Probing Molecular Docking in a Charged Model Binding Site

Abstract

A model binding site was used to investigate charge-charge interactions in molecular docking. This simple site, a small (180A(3)) engineered cavity in cyctochrome c peroxidase (CCP), is negatively charged and completely buried from solvent, allowing us to explore the balance between electrostatic energy and ligand desolvation energy in a system where many of the common approximations in docking do not apply. A database with about 5300 molecules was docked into this cavity. Retrospective testing with known ligands and decoys showed that overall the balance between electrostatic interaction and desolvation energy was captured. More interesting were prospective docking scre"ens that looked for novel ligands, especially those that might reveal problems with the docking and energy methods. Based on screens of the 5300 compound database, both high-scoring and low-scoring molecules were acquired and tested for binding. Out of 16 new, high-scoring compounds tested, 15 were observed to bind. All of these were small heterocyclic cations. Binding constants were measured for a few of these, they ranged between 20microM and 60microM. Crystal structures were determined for ten of these ligands in complex with the protein. The observed ligand geometry corresponded closely to that predicted by docking. Several low-scoring alkyl amino cations were also tested and found to bind. The low docking score of these molecules owed to the relatively high charge density of the charged amino group and the corresponding high desolvation penalty. When the complex structures of those ligands were determined, a bound water molecule was observed interacting with the amino group and a backbone carbonyl group of the cavity. This water molecule mitigates the desolvation penalty and improves the interaction energy relative to that of the "naked" site used in the docking screen. Finally, six low-scoring neutral molecules were also tested, with a view to looking for false negative predictions. Whereas most of these did not bind, two did (phenol and 3-fluorocatechol). Crystal structures for these two ligands in complex with the cavity site suggest reasons for their binding. That these neutral molecules do, in fact bind, contradicts previous results in this site and, along with the alkyl amines, provides instructive false negatives that help identify weaknesses in our scoring functions. Several improvements of these are considered.

Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?

“…The W191G cavity of cytochrome c peroxidase is used as a model system for introducing small molecule oxidation in an artificially created cavity. Goodin et al [28][29][30][31][32][33] studied the binding modes of several small molecules of structural types XII~XVI to the cytochrome c peroxidase. They are listed in Table 8.…”

“…The binding position of N-NH 2 group of Compound 8-5 is significantly different from the other two. In the studies of Goodin et al [33] the binding modes of two phenol derivatives (structural type XVI) were also examined: phenol (8-22, 2AS3, green) and 3-fluorocatechol (8-23, 2AS4, gray). Figure 7f shows these two molecules after overlapping the two corresponding protein structures.…”

(Thermo)dynamic Role of Receptor Flexibility, Entropy, and Motional Correlation in Protein–Ligand Binding

“…[1][2][3][4][5][6][7][8] The binding of 2-amino-5-methylthiazole (2a5mt) to the W191G cavity mutant of cytochrome c peroxidase from E. coli (W191G) has been characterized by X-ray crystallography [9][10][11][12] and isothermal titration calorimetry [12] experiments, as well as by computational techniques. [13,14] This system is an ideal test case to investigate the magnitude of the entropy penalty to the binding free energy due to changes in receptor flexibility. Ligand binding affects the flexibility of both the W191G cavity and 190-195 gating-loop regions, [10,14] which may induce full opening of the gating loop in the case of benzimidazole (bzi).…”

Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors

“…Water molecules present in the active site further complicate the problem because of their ability to act as Lewis bases and/or acids. Computational studies on a binding pocket in the engineered cavity of cytochrome c peroxidase [203], showed better docking results when a single conserved water was allowed to move. Crystallographers and computational chemists have been interested in the proper placement and optimization of polar protons for decades.…”