how to check inhibition constant in autodock vina

High MTA sensitizes MTAP−/− cells to partial PRMT5 inhibition that spares MTAP+ cells 31– 33. ~15% of all human cancers lack MTAP (MTAP-) and accumulate by 5–20 folds a metabolic derivative-5′-methylthioadenosine (MTA)-of S-adenosyl- l-methionine (SAM), the cofactor for PRMT5 catalytic activity. It is overexpressed in various human cancers 23– 28, and its inhibition causes cell death 29, 30, especially in cancer cells lacking 5′-methylthioadenosine phosphorylase (MTAP). PRMT5 is epigenetically important 14– 16, because it regulates gene transcription 17, cell signaling 18, RNA splicing 19, DNA repair 20, chromatin remodeling 21 and cell cycle 22. We started to test this possibility in 2015, using human protein arginine methyltransferase 5 (PRMT5) as a target. With advancements in computational analysis of ligand configurations (poses) 12, 13, virtual screening, docking and energy minimization of ligands could be utilized to enhance cryo-EM SBDD. These developments promised a high potential of cryo-EM SBDD, which may be realized for many important biological or pharmacological targets but such potential is still not well materialized, in part because most cryo-EM structures (>85%) are not resolved to 1.0–2.5 Å, where X-ray SBDD has been quite successful 2. Although atomic resolutions (~1.2 Å) for high-symmetry complexes were achieved recently 10, 11, most near-atomic resolution cryo-EM structures of low- or no-symmetry have been resolved at 2.5–4.5 Å. Although single particle cryo-EM often lags behind crystallography in resolution because a majority of cryo-EM structures are still of 3.5 Å resolution or worse, it is still expected to usher a new era in structure-based drug design (SBDD), which has been successful with high-resolution crystal structures and fragment-based design. Many of these structures represent biomacromolecules complexed with small molecule agonists, antagonists, or modulators 2, 9. The so-called “resolution revolution” in single particle cryo-EM has produced hundreds of structures of 2.5–4.5 Å resolutions in ten years 1– 8. These data suggest the feasibility of employing near-atomic resolution cryo-EM structures and computational analysis of ligand poses for small molecule therapeutics. One of them, after synthesis, is ~4 fold more efficient in inhibiting PRMT5 catalysis than 11-2 F, with strong MTA-synergy. Structural analysis of ligands in the binding pockets is performed to compare poses of 11-2 F and its redesigned analogs and identifies three new analogs predicted to have significantly better potency. Computational analysis predicts subtype specificity of 11-2 F among PRMTs. Cryo-EM structures of 11-2 F / MTA-bound human PRMT5/MEP50 complex and its apo form resolved at 3.1 and 3.2 Å respectively show that 11-2 F in the catalytic pocket shifts the cofactor-binding pocket away by ~2.0 Å, contributing to positive cooperativity. To achieve MTA-synergic inhibition, a pharmacophore from virtual screen leads to a specific inhibitor (11-2 F). PRMT5, an oncogenic target for various cancer types, has many inhibitors manifesting little cooperativity with MTA, a co-factor analog accumulated in MTAP−/− cells. Here we show that a 3.1 Å structure of PRMT5 is suitable for selecting computed poses of a chemical inhibitor and its analogs for enhanced potency. Projected potential of 2.5–4.0 Å cryo-EM structures for structure-based drug design is not well realized yet.

How to check inhibition constant in autodock vina