1
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Petrov D, Perthold JW, Oostenbrink C, de Groot BL, Gapsys V. Guidelines for Free-Energy Calculations Involving Charge Changes. J Chem Theory Comput 2024; 20:914-925. [PMID: 38164763 PMCID: PMC10809403 DOI: 10.1021/acs.jctc.3c00757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
The Coulomb interactions in molecular simulations are inherently approximated due to the finite size of the molecular box sizes amenable to current-day compute power. Several methods exist for treating long-range electrostatic interactions, yet these approaches are subject to various finite-size-related artifacts. Lattice-sum methods are frequently used to approximate long-range interactions; however, these approaches also suffer from artifacts which become particularly pronounced for free-energy calculations that involve charge changes. The artifacts, however, also affect the sampling when plain simulations are performed, leading to a biased ensemble. Here, we investigate two previously described model systems to determine if artifacts continue to play a role when overall neutral boxes are considered, in the context of both free-energy calculations and sampling. We find that ensuring that no net-charge changes take place, while maintaining a neutral simulation box, may be sufficient provided that the simulation boxes are large enough. Addition of salt to the solution (when appropriate) can further alleviate the remaining artifacts in the sampling or the calculated free-energy differences. We provide practical guidelines to avoid finite-size artifacts.
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Affiliation(s)
- Drazen Petrov
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna, Vienna 1190, Austria
| | - Jan Walther Perthold
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna, Vienna 1190, Austria
| | - Chris Oostenbrink
- Institute
for Molecular Modeling and Simulation, Department of Material Sciences
and Process Engineering, University of Natural
Resources and Life Sciences, Vienna, Vienna 1190, Austria
- Christian
Doppler Laboratory for Molecular Informatics in the Biosciences, University of Natural Resources and Life Sciences, Vienna, Vienna 1190, Austria
| | - Bert L. de Groot
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, Göttingen 37077, Germany
| | - Vytautas Gapsys
- Computational
Biomolecular Dynamics Group, Department of Theoretical and Computational
Biophysics, Max Planck Institute for Multidisciplinary
Sciences, Göttingen 37077, Germany
- Computational
Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg
30, Beerse B-2340, Belgium
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2
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Öhlknecht C, Perthold JW, Lier B, Oostenbrink C. Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest-Host Systems. J Chem Theory Comput 2020; 16:7721-7734. [PMID: 33136389 PMCID: PMC7726903 DOI: 10.1021/acs.jctc.0c00719] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Indexed: 01/24/2023]
Abstract
Currently, two different methods dominate the field of biomolecular free-energy calculations for the prediction of binding affinities. Pathway methods are frequently used for large ligands that bind on the surface of a host, such as protein-protein complexes. Alchemical methods, on the other hand, are preferably applied for small ligands that bind to deeply buried binding sites. The latter methods are also widely known to be heavily artifacted by the representation of electrostatic energies in periodic simulation boxes, in particular, when net-charge changes are involved. Different methods have been described to deal with these artifacts, including postsimulation correction schemes and instantaneous correction schemes (e.g., co-alchemical perturbation of ions). Here, we use very simple test systems to show that instantaneous correction schemes with no change in the system net charge lower the artifacts but do not eliminate them. Furthermore, we show that free energies from pathway methods suffer from the same artifacts.
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Affiliation(s)
- Christoph Öhlknecht
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Jan Walther Perthold
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Bettina Lier
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna 1190, Austria
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3
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Kellett K, Slochower DR, Schauperl M, Duggan BM, Gilson MK. Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. J Comput Aided Mol Des 2020; 35:95-104. [PMID: 33037548 DOI: 10.1007/s10822-020-00350-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022]
Abstract
We investigate the binding of native β-cyclodextrin (β-CD) and eight novel β-CD derivatives with two different guest compounds, using isothermal calorimetry and 2D NOESY NMR. In all cases, the stoichiometry is 1:1 and binding is exothermic. Overall, modifications at the 3' position of β-CD, which is at the secondary face, weaken binding by several kJ/mol relative to native β-CD, while modifications at the 6' position (primary face) maintain or somewhat reduce the binding affinity. The variations in binding enthalpy are larger than the variations in binding free energy, so entropy-enthalpy compensation is observed. Characterization of the bound conformations with NOESY NMR shows that the polar groups of the guests may be situated at either face, depending on the host molecule, and, in some cases, both orientations are populated. The present results were used in the SAMPL7 blinded prediction challenge whose results are detailed in the same special issue of JCAMD.
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Affiliation(s)
- K Kellett
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - D R Slochower
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - M Schauperl
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - B M Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - M K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA.
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4
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Perthold JW, Petrov D, Oostenbrink C. Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). J Chem Inf Model 2020; 60:5395-5406. [PMID: 32492343 PMCID: PMC7686955 DOI: 10.1021/acs.jcim.0c00456] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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Free-energy
perturbation (FEP) methods are commonly used in drug
design to calculate relative binding free energies of different ligands
to a common host protein. Alchemical ligand transformations are usually
performed in multiple steps which need to be chosen carefully to ensure
sufficient phase-space overlap between neighboring states. With one-step
or single-step FEP techniques, a single reference state is designed
that samples phase-space not only representative of a full transformation
but also ideally resembles multiple ligand end states and hence allows
for efficient multistate perturbations. Enveloping distribution sampling
(EDS) is one example for such a method in which the reference state
is created by a mathematical combination of the different ligand end
states based on solid statistical mechanics. We have recently proposed
a novel approach to EDS which enables efficient barrier crossing between
the different end states, termed accelerated EDS (A-EDS). In this
work, we further simplify the parametrization of the A-EDS reference
state and demonstrate the automated calculation of multiple free-energy
differences between different ligands from a single simulation in
three different well-described drug design model systems.
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Affiliation(s)
- Jan Walther Perthold
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Dražen Petrov
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190 Vienna, Austria
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5
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Karandashev K, Vaníček J. Accelerating equilibrium isotope effect calculations. II. Stochastic implementation of direct estimators. J Chem Phys 2019; 151:134116. [PMID: 31594323 DOI: 10.1063/1.5124995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Path integral calculations of equilibrium isotope effects and isotopic fractionation are expensive due to the presence of path integral discretization errors, statistical errors, and thermodynamic integration errors. Whereas the discretization errors can be reduced by high-order factorization of the path integral and statistical errors by using centroid virial estimators, two recent papers proposed alternative ways to completely remove the thermodynamic integration errors: Cheng and Ceriotti [J. Chem. Phys. 141, 244112 (2015)] employed a variant of free-energy perturbation called "direct estimators," while Karandashev and Vaníček [J. Chem. Phys. 143, 194104 (2017)] combined the thermodynamic integration with a stochastic change of mass and piecewise-linear umbrella biasing potential. Here, we combine the former approach with the stochastic change in mass in order to decrease its statistical errors when applied to larger isotope effects and perform a thorough comparison of different methods by computing isotope effects first on a harmonic model and then on methane and methanium, where we evaluate all isotope effects of the form CH4-xDx/CH4 and CH5-xDx +/CH5 +, respectively. We discuss the reasons for a surprising behavior of the original method of direct estimators, which performed well for a much larger range of isotope effects than what had been expected previously, as well as some implications of our work for the more general problem of free energy difference calculations.
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Affiliation(s)
- Konstantin Karandashev
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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6
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Perthold JW, Oostenbrink C. Accelerated Enveloping Distribution Sampling: Enabling Sampling of Multiple End States while Preserving Local Energy Minima. J Phys Chem B 2018; 122:5030-5037. [DOI: 10.1021/acs.jpcb.8b02725] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jan Walther Perthold
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190 Vienna, Austria
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7
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Jandova Z, Fast D, Setz M, Pechlaner M, Oostenbrink C. Saturation Mutagenesis by Efficient Free-Energy Calculation. J Chem Theory Comput 2018; 14:894-904. [PMID: 29262673 PMCID: PMC5813279 DOI: 10.1021/acs.jctc.7b01099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Single-point mutations
in proteins can greatly influence protein
stability, binding affinity, protein function or its expression per
se. Here, we present accurate and efficient predictions of the free
energy of mutation of amino acids. We divided the complete mutational
free energy into an uncharging step, which we approximate by a third-power
fitting (TPF) approach, and an annihilation step, which we approximate
using the one-step perturbation (OSP) method. As a diverse set of
test systems, we computed the solvation free energy of all amino acid
side chain analogues and obtained an excellent agreement with thermodynamic
integration (TI) data. Moreover, we calculated mutational free energies
in model tripeptides and established an efficient protocol involving
a single reference state. Again, the approximate methods agreed excellently
with the TI references, with a root-mean-square error of only 3.6
kJ/mol over 17 mutations. Our combined TPF+OSP approach does show
not only a very good agreement but also a 2-fold higher efficiency
than full blown TI calculations.
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Affiliation(s)
- Zuzana Jandova
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Daniel Fast
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Martina Setz
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Maria Pechlaner
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna A-1190, Austria
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8
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Reif MM, Zacharias M. Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules. J Comput Chem 2016; 37:1711-24. [DOI: 10.1002/jcc.24390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Maria M. Reif
- Physics Department (T38); Technische Universität München; James-Franck-Str. 1 85748 Garching Germany
| | - Martin Zacharias
- Physics Department (T38); Technische Universität München; James-Franck-Str. 1 85748 Garching Germany
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9
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Solovyeva A, von Lilienfeld OA. Alchemical screening of ionic crystals. Phys Chem Chem Phys 2016; 18:31078-31091. [DOI: 10.1039/c6cp04258a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We introduce alchemical perturbations as a rapid and accurate tool to estimate fundamental structural and energetic properties in pure and mixed ionic crystals.
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Affiliation(s)
- Alisa Solovyeva
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials MARVEL
- Department of Chemistry
- University of Basel
- 4056 Basel
- Switzerland
| | - O. Anatole von Lilienfeld
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials MARVEL
- Department of Chemistry
- University of Basel
- 4056 Basel
- Switzerland
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10
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Naden LN, Shirts MR. Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions. J Chem Theory Comput 2015; 11:2536-49. [DOI: 10.1021/ct501047e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Levi N. Naden
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Michael R. Shirts
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
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11
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Kang SG, Das P, McGrane SJ, Martin AJ, Huynh T, Royyuru AK, Taylor AJ, Jones PG, Zhou R. Molecular recognition of metabotropic glutamate receptor type 1 (mGluR1): synergistic understanding with free energy perturbation and linear response modeling. J Phys Chem B 2014; 118:6393-404. [PMID: 24635567 DOI: 10.1021/jp410232j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metabotropic glutamate receptors (mGluRs) constitute an important family of the G-protein coupled receptors. Due to their widespread distribution in the central nervous system (CNS), these receptors are attractive candidates for understanding the molecular basis of various cognitive processes as well as for designing inhibitors for relevant psychiatric and neurological disorders. Despite many studies on drugs targeting the mGluR receptors to date, the molecular level details on the ligand binding dynamics still remain unclear. In this study, we performed in silico experiments for mGluR1 with 29 different ligands including known synthetic agonists and antagonists as well as natural amino acids. The ligand-receptor binding affinities were estimated by the use of atomistic simulations combined with the mathematically rigorous, Free Energy Perturbation (FEP) method, which successfully recognized the native agonist l-glutamate among the highly favorable binders, and also accurately distinguished antagonists from agonists. Comparative contact analysis also revealed the binding mode differences between natural and non-natural amino acid-based ligands. Several factors potentially affecting the ligand binding affinity and specificity were identified including net charges, dipole moments, and the presence of aromatic rings. On the basis of these findings, linear response models (LRMs) were built for different sets of ligands that showed high correlations (R(2) > 0.95) to the corresponding FEP binding affinities. These results identify some key factors that determine ligand-mGluR1 binding and could be used for future inhibitor designs and support a role for in silico modeling for understanding receptor ligand interactions.
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Affiliation(s)
- Seung-gu Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center , Yorktown Heights, New York 10598, United States
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12
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Reif MM, Oostenbrink C. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. J Comput Chem 2014; 35:227-43. [PMID: 24249099 PMCID: PMC4237198 DOI: 10.1002/jcc.23490] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/13/2013] [Indexed: 12/11/2022]
Abstract
The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio-)chemical thermodynamics. Many important endogenous receptor-binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice-summation scheme or a cutoff-truncation scheme with Barker-Watts reaction-field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest-host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free-energy calculation studies if changes in the net charge are involved.
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Affiliation(s)
- Maria M Reif
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences ViennaMuthgasse 18, 1190, Wien, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences ViennaMuthgasse 18, 1190, Wien, Austria
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13
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Bachmann SJ, Lin Z, Stafforst T, van Gunsteren WF, Dolenc J. On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters. J Chem Theory Comput 2013; 10:391-400. [DOI: 10.1021/ct400652w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Zhixiong Lin
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Thorsten Stafforst
- Laboratory
of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | | | - Jožica Dolenc
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Faculty
of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
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14
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Wickstrom L, He P, Gallicchio E, Levy RM. Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. J Chem Theory Comput 2013; 9:3136-3150. [PMID: 25147485 DOI: 10.1021/ct400003r] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Host-guest inclusion complexes are useful models for understanding the structural and energetic aspects of molecular recognition. Due to their small size relative to much larger protein-ligand complexes, converged results can be obtained rapidly for these systems thus offering the opportunity to more reliably study fundamental aspects of the thermodynamics of binding. In this work, we have performed a large scale binding affinity survey of 57 β-cyclodextrin (CD) host guest systems using the binding energy distribution analysis method (BEDAM) with implicit solvation (OPLS-AA/AGBNP2). Converged estimates of the standard binding free energies are obtained for these systems by employing techniques such as parallel Hamitionian replica exchange molecular dynamics, conformational reservoirs and multistate free energy estimators. Good agreement with experimental measurements is obtained in terms of both numerical accuracy and affinity rankings. Overall, average effective binding energies reproduce affinity rank ordering better than the calculated binding affinities, even though calculated binding free energies, which account for effects such as conformational strain and entropy loss upon binding, provide lower root mean square errors when compared to measurements. Interestingly, we find that binding free energies are superior rank order predictors for a large subset containing the most flexible guests. The results indicate that, while challenging, accurate modeling of reorganization effects can lead to ligand design models of superior predictive power for rank ordering relative to models based only on ligand-receptor interaction energies.
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Affiliation(s)
- Lauren Wickstrom
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854 ; Department of Chemistry, Lehman College, The City University of New York, Bronx, NY 10468
| | - Peng He
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Emilio Gallicchio
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Ronald M Levy
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
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15
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Klvaňa M, Murphy DL, Jeřábek P, Goodman MF, Warshel A, Sweasy JB, Florián J. Catalytic effects of mutations of distant protein residues in human DNA polymerase β: theory and experiment. Biochemistry 2012; 51:8829-43. [PMID: 23013478 DOI: 10.1021/bi300783t] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We carried out free-energy calculations and transient kinetic experiments for the insertion of the right (dC) and wrong (dA) nucleotides by wild-type (WT) and six mutant variants of human DNA polymerase β (Pol β). Since the mutated residues in the point mutants, I174S, I260Q, M282L, H285D, E288K, and K289M, were not located in the Pol β catalytic site, we assumed that the WT and its point mutants share the same dianionic phosphorane transition-state structure of the triphosphate moiety of deoxyribonucleotide 5'-triphosphate (dNTP) substrate. On the basis of this assumption, we have formulated a thermodynamic cycle for calculating relative dNTP insertion efficiencies, Ω = (k(pol)/K(D))(mut)/(k(pol)/K(D))(WT) using free-energy perturbation (FEP) and linear interaction energy (LIE) methods. Kinetic studies on five of the mutants have been published previously using different experimental conditions, e.g., primer-template sequences. We have performed a presteady kinetic analysis for the six mutants for comparison with wild-type Pol β using the same conditions, including the same primer/template DNA sequence proximal to the dNTP insertion site used for X-ray crystallographic studies. This consistent set of kinetic and structural data allowed us to eliminate the DNA sequence from the list of factors that can adversely affect calculated Ω values. The calculations using the FEP free energies scaled by 0.5 yielded 0.9 and 1.1 standard deviations from the experimental log Ω values for the insertion of the right and wrong dNTP, respectively. We examined a hybrid FEP/LIE method in which the FEP van der Waals term for the interaction of the mutated amino acid residue with its surrounding environment was replaced by the corresponding van der Waals term calculated using the LIE method, resulting in improved 0.4 and 1.0 standard deviations from the experimental log Ω values. These scaled FEP and FEP/LIE methods were also used to predict log Ω for R283A and R283L Pol β mutants.
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Affiliation(s)
- Martin Klvaňa
- Department of Chemistry, Loyola University, Chicago, Illinois 60626, United States
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16
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Lin Z, van Gunsteren WF. On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment. J Comput Chem 2012; 34:387-93. [DOI: 10.1002/jcc.23146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/10/2012] [Accepted: 09/13/2012] [Indexed: 11/09/2022]
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17
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Lai B, Oostenbrink C. Binding free energy, energy and entropy calculations using simple model systems. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1272-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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de Ruiter A, Oostenbrink C. Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors. J Chem Theory Comput 2012; 8:3686-95. [PMID: 26593013 DOI: 10.1021/ct200750p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several combinations of free energy calculation methods have been applied to determine the relative free energies of binding between eight para-substituted benzamidines in complex with the serine protease trypsin. With the aim to improve efficiency and maintain accuracy, the linear response approximation (LRA), linear interaction energy (LIE) and third power fitting (TPF) are combined with the one-step perturbation (OSP) to determine the polar and apolar contributions to the free energy, respectively. It is shown that the combination TPF/OSP gives the most accurate results and is 4.5 times more efficient than the rigorous thermodynamic integration (TI). By projecting the electrostatic preorganization energy from the OSP simulations, an increase in efficiency of a factor 7.5 can even be achieved. Loss of accuracy with respect to the TI data is limited to 3.9 and 5.6 kJ/mol, respectively, making it an attractive approach for lead optimization programs in drug research.
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Affiliation(s)
- Anita de Ruiter
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU) , Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU) , Vienna, Austria
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Abstract
The one-step perturbation approach offers an efficient means to estimate free energy differences. It may be applied to estimate solvation free energies, conformational preferences or relative free energies of binding of series of compounds to a common receptor. Applicability of the method depends on the possibility to define a proper reference state which may in itself be an unphysical molecule. Here, we describe practical considerations and explicit guidelines to define a proper reference state, and to efficiently calculate relative free energies. The strengths and limitations of the method are highlighted and special considerations are noted. The method may be applied using many different simulation programs. Here, analyses are exemplified at the hand of the GROMOS simulation package.
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Affiliation(s)
- Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria.
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20
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Pérez A, von Lilienfeld OA. Path Integral Computation of Quantum Free Energy Differences Due to Alchemical Transformations Involving Mass and Potential. J Chem Theory Comput 2011; 7:2358-69. [PMID: 26606611 DOI: 10.1021/ct2000556] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Thermodynamic integration, perturbation theory, and λ-dynamics methods were applied to path integral molecular dynamics calculations to investigate free energy differences due to "alchemical" transformations. Several estimators were formulated to compute free energy differences in solvable model systems undergoing changes in mass and/or potential. Linear and nonlinear alchemical interpolations were used for the thermodynamic integration. We find improved convergence for the virial estimators, as well as for the thermodynamic integration over nonlinear interpolation paths. Numerical results for the perturbative treatment of changes in mass and electric field strength in model systems are presented. We used thermodynamic integration in ab initio path integral molecular dynamics to compute the quantum free energy difference of the isotope transformation in the Zundel cation. The performance of different free energy methods is discussed.
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Affiliation(s)
- Alejandro Pérez
- Department of Chemistry, New York University , New York, New York 10003, United States, Nano-bio spectroscopy group, Centro Joxe Mari Korta , Avenida de Tolosa, 72, E-20018 Donostia-San Sebastian, Spain, and Institute of Pure and Applied Mathematics, University of California Los Angeles , Los Angeles, California 90095, United States.,Surface and Interface Sciences Department, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States, Argonne Leadership Computing Facility, Argonne National Laboratory , Argonne, Illinois 60439, United States, and Institute of Pure and Applied Mathematics, University of California Los Angeles , Los Angeles, California 90095, United States
| | - O Anatole von Lilienfeld
- Department of Chemistry, New York University , New York, New York 10003, United States, Nano-bio spectroscopy group, Centro Joxe Mari Korta , Avenida de Tolosa, 72, E-20018 Donostia-San Sebastian, Spain, and Institute of Pure and Applied Mathematics, University of California Los Angeles , Los Angeles, California 90095, United States.,Surface and Interface Sciences Department, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States, Argonne Leadership Computing Facility, Argonne National Laboratory , Argonne, Illinois 60439, United States, and Institute of Pure and Applied Mathematics, University of California Los Angeles , Los Angeles, California 90095, United States
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21
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Free energy calculations of protein-ligand interactions. Curr Opin Chem Biol 2011; 15:547-52. [PMID: 21684797 DOI: 10.1016/j.cbpa.2011.05.021] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 05/03/2011] [Accepted: 05/23/2011] [Indexed: 01/25/2023]
Abstract
In the calculation of free energies of binding for protein-ligand complexes, we distinguish endpoint methods, methods involving alchemical modifications and methods that physically displace the ligand from the protein. Most methodological advances seem to come from a clever combination of multiple existing methods to enhance the sampling or to utilize specific advantages of various approaches. The coupling parameters common in thermodynamic integration and in Hamiltonian replica exchange are for instance combined to yield replica exchange thermodynamic integration. As new methods mostly aim to improve efficiency or to attain more complete sampling, there are good prospects to understand and tackle the sampling problem better and to shift the focus towards the scoring problem in the context of more robust and accurate force fields.
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22
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Lin Z, Hodel FH, van Gunsteren WF. Influence of Variation of a Side Chain on the Folding Equilibrium of a β-Peptide. Helv Chim Acta 2011. [DOI: 10.1002/hlca.201100003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Dolenc J, Gerster S, van Gunsteren WF. Molecular Dynamics Simulations Shed Light on the Enthalpic and Entropic Driving Forces That Govern the Sequence Specific Recognition between Netropsin and DNA. J Phys Chem B 2010; 114:11164-72. [DOI: 10.1021/jp100483f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jožica Dolenc
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH-8093 Zürich, Switzerland, and Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Sarah Gerster
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH-8093 Zürich, Switzerland, and Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wilfred F. van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH-8093 Zürich, Switzerland, and Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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Tavlarakis A, Zhou R. Linear interaction energy approximation for binding affinities of nevirapine and HEPT analogues with HIV-1 reverse transcriptase. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020902929828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Anatole von Lilienfeld O. Accurate ab initio energy gradients in chemical compound space. J Chem Phys 2009; 131:164102. [DOI: 10.1063/1.3249969] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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