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 ha

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

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.

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Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes

Structure-based virtual screening plays an important role in drug discovery and complements other screening approaches. In general, protein crystal structures are prepared prior to docking in order to add hydrogen atoms, optimize hydrogen bonds, remove atomic clashes, and perform other operations that are not part of the x-ray crystal structure refinement process. In addition, ligands must be prepared to create 3-dimensional geometries, assign proper bond orders, and generate accessible tautomer and ionization states prior to virtual screening. While the prerequisite for proper system preparation is generally accepted in the field, an extensive study of the preparation steps and their effect on virtual screening enrichments has not been performed. In this work, we systematically explore each of the steps involved in preparing a system for virtual screening. We first explore a large number of parameters using the Glide validation set of 36 crystal structures and 1,000 decoys. We then apply a subset of protocols to the DUD database. We show that database enrichment is improved with proper preparation and that neglecting certain steps of the preparation process produces a systematic degradation in enrichments, which can be large for some targets. We provide examples illustrating the structural changes introduced by the preparation that impact database enrichment. While the work presented here was performed with the Protein Preparation Wizard and Glide, the insights and guidance are expected to be generalizable to structure-based virtual screening with other docking methods.

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

We present results of improving the OPLS-AA force field for peptides by means of refitting the key Fourier torsional coefficients. The fitting technique combines using accurate ab initio data as the target, choosing an efficient fitting subspace of the whole potential-energy surface, and determining weights for each of the fitting points based on magnitudes of the potential-energy gradient. The average energy RMS deviation from the LMP2/cc-pVTZ(-f)//HF/6-31G** data is reduced by ca. 40% from 0.81 to 0.47 kcal/mol as a result of the fitting for the electrostatically uncharged dipeptides. Transferability of the parameters is demonstrated by using the same alanine dipeptide-fitted backbone torsional parameters for all of the other dipeptides (with the appropriate side-chain refitting) and the alanine tetrapeptide. Parameters of nonbonded interactions have also been refitted for the sulfur-containing dipeptides (cysteine and methionine), and the validity of the new Coulombic charges and the van der Waals σ's ...

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Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides†

Computational approaches that 'dock' small molecules into the structures of macromolecular targets and 'score' their potential complementarity to binding sites are widely used in hit identification and lead optimization Indeed, there are now a number of drugs whose development was heavily influenced by or based on structure-based design and screening strategies, such as HIV protease inhibitors Nevertheless, there remain significant challenges in the application of these approaches, in particular in relation to current scoring schemes Here, we review key concepts and specific features of small-molecule-protein docking methods, highlight selected applications and discuss recent advances that aim to address the acknowledged limitations of established approaches

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Docking and scoring in virtual screening for drug discovery: methods and applications.

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−protei...

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

We present a new method for solving the Redfield equation, which describes the evolution of the reduced density matrix of a multilevel quantum‐mechanical system interacting with a thermal bath. The method is based on a new decomposition of the Redfield relaxation tensor that makes possible its direct application to the density matrix without explicit construction of the full tensor. In the resulting expressions, only ordinary matrices are involved and so any quantum system whose Hamiltonian can be diagonalized can be treated with the full Redfield theory. To efficiently solve the equation of motion for the density matrix, we introduce a generalization of the short‐iterative‐Lanczos propagator. Together, these contributions allow the complete Redfield theory to be applied to significantly larger systems than was previously possible. Several model calculations are presented to illustrate the methodology, including one example with 172 quantum states.

Solution of the Redfield equation for the dissipative quantum dynamics of multilevel systems

We discuss computational methods for carrying out correlated ab initio electronic structure calculations for large systems. The focus is on two types of methods:  density functional theory (DFT) and localized orbital methods such as local MP2 (LMP2) and a multireference version based upon a generalized valence bond reference wave function, GVB-LMP2. The computational performance of both approaches using pseudospectral numerical methods is documented, and calculated thermochemical and conformational energetics are compared to experimental data.

Correlated ab Initio Electronic Structure Calculations for Large Molecules

The large spectral width of ultrashort optical pulses makes it possible to measure the complete time‐resolved absorption spectrum of a sample with a single pulse, offering simultaneously high resolution in both the time and frequency domains. To quantitatively interpret these experiments, we start with the usual perturbative density matrix theory for the third‐order susceptibility of a multilevel system. However, the theory is formulated in terms of four‐time correlation functions which are interpreted as the time‐dependent overlap of bra and ket vibrational wave packets propagating independently on the ground and excited electronic state potential surfaces. This approach captures the critical distinction between electronic population decay and pure dephasing processes, while retaining the intuitive physical picture offered by the time‐dependent wave packet theories of molecular spectroscopy. A useful simplification is achieved by considering the absorption of the probe pulse as the first‐order spectrosco...

Wave packet theory of dynamic absorption spectra in femtosecond pump–probe experiments

The density matrix formalism is used to consider long-range electron transfer through a delocalized bridge system that is dissipatively coupled to a thermal bath. Under conditions when the bridge is weakly populated, a distance-independent transfer mechanism arises that eventually dominates the exponentially distance-dependent nonadiabatic tunneling process typically observed. This model offers a possible explanation for the anomalously rapid long-range photoelectron transfer recently observed by Barton and Turro et al, for donor and acceptor species intercalated into a DNA double helix. Predicted electron-transfer rates are obtained by numerically solving the Redfield equation for the density matrix of the full donor-bridge-acceptor system in the presence of stochastic fluctuations induced by the bath. 43 refs., 17 figs., 4 tabs.

W. Thomas Pollard

Papers

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

Solution of the Redfield equation for the dissipative quantum dynamics of multilevel systems

Correlated ab Initio Electronic Structure Calculations for Large Molecules

Wave packet theory of dynamic absorption spectra in femtosecond pump–probe experiments

Multilevel Redfield Treatment of Bridge-Mediated Long-Range Electron Transfer: A Mechanism for Anomalous Distance Dependence