Dynamics and design of enzymes and inhibitors

Wong, Chung F.; McCammon, J. Andrew

doi:10.1021/ja00273a048

Cited by 258 publications

(148 citation statements)

References 7 publications

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“…[10][11][12][13][14][15] Subsequent efforts since that original seminal work have reported anecdotal results for a small number of protein-ligand complexes, but suffered from a lack of computing power and inadequacies in both sampling algorithms and molecular mechanics force fields. 1,5,8 As a result, use of free energy calculations was limited in an industrial drug discovery setting, where high throughput, predictive accuracy, and robustness are required to make a significant impact.…”

Section: Introductionmentioning

confidence: 99%

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

et al. 2015

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Designing tight binding ligands is a primary objective of small molecule drug discovery.Over the past few decades, free energy calculations have benefited from improved force fields and sampling algorithms, as well as the advent of low cost parallel computing.However, it has proven to be challenging to reliably achieve the level of accuracy that would be needed to guide lead optimization (~5X in binding affinity) for a wide range of ligands and protein targets. Not surprisingly, widespread commercial application of free energy simulations has been limited due to the lack of large-scale validation coupled with the technical challenges traditionally associated with running these types of calculations.Here, we report an approach that achieves an unprecedented level of accuracy across a broad range of target classes and ligands, with retrospective results encompassing 200 ligands and a wide variety of chemical perturbations, many of which involve significant changes in ligand chemical structures. In addition, we have applied the method in prospective drug discovery projects and found a significant improvement in the quality of the compounds synthesized that have been predicted to be potent. Compounds predicted to be potent by this approach have a substantial reduction in false positives relative to compounds synthesized based on other computational or medicinal chemistry approaches. Furthermore, the results are consistent with those obtained from our retrospective studies, demonstrating the robustness and broad range of applicability of this approach, which can be used to drive decisions in lead optimization.3

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Section: Introductionmentioning

confidence: 99%

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

et al. 2015

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“…In the single topology approach, there is one ligand molecule in all simulations, which morphs from being in state A (having a particular chemical structure and interaction parameters), to a different state B, where the structure and interaction parameters are different. [4][5][6][7][8][9][10][11][12][13] In some transformations, there could be atoms on A that have no direct analog on B. During the computational morphing process, these atoms will have their non-bonded interactions decoupled from the rest of the sysa) Author to whom correspondence should be addressed.…”

Section: Introductionmentioning

confidence: 99%

Separated topologies—A method for relative binding free energy calculations using orientational restraints

Rocklin

Mobley

Dill

2013

The Journal of Chemical Physics

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Orientational restraints can improve the efficiency of alchemical free energy calculations, but they are not typically applied in relative binding calculations, which compute the affinity difference been two ligands. Here, we describe a new "separated topologies" method, which computes relative binding free energies using orientational restraints and which has several advantages over existing methods. While standard approaches maintain the initial and final ligand in a shared orientation, the separated topologies approach allows the initial and final ligands to have distinct orientations. This avoids a slowly converging reorientation step in the calculation. The separated topologies approach can also be applied to determine the relative free energies of multiple orientations of the same ligand. We illustrate the approach by calculating the relative binding free energies of two compounds to an engineered site in Cytochrome C Peroxidase.

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“…We compare both L-Asp and D-Asp, in regular and inverted orientations, and the metabolite succinate, where the ammonium group is removed altogether and the ligand has an additional negative charge. This is done with a state of the art molecular dynamics free energy (MDFE) technique (21)(22)(23)(24)(25)(32)(33)(34)(35)(36)(37)(38)(39), by computing the change in binding free energy when an ammonium group is inserted at either possible position on either succinate methylene group.By scanning all possible ammonium positions on the ligand, we can also address an interesting, secondary question: the strength of electrostatic interactions in the active site. Simulations have played a significant role in establishing the impor-…”

mentioning

confidence: 99%

Ammonium Scanning in an Enzyme Active Site

Thompson

Lazennec

Plateau

et al. 2007

Journal of Biological Chemistry

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The aminoacyl-tRNA synthetases (aaRSs) 3 play a crucial role in preserving the accuracy of genetic code translation, linking each amino acid to a cognate tRNA, which carries the corresponding anticodon. Each of the 20 aaRSs must bind its target amino acid substrate with a high specificity (1-8). In the "class IIb" subgroup, formed of AspRS (9 -16, 21-26), AsnRS (17,24),25), a network of electrostatic interactions ensures binding specificity for the cognate amino acid side chain in each case. Experimental and theoretical studies show, for example, that the preference of AspRS for Asp over its neutral analogue, Asn, involves a complex mechanism (24, 25). Proton binding, ATP binding, and long-range electrostatic interactions play important roles, and net positive electrostatic potential in the active site permits AspRS to bind L-Asp much more strongly than L-Asn.The translation apparatus must also preserve the homochirality of proteins, and aaRSs should be specific for L-amino acids. Kinetic experiments show, however, that AspRS does not strongly distinguish between the "left-handed" L-Asp and "right-handed" D-Asp stereoisomers. Indeed, D-Asp-tRNA Asp is produced at detectable levels by Escherichia coli AspRS (26), at a rate only 4,000 times lower than L-Asp-tRNA Asp . To preserve homochirality in vivo (27), editing (28) of D-Asp-tRNA Asp by a D-aminoacyl-tRNA deacylase is performed (26). For biotechnology applications, it is not always desirable to preserve homochirality, and D-amino acids are of great potential interest in protein engineering and design. For example, mixed L-and D-amino acid proteins are used in the development of synthetic vaccines (29,30). It is hence of interest, both from a fundamental and an engineering perspective, to better understand how aaRSs distinguish between L-and D-amino acids.In the present work, we use simulations and experiments to investigate the origins of chiral specificity of E. coli AspRS for its L-aspartate substrate (L-Asp). Asp has a pseudosymmetry, broken only by its ammonium group, and so the enzyme must protect not only against D-Asp, but against an alternate, "inverted" orientation where the two substrate carboxylates are swapped (Fig. 1A). The inverted orientation is seen in the crystal structure of a homologous enzyme, asparagine synthetase (31). We compare both L-Asp and D-Asp, in regular and inverted orientations, and the metabolite succinate, where the ammonium group is removed altogether and the ligand has an additional negative charge. This is done with a state of the art molecular dynamics free energy (MDFE) technique (21)(22)(23)(24)(25)(32)(33)(34)(35)(36)(37)(38)(39), by computing the change in binding free energy when an ammonium group is inserted at either possible position on either succinate methylene group.By scanning all possible ammonium positions on the ligand, we can also address an interesting, secondary question: the strength of electrostatic interactions in the active site. Simulations have played a significant role in establishing the impor-

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Dynamics and design of enzymes and inhibitors

Cited by 258 publications

References 7 publications

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Separated topologies—A method for relative binding free energy calculations using orientational restraints

Ammonium Scanning in an Enzyme Active Site

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