1
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Nguyen H, Nguyen HL, Li MS. Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation. J Phys Chem B 2024; 128:7033-7042. [PMID: 39007765 DOI: 10.1021/acs.jpcb.4c01391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Experimental evidence has established that SARS-CoV-2 NSP1 acts as a factor that restricts cellular gene expression and impedes mRNA translation within the ribosome's 40S subunit. However, the precise molecular mechanisms underlying this phenomenon have remained elusive. To elucidate this issue, we employed a combination of all-atom steered molecular dynamics and coarse-grained alchemical simulations to explore the binding affinity of mRNA to the 40S ribosome, both in the presence and absence of SARS-CoV-2 NSP1. Our investigations revealed that the binding of SARS-CoV-2 NSP1 to the 40S ribosome leads to a significant enhancement in the binding affinity of mRNA. This observation, which aligns with experimental findings, strongly suggests that SARS-CoV-2 NSP1 has the capability to inhibit mRNA translation. Furthermore, we identified electrostatic interactions between mRNA and the 40S ribosome as the primary driving force behind mRNA translation. Notably, water molecules were found to play a pivotal role in stabilizing the mRNA-40S ribosome complex, underscoring their significance in this process. We successfully pinpointed the specific SARS-CoV-2 NSP1 residues that play a critical role in triggering the translation arrest.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang City 550000, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Quang Trung Software City, Life Science Lab, Institute for Computational Science and Technology, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam
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2
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Lagardère L, Maurin L, Adjoua O, El Hage K, Monmarché P, Piquemal JP, Hénin J. Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation. J Chem Theory Comput 2024; 20:4481-4498. [PMID: 38805379 DOI: 10.1021/acs.jctc.3c01249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
We introduce the lambda-Adaptive Biasing Force (lambda-ABF) method for the computation of alchemical free-energy differences. We propose a software implementation and showcase it on biomolecular systems. The method arises from coupling multiple-walker adaptive biasing force with λ-dynamics. The sampling of the alchemical variable is continuous and converges toward a uniform distribution, making manual optimization of the λ schedule unnecessary. Contrary to most other approaches, alchemical free-energy estimates are obtained immediately without any postprocessing. Free diffusion of λ improves orthogonal relaxation compared to fixed-λ thermodynamic integration or free-energy perturbation. Furthermore, multiple walkers provide generic orthogonal space coverage with minimal user input and negligible computational overhead. We show that our high-performance implementations coupling the Colvars library with NAMD and Tinker-HP can address real-world cases including ligand-receptor binding with both fixed-charge and polarizable models, with a demonstrably richer sampling than fixed-λ methods. The implementation is fully open-source, publicly available, and readily usable by practitioners of current alchemical methods. Thanks to the portable Colvars library, lambda-ABF presents a unified user interface regardless of the back-end (NAMD, Tinker-HP, or any software to be interfaced in the future), sparing users the effort of learning multiple interfaces. Finally, the Colvars Dashboard extension of the visual molecular dynamics (VMD) software provides an interactive monitoring and diagnostic tool for lambda-ABF simulations.
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Affiliation(s)
- Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, Institut Parisien de Chimie Physique et Théorique, FR2622 CNRS, 75005 Paris, France
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Lise Maurin
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, Laboratoire Jacques-Louis Lions, UMR 7589 CNRS, 75005 Paris, France
| | - Olivier Adjoua
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
| | - Krystel El Hage
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Pierre Monmarché
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, Laboratoire Jacques-Louis Lions, UMR 7589 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, Université Paris Cité, CNRS, UPR 9080, 75005 Paris, France
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3
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Nam K, Arattu Thodika AR, Grundström C, Sauer UH, Wolf-Watz M. Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. J Chem Inf Model 2024; 64:150-163. [PMID: 38117131 PMCID: PMC10778088 DOI: 10.1021/acs.jcim.3c01618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
This study explores ligand-driven conformational changes in adenylate kinase (AK), which is known for its open-to-close conformational transitions upon ligand binding and release. By utilizing string free energy simulations, we determine the free energy profiles for both enzyme opening and ligand release and compare them with profiles from the apoenzyme. Results reveal a three-step ligand release process, which initiates with the opening of the adenosine triphosphate-binding subdomain (ATP lid), followed by ligand release and concomitant opening of the adenosine monophosphate-binding subdomain (AMP lid). The ligands then transition to nonspecific positions before complete dissociation. In these processes, the first step is energetically driven by ATP lid opening, whereas the second step is driven by ATP release. In contrast, the AMP lid opening and its ligand release make minor contributions to the total free energy for enzyme opening. Regarding the ligand binding mechanism, our results suggest that AMP lid closure occurs via an induced-fit mechanism triggered by AMP binding, whereas ATP lid closure follows conformational selection. This difference in the closure mechanisms provides an explanation with implications for the debate on ligand-driven conformational changes of AK. Additionally, we determine an X-ray structure of an AK variant that exhibits significant rearrangements in the stacking of catalytic arginines, explaining its reduced catalytic activity. In the context of apoenzyme opening, the sequence of events is different. Here, the AMP lid opens first while the ATP lid remains closed, and the free energy associated with ATP lid opening varies with orientation, aligning with the reported AK opening and closing rate heterogeneity. Finally, this study, in conjunction with our previous research, provides a comprehensive view of the intricate interplay between various structural elements, ligands, and catalytic residues that collectively contribute to the robust catalytic power of the enzyme.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Abdul Raafik Arattu Thodika
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | | | - Uwe H. Sauer
- Department
of Chemistry, Umeå University, Umeå 90187, SE, Sweden
| | - Magnus Wolf-Watz
- Department
of Chemistry, Umeå University, Umeå 90187, SE, Sweden
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4
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Nam K, Tao Y, Ovchinnikov V. Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway. J Phys Chem B 2023; 127:5789-5798. [PMID: 37363953 PMCID: PMC10332359 DOI: 10.1021/acs.jpcb.3c01804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/22/2023] [Indexed: 06/28/2023]
Abstract
Modulating the transitions between active and inactive conformations of protein kinases is the primary means of regulating their catalytic activity, achieved by phosphorylation of the activation loop (A-loop). To elucidate the mechanism of this conformational activation, we applied the string method to determine the conformational transition path of insulin receptor kinase between the active and inactive conformations and the corresponding free-energy profiles with and without A-loop phosphorylation. The conformational change was found to proceed in three sequential steps: first, the flipping of the DFG motif of the active site; second, rotation of the A-loop; finally, the inward movement of the αC helix. The main energetic bottleneck corresponds to the conformational change in the A-loop, while changes in the DFG motif and αC helix occur before and after A-loop conformational change, respectively. In accordance with this, two intermediate states are identified, the first state just after the DFG flipping and the second state after the A-loop rotation. These intermediates exhibit structural features characteristic of the corresponding inactive and active conformations of other protein kinases. To understand the impact of A-loop phosphorylation on kinase conformation, the free energies of A-loop phosphorylation were determined at several states along the conformational transition path using the free-energy perturbation simulations. The calculated free energies reveal that while the unphosphorylated kinase interconverts between the inactive and active conformations, A-loop phosphorylation restricts access to the inactive conformation, thereby increasing the active conformation population. Overall, this study suggests a consensus mechanism of conformational activation between different protein kinases.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yunwen Tao
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Victor Ovchinnikov
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
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5
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Yu Y, Wang Z, Wang L, Wang Q, Tang R, Xiang S, Deng Q, Hou T, Sun H. Deciphering the Shared and Specific Drug Resistance Mechanisms of Anaplastic Lymphoma Kinase via Binding Free Energy Computation. RESEARCH (WASHINGTON, D.C.) 2023; 6:0170. [PMID: 37342628 PMCID: PMC10278961 DOI: 10.34133/research.0170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023]
Abstract
Anaplastic lymphoma kinase (ALK), a tyrosine receptor kinase, has been proven to be associated with the occurrence of numerous malignancies. Although there have been already at least 3 generations of ALK inhibitors approved by FDA or in clinical trials, the occurrence of various mutations seriously attenuates the effectiveness of the drugs. Unfortunately, most of the drug resistance mechanisms still remain obscure. Therefore, it is necessary to reveal the bottom reasons of the drug resistance mechanisms caused by the mutations. In this work, on the basis of verifying the accuracy of 2 main kinds of binding free energy calculation methodologies [end-point method of Molecular Mechanics with Poisson-Boltzmann/Generalized Born and Surface Area (MM/PB(GB)SA) and alchemical method of Thermodynamic Integration (TI)], we performed a systematic analysis on the ALK systems to explore the underlying shared and specific drug resistance mechanisms, covering the one-drug-multiple-mutation and multiple-drug-one-mutation cases. Through conventional molecular dynamics (cMD) simulation in conjunction with MM/PB(GB)SA and umbrella sampling (US) in conjunction with contact network analysis (CNA), the resistance mechanisms of the in-pocket, out-pocket, and multiple-site mutations were revealed. Especially for the out-pocket mutation, a possible transfer chain of the mutation effect was revealed, and the reason why different drugs exhibited various sensitivities to the same mutation was also uncovered. The proposed mechanisms may be prevalent in various drug resistance cases.
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Affiliation(s)
- Yang Yu
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine ofZhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Lingling Wang
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Qinghua Wang
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Rongfan Tang
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Sutong Xiang
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Qirui Deng
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine ofZhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Huiyong Sun
- Department of Medicinal Chemistry,
China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
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6
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Jorge M, Barrera MC, Milne AW, Ringrose C, Cole DJ. What is the Optimal Dipole Moment for Nonpolarizable Models of Liquids? J Chem Theory Comput 2023; 19:1790-1804. [PMID: 36827585 DOI: 10.1021/acs.jctc.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
In classical nonpolarizable models, electrostatic interactions are usually described by assigning fixed partial charges to interaction sites. Despite the multitude of methods and theories proposed over the years for partial charge assignment, a fundamental question remains─what is the correct degree of polarization that a fixed-charge model should possess to provide the best balance of interactions (including induction effects) and yield the best description of the potential energy surface of a liquid phase? We address this question by approaching it from two separate and independent viewpoints: the QUantum mechanical BEspoke (QUBE) approach, which assigns bespoke force field parameters for individual molecules from ab initio calculations with minimal empirical fitting, and the Polarization-Consistent Approach (PolCA) force field, based on empirical fitting of force field parameters with an emphasis on transferability by rigorously accounting for polarization effects in the parameterization process. We show that the two approaches yield consistent answers to the above question, namely, that the dipole moment of the model should be approximately halfway between those of the gas and the liquid phase. Crucially, however, the reference liquid-phase dipole needs to be estimated using methods that explicitly consider both mean-field and local contributions to polarization. In particular, continuum dielectric models are inadequate for this purpose because they cannot account for local effects and therefore significantly underestimate the degree of polarization of the molecule. These observations have profound consequences for the development, validation, and testing of nonpolarizable models.
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Affiliation(s)
- Miguel Jorge
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Maria Cecilia Barrera
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral St, Glasgow G4 0RE, United Kingdom
| | - Andrew W Milne
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Chris Ringrose
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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7
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Sun Y, He X, Hou T, Cai L, Man VH, Wang J. Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method. J Comput Chem 2023; 44:1334-1346. [PMID: 36807356 DOI: 10.1002/jcc.27089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/22/2022] [Accepted: 01/29/2023] [Indexed: 02/23/2023]
Abstract
Accurate estimation of solvation free energy (SFE) lays the foundation for accurate prediction of binding free energy. The Poisson-Boltzmann (PB) or generalized Born (GB) combined with surface area (SA) continuum solvation method (PBSA and GBSA) have been widely used in SFE calculations because they can achieve good balance between accuracy and efficiency. However, the accuracy of these methods can be affected by several factors such as the charge models, polar and nonpolar SFE calculation methods and the atom radii used in the calculation. In this work, the performance of the ABCG2 (AM1-BCC-GAFF2) charge model as well as other two charge models, that is, RESP (Restrained Electrostatic Potential) and AM1-BCC (Austin Model 1-bond charge corrections), on the SFE prediction of 544 small molecules in water by PBSA/GBSA was evaluated. In order to improve the performance of the PBSA prediction based on the ABCG2 charge, we further explored the influence of atom radii on the prediction accuracy and yielded a set of atom radius parameters for more accurate SFE prediction using PBSA based on the ABCG2/GAFF2 by reproducing the thermodynamic integration (TI) calculation results. The PB radius parameters of carbon, oxygen, sulfur, phosphorus, chloride, bromide and iodine, were adjusted. New atom types, on, oi, hn1, hn2, hn3, were introduced to further improve the fitting performance. Then, we tuned the parameters in the nonpolar SFE model using the experimental SFE data and the PB calculation results. By adopting the new radius parameters and new nonpolar SFE model, the root mean square error (RMSE) of the SFE calculation for the 544 molecules decreased from 2.38 to 1.05 kcal/mol. Finally, the new radius parameters were applied in the prediction of protein-ligand binding free energies using the MM-PBSA method. For the eight systems tested, we could observe higher correlation between the experiment data and calculation results and smaller prediction errors for the absolute binding free energies, demonstrating that our new radius parameters can improve the free energy calculation using the MM-PBSA method.
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Affiliation(s)
- Yuchen Sun
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lianjin Cai
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Viet Hoag Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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8
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At least three xenon binding sites in the glycine binding domain of the N-methyl D-aspartate receptor. Arch Biochem Biophys 2022; 724:109265. [DOI: 10.1016/j.abb.2022.109265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022]
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9
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Golubev VA, Gurina DL. Dissolving power of the binary solvent carbon tetrachloride – methanol. Solubility of caffeine: Experiment, ASL model, and MD simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Petrov D. Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder. J Chem Inf Model 2021; 61:4382-4390. [PMID: 34415755 PMCID: PMC8479811 DOI: 10.1021/acs.jcim.1c00428] [Citation(s) in RCA: 10] [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: 04/15/2021] [Indexed: 11/30/2022]
Abstract
Free-energy calculations play an important role in the application of computational chemistry to a range of fields, including protein biochemistry, rational drug design, or materials science. Importantly, the free-energy difference is directly related to experimentally measurable quantities such as partition and adsorption coefficients, water activity, and binding affinities. Among several techniques aimed at predicting free-energy differences, perturbation approaches, involving the alchemical transformation of one molecule into another through intermediate states, stand out as rigorous methods based on statistical mechanics. However, despite the importance of free-energy calculations, the applicability of the perturbation approaches is still largely impeded by a number of challenges, including the definition of the perturbation path, i.e., alchemical changes leading to the transformation of one molecule to the other. To address this, an automatic perturbation topology builder based on a graph-matching algorithm is developed, which can identify the maximum common substructure (MCS) of two or multiple molecules and provide the perturbation topologies suitable for free-energy calculations using the GROMOS and the GROMACS simulation packages. Various MCS search options are presented leading to alternative definitions of the perturbation pathway. Moreover, perturbation topologies generated using the default multistate MCS search are used to calculate the changes in free energy between lysine and its two post-translational modifications, 3-methyllysine and acetyllysine. The pairwise free-energy calculations performed on this test system led to a cycle closure of 0.5 ± 0.3 and 0.2 ± 0.2 kJ mol-1, with GROMOS and GROMACS simulation packages, respectively. The same relative free energies between the three states are obtained by employing the enveloping distribution sampling (EDS) approach when compared to the pairwise perturbations. Importantly, this toolkit is made available online as an open-source Python package (https://github.com/drazen-petrov/SMArt).
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Affiliation(s)
- Drazen Petrov
- Department of Material Sciences
and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences
Vienna, Muthgasse 18, A-1190 Vienna, Austria
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11
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King E, Aitchison E, Li H, Luo R. Recent Developments in Free Energy Calculations for Drug Discovery. Front Mol Biosci 2021; 8:712085. [PMID: 34458321 PMCID: PMC8387144 DOI: 10.3389/fmolb.2021.712085] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/27/2021] [Indexed: 01/11/2023] Open
Abstract
The grand challenge in structure-based drug design is achieving accurate prediction of binding free energies. Molecular dynamics (MD) simulations enable modeling of conformational changes critical to the binding process, leading to calculation of thermodynamic quantities involved in estimation of binding affinities. With recent advancements in computing capability and predictive accuracy, MD based virtual screening has progressed from the domain of theoretical attempts to real application in drug development. Approaches including the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA), Linear Interaction Energy (LIE), and alchemical methods have been broadly applied to model molecular recognition for drug discovery and lead optimization. Here we review the varied methodology of these approaches, developments enhancing simulation efficiency and reliability, remaining challenges hindering predictive performance, and applications to problems in the fields of medicine and biochemistry.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, United States
- Department of Materials Science and Engineering, University of California, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
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12
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Kashefolgheta S, Wang S, Acree WE, Hünenberger PH. Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free energies. Phys Chem Chem Phys 2021; 23:13055-13074. [PMID: 34105547 PMCID: PMC8207520 DOI: 10.1039/d1cp00215e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/28/2021] [Indexed: 12/02/2022]
Abstract
Experimental solvation free energies are nowadays commonly included as target properties in the validation of condensed-phase force fields, sometimes even in their calibration. In a previous article [Kashefolgheta et al., J. Chem. Theory. Comput., 2020, 16, 7556-7580], we showed how the involved comparison between experimental and simulation results could be made more systematic by considering a full matrix of cross-solvation free energies . For a set of N molecules that are all in the liquid state under ambient conditions, such a matrix encompasses N×N entries for considering each of the N molecules either as solute (A) or as solvent (B). In the quoted study, a cross-solvation matrix of 25 × 25 experimental value was introduced, considering 25 small molecules representative for alkanes, chloroalkanes, ethers, ketones, esters, alcohols, amines, and amides. This experimental data was used to compare the relative accuracies of four popular condensed-phase force fields, namely GROMOS-2016H66, OPLS-AA, AMBER-GAFF, and CHARMM-CGenFF. In the present work, the comparison is extended to five additional force fields, namely GROMOS-54A7, GROMOS-ATB, OPLS-LBCC, AMBER-GAFF2, and OpenFF. Considering these nine force fields, the correlation coefficients between experimental values and simulation results range from 0.76 to 0.88, the root-mean-square errors (RMSEs) from 2.9 to 4.8 kJ mol-1, and average errors (AVEEs) from -1.5 to +1.0 kJ mol-1. In terms of RMSEs, GROMOS-2016H66 and OPLS-AA present the best accuracy (2.9 kJ mol-1), followed by OPLS-LBCC, AMBER-GAFF2, AMBER-GAFF, and OpenFF (3.3 to 3.6 kJ mol-1), and then by GROMOS-54A7, CHARM-CGenFF, and GROMOS-ATB (4.0 to 4.8 kJ mol-1). These differences are statistically significant but not very pronounced, and are distributed rather heterogeneously over the set of compounds within the different force fields.
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Affiliation(s)
- Sadra Kashefolgheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 55 03
| | - Shuzhe Wang
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 55 03
| | - William E. Acree
- Department of Chemistry, University of North Texas1155 Union Circle Drive #305070DentonTexas 76203USA
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 55 03
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13
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Giese TJ, York DM. Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints. J Chem Theory Comput 2021; 17:1326-1336. [PMID: 33528251 PMCID: PMC8011336 DOI: 10.1021/acs.jctc.0c01219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We describe an efficient method for the simultaneous solution of all free energies within a relative binding free-energy (RBFE) network with cycle closure and experimental/reference constraint conditions using Bennett Acceptance Ratio (BAR) and Multistate BAR (MBAR) analysis. Rather than solving the BAR or MBAR equations for each transformation independently, the simultaneous solution of all transformations are obtained by performing a constrained minimization of a global objective function. The nonlinear optimization of the objective function is subjected to affine linear constraints that couple the free energies between the network edges. The constraints are used to enforce the closure of thermodynamic cycles within the RBFE network, and to enforce an additional set of linear constraint conditions demonstrated here to be subsets of (1 or 2) experimental values. We describe details of the practical implementation of the network BAR/MBAR procedure, including use of generalized coordinates in the minimization of the free-energy objective function, propagation of bootstrap errors from those coordinates, and performance and memory optimization. In some cases it is found that use of restraints in the optimization is more practical than use of generalized coordinates for enforcing constraint conditions. The fast BARnet and MBARnet methods are used to analyze the RBFEs of six prototypical protein-ligand systems, and it is shown that enforcement of cycle closure conditions reduces the error in the predictions only modestly, and further reduction in errors can be achieved when one or two experimental RBFEs are included in the optimization procedure. These methods have been implemented into FE-ToolKit, a new free-energy analysis toolkit. The BARnet/MBARnet framework presented here opens the door to new, more efficient and robust free-energy analysis with enhanced predictive capability for drug discovery applications.
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Affiliation(s)
- Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087 USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087 USA
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14
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Lee TS, Allen BK, Giese TJ, Guo Z, Li P, Lin C, McGee TD, Pearlman DA, Radak BK, Tao Y, Tsai HC, Xu H, Sherman W, York DM. Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. J Chem Inf Model 2020; 60:5595-5623. [PMID: 32936637 PMCID: PMC7686026 DOI: 10.1021/acs.jcim.0c00613] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Predicting protein-ligand binding affinities and the associated thermodynamics of biomolecular recognition is a primary objective of structure-based drug design. Alchemical free energy simulations offer a highly accurate and computationally efficient route to achieving this goal. While the AMBER molecular dynamics package has successfully been used for alchemical free energy simulations in academic research groups for decades, widespread impact in industrial drug discovery settings has been minimal because of the previous limitations within the AMBER alchemical code, coupled with challenges in system setup and postprocessing workflows. Through a close academia-industry collaboration we have addressed many of the previous limitations with an aim to improve accuracy, efficiency, and robustness of alchemical binding free energy simulations in industrial drug discovery applications. Here, we highlight some of the recent advances in AMBER20 with a focus on alchemical binding free energy (BFE) calculations, which are less computationally intensive than alternative binding free energy methods where full binding/unbinding paths are explored. In addition to scientific and technical advances in AMBER20, we also describe the essential practical aspects associated with running relative alchemical BFE calculations, along with recommendations for best practices, highlighting the importance not only of the alchemical simulation code but also the auxiliary functionalities and expertise required to obtain accurate and reliable results. This work is intended to provide a contemporary overview of the scientific, technical, and practical issues associated with running relative BFE simulations in AMBER20, with a focus on real-world drug discovery applications.
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Affiliation(s)
- Tai-Sung Lee
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
| | - Bryce K. Allen
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Timothy J. Giese
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
| | - Zhenyu Guo
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Pengfei Li
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Charles Lin
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - T. Dwight McGee
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - David A. Pearlman
- QSimulate Incorporated, Cambridge, Massachusetts 02139, United States
| | - Brian K. Radak
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Yujun Tao
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
| | - Hsu-Chun Tsai
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
| | - Huafeng Xu
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Woody Sherman
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Darrin M. York
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
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15
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Ishak MAI, Jumbri K, Daud S, Abdul Rahman MB, Abdul Wahab R, Yamagishi H, Yamamoto Y. Molecular simulation on the stability and adsorption properties of choline-based ionic liquids/IRMOF-1 hybrid composite for selective H 2S/CO 2 capture. JOURNAL OF HAZARDOUS MATERIALS 2020; 399:123008. [PMID: 32502857 DOI: 10.1016/j.jhazmat.2020.123008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
The compatibility and performance of an Isoreticular Metal-Organic Frameworks (IRMOF-1) impregnated with choline-based ionic liquids (ILs) for selective adsorption of H2S/CO2, were studied by molecular dynamics (MD) simulation. Cholinium alanate ([Chl][Ala]) was nominated as the suitable IL for impregnation into IRMOF-1, consistent with the low RMSD values (0.546 nm, 0.670 nm, 0.776 nm) at three IL/IRMOF-1 w/w ratios (WIL/IRMOF-1 = 0.4, 0.8, and 1.2). The [Chl]+ and [Ala]- ion pair was located preferentially around the carboxylate group within the IRMOF-1 framework, with the latter interacting strongly with the host than the [Chl]+. Results of radius of gyration (Rg) and root mean square displacement (RMSD) revealed that a ratio of 0.4 w/w of IL/IRMOF-1 (Rg = 1.405 nm; RMSD = 0.546 nm) gave the best conformation to afford an exceptionally stable IL/IRMOF-1 composite. It was discovered that the IL/IRMOF-1 composite was more effective in capturing H2S and CO2 compared to pristine IRMOF-1. The gases adsorbed in higher quantities in the IL/IRMOF-1 composite phase compared to the bulk phase, with a preferential adsorption for H2S, as shown by the uppermost values of adsorption ( [Formula: see text] = 17.954 mol L-1 bar-1) and an adsorption selectivity ( [Formula: see text] = 43.159) at 35 IL loading.
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Affiliation(s)
- Mohd Adil Iman Ishak
- Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS, 32610, Bandar Seri Iskandar, Perak, Malaysia
| | - Khairulazhar Jumbri
- Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS, 32610, Bandar Seri Iskandar, Perak, Malaysia; Centre of Research in Ionic Liquids (CORIL), Universiti Teknologi PETRONAS, 32610 Bandar Seri Iskandar, Perak, Malaysia.
| | - Shaari Daud
- Faculty of Applied Sciences, Universiti Teknologi MARA, Bandar Jengka, 26400, Bandar Tun Razak, Pahang, Malaysia
| | | | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, UTM Johor Bahru, Johor, Malaysia
| | - Hiroshi Yamagishi
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan
| | - Yohei Yamamoto
- Division of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan
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16
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König G, Glaser N, Schroeder B, Kubincová A, Hünenberger PH, Riniker S. An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. J Chem Inf Model 2020; 60:5407-5423. [PMID: 32794763 DOI: 10.1021/acs.jcim.0c00520] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Alchemical free energy calculations typically rely on intermediate states to bridge between the relevant phase spaces of the two end states. These intermediate states are usually created by mixing the energies or parameters of the end states according to a coupling parameter λ. The choice of the procedure has a strong impact on the efficiency of the calculation, as it affects both the encountered energy barriers and the phase space overlap between the states. The present work builds on the connection between the minimum variance pathway (MVP) and enveloping distribution sampling (EDS). It is shown that both methods can be regarded as special cases of a common scheme referred to as λ-EDS, which can also reproduce the behavior of conventional λ-intermediate states. A particularly attractive feature of λ-EDS is its ability to emulate the use of soft core potentials (SCP) while avoiding the associated computational overhead when applying efficient free energy estimators such as the multistate Bennett's acceptance ratio (MBAR). The method is illustrated for both relative and absolute free energy calculations considering five benchmark systems. The first two systems (charge inversion and cavity creation in a dipolar solvent) demonstrate the use of λ-EDS as an alternative coupling scheme in the context of thermodynamic integration (TI). The three other systems (change of bond length, change of dihedral angles, and cavity creation in water) investigate the efficiency and optimal choice of parameters in the context of free energy perturbation (FEP) and Bennett's acceptance ratio (BAR). It is shown that λ-EDS allows larger steps along the alchemical pathway than conventional intermediate states.
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Affiliation(s)
- Gerhard König
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Nina Glaser
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Benjamin Schroeder
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Alžbeta Kubincová
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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17
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Petrov D, Tunega D, Gerzabek MH, Oostenbrink C. Molecular modelling of sorption processes of a range of diverse small organic molecules in Leonardite humic acid. EUROPEAN JOURNAL OF SOIL SCIENCE 2020; 71:831-844. [PMID: 33041627 PMCID: PMC7540484 DOI: 10.1111/ejss.12868] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 05/08/2023]
Abstract
Soil organic matter (SOM) is abundant in the environment and plays an important role in several biogeochemical processes, including microbial activity, soil aggregation, plant growth and carbon storage. One of its key functions is the retention and release of various chemical compounds, primarily governed by the sorption process, which strongly affects the environmental fate of nutrients and pollutants. Sorption largely depends on the composition of SOM, as well as its structure, dynamics and the thermodynamic conditions. Although several approaches are available, experimental characterization of sorption mechanisms is not easy. Computational models for predicting sorption coefficients often require a wealth of experimental data for training and are only applicable to compounds and conditions related to the training dataset. Here, we use molecular dynamics (MD) simulations to study the sorption of a range of small organic compounds. As a model SOM system we use the standard Leonardite humic acid (LHA) sample, which physicochemical properties have recently been characterized computationally in detail. This model allowed us to estimate sorption propensities of the systems at two different hydration levels (water activities close to 0 and 1), showing a remarkable correlation with experimental data. Importantly, this molecular modelling approach based on perturbation free-energy calculations is rigorously derived from statistical thermodynamics and requires no experimental sorption data for training. It is therefore in principle applicable to any SOM model or thermodynamic condition. Moreover, the power of MD simulations to provide high-resolution insight into atomistic and molecular interactions was employed to explore how sorbate molecules associate with the LHA matrix and which contacts they form. The heteroatoms of both sorbate and sorbent play an important role and water molecules are identified as further key players in facilitating the sorption process. HIGHLIGHTS Modelling of the sorption processes in soil organic matter at atomistic level.Rigorous, physics-based approach applicable to a range of SOM systems and conditions.Remarkable level of matching with experimental data with additional insight into the molecular mechanism.Interactions between the sorbate and local environment strongly affects the sorption process.
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Affiliation(s)
- Drazen Petrov
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
| | - Daniel Tunega
- Department of Forest and Soil SciencesInstitute of Soil Research, University of Natural Resources and Life Sciences ViennaViennaAustria
- School of Pharmaceutical Science and Technology, Tianjin UniversityTianjinPeople's Republic of China
| | - Martin H. Gerzabek
- Department of Forest and Soil SciencesInstitute of Soil Research, University of Natural Resources and Life Sciences ViennaViennaAustria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life Sciences ViennaViennaAustria
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18
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Ito S, Cui Q. Multi-level free energy simulation with a staged transformation approach. J Chem Phys 2020; 153:044115. [PMID: 32752685 DOI: 10.1063/5.0012494] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Combining multiple levels of theory in free energy simulations to balance computational accuracy and efficiency is a promising approach for studying processes in the condensed phase. While the basic idea has been proposed and explored for quite some time, it remains challenging to achieve convergence for such multi-level free energy simulations as it requires a favorable distribution overlap between different levels of theory. Previous efforts focused on improving the distribution overlap by either altering the low-level of theory for the specific system of interest or ignoring certain degrees of freedom. Here, we propose an alternative strategy that first identifies the degrees of freedom that lead to gaps in the distributions of different levels of theory and then treats them separately with either constraints or restraints or by introducing an intermediate model that better connects the low and high levels of theory. As a result, the conversion from the low level to the high level model is done in a staged fashion that ensures a favorable distribution overlap along the way. Free energy components associated with different steps are mostly evaluated explicitly, and thus, the final result can be meaningfully compared to the rigorous free energy difference between the two levels of theory with limited and well-defined approximations. The additional free energy component calculations involve simulations at the low level of theory and therefore do not incur high computational costs. The approach is illustrated with two simple but non-trivial solution examples, and factors that dictate the reliability of the result are discussed.
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Affiliation(s)
- Shingo Ito
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
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19
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Li Y, Nam K. Repulsive Soft-Core Potentials for Efficient Alchemical Free Energy Calculations. J Chem Theory Comput 2020; 16:4776-4789. [PMID: 32559374 DOI: 10.1021/acs.jctc.0c00163] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In alchemical free energy (FE) simulations, annihilation and creation of atoms are generally achieved with the soft-core potential that shifts the interparticle separations. While this soft-core potential eliminates the numerical instability occurring near the two end states of the transformation, it makes the hybrid Hamiltonian vary nonlinearly with respect to the parameter λ, which interpolates between the Hamiltonians representing the two end states. This complicates FE estimation by Bennett acceptance ratio (BAR), free energy perturbation (FEP), and thermodynamic integration (TI) methods, thus reducing their calculation efficiency. In this work, we develop a new type of repulsive soft-core potential, called Gaussian soft-core (GSC) potential, with two parameters controlling its maximum and width. The main advantage of this potential is the linearity of the hybrid Hamiltonian with respect to λ, thus permitting the direct application of BAR, FEP, TI, and other variant FE methods. The accuracy and efficiency of the GSC potential are demonstrated by comparing the free energies of annihilation determined for 13 small molecules and an alchemical mutation of a protein side chain. In addition, in combination with a TI integrand (∂H/∂λ) estimation strategy, we show that GSC can considerably reduce the number of λ simulations compared to the commonly used separation-shifted soft-core potential.
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Affiliation(s)
- Yaozong Li
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.,Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Kwangho Nam
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.,Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019-0065, United States
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20
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Evaluating the Performance of a Non-Bonded Cu 2+ Model Including Jahn-Teller Effect into the Binding of Tyrosinase Inhibitors. Int J Mol Sci 2020; 21:ijms21134783. [PMID: 32640730 PMCID: PMC7369908 DOI: 10.3390/ijms21134783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 02/08/2023] Open
Abstract
Tyrosinase (TYR) is a metalloenzyme classified as a type-3 copper protein, which is involved in the synthesis of melanin through a catalytic process beginning with the conversion of the amino acid l-Tyrosine (l-Tyr) to l-3,4-dihydroxyphenylalanine (l-DOPA). It plays an important role in the mechanism of melanogenesis in various organisms including mammals, plants, and fungi. Herein, we used a combination of computational molecular modeling techniques including molecular dynamic (MD) simulations and the linear interaction energy (LIE) model to evaluate the binding free energy of a set of analogs of kojic acid (KA) in complex with TYR. For the MD simulations, we used a dummy model including the description of the Jahn–Teller effect for Cu2+ ions in the active site of this enzyme. Our results show that the LIE model predicts the TYR binding affinities of the inhibitor in close agreement to experimental results. Overall, we demonstrate that the classical model provides a suitable description of the main interactions between analogs of KA and Cu2+ ions in the active site of TYR.
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21
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Lavino AD, Carbone P, Marchisio D. MARTINI
coarse‐grained model for poly‐ε‐caprolactone in acetone‐water mixtures. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Alessio D. Lavino
- Department of Applied Science and TechnologyPolitecnico di Torino Torino Italy
| | - Paola Carbone
- School of Chemical Engineering & Analytical ScienceThe University of Manchester Manchester UK
| | - Daniele Marchisio
- Department of Applied Science and TechnologyPolitecnico di Torino Torino Italy
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22
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Choline-Based Ionic Liquids-Incorporated IRMOF-1 for H2S/CH4 Capture: Insight from Molecular Dynamics Simulation. Processes (Basel) 2020. [DOI: 10.3390/pr8040412] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The removal of H2S and CH4 from natural gas is crucial as H2S causes environmental contamination, corrodes the gas stream pipelines, and decreases the feedstock for industrial productions. Many scientific researches have shown that the metal-organic framework (MOF)/ionic liquids (ILs) have great potential as alternative adsorbents to capture H2S. In this work, molecular dynamics (MD) simulation was carried out to determine the stability of ILs/IRMOF-1 as well as to study the solubility of H2S and CH4 gases in this ILs/IRMOF-1 hybrid material. Three choline-based ILs were incorporated into IRMOF-1 with different ratios of 0.4, 0.8, and 1.2% w/w, respectively, in which the most stable choline-based ILs/IRMOF-1 composite was analysed for H2S/CH4 solubility selectivity. Among the three choline-based ILs/IRMOF-1, [Chl] [SCN]/IRMOF-1 shows the most stable incorporation. However, the increment of ILs loaded in the IRMOF-1 significantly reduced the stability of the hybrid due to the crowding effect. Solvation free energy was then computed to determine the solubility of H2S and CH4 in the [Chl] [SCN]/IRMOF-1. H2S showed higher solubility compared to CH4, where its solubility declined with the increase of choline-based IL loading.
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23
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Barrera M, Jorge M. A Polarization-Consistent Model for Alcohols to Predict Solvation Free Energies. J Chem Inf Model 2020; 60:1352-1367. [PMID: 31977210 PMCID: PMC7145284 DOI: 10.1021/acs.jcim.9b01005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Indexed: 11/28/2022]
Abstract
Classical nonpolarizable models, normally based on a combination of Lennard-Jones sites and point charges, are extensively used to model thermodynamic properties of fluids, including solvation. An important shortcoming of these models is that they do not explicitly account for polarization effects, i.e., a description of how the electron density responds to changes in the molecular environment. Instead, polarization is implicitly included, in a mean-field sense, into the parameters of the model, usually by fitting to pure liquid properties (e.g., density). This causes problems when trying to describe thermodynamic properties that involve a change of phase (e.g., enthalpy of vaporization), that directly depend on the electronic response of the medium (e.g., dielectric constant), and that require mixing or solvation in different media (e.g., solvation free energies). Fully polarizable models present a natural route for addressing these limitations but at the price of a much higher computational cost. In this work, we combine the best of those two approaches by running fast simulations using nonpolarizable models and applying post facto corrections to the computed properties in order to account for the effects of polarization. By applying this new paradigm, a new united-atom force field for alcohols is developed that is able to predict both pure liquid properties, including dielectric constant, and solvation free energies in different solvents with a high degree of accuracy. This paves the way for the development of a generic classical nonpolarizable force field that can predict solvation of drug-like molecules in a variety of solvents.
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Affiliation(s)
- Maria
Cecilia Barrera
- Department of Chemical and
Process Engineering, University of Strathclyde, Glasgow G1 1XJ, United Kingdom
| | - Miguel Jorge
- Department of Chemical and
Process Engineering, University of Strathclyde, Glasgow G1 1XJ, United Kingdom
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24
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Mirabzadeh CA, Ytreberg FM. Implementation of adaptive integration method for free energy calculations in molecular systems. PeerJ Comput Sci 2020; 6:e264. [PMID: 33457645 PMCID: PMC7808261 DOI: 10.7717/peerj-cs.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/10/2020] [Indexed: 11/20/2022]
Abstract
Estimating free energy differences by computer simulation is useful for a wide variety of applications such as virtual screening for drug design and for understanding how amino acid mutations modify protein interactions. However, calculating free energy differences remains challenging and often requires extensive trial and error and very long simulation times in order to achieve converged results. Here, we present an implementation of the adaptive integration method (AIM). We tested our implementation on two molecular systems and compared results from AIM to those from a suite of other methods. The model systems tested here include calculating the solvation free energy of methane, and the free energy of mutating the peptide GAG to GVG. We show that AIM is more efficient than other tested methods for these systems, that is, AIM results converge to a higher level of accuracy and precision for a given simulation time.
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Affiliation(s)
| | - F. Marty Ytreberg
- Department of Physics, University of Idaho, Moscow, ID, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States of America
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25
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Rondina GG, Böhm MC, Müller-Plathe F. Predicting the Mobility Increase of Coarse-Grained Polymer Models from Excess Entropy Differences. J Chem Theory Comput 2020; 16:1431-1447. [DOI: 10.1021/acs.jctc.9b01088] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gustavo G. Rondina
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - Michael C. Böhm
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 8, 64287 Darmstadt, Germany
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26
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Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies. J Comput Aided Mol Des 2019; 34:71-82. [PMID: 31781991 DOI: 10.1007/s10822-019-00261-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
Abstract
Accurate solvation free energy ΔGsolv predictions require well parametrized force fields. In order to refit Lennard-Jones (LJ) parameters for improved ΔGsolv predictions for a variety of compound classes and chemical environments, a large number of ΔGsolv calculations is required. As the calculation of ΔGsolv is computational expensive, there is need for efficient but precise calculation methods. In this work, we focus on the computation of non-aqueous solvation free energies. We compare ΔGsolv results from highly precise reference simulations for transferring a solute from the vacuum into a condensed phase and results obtained from a thermodynamic cycle implementation. As test systems, we alter LJ parameters ε and σ of widely used GAFF atom types ca, cl, n1, oh and os in various solute/solvent combinations. We examine the degree of configurational space overlap and find an impact by hydrogen bonds and the solvent accessible surface area. We conclude that the application of a thermodynamic cycle for the parametrization of force fields targeting ΔGsolv is useful if the adaptation of LJ parameters is limited to atom types in the solute or if only ε is changed.
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27
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Theiss M, van Westen T, Gross J. An equation of state for Stockmayer fluids based on a perturbation theory for dipolar hard spheres. J Chem Phys 2019; 151:104102. [PMID: 31521101 DOI: 10.1063/1.5116912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We develop a perturbation theory for the difference between the Helmholtz energy of a Stockmayer fluid, i.e., a fluid interacting by a Lennard-Jones plus point-dipole potential, and a Lennard-Jones fluid. We show that the difference can be approximated by the perturbational Helmholtz energy contribution of a dipolar hard-sphere fluid with a suitably chosen effective hard-sphere diameter, relative to a hard-sphere fluid with the same effective diameter. We analyze both a third and fourth order perturbation theory, both written as Padé approximations. Several recipes for calculating the hard-sphere diameter are investigated; we find that the Weeks-Chandler-Andersen diameter is most suitable. Results of the perturbation theory are shown to be in good agreement with reference data for the Helmholtz energy, internal energy, and isochoric heat capacity as obtained from molecular simulations performed in this work and to vapor-liquid equilibrium data from the literature. Theoretical predictions of the proposed model are compared to results from the perturbation theory of Gubbins and Twu [Chem. Eng. Sci. 33, 863 (1978)], which is a theory based on a Lennard-Jones reference fluid. We find the theories are in good agreement. Our approach can easily be applied to van der Waals potentials, other than Lennard-Jones potentials. If a dipolar Mie fluid is considered, the approach merely requires calculation of the effective hard-sphere diameter for a Mie potential. We further note that the approach has a reduction in the variable space of the underlying correlation integrals, i.e., the correlation functions of a hard-sphere fluid depend on density only, whereas the Lennard-Jones reference correlation functions depend on density and temperature.
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Affiliation(s)
- Marc Theiss
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Thijs van Westen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
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28
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Abstract
In practical free energy estimation, the bias is often neglected once it has been shown to vanish in the large-sample limit. Yet finite-sample bias always exists and ought to be considered in any rigorous study. This work develops a metric for bias in a broad class of free energy "bridge estimators" (e.g., Bennett's method). The framework complements existing variance estimation methods and provides a means for comparing systematic and statistical errors. Examples show that, contrary to what is often assumed, the bias can be quite substantial when the sample size is modest.
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Affiliation(s)
- Brian K Radak
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801-2325, USA
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29
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Peters LDM, Dietschreit JCB, Kussmann J, Ochsenfeld C. Calculating free energies from the vibrational density of states function: Validation and critical assessment. J Chem Phys 2019; 150:194111. [DOI: 10.1063/1.5079643] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Laurens D. M. Peters
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
| | - Johannes C. B. Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5–13, D-81377 München, Germany
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30
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Taddese T, Kitabata M, Okazaki S. All-atom molecular dynamics study on the non-solvent induced phase separation: Thermodynamics of adding water to poly(vinylidene fluoride)/N-methyl-2-pyrrolidone solution. J Chem Phys 2019; 150:184505. [PMID: 31091903 DOI: 10.1063/1.5094088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The change in the thermodynamics when adding water in poly(vinylidene fluoride) (PVDF)/N-methyl-2-pyrrolidone (NMP) solution is studied from all atom molecular dynamics (MD) simulations. This is done by estimating the free energy of mixing of PVDF/NMP solution with increasing volume fraction of water (ϕw) using an appropriately chosen thermodynamic cycle and the Bennett acceptance ratio method. The MD calculations predict the thermodynamic phase separation point of water/NMP/PVDF to be at ϕw = 0.08, in close agreement with the experimental cloud point measurement (ϕw = 0.05). Examining the enthalpic and entropic components of the free energy of mixing reveals that at low concentrations of water, the enthalpy term has the most significant contribution to the miscibility of the ternary system, whereas at higher concentrations of water, the entropy term dominates. Finally, the free energy of mixing was compared with the Flory-Huggins (FH) free energy of mixing by computing the concentration-dependent interaction parameters from MD simulations. The FH model inadequately predicted the miscibility of the PVDF solution, mainly due to its negligence of the excess entropy of mixing.
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Affiliation(s)
- Tseden Taddese
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi 464-8603, Japan
| | - Masahiro Kitabata
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi 464-8603, Japan
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31
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Hahn DF, Hünenberger PH. Alchemical Free-Energy Calculations by Multiple-Replica λ-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme. J Chem Theory Comput 2019; 15:2392-2419. [PMID: 30821973 DOI: 10.1021/acs.jctc.8b00782] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A new method is proposed to calculate alchemical free-energy differences based on molecular dynamics (MD) simulations, called the conveyor belt thermodynamic integration (CBTI) scheme. As in thermodynamic integration (TI), K replicas of the system are simulated at different values of the alchemical coupling parameter λ. The number K is taken to be even, and the replicas are equally spaced on a forward-turn-backward-turn path, akin to a conveyor belt (CB) between the two physical end-states; and as in λ-dynamics (λD), the λ-values associated with the individual systems evolve in time along the simulation. However, they do so in a concerted fashion, determined by the evolution of a single dynamical variable Λ of period 2π controlling the advance of the entire CB. Thus, a change of Λ is always associated with K/2 equispaced replicas moving forward and K/2 equispaced replicas moving backward along λ. As a result, the effective free-energy profile of the replica system along Λ is periodic of period 2 πK-1, and the magnitude of its variations decreases rapidly upon increasing K, at least as K-1 in the limit of large K. When a sufficient number of replicas is used, these variations become small, which enables a complete and quasi-homogeneous coverage of the λ-range by the replica system, without application of any biasing potential. If desired, a memory-based biasing potential can still be added to further homogenize the sampling, the preoptimization of which is computationally inexpensive. The final free-energy profile along λ is calculated similarly to TI, by binning of the Hamiltonian λ-derivative as a function of λ considering all replicas simultaneously, followed by quadrature integration. The associated quadrature error can be kept very low owing to the continuous and quasi-homogeneous λ-sampling. The CBTI scheme can be viewed as a continuous/deterministic/dynamical analog of the Hamiltonian replica-exchange/permutation (HRE/HRP) schemes or as a correlated multiple-replica analog of the λD or λ-local elevation umbrella sampling (λ-LEUS) schemes. Compared to TI, it shares the advantage of the latter schemes in terms of enhanced orthogonal sampling, i.e. the availability of variable-λ paths to circumvent conformational barriers present at specific λ-values. Compared to HRE/HRP, it permits a deterministic and continuous sampling of the λ-range, is expected to be less sensitive to possible artifacts of the thermo- and barostating schemes, and bypasses the need to carefully preselect a λ-ladder and a swapping-attempt frequency. Compared to λ-LEUS, it eliminates (or drastically reduces) the dead time associated with the preoptimization of a biasing potential. The goal of this article is to provide the mathematical/physical formulation of the proposed CBTI scheme, along with an initial application of the method to the calculation of the hydration free energy of methanol.
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Affiliation(s)
- David F Hahn
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Philippe H Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
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32
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Wei W, Chen Y, Xie D, Zhou Y. Molecular insight into chymotrypsin inhibitor 2 resisting proteolytic degradation. Phys Chem Chem Phys 2019; 21:5049-5058. [PMID: 30762035 DOI: 10.1039/c8cp07784c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chymotrypsin inhibitor 2 (CI2) is a special serine protease inhibitor which can resist hydrolysis for several days with a rapid equilibrium between the Michaelis complex and acyl-enzyme intermediate. The energies and conformational changes for subtilisin-catalyzed proteolysis of CI2 were examined in this paper for the first time by employing pseudo bond ab initio QM/MM MD simulations. In the acylation reaction, a low-barrier hydrogen bond between His64 and Asp32 in the transition state together with the lack of covalent backbone constraints makes the peptide bonds of CI2 break more easily than in other serine protease inhibitors. After acyl-enzyme formation, molecular dynamics simulations showed that the access of hydrolytic water to the active site requires partial dissociation of the leaving group. However, retention of the leaving group mainly by the intra- and inter-molecular H-bonding networks hinders the access of water and retards the deacylation reaction. Instead of the dissociation constant of inhibitors, we suggest employing the free energy at the acyl-enzyme state to predict the relative hydrolysis rates of CI2 mutants, which are testified by the experimental relative hydrolysis rates.
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Affiliation(s)
- Wanqing Wei
- Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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33
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Nilsson L, Villa A. Modeling and Simulation of Oligonucleotide Hybrids: Outlining a Strategy. Methods Mol Biol 2019; 2036:113-126. [PMID: 31410793 DOI: 10.1007/978-1-4939-9670-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular dynamics simulations with a state-of-the-art force field provide an atomistic detailed description of the structural and thermodynamic features of biomolecules. Effects of chemical modifications and of the environment such as sequence, solvent, and ionic strength can explicitly be taken into account. Molecular simulation techniques can also provide insight in change in binding affinity, in protonation (pKa shift) and tautomeric propensity due to changes in the environment or in the molecular system. The quality and reliability of a simulation depend on the quality of the force field and on the reproducibility of the data, and validation depends on the availability of suitable experimental data. Here, we describe the workflow to investigate oligonucleotide hybrids using molecular simulation including hardware and software information.
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Affiliation(s)
- Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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34
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König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM. A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules 2018; 23:E2695. [PMID: 30347691 PMCID: PMC6222909 DOI: 10.3390/molecules23102695] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/01/2022] Open
Abstract
Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.
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Affiliation(s)
- Gerhard König
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Frank C Pickard
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jing Huang
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
- School of Life Sciences, Westlake University, 18 Shilongshan Street, Hangzhou 310024, China.
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany.
| | - Alexander D MacKerell
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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35
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Maurer M, Hansen N, Oostenbrink C. Comparison of free-energy methods using a tripeptide-water model system. J Comput Chem 2018; 39:2226-2242. [PMID: 30280398 PMCID: PMC6220940 DOI: 10.1002/jcc.25537] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 06/29/2018] [Accepted: 06/30/2018] [Indexed: 11/24/2022]
Abstract
We investigate the ability of several free-energy calculation methods to combine two alchemical changes. We use Bennett acceptance ratio (BAR), thermodynamic integration (TI), extended TI (X-TI), and enveloping distribution sampling (EDS) to perturb a water molecule, which is restrained to an amino acid that is also being perturbed. In addition to these pairwise methods, we present two two-dimensional approaches, EDS-TI and two-dimensional TI (2D-TI). We compare feasibility, efficiency and usability of these methods in regard to our simple model system, which mimics the displacement of a water molecule in the active site of a protein on residue mutation. The correct treatment of structural water has been shown to greatly aid binding affinity calculations in some cases that remained elusive otherwise. This is of broad interest in, for example, drug design, and we conclude that thus far, the pairwise method BAR and also the newer X-TI remain the most suitable methods to treat this problem as long as few end states are involved. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Manuela Maurer
- Department of Material Sciences and Process EngineeringInstitute of Molecular Modeling and Simulation, University of Natural Resources and Life SciencesMuthgasse 18, A‐1190, ViennaAustria
| | - Niels Hansen
- Department of Energy‐, Process‐ and Bio‐Engineering, University of StuttgartInstitute of Thermodynamics and Thermal Process EngineeringPfaffenwaldring 9, 70569, StuttgartGermany
| | - Chris Oostenbrink
- Department of Material Sciences and Process EngineeringInstitute of Molecular Modeling and Simulation, University of Natural Resources and Life SciencesMuthgasse 18, A‐1190, ViennaAustria
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36
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Lee TS, Cerutti DS, Mermelstein D, Lin C, LeGrand S, Giese TJ, Roitberg A, Case DA, Walker RC, York DM. GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. J Chem Inf Model 2018; 58:2043-2050. [PMID: 30199633 DOI: 10.1021/acs.jcim.8b00462] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report progress in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber18. Of particular interest is the development of alchemical free energy algorithms, including free energy perturbation and thermodynamic integration methods with support for nonlinear soft-core potential and parameter interpolation transformation pathways. These methods can be used in conjunction with enhanced sampling techniques such as replica exchange, constant-pH molecular dynamics, and new 12-6-4 potentials for metal ions. Additional performance enhancements have been made that enable appreciable speed-up on GPUs relative to the previous software release.
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Affiliation(s)
- Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - David S Cerutti
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Dan Mermelstein
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Charles Lin
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Scott LeGrand
- A9.com , Palo Alto , California 94301 , United States
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Adrian Roitberg
- Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - David A Case
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Ross C Walker
- GlaxoSmithKline PLC , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
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37
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Theiss M, Gross J. A third and fourth order perturbation theory for dipolar hard spheres. J Chem Phys 2018; 149:044901. [DOI: 10.1063/1.5035421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marc Theiss
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
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38
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Schieber NP, Dybeck EC, Shirts MR. Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams. J Chem Phys 2018; 148:144104. [PMID: 29655343 DOI: 10.1063/1.5013273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of semiconductors. Predicting the most stable crystalline form at a given temperature and pressure requires determining the crystalline form with the lowest relative Gibbs free energy. Effective computational prediction of the most stable polymorph could save significant time and effort in the design of novel molecular crystalline solids or predict their behavior under new conditions. In this study, we introduce a new approach using multistate reweighting to address the problem of determining solid-solid phase diagrams and apply this approach to the phase diagram of solid benzene. For this approach, we perform sampling at a selection of temperature and pressure states in the region of interest. We use multistate reweighting methods to determine the reduced free energy differences between T and P states within a given polymorph and validate this phase diagram using several measures. The relative stability of the polymorphs at the sampled states can be successively interpolated from these points to create the phase diagram by combining these reduced free energy differences with a reference Gibbs free energy difference between polymorphs. The method also allows for straightforward estimation of uncertainties in the phase boundary. We also find that when properly implemented, multistate reweighting for phase diagram determination scales better with the size of the system than previously estimated.
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Affiliation(s)
- Natalie P Schieber
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Eric C Dybeck
- Department of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, USA
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39
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König G, Brooks BR, Thiel W, York DM. On the convergence of multi-scale free energy simulations. MOLECULAR SIMULATION 2018; 44:1062-1081. [PMID: 30581251 DOI: 10.1080/08927022.2018.1475741] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
In this work we employ simple model systems to evaluate the relative performance of two of the most important free energy methods: The Zwanzig equation (also known as "Free energy perturbation") and Bennett's acceptance ratio method (BAR). Although our examples should be transferable to other kinds of free energy simulations, we focus on applications of multi-scale free energy simulations. Such calculations are especially complex, since they connect two different levels of theory with very different requirements in terms of speed, accuracy, sampling and parallelizability. We try to reconcile all those different factors by developing some simple criteria to guide the early stages of the development of a free energy protocol. This is accomplished by quantifying how many λ intermediate steps and how many potential energy evaluations are necessary in order to reach a certain level of convergence.
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Affiliation(s)
- Gerhard König
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany, EU.,Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.,Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany, EU
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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40
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Mermelstein DJ, Lin C, Nelson G, Kretsch R, McCammon JA, Walker RC. Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. J Comput Chem 2018. [PMID: 29532496 DOI: 10.1002/jcc.25187] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD-based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907-atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel J Mermelstein
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Charles Lin
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093.,GlaxoSmithKline PLC, 1250 S. Collegeville Rd, Collegeville, Pennsylvania, 19426
| | - Gard Nelson
- NantBioscience, Inc., 9920 Jefferson Boulevard, Culver City, California, 90232
| | - Rachael Kretsch
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093.,Harvey Mudd College, 301 Platt Blvd, Claremont, California, 91711
| | - J Andrew McCammon
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093
| | - Ross C Walker
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093.,GlaxoSmithKline PLC, 1250 S. Collegeville Rd, Collegeville, Pennsylvania, 19426
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41
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Li PF, Jia XY, Wang MT, Mei Y. Comparison of Accuracy and Convergence Rate between Equilibrium and Nonequilibrium Alchemical Transformations for Calculation of Relative Binding Free Energy. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1711204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Peng-fei Li
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Xiang-yu Jia
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Mei-ting Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman OK 73019, USA
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42
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Demuynck R, Rogge SMJ, Vanduyfhuys L, Wieme J, Waroquier M, Van Speybroeck V. Efficient Construction of Free Energy Profiles of Breathing Metal-Organic Frameworks Using Advanced Molecular Dynamics Simulations. J Chem Theory Comput 2017; 13:5861-5873. [PMID: 29131647 PMCID: PMC5729547 DOI: 10.1021/acs.jctc.7b01014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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In order to reliably
predict and understand the breathing behavior
of highly flexible metal–organic frameworks from thermodynamic
considerations, an accurate estimation of the free energy difference
between their different metastable states is a prerequisite. Herein,
a variety of free energy estimation methods are thoroughly tested
for their ability to construct the free energy profile as a function
of the unit cell volume of MIL-53(Al). The methods comprise free energy
perturbation, thermodynamic integration, umbrella sampling, metadynamics,
and variationally enhanced sampling. A series of molecular dynamics
simulations have been performed in the frame of each of the five methods
to describe structural transformations in flexible materials with
the volume as the collective variable, which offers a unique opportunity
to assess their computational efficiency. Subsequently, the most efficient
method, umbrella sampling, is used to construct an accurate free energy
profile at different temperatures for MIL-53(Al) from first principles
at the PBE+D3(BJ) level of theory. This study yields insight into
the importance of the different aspects such as entropy contributions
and anharmonic contributions on the resulting free energy profile.
As such, this thorough study provides unparalleled insight in the
thermodynamics of the large structural deformations of flexible materials.
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Affiliation(s)
- Ruben Demuynck
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - Sven M J Rogge
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - Louis Vanduyfhuys
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - Jelle Wieme
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - Michel Waroquier
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, B-9052 Zwijnaarde, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, B-9052 Zwijnaarde, Belgium
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43
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Mecklenfeld A, Raabe G. Comparison of RESP and IPolQ-Mod Partial Charges for Solvation Free Energy Calculations of Various Solute/Solvent Pairs. J Chem Theory Comput 2017; 13:6266-6274. [PMID: 29125770 DOI: 10.1021/acs.jctc.7b00692] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The calculation of solvation free energies ΔGsolv by molecular simulations is of great interest as they are linked to other physical properties such as relative solubility, partition coefficient, and activity coefficient. However, shortcomings in molecular models can lead to ΔGsolv deviations from experimental data. Various studies have demonstrated the impact of partial charges on free energy results. Consequently, calculation methods for partial charges aimed at more accurate ΔGsolv predictions are the subject of various studies in the literature. Here we compare two methods to derive partial charges for the general AMBER force field (GAFF), i.e. the default RESP as well as the physically motivated IPolQ-Mod method that implicitly accounts for polarization costs. We study 29 solutes which include characteristic functional groups of drug-like molecules, and 12 diverse solvents were examined. In total, we consider 107 solute/solvent pairs including two water models TIP3P and TIP4P/2005. Comparison with experimental results yields better agreement for TIP3P, regardless of the partial charge scheme. The overall performance of GAFF/RESP and GAFF/IPolQ-Mod is similar, though specific shortcomings in the description of ΔGsolv for both RESP and IPolQ-Mod can be identified. However, the high correlation between free energies obtained with GAFF/RESP and GAFF/IPolQ-Mod demonstrates the compatibility between the modified charges and remaining GAFF parameters.
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Affiliation(s)
- Andreas Mecklenfeld
- Institut für Thermodynamik, Technische Universität Braunschweig , Hans-Sommer-Strasse 5, 38106 Braunschweig, Germany.,Center of Pharmaceutical Engineering, Technische Universität Braunschweig , Franz-Liszt-Strasse 35a, 38106 Braunschweig, Germany
| | - Gabriele Raabe
- Institut für Thermodynamik, Technische Universität Braunschweig , Hans-Sommer-Strasse 5, 38106 Braunschweig, Germany
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44
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Lee TS, Hu Y, Sherborne B, Guo Z, York DM. Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration. J Chem Theory Comput 2017; 13:3077-3084. [PMID: 28618232 DOI: 10.1021/acs.jctc.7b00102] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report the implementation of the thermodynamic integration method on the pmemd module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically delivers over 2 orders of magnitude of speed-up relative to a single CPU core for the calculation of ligand-protein binding affinities with no statistically significant numerical differences and thus provides a powerful new tool for drug discovery applications.
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Affiliation(s)
- Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Yuan Hu
- Department of Chemistry, Modeling and Informatics, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brad Sherborne
- Department of Chemistry, Modeling and Informatics, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Zhuyan Guo
- Department of Chemistry, Modeling and Informatics, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
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45
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Göke K, Lorenz T, Repanas A, Schneider F, Steiner D, Baumann K, Bunjes H, Dietzel A, Finke JH, Glasmacher B, Kwade A. Novel strategies for the formulation and processing of poorly water-soluble drugs. Eur J Pharm Biopharm 2017; 126:40-56. [PMID: 28532676 DOI: 10.1016/j.ejpb.2017.05.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/10/2017] [Accepted: 05/15/2017] [Indexed: 12/31/2022]
Abstract
Low aqueous solubility of active pharmaceutical ingredients presents a serious challenge in the development process of new drug products. This article provides an overview on some of the current approaches for the formulation of poorly water-soluble drugs with a special focus on strategies pursued at the Center of Pharmaceutical Engineering of the TU Braunschweig. These comprise formulation in lipid-based colloidal drug delivery systems and experimental as well as computational approaches towards the efficient identification of the most suitable carrier systems. For less lipophilic substances the preparation of drug nanoparticles by milling and precipitation is investigated for instance by means of microsystem-based manufacturing techniques and with special regard to the preparation of individualized dosage forms. Another option to overcome issues with poor drug solubility is the incorporation into nanospun fibers.
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Affiliation(s)
- Katrin Göke
- Technische Universität Braunschweig, Institut für Pharmazeutische Technologie, Mendelssohnstr. 1, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Thomas Lorenz
- Technische Universität Braunschweig, Institut für Mikrotechnik, Alte Salzdahlumer Str. 203, 38124 Braunschweig, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Alexandros Repanas
- Leibniz Universität Hannover, Institut für Mehrphasenprozesse, Callinstr. 36, 30167 Hannover, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Frederic Schneider
- Technische Universität Braunschweig, Institut für Medizinische und Pharmazeutische Chemie, Beethovenstr. 55, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Denise Steiner
- Technische Universität Braunschweig, Institut für Partikeltechnik, Volkmaroder Str. 5, 38104 Braunschweig, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Knut Baumann
- Technische Universität Braunschweig, Institut für Medizinische und Pharmazeutische Chemie, Beethovenstr. 55, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Heike Bunjes
- Technische Universität Braunschweig, Institut für Pharmazeutische Technologie, Mendelssohnstr. 1, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Andreas Dietzel
- Technische Universität Braunschweig, Institut für Mikrotechnik, Alte Salzdahlumer Str. 203, 38124 Braunschweig, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Jan H Finke
- Technische Universität Braunschweig, Institut für Partikeltechnik, Volkmaroder Str. 5, 38104 Braunschweig, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Birgit Glasmacher
- Leibniz Universität Hannover, Institut für Mehrphasenprozesse, Callinstr. 36, 30167 Hannover, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
| | - Arno Kwade
- Technische Universität Braunschweig, Institut für Partikeltechnik, Volkmaroder Str. 5, 38104 Braunschweig, Germany; Technische Universität Braunschweig, Zentrum für Pharmaverfahrenstechnik (PVZ), Franz-Liszt-Str. 35a, 38106 Braunschweig, Germany.
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46
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Kearns FL, Hudson PS, Woodcock HL, Boresch S. Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities. J Comput Chem 2017; 38:1376-1388. [PMID: 28272811 DOI: 10.1002/jcc.24706] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/29/2016] [Indexed: 01/09/2023]
Abstract
We demonstrate that Jarzynski's equation can be used to reliably compute free energy differences between low and high level representations of systems. The need for such a calculation arises when employing the so-called "indirect" approach to free energy simulations with mixed quantum mechanical/molecular mechanical (QM/MM) Hamiltonians; a popular technique for circumventing extensive simulations involving quantum chemical computations. We have applied this methodology to several small and medium sized organic molecules, both in the gas phase and explicit solvent. Test cases include several systems for which the standard approach; that is, free energy perturbation between low and high level description, fails to converge. Finally, we identify three major areas in which the difference between low and high level representations make the calculation of ΔAlow→high difficult: bond stretching and angle bending, different preferred conformations, and the response of the MM region to the charge distribution of the QM region. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Fiona L Kearns
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, CHE205, Tampa, Florida, 33620-5250
| | - Phillip S Hudson
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, CHE205, Tampa, Florida, 33620-5250
| | - Henry L Woodcock
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, CHE205, Tampa, Florida, 33620-5250
| | - Stefan Boresch
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Währingerstraße 17, Vienna, A-1090, Austria
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47
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Mecklenfeld A, Raabe G. Efficient solvation free energy simulations: impact of soft-core potential and a new adaptive λ-spacing method. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1292008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Andreas Mecklenfeld
- Institut für Thermodynamik, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
| | - Gabriele Raabe
- Institut für Thermodynamik, Technische Universität Braunschweig, Braunschweig, Germany
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48
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Taddese T, Carbone P. Effect of Chain Length on the Partition Properties of Poly(ethylene oxide): Comparison between MARTINI Coarse-Grained and Atomistic Models. J Phys Chem B 2017; 121:1601-1609. [PMID: 28151665 DOI: 10.1021/acs.jpcb.6b10858] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The MARTINI coarse-grained beads are parameterized to match the partition coefficients of several organic molecules in different solvents. Here, we test the method when modeling the partitioning properties of poly(ethylene oxide) between solvents of different polarities. We show that, among the existing models, the latest model developed by Lee and co-workers [ Lee , H. ; Pastor , R. W. J. Phys. Chem. B 2011 , 115 , 7830 - 7837 ] is the one that most successfully reproduces the hydration free energy of short oligomers, although it predicts highly negative solvation free energies in octanol and hexane. We develop a new CG model matching the solvation free energy of the monomer in different solvents and propose a simple method to select the Lennard-Jones parameters that reproduce the desired partition coefficients. The model correctly reproduces water/hexane partition properties for oligomers up to 10 monomers but still suffers from a transferability problem for larger molecular weight.
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Affiliation(s)
- Tseden Taddese
- School of Chemical Engineering and Analytical Science, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K
| | - Paola Carbone
- School of Chemical Engineering and Analytical Science, The University of Manchester , Oxford Road, Manchester M13 9PL, U.K
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49
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Xu Y, Villa A, Nilsson L. The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid. J Comput Chem 2017; 38:1147-1157. [PMID: 28101966 PMCID: PMC5434909 DOI: 10.1002/jcc.24692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/01/2016] [Accepted: 11/08/2016] [Indexed: 01/09/2023]
Abstract
Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy. We validate the approach on the solvation free energy difference for the nucleosides thymidine, cytosine, and 5-methyl-cytosine. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- You Xu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SE-141 83, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SE-141 83, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SE-141 83, Sweden
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50
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Tofoleanu F, Lee J, Pickard Iv FC, König G, Huang J, Baek M, Seok C, Brooks BR. Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. J Comput Aided Mol Des 2017; 31:107-118. [PMID: 27696242 PMCID: PMC6472255 DOI: 10.1007/s10822-016-9965-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/02/2016] [Indexed: 02/07/2023]
Abstract
As part of the SAMPL5 blind prediction challenge, we calculate the absolute binding free energies of six guest molecules to an octa-acid (OAH) and to a methylated octa-acid (OAMe). We use the double decoupling method via thermodynamic integration (TI) or Hamiltonian replica exchange in connection with the Bennett acceptance ratio (HREM-BAR). We produce the binding poses either through manual docking or by using GalaxyDock-HG, a docking software developed specifically for this study. The root mean square deviations for our most accurate predictions are 1.4 kcal mol-1 for OAH with TI and 1.9 kcal mol-1 for OAMe with HREM-BAR. Our best results for OAMe were obtained for systems with ionic concentrations corresponding to the ionic strength of the experimental solution. The most problematic system contains a halogenated guest. Our attempt to model the σ-hole of the bromine using a constrained off-site point charge, does not improve results. We use results from molecular dynamics simulations to argue that the distinct binding affinities of this guest to OAH and OAMe are due to a difference in the flexibility of the host. We believe that the results of this extensive analysis of host-guest complexes will help improve the protocol used in predicting binding affinities for larger systems, such as protein-substrate compounds.
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Affiliation(s)
- Florentina Tofoleanu
- Laboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA.
| | - Juyong Lee
- Laboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA
| | - Frank C Pickard Iv
- Laboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA
| | - Gerhard König
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Jing Huang
- Laboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA
| | - Minkyung Baek
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Institutes of Health - National Heart, Lung, and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA
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