Identifying and characterizing binding sites and assessing druggability.

Identification and characterization of binding sites is key in the process of structure-based drug design. In some cases there may not be any information about the binding site for a target of interest. In other cases, a putative binding site has been identified by computational or experimental means, but the druggability of the target is not known. Even when a site for a given target is known, it may be desirable to find additional sites whose targeting could produce a desired biological response. A new program, called SiteMap, is presented for identifying and analyzing binding sites and for predicting target druggability. In a large-scale validation, SiteMap correctly identifies the known binding site as the top-ranked site in 86% of the cases, with best results (>98%) coming for sites that bind ligands with subnanomolar affinity. In addition, a modified version of the score employed for binding-site identification allows SiteMap to accurately classify the druggability of proteins as measured by their ability to bind passively absorbed small molecules tightly. In characterizing binding sites, SiteMap provides quantitative and graphical information that can help guide efforts to critically assess virtual hits in a lead-discovery application or to modify ligand structure to enhance potency or improve physical properties in a lead-optimization context.

Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.

A novel scoring function to estimate protein-ligand binding affinities has been developed and implemented as the Glide 4.0 XP scoring function and docking protocol. In addition to unique water desolvation energy terms, protein-ligand structural motifs leading to enhanced binding affinity are included: (1) hydrophobic enclosure where groups of lipophilic ligand atoms are enclosed on opposite faces by lipophilic protein atoms, (2) neutral-neutral single or correlated hydrogen bonds in a hydrophobically enclosed environment, and (3) five categories of charged-charged hydrogen bonds. The XP scoring function and docking protocol have been developed to reproduce experimental binding affinities for a set of 198 complexes (RMSDs of 2.26 and 1.73 kcal/mol over all and well-docked ligands, respectively) and to yield quality enrichments for a set of fifteen screens of pharmaceutical importance. Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives.

Integrated Modeling Program, Applied Chemical Theory (IMPACT).

We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high-throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function.

A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions.

A polarizable force field, and associated continuum solvation model, have been developed for the explicit purpose of computing and studying the energetics and structural features of protein binding to the wide range of ligands with potential for medicinal applications. Parameters for the polarizable force field (PFF) are derived from gas-phase ab initio calculations and then utilized for applications in which the protein binding to ligands occurs in aqueous solvents, wherein the charge distributions of proteins and ligands can be dramatically altered. The continuum solvation model is based on a self-consistent reaction field description of solvation, incorporating an analytical gradient, that allows energy minimizations (and, potentially, molecular dynamics simulations) of protein/ligand systems in continuum solvent. This technology includes a nonpolar model describing the cost of cavity formation, and van der Waals interactions, between the continuum solvent and protein/ligand solutes. Tests of the structural accuracy and computational stability of the methodology, and timings for energy minimizations of proteins and protein/ligand systems in the condensed phase, are reported. In addition, the derivation of polarizability, electrostatic, exchange repulsion, and torsion parameters from ab initio data is described, along with the use of experimental solvation energies for determining parameters for the solvation model.

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 A in nearly half of the cases and are greater than 2 A in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.

Glide's ability to identify active compounds in a database screen is characterized by applying Glide to a diverse set of nine protein receptors. In many cases, two, or even three, protein sites are employed to probe the sensitivity of the results to the site geometry. To make the database screens as realistic as possible, the screens use sets of "druglike" decoy ligands that have been selected to be representative of what we believe is likely to be found in the compound collection of a pharmaceutical or biotechnology company. Results are presented for releases 1.8, 2.0, and 2.5 of Glide. The comparisons show that average measures for both "early" and "global" enrichment for Glide 2.5 are 3 times higher than for Glide 1.8 and more than 2 times higher than for Glide 2.0 because of better results for the least well-handled screens. This improvement in enrichment stems largely from the better balance of the more widely parametrized GlideScore 2.5 function and the inclusion of terms that penalize ligand-protein interactions that violate established principles of physical chemistry, particularly as it concerns the exposure to solvent of charged protein and ligand groups. Comparisons to results for the thymidine kinase and estrogen receptors published by Rognan and co-workers (J. Med. Chem. 2000, 43, 4759-4767) show that Glide 2.5 performs better than GOLD 1.1, FlexX 1.8, or DOCK 4.01.

Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests.

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.

MMFF VI. MMFF94s option for energy minimization studies.

This article describes the derivation of MMFF94s, which is the "s" (static) variant of MMFF94. MMFF94s incorporates altered out of plane bending parameters that yield planar (or nearly planar) energy-minimized geometries at unstrained delocalized trigonal nitrogen centers. Some experimental and most theoretical structures show appreciable puckering at nitrogen in isolated structures. However, condensed-phase effects or even strong intermolecular hydrogen bonding tends to reduce, but need not eliminate, such puckering; in contravention to results reported on the lower level Hartree-Fock surface, we show in the correlated LMP2/6-31G** calculations for the Watson-Crick guanine-cytosine base pair that one of the hydrogen-bonded NH2 groups remains appreciably puckered. The resultant MMFF94s geometries emulate the "time-averaged" structures typically observed in crystallographic and most other experimental structure determinations. MMFF94s also employs modified torsion parameters for interactions that involve such centers, but is identical to MMFF94 for other systems. Isolated instances are found in which MMFF94s fails to locate a (probably shallow) local minimum found on the MMFF94 and reference MP2/6-31G* surfaces. In general, however, MMFF94s describes conformation energies for delocalized trigonal nitrogen systems nearly as well as MMFF94 does. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 720-729, 1999.

MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries.

This article provides extensive comparisons for the MMFF94, MMFF94s, CFF95, CVFF, MSI CHARMm, AMBER*, OPLS*, MM2*, and MM3* force fields to experimental and high-quality ab initio data for conformational energies and to scaled ab initio data for hydrogen-bonded complexes. Some comparisons are also presented for CHARMM 22. The tests of conformational energies consisted of two sets of comparisons to experiment and one more extensive set of comparisons to relatively high-quality ab initio data. As in the derivation of MMFF94, scaled HF/6-31G* energies and geometries were used to assess the reasonableness of the calculated intermolecular interaction energies and geometries. The comparisons for intermolecular interactions appear to be the first broadly based comparisons to appear in the chemical literature. Taken together, the comparisons reveal that most of the force fields make sizable errors and frequently produce qualitatively incorrect results for both conformational and intermolecular-interaction energies. For example, three of the force fields produce individual errors in conformational energy of more than 10 kcal/mol, and four rate thiophene as a stronger hydrogen-bond acceptor than ammonia. Only MMFF94 and MMFF94s perform consistently well. Some MMFF deficiencies are apparent, however, particularly for conformational energies of halocyclohexanes. These deficiencies, and others recently found for condensed-phase simulations, will need to be addressed in any future reparameterization of MMFF. The quantum-chemical data used in this work have been placed on the Computational Chemistry List web site. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 730-748, 1999.