a DHODH inhibitor named BAY 2402234 on the basis of Christian’s study [37]. A total of 10,152 molecule compounds obtained from the ZINC database [38] were utilized for docking so that we were able to find some of these approved drugs that could inhibit the DHODH protein and act on the UMPS protein at the same time.

The “Dock Ligands (LigandFit)” protocol followed three stages: docking, in situ ligand minimization, and scoring. During the docking process, the docked poses were used to be minimized with the Chemistry at Harvard Molecular Mechanics (CHARMM) and evaluated with a set of scoring functions, including LigScore1, LigScore2, PLP1, PLP2, Jain, PMF, PMF04, Ludi energy estimate 1, Ludi energy estimate 2, and Ludi energy estimate 3. Here, we also illustrated some other parameter settings. The DREIDING force field was chosen for calculating interaction energies for each ligand and the specified receptor. The numbers of Monte Carlo trials were set to “2500 120, 4 1200 300, 6 1500 350, 10 2000 500, 25 3000 750”, and the minimization algorithm was set to “Do not minimize”. Lastly, we set the parallel processing as “True” and the batch size as 25 in order to speed up the docking process.