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Bao X, Liu X, Dou R, Xu S, Liu D, Luo J, Gong X, Wong CF, Zhou B. How are N-methylcarbamates encapsulated by β-cyclodextrin: insight into the binding mechanism. Phys Chem Chem Phys 2023; 25:13923-13932. [PMID: 37184134 DOI: 10.1039/d3cp01252b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Guest molecules containing chromophore groups encapsulated by β-cyclodextrin (β-CD) generate circular dichroism (CD) signals, which enables a preliminary prediction of their binding modes. However, the accurate determination of the representative binding conformation (RC) remains a challenging task due to the complex conformational space of these host-guest systems. Here, we combine a molecular dynamics/quantum mechanics/continuum solvent model (MD/QM/CSM) with induced circular dichroism (ICD) data (N. L. Pacioni, A. B. Pierini and A. V. Veglia, Spectrochim. Acta A Mol. Biomol. Spectrosc., 2013, 103, 319-324.) to explore the binding mechanism of β-CD with four N-methylcarbamate molecules: promecarb (PC), bendiocarb (BC), carbaryl (CY) and carbofuran (CF). In aqueous solution, their stability decreases as: PC > BC > CY > CF. Comparing the ECD spectra computed from TD-DFT with the ICD data can help eliminate many common binding configurations and identify the RC. The host-guest binding affinities (BAs) estimated using a ONIOM2(B971:PM6)/SMD model reproduce the measured binding trend, reveal the competition between the non-covalent interaction and solvent effect and explain the large difference in their binding modes. We also examine the fluctuations in the computed BA using similar structures.
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Affiliation(s)
- Xiaofang Bao
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Xiao Liu
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Ran Dou
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Sen Xu
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Dabin Liu
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Jun Luo
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Xuedong Gong
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Chung F Wong
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri-Saint Louis, One University Boulevard, Saint Louis, MO 63121, USA
| | - Baojing Zhou
- Computational Institute for Molecules and Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
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Akkus E, Tayfuroglu O, Yildiz M, Kocak A. Accurate Binding Free Energy Method from End-State MD Simulations. J Chem Inf Model 2022; 62:4095-4106. [PMID: 35972783 PMCID: PMC9472276 DOI: 10.1021/acs.jcim.2c00601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
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Herein, we introduce a new strategy to estimate binding
free energies
using end-state molecular dynamics simulation trajectories. The method
is adopted from linear interaction energy (LIE) and ANI-2x neural
network potentials (machine learning) for the atomic simulation environment
(ASE). It predicts the single-point interaction energies between ligand–protein
and ligand–solvent pairs at the accuracy of the wb97x/6-31G*
level for the conformational space that is sampled by molecular dynamics
(MD) simulations. Our results on 54 protein–ligand complexes
show that the method can be accurate and have a correlation of R = 0.87–0.88 to the experimental binding free energies,
outperforming current end-state methods with reduced computational
cost. The method also allows us to compare BFEs of ligands with different
scaffolds. The code is available free of charge (documentation and
test files) at https://github.com/otayfuroglu/deepQM.
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Affiliation(s)
- Ebru Akkus
- Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli, Turkey
| | - Omer Tayfuroglu
- Department of Chemistry, Gebze Technical University, 41400 Gebze, Kocaeli, Turkey
| | - Muslum Yildiz
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400 Gebze, Kocaeli, Turkey
| | - Abdulkadir Kocak
- Department of Chemistry, Gebze Technical University, 41400 Gebze, Kocaeli, Turkey
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Gundelach L, Fox T, Tautermann CS, Skylaris CK. Protein–ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange–correlation functional. Phys Chem Chem Phys 2021; 23:9381-9393. [DOI: 10.1039/d1cp00206f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum mechanical binding free energies based on thousands of full-protein DFT calculations are tractable, reproducible and converge well.
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Affiliation(s)
- Lennart Gundelach
- University of Southampton Faculty of Engineering Science and Mathematics, Chemistry
- University Road
- Southampton
- UK
| | - Thomas Fox
- Boehringer Ingelheim Pharma GmbH & Co KG
- Medicinal Chemistry
- 88397 Biberach an der Riss
- Germany
| | | | - Chris-Kriton Skylaris
- University of Southampton Faculty of Engineering Science and Mathematics, Chemistry
- University Road
- Southampton
- UK
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Liu J, He X. Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids. Phys Chem Chem Phys 2020; 22:12341-12367. [PMID: 32459230 DOI: 10.1039/d0cp01095b] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To study large molecular systems beyond the system size that the current state-of-the-art ab initio electronic structure methods could handle, fragment-based quantum mechanical (QM) approaches have been developed over the past years, and proved to be efficient in dealing with large molecular systems at various ab initio levels. According to the fragmentation approach, a large molecular system can be divided into subsystems (fragments), and subsequently the property of the whole system can be approximately obtained by taking a proper combination of the corresponding terms of individual fragments. Therefore, the standard QM calculation of a large system could be circumvented by carrying out a series of calculations on small fragments, which significantly promotes computational efficiency. The electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method is one of the fragment-based QM approaches which has been developed by our research group in recent years. This Perspective presents the theoretical framework of this fragmentation method and its applications in biomolecules, molecular clusters, molecular crystals and liquids, including total energy calculation, protein-ligand/protein binding affinity prediction, geometry optimization, vibrational spectrum simulation, ab initio molecular dynamics simulation, and prediction of excited-state properties.
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Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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5
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QM Implementation in Drug Design: Does It Really Help? Methods Mol Biol 2020. [PMID: 32016884 DOI: 10.1007/978-1-0716-0282-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Computational chemistry allows one to characterize the structure, dynamics, and energetics of protein-ligand interactions, which makes it a valuable tool in drug discovery in both academic research and pharmaceutical industry. Molecular mechanics (MM)-based approaches are widely utilized to assist the discovery of new drug candidates. However, the complexity of protein-ligand interactions challenges the accuracy and efficiency of the commonly used empirical methods. Aiming to provide better accuracy in the description of protein-ligand interactions, quantum mechanics (QM)-based approaches are becoming increasingly explored. In principle, QM calculation includes all contributions to the energy, accounting for terms usually missing in empirical force fields, and provides a greater degree of transferability. The usefulness of QM in drug design cannot be overemphasized. In this chapter, we present recent developments and applications of fragment-based QM method in studying the protein-ligand and protein-protein interactions. We critically discuss the performance of the fragment-based QM method at different ab initio levels while trying to answer a critical question: do QM-based methods really help in drug design?
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A new approach for the acceleration of large-scale serial quantum chemical calculations of docking complexes. Russ Chem Bull 2018. [DOI: 10.1007/s11172-018-2186-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Caldararu O, Olsson MA, Riplinger C, Neese F, Ryde U. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T). J Comput Aided Mol Des 2017; 31:87-106. [PMID: 27600554 PMCID: PMC5239813 DOI: 10.1007/s10822-016-9957-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/25/2016] [Indexed: 10/27/2022]
Abstract
We have tried to calculate the free energy for the binding of six small ligands to two variants of the octa-acid deep cavitand host in the SAMPL5 blind challenge. We employed structures minimised with dispersion-corrected density-functional theory with small basis sets and energies were calculated using large basis sets. Solvation energies were calculated with continuum methods and thermostatistical corrections were obtained from frequencies calculated at the HF-3c level. Care was taken to minimise the effects of the flexibility of the host by keeping the complexes as symmetric and similar as possible. In some calculations, the large net charge of the host was reduced by removing the propionate and benzoate groups. In addition, the effect of a restricted molecular dynamics sampling of structures was tested. Finally, we tried to improve the energies by using the DLPNO-CCSD(T) approach. Unfortunately, results of quite poor quality were obtained, with no correlation to the experimental data, systematically too positive affinities (by ~50 kJ/mol) and a mean absolute error (after removal of the systematic error) of 11-16 kJ/mol. DLPNO-CCSD(T) did not improve the results, so the accuracy is not limited by the energy function. Instead, four likely sources of errors were identified: first, the minimised structures were often incorrect, owing to the omission of explicit solvent. They could be partly improved by performing the minimisations in a continuum solvent with four water molecules around the charged groups of the ligands. Second, some ligands could bind in several different conformations, requiring sampling of reasonable structures. Third, there is an indication the continuum-solvation model has problems to accurately describe the binding of both the negatively and positively charged guest molecules. Fourth, different methods to calculate the thermostatistical corrections gave results that differed by up to 30 kJ/mol and there is an indication that HF-3c overestimates the entropy term. In conclusion, it is a challenge to calculate binding affinities for this octa-acid system with quantum-mechanical methods.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden
| | - Martin A Olsson
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden
| | - Christoph Riplinger
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden.
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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9
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Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
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Yilmazer ND, Heitel P, Schwabe T, Korth M. Benchmark of electronic structure methods for protein–ligand interactions based on high-level reference data. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633615400015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The accurate prediction of the strength of protein–ligand interactions is a very difficult problem despite impressive advances in the field of biomolecular modeling. There are good reasons to believe that quantum mechanical methods can help with this task, but the application of such methods in the context of scoring is still in its infancy. Here we benchmark several wave function theory (WFT), density functional theory (DFT) and semiempirical quantum mechanical (SQM) approaches against high-level theoretical references for realistic test cases. Based on our findings for systematically generated model systems of real protein/ligand complexes from the PDB-bind database, we can recommend SCS-MP2 and B2-PLYP-D3 as reference methods, TPSS-D3+Dabc/def-TZVPP as the best DFT approach and PM6-DH+ as a fast and accurate alternative to full ab initio treatments.
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Affiliation(s)
- Nusret Duygu Yilmazer
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Pascal Heitel
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Tobias Schwabe
- Center for Bioinformatics and Institute of Physical Chemistry, University of Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
| | - Martin Korth
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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11
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Chaskar P, Zoete V, Röhrig UF. Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function. J Chem Inf Model 2014; 54:3137-52. [DOI: 10.1021/ci5004152] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prasad Chaskar
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
| | - Ute F. Röhrig
- Swiss Institute of Bioinformatics, Molecular Modeling Group,
Quartier Sorge, Bâtiment
Génopode, CH-1015 Lausanne, Switzerland
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12
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Mikulskis P, Cioloboc D, Andrejić M, Khare S, Brorsson J, Genheden S, Mata RA, Söderhjelm P, Ryde U. Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies. J Comput Aided Mol Des 2014; 28:375-400. [DOI: 10.1007/s10822-014-9739-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/24/2014] [Indexed: 01/09/2023]
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13
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Abstract
Docking methodology aims to predict the experimental binding modes and affinities of small molecules within the binding site of particular receptor targets and is currently used as a standard computational tool in drug design for lead compound optimisation and in virtual screening studies to find novel biologically active molecules. The basic tools of a docking methodology include a search algorithm and an energy scoring function for generating and evaluating ligand poses. In this review, we present the search algorithms and scoring functions most commonly used in current molecular docking methods that focus on protein-ligand applications. We summarise the main topics and recent computational and methodological advances in protein-ligand docking. Protein flexibility, multiple ligand binding modes and the free-energy landscape profile for binding affinity prediction are important and interconnected challenges to be overcome by further methodological developments in the docking field.
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Honarparvar B, Govender T, Maguire GEM, Soliman MES, Kruger HG. Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity. Chem Rev 2013; 114:493-537. [DOI: 10.1021/cr300314q] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bahareh Honarparvar
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Glenn E. M. Maguire
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Hendrik G. Kruger
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
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Ferenczy* GG, Keserű* GM. Thermodynamics of Ligand Binding. PHYSICO-CHEMICAL AND COMPUTATIONAL APPROACHES TO DRUG DISCOVERY 2012. [DOI: 10.1039/9781849735377-00023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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16
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Antony J, Grimme S. Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory. J Comput Chem 2012; 33:1730-9. [PMID: 22570225 DOI: 10.1002/jcc.23004] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 01/31/2023]
Abstract
Dispersion corrected density functional theory (DFT-D3) is used for fully ab initio protein-ligand (PL) interaction energy calculation via molecular fractionation with conjugated caps (MFCC) and applied to PL complexes from the PDB comprising 3680, 1798, and 1060 atoms. Molecular fragments with n amino acids instead of one in the original MFCC approach are considered, thereby allowing for estimating the three-body and higher many-body terms. n > 1 is recommended both in terms of accuracy and efficiency of MFCC. For neutral protein side-chains, the computed PL interaction energy is visibly independent of the fragment length n. The MFCC fractionation error is determined by comparison to a full-system calculation for the 1060 atoms containing PL complex. For charged amino acid side-chains, the variation of the MFCC result with n is increased. For these systems, using a continuum solvation model with a dielectricity constant typical for protein environments (ϵ = 4) reduces both the variation with n and improves the stability of the DFT calculations considerably. The PL interaction energies for two typical complexes obtained ab initio for the first time are found to be rather large (-30 and -54 kcal/mol).
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Affiliation(s)
- Jens Antony
- Universität Münster, Organisch-Chemisches Institut, Germany
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Antony J, Grimme S, Liakos DG, Neese F. Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods. J Phys Chem A 2011; 115:11210-20. [PMID: 21842894 DOI: 10.1021/jp203963f] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.
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Affiliation(s)
- Jens Antony
- Organisch-Chemisches Institut, Universität Münster, Münster, Germany
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Ciancetta A, Genheden S, Ryde U. A QM/MM study of the binding of RAPTA ligands to cathepsin B. J Comput Aided Mol Des 2011; 25:729-42. [PMID: 21701919 DOI: 10.1007/s10822-011-9448-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/13/2011] [Indexed: 11/28/2022]
Abstract
We have carried out quantum mechanical (QM) and QM/MM (combined QM and molecular mechanics) calculations, as well as molecular dynamics (MD) simulations to study the binding of a series of six RAPTA (Ru(II)-arene-1,3,5-triaza-7-phosphatricyclo-[3.3.1.1] decane) complexes with different arene substituents to cathepsin B. The recently developed QM/MM-PBSA approach (QM/MM combined with Poisson-Boltzmann solvent-accessible surface area solvation) has been used to estimate binding affinities. The QM calculations reproduce the antitumour activities of the complexes with a correlation coefficient (r (2)) of 0.35-0.86 after a conformational search. The QM/MM-PBSA method gave a better correlation (r (2) = 0.59) when the protein was fixed to the crystal structure, but more reasonable ligand structures and absolute binding energies were obtained if the protein was allowed to relax, indicating that the ligands are strained when the protein is kept fixed. In addition, the best correlation (r (2) = 0.80) was obtained when only the QM energies were used, which suggests that the MM and continuum solvation energies are not accurate enough to predict the binding of a charged metal complex to a charged protein. Taking into account the protein flexibility by means of MD simulations slightly improves the correlation (r (2) = 0.91), but the absolute energies are still too large and the results are sensitive to the details in the calculations, illustrating that it is hard to obtain stable predictions when full flexible protein is included in the calculations.
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Affiliation(s)
- Antonella Ciancetta
- Dipartimento di Scienze del Farmaco, Università degli Studi "G. D'Annunzio" Chieti-Pescara, Italy
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Genheden S, Luchko T, Gusarov S, Kovalenko A, Ryde U. An MM/3D-RISM approach for ligand binding affinities. J Phys Chem B 2010; 114:8505-16. [PMID: 20524650 DOI: 10.1021/jp101461s] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have modified the popular MM/PBSA or MM/GBSA approaches (molecular mechanics for a biomolecule, combined with a Poisson-Boltzmann or generalized Born electrostatic and surface area nonelectrostatic solvation energy) by employing instead the statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D reference interaction site model, or 3D-RISM-KH) coupled with molecular mechanics or molecular dynamics ( Blinov , N. ; et al. Biophys. J. 2010 ; Luchko , T. ; et al. J. Chem. Theory Comput. 2010 ). Unlike the PBSA or GBSA semiempirical approaches, the 3D-RISM-KH theory yields a full molecular picture of the solvation structure and thermodynamics from the first principles, with proper account of chemical specificities of both solvent and biomolecules, such as hydrogen bonding, hydrophobic interactions, salt bridges, etc. We test the method on the binding of seven biotin analogues to avidin in aqueous solution and show it to work well in predicting the ligand-binding affinities. We have compared the results of 3D-RISM-KH with four different generalized Born and two Poisson-Boltzmann methods. They give absolute binding energies that differ by up to 208 kJ/mol and mean absolute deviations in the relative affinities of 10-43 kJ/mol.
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Affiliation(s)
- Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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