101
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Rasheed M, Clement N, Bhowmick A, Bajaj CL. Statistical Framework for Uncertainty Quantification in Computational Molecular Modeling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:1154-1167. [PMID: 29989988 PMCID: PMC6857703 DOI: 10.1109/tcbb.2017.2771240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
As computational modeling, simulation, and predictions are becoming integral parts of biomedical pipelines, it behooves us to emphasize the reliability of the computational protocol. For any reported quantity of interest (QOI), one must also compute and report a measure of the uncertainty or error associated with the QOI. This is especially important in molecular modeling, since in most practical applications the inputs to the computational protocol are often noisy, incomplete, or low-resolution. Unfortunately, currently available modeling tools do not account for uncertainties and their effect on the final QOIs with sufficient rigor. We have developed a statistical framework that expresses the uncertainty of the QOI as the probability that the reported value deviates from the true value by more than some user-defined threshold. First, we provide a theoretical approach where this probability can be bounded using Azuma-Hoeffding like inequalities. Second, we approximate this probability empirically by sampling the space of uncertainties of the input and provide applications of our framework to bound uncertainties of several QOIs commonly used in molecular modeling. Finally, we also present several visualization techniques to effectively and quantitavely visualize the uncertainties: in the input, final QOIs, and also intermediate states.
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102
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Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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103
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Development of sodium glucose co-transporter 2 (SGLT2) inhibitors with novel structure by molecular docking and dynamics simulation. J Mol Model 2019; 25:175. [PMID: 31154518 DOI: 10.1007/s00894-019-4067-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 05/17/2019] [Indexed: 01/09/2023]
Abstract
In this study, molecular docking studies were carried out to explore the binding interactions of sodium glucose co-transporter 2 (SGLT2) with its inhibitors. A correlation between the docking scores and the experimental bioactivity was observed (R2 = 0.8368, N = 24). The new inhibitors were designed using the 3D quantitative structure activity relationship (3D-QSAR) method, and the activities were predicted by the docking method. In order to understand the structure-activity correlation of compound 1 m (the highest score of docking) and compound 1 t (the lowest score), we carried out a combined molecular dynamics simulation and MM-GBSA method. It was found that, in the system of SGLT2-1 m, the interaction between Gln271 and Val272 exhibited significant effects, which were absent in the SGLT2-1 t system. This study is expected to shed light on the mechanism of action of compound 1 m, leading to development of active drug candidates targeting SGLT2.
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104
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Molecular dynamics of carbon nanohorns and their complexes with cisplatin in aqueous solution. J Mol Graph Model 2019; 89:167-177. [DOI: 10.1016/j.jmgm.2019.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 11/21/2022]
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105
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Abstract
It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. These approaches model hydration effects and provide solvent-dependent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as such, they can be incorporated into MD or other conformational searching strategies in a straightforward manner. The foundations of the GB model are reviewed, followed by examples of newer, emerging models and examples of important applications. We discuss their strengths and weaknesses, both for fidelity to the underlying continuum model and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations.
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Affiliation(s)
- Alexey V Onufriev
- Departments of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24060, USA;
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA;
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106
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Spiriti J, Subramanian SR, Palli R, Wu M, Zuckerman DM. Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α. PLoS One 2019; 14:e0215694. [PMID: 31013302 PMCID: PMC6478315 DOI: 10.1371/journal.pone.0215694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/06/2019] [Indexed: 12/17/2022] Open
Abstract
There is a vast gulf between the two primary strategies for simulating protein-ligand interactions. Docking methods significantly limit or eliminate protein flexibility to gain great speed at the price of uncontrolled inaccuracy, whereas fully flexible atomistic molecular dynamics simulations are expensive and often suffer from limited sampling. We have developed a flexible docking approach geared especially for highly flexible or poorly resolved targets based on mixed-resolution Monte Carlo (MRMC), which is intended to offer a balance among speed, protein flexibility, and sampling power. The binding region of the protein is treated with a standard atomistic force field, while the remainder of the protein is modeled at the residue level with a Gō model that permits protein flexibility while saving computational cost. Implicit solvation is used. Here we assess three facets of the MRMC approach with implications for other docking studies: (i) the role of receptor flexibility in cross-docking pose prediction; (ii) the use of non-equilibrium candidate Monte Carlo (NCMC) and (iii) the use of pose-clustering in scoring. We examine 61 co-crystallized ligands of estrogen receptor α, an important cancer target known for its flexibility. We also compare the performance of the MRMC approach with Autodock smina. Adding protein flexibility, not surprisingly, leads to significantly lower total energies and stronger interactions between protein and ligand, but notably we document the important role of backbone flexibility in the improvement. The improved backbone flexibility also leads to improved performance relative to smina. Somewhat unexpectedly, our implementation of NCMC leads to only modestly improved sampling of ligand poses. Overall, the addition of protein flexibility improves the performance of docking, as measured by energy-ranked poses, but we do not find significant improvements based on cluster information or the use of NCMC. We discuss possible improvements for the model including alternative coarse-grained force fields, improvements to the treatment of solvation, and adding additional types of NCMC moves.
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Affiliation(s)
- Justin Spiriti
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States of America
| | - Sundar Raman Subramanian
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Rohith Palli
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Maria Wu
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Daniel M. Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States of America
- * E-mail:
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107
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Ou SC, Pettitt BM. Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles. J Chem Theory Comput 2019; 15:2649-2658. [PMID: 30768893 DOI: 10.1021/acs.jctc.8b01157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Techniques to calculate the free energy changes of a system are very useful in the study of biophysical and biochemical properties. In practice, free energy changes can be described with thermodynamic cycles, and the free energy change of an individual process can be computed by sufficiently sampling the corresponding configurations. However, this is still time-consuming especially for large biomolecular systems. Previously, we have shown that by utilizing precomputed solute-solvent correlations, so-called proximal distribution functions (pDF), we are capable of reconstructing the solvent environment near solute atoms, thus estimating the solute-solvent interactions and solvation free energies of molecules. In this contribution, we apply the technique of pDF-reconstructions to calculate chemical potentials and use this information in thermodynamic cycles. This illustrates how free energy changes of nontrivial chemical processes in aqueous solution systems can be rapidly estimated.
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Affiliation(s)
- Shu-Ching Ou
- Sealy Center for Structural Biology and Molecular Biophysics , University of Texas Medical Branch , 301 University Boulevard , Galveston , Texas 77555-0304 , United States
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics , University of Texas Medical Branch , 301 University Boulevard , Galveston , Texas 77555-0304 , United States
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108
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Pal A, Neo K, Rajamani L, Ferrer FJ, Lane DP, Verma CS, Mortellaro A. Inhibition of NLRP3 inflammasome activation by cell-permeable stapled peptides. Sci Rep 2019; 9:4913. [PMID: 30894604 PMCID: PMC6426897 DOI: 10.1038/s41598-019-41211-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/22/2019] [Indexed: 12/12/2022] Open
Abstract
Interleukin-1β (IL-1β) is a major cytokine that initiates and enhances inflammatory responses. Excessive IL-1β production is a characteristic of most chronic inflammatory diseases, including atherosclerosis, type 2 diabetes, and obesity, which affect a large proportion of the global population. The production of bioactive IL-1β is mediated by a caspase-1-activating complex known as an 'inflammasome'. The NLRP3 inflammasome has been associated with several human inflammatory and autoimmune diseases and represents a potential therapeutic target for disrupting IL-1β production. We used molecular modeling guided by molecular dynamics simulations to design α-helical stapled peptides targeting the pyrin domain of the adaptor protein ASC to interrupt the development of its filament, which is crucial for NLRP3 inflammasome formation. The peptides were effectively internalized by human monocytic cells and efficiently suppressed the release of the inflammasome-regulated cytokines IL-1β and IL-18, following exogenous activation of the NLRP3 inflammasome. The peptides reduced ASC speck formation and caspase-1 processing thereby suppressing pro-IL-1β processing and release of active IL-1β. This is the first demonstration of the successful use of stapled peptides designed to target the adaptor protein ASC, and can be extended to other inflammatory pathways to disrupt excessive IL-1β production.
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Affiliation(s)
- Arumay Pal
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Kurt Neo
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8a Biomedical Grove, Singapore, 138648, Singapore
| | - Lakshminarayanan Rajamani
- Singapore Eye Research Institute (SERI), The Academia, 20 College Road, Discovery Tower Level 6, Singapore, 169856, Singapore
| | - Fernando Jose Ferrer
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - David P Lane
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore, 138648, Singapore
| | - Chandra S Verma
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
| | - Alessandra Mortellaro
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8a Biomedical Grove, Singapore, 138648, Singapore. .,San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milano, Italy.
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109
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Berthoumieux H, Paillusson F. Dielectric response in the vicinity of an ion: A nonlocal and nonlinear model of the dielectric properties of water. J Chem Phys 2019; 150:094507. [PMID: 30849905 DOI: 10.1063/1.5080183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The goal of this work is to propose a simple continuous model that captures the dielectric properties of water at the nanometric scale. We write an electrostatic energy as a functional of the polarisation field containing a term in P4 and non-local Gaussian terms. Such a hamiltonian can reproduce two key properties of water: the saturation of the polarisation response of water in the presence of a strong electrostatic field and the nanometric dipolar correlations of the solvent molecules modifying the long range van der waals interaction. This model explores thus two fundamental aspects that have to be included in implicit models of electrolytes for a relevant description of electrostatic interactions at nanometric scales.
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Affiliation(s)
| | - F Paillusson
- School of Mathematics and Physics, University of Lincoln, Lincoln LN6 7TS, United Kingdom
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110
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Yamasaki S, Amemiya T, Yabuki Y, Horimoto K, Fukui K. ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow. J Comput Aided Mol Des 2019; 33:497-507. [PMID: 30840170 PMCID: PMC7088279 DOI: 10.1007/s10822-019-00195-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/28/2019] [Indexed: 12/22/2022]
Abstract
Recent progress in molecular biology has revealed that many non-coding RNAs regulate gene expression or catalyze biochemical reactions in tumors, viruses and several other diseases. The tertiary structure of RNA molecules and RNA–RNA/protein interaction sites are of increasing importance as potential targets for new medicines that treat a broad array of human diseases. Current RNA drugs are split into two groups: antisense RNA molecules and aptamers. In this report, we present a novel workflow to predict RNA tertiary structures and RNA–RNA/protein interactions using the KNIME environment, which enabled us to assemble a combination of RNA-related analytical tools and databases. In this study, three analytical workflows for comprehensive structural analysis of RNA are introduced: (1) prediction of the tertiary structure of RNA; (2) prediction of the structure of RNA–RNA complexes and analysis of their interactions; and (3) prediction of the structure of RNA–protein complexes and analysis of their interactions. In an RNA–protein case study, we modeled the tertiary structure of pegaptanib, an aptamer drug, and performed docking calculations of the pegaptanib-vascular endothelial growth factor complex using a fragment of the interaction site of the aptamer. We also present molecular dynamics simulations of the RNA–protein complex to evaluate the affinity of the complex by mutating bases at the interaction interface. The results provide valuable information for designing novel features of aptamer-protein complexes.
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Affiliation(s)
- Satoshi Yamasaki
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan. .,Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo (IMSUT), 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
| | - Takayuki Amemiya
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yukimitsu Yabuki
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,IMSBIO Co., Ltd, 4-21-1-601 Higashi-Ikebukuro, Toshima-ku, Tokyo, 170-0013, Japan
| | - Katsuhisa Horimoto
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuhiko Fukui
- Molecular Profiling for Drug Discovery Research Center (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
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111
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Depta PN, Jandt U, Dosta M, Zeng AP, Heinrich S. Toward Multiscale Modeling of Proteins and Bioagglomerates: An Orientation-Sensitive Diffusion Model for the Integration of Molecular Dynamics and the Discrete Element Method. J Chem Inf Model 2019; 59:386-398. [PMID: 30550276 DOI: 10.1021/acs.jcim.8b00613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most processes involved in biological and biotechnological systems spread over many scales in space and time. For example, the interaction of multiple enzymes in heterogeneous enzymatic agglomerates or clusters, necessary for efficient enzymatic conversion, is of high interest for research and enzyme engineering. In order to understand and predict their overall behavior and performance, it is important to describe these scales as completely as possible, known as multiscale modeling. While many different approaches have been presented in recent years, knowledge about protein formation and bioagglomeration at the micro scale is still very limited. In an attempt to address such systems, we propose a bottom- up multiscale modeling methodology, bridging the gaps between molecular dynamics (MD) with an explicit solvent and the larger scale discrete element method (DEM) using an implicit solvent and abstracting macromolecules (e.g., proteins) as objects with anisotropic properties. We term this approach the molecular discrete element method (MDEM). For this, we present an orientation-sensitive diffusion model for DEM, which describes the dynamics of anisotropic translational and rotational diffusion, while implicitly considering solvent molecules and enforcing a canonical ensemble. A general-purpose model and parametrization approach is presented, which can be used to simulate any process involving diffusion of discrete particles. Effects of temperature and viscosity changes can be considered, and guidance is provided concerning time step selection. This model is generally applicable and serves as a precondition to enforce the proper dynamics (i.e., diffusion characteristics and canonical ensemble, similar to a thermostat in MD) for the proposed multiscale modeling methodology with anisotropic properties. Thereby, it presents a first step toward modeling at the micro scale and is integral to enforcing dynamics of such systems and therefore extensively validated. As a next step, interaction models are to be defined and added to the presented model. In comparison to atomistic and coarse-grained (CG) MD, a speedup of 5-7 orders of magnitude can be achieved. The approach is demonstrated on multiple components of the pyruvate dehydrogenase enzyme complex, a multienzymatic machinery that involves very different types of enzymes and is of high value to further elucidate the mechanisms of bioagglomeration and metabolic channeling.
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112
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Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach. PLoS One 2019; 14:e0211227. [PMID: 30682119 PMCID: PMC6347273 DOI: 10.1371/journal.pone.0211227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/09/2019] [Indexed: 02/08/2023] Open
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, a neglected infection affecting millions of people in tropical regions. There are several chemotherapeutic agents for the treatment of this disease, but most of them are highly toxic and generate resistance. Currently, the development of allosteric inhibitors constitutes a promising research field, since it can improve the accessibility to more selective and less toxic medicines. To date, the allosteric drugs prediction is a state-of-the-art topic in rational structure-based computational design. In this work, a simulation strategy was developed for computational discovery of allosteric inhibitors, and it was applied to cruzain, a promising target and the major cysteine protease of T. cruzi. Molecular dynamics simulations, binding free energy calculations and network-based modelling of residue interactions were combined to characterize and compare molecular distinctive features of the apo form and the cruzain-allosteric inhibitor complexes. By using geometry-based criteria on trajectory snapshots, we predicted two main allosteric sites suitable for drug targeting. The results suggest dissimilar mechanisms exerted by the same allosteric site when binding different potential allosteric inhibitors. Finally, we identified the residues involved in suboptimal paths linking the identified site and the orthosteric site. The present study constitutes the first approximation to the design of cruzain allosteric inhibitors and may serve for future pharmacological intervention. Here, no major effects on active site structure were observed due to compound binding (modification of distance and angles between catalytic residues), which indicates that allosteric regulation in cruzain might be mediated via alterations of its dynamical properties similarly to allosteric inhibition of human cathepsin K (HCatK). The current findings are particularly relevant for the design of allosteric modulators of papain-like cysteine proteases.
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113
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Roshanzamir K, Kashani-Amin E, Ebrahim-Habibi A, Navidpour L. Aurones as New Porcine Pancreatic α-Amylase Inhibitors. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180712150600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background: Aurones, (Z)-2-benzylidenebenzofuran-3-one derivatives, are naturallyoccurring
structural isomers of flavones, with promising pharmacological potential.
</P><P>
Methods: In this study, the structural requirements for the inhibition of porcine pancreatic α-
amylase by hydroxylated or methoxylated aurone derivatives were investigated by assessing their in
vitro biological activities against porcine pancreatic α-amylase.
</P><P>
Results: The structure-activity relationship of these inhibitors based on both in vitro and in silico
findings showed that the hydrogen bonds between the OH groups of the A or B ring of (Z)-
benzylidenebenzofuran-3-one derivatives and the catalytic residues of the binding site are crucial
for their inhibitory activities.
</P><P>
Conclusion: It seems that the OH groups in aurones inhibit α-amylase in a manner similar to that of
OH groups in flavones and flavonols.
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Affiliation(s)
- Khashayar Roshanzamir
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 14176, Iran
| | - Elaheh Kashani-Amin
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Ebrahim-Habibi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Latifeh Navidpour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 14176, Iran
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114
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Tian S, Zeng J, Liu X, Chen J, Zhang JZH, Zhu T. Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling. Phys Chem Chem Phys 2019; 21:22103-22112. [DOI: 10.1039/c9cp03598b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular dynamics simulations and binding free energy calculations are combined to investigate the selectivity of inhibitors toward type III phosphatidylinositol 4 kinases.
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Affiliation(s)
- Shuaizhen Tian
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Jinzhe Zeng
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Xiao Liu
- School of Mathematics, Physics and Statistics
- Shanghai University of Engineering Science
- Shanghai 201620
- China
| | - Jianzhong Chen
- School of Science
- Shandong Jiaotong University
- Jinan 250357
- China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
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115
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Mujika JI, Dalla Torre G, Lachowicz JI, Lopez X. In silico design of mimosine containing peptides as new efficient chelators of aluminum. RSC Adv 2019; 9:7688-7697. [PMID: 35521183 PMCID: PMC9061177 DOI: 10.1039/c8ra10139f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/26/2019] [Indexed: 12/16/2022] Open
Abstract
The design of new and efficient chelators that can remove aluminium(iii), a metal with increasing recognition as a potential toxic agent, from biological systems is an area of high therapeutic relevance. In the present paper, we present an extensive computational study of a new promising type of these chelators based on mimosine containing peptides. The reason to choose mimosine is that the sidechain of this residue is similar to deferiprone, a ligand known to tightly interact with highly-valent metals, and in particular with Al(iii). In this article we analyze systematically, using a combination of methods that include QM/MM MD simulations, how the size and sequence of the polypeptides can alter the fundamental binding patterns to aluminum, in comparison with the binding to deferiprone. Particular attention is given towards the identification of the smallest peptide that interacts efficiently with aluminum, since polypeptide size is a fundamental factor to allow a given polypeptide to efficiently cross the cell membrane. The results indicate that the longest peptides, with 8 or 9 amino acids, show no difficulties interacting with Al(iii) in an optimum arrangement. By contrast, when the peptide contains five or six amino acids Al(iii) is pentacoordinated, reducing the stability of the resultant complex. In summary, our study demonstrates that the mimosine containing peptides can efficiently coordinate highly valent metals such as Al(iii), with a subtle dependence of the binding on the specific chain-lengths of the polypeptide. We believe that the present study sheds light on the adequacy of this new type of chelator towards aluminum binding. A novel chelator of aluminum is presented, a peptide containing three mimosine residues.![]()
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Affiliation(s)
- J. I. Mujika
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea UPV/EHU
- Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - G. Dalla Torre
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea UPV/EHU
- Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
| | - J. I. Lachowicz
- University of Cagliari
- Department of Chemical and Geological Sciences
- Cittadella Universitaria
- Monserrato
- Italy
| | - X. Lopez
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea UPV/EHU
- Donostia International Physics Center (DIPC)
- 20080 Donostia
- Spain
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Qi R, Luo R. Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units. J Chem Inf Model 2018; 59:409-420. [PMID: 30550277 DOI: 10.1021/acs.jcim.8b00761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Poisson-Boltzmann equation (PBE) based continuum electrostatics models have been widely used in modeling electrostatic interactions in biochemical processes, particularly in estimating protein-ligand binding affinities. Fast convergence of PBE solvers is crucial in binding affinity computations as numerous snapshots need to be processed. Efforts have been reported to develop PBE solvers on graphics processing units (GPUs) for efficient modeling of biomolecules, though only relatively simple successive over-relaxation and conjugate gradient methods were implemented. However, neither convergence nor scaling properties of the two methods are optimal for large biomolecules. On the other hand, geometric multigrid (MG) has been shown to be an optimal solver on CPUs, though no MG have been reported for biomolecular applications on GPUs. This is not a surprise as it is a more complex method and depends on simpler but limited iterative methods such as Gauss-Seidel in its core relaxation procedure. The robustness and efficiency of MG on GPUs are also unclear. Here we present an implementation and a thorough analysis of MG on GPUs. Our analysis shows that robustness is a more pronounced issue than efficiency for both MG and other tested solvers when the single precision is used for complex biomolecules. We further show how to balance robustness and efficiency utilizing MG's overall efficiency and conjugate gradient's robustness, pointing to a hybrid GPU solver with a good balance of efficiency and accuracy. The new PBE solver will significantly improve the computational throughput for a range of biomolecular applications on the GPU platforms.
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Zaka M, Abbasi BH, Durdagi S. Novel tumor necrosis factor-α (TNF-α) inhibitors from small molecule library screening for their therapeutic activity profiles against rheumatoid arthritis using target-driven approaches and binary QSAR models. J Biomol Struct Dyn 2018; 37:2464-2476. [PMID: 30047845 DOI: 10.1080/07391102.2018.1491423] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Tumor necrosis factor alpha (TNF-α) is a multifunctional cytokine that acts as a central biological mediator for critical immune functions, including inflammation, infection, and antitumor responses. It plays pivotal role in autoimmune diseases like rheumatoid arthritis (RA). The synthetic antibodies etanercept, infliximab, and adalimumab are approved drugs for the treatment of inflammatory diseases bind to TNF-α directly, preventing its association with the tumor necrosis factor receptor (TNFR). These biologics causes serious side effects such as triggering an autoimmune anti-antibody response or the weakening of the body's immune defenses. Therefore, alternative small-molecule based therapies for TNF-α inhibition is a hot topic both in academia and industry. Most of small-molecule inhibitors reported in the literature target TNF-α, indirectly. In this study, combined in silico approaches have been applied to better understand the important direct interactions between TNF-α and small inhibitors. Our effort executed with the extensive literature review to select the compounds that inhibit TNF-α. High-throughput structure-based and ligand-based virtual screening methods are applied to identify TNF-α inhibitors from 3 different small molecule databases (∼256.000 molecules from Otava drug-like green chemical collection, ∼ 500.000 molecules from Otava Tangible database, ∼2.500.000 Enamine small molecule database) and ∼240.000 molecules from ZINC natural products libraries. Moreover, therapeutic activity prediction, as well as pharmacokinetic and toxicity profiles are also investigated using MetaCore/MetaDrug platform which is based on a manually curated database of molecular interactions, molecular pathways, gene-disease associations, chemical metabolism and toxicity information, uses binary QSAR models. Particular therapeutic activity and toxic effect predictions are based on the ChemTree ability to correlate structural descriptors to that property using recursive partitioning algorithm. Molecular Dynamics (MD) simulations were also performed for selected hits to investigate their detailed structural and dynamical analysis beyond docking studies. As a result, at least one hit from each database were identified as novel TNF-α inhibitors after comprehensive virtual screening, multiple docking, e-Pharmacophore modeling (structure-based pharmacophore modeling), MD simulations, and MetaCore/MetaDrug analysis. Identified hits show predicted promising anti-arthritic activity and no toxicity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mehreen Zaka
- a Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory , Bahcesehir University (BAU) , Istanbul , Turkey.,b Department of Biotechnology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Bilal Haider Abbasi
- b Department of Biotechnology , Quaid-i-Azam University , Islamabad , Pakistan
| | - Serdar Durdagi
- a Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory , Bahcesehir University (BAU) , Istanbul , Turkey.,c Neuroscience Program, Institute of Health Sciences , Bahcesehir University , Istanbul , Turkey
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118
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Medina FE, Neves RPP, Ramos MJ, Fernandes PA. QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02616] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabiola E. Medina
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P. P. Neves
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Proposing novel TNFα direct inhibitor Scaffolds using fragment-docking based e-pharmacophore modeling and binary QSAR-based virtual screening protocols pipeline. J Mol Graph Model 2018; 85:111-121. [DOI: 10.1016/j.jmgm.2018.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 01/08/2023]
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120
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Fernández-Ramírez MDC, Hervás R, Galera-Prat A, Laurents DV, Carrión-Vázquez M. Efficient and simplified nanomechanical analysis of intrinsically disordered proteins. NANOSCALE 2018; 10:16857-16867. [PMID: 30168565 DOI: 10.1039/c8nr02785d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a tertiary structure. Amyloidogenic IDPs (aIDPs) in particular have attracted great interest due to their implication in several devastating diseases as well as in critical biological functions. However, the conformational changes that trigger amyloid formation in aIDPs are largely unknown. aIDPs' conformational polymorphism at the monomer level encumbers their study using bulk techniques. Single-molecule techniques like atomic force microscopy-based single-molecule force spectroscopy represent a promising approach and a "carrier-guest" strategy, in which the protein of interest is mechanically protected, was developed to overcome the spurious signals from the noisy proximal region. However, since the carrier and single-molecule markers have similar mechanostabilities, their signals can intermingle in the force-extension recordings, making peak selection and analysis very laborious, cumbersome and prone to error for the non-expert. Here we have developed a new carrier, the c8C module from the CipC scaffoldin, with a higher mechanostability so that the signals from the protected protein will appear at the end of the recordings. This assures an accurate, more efficient and expert-independent analysis, simplifying both the selection and analysis of the single-molecule data. Furthermore, this modular design can be integrated into any SMFS polyprotein-based vector, thus constituting a useful utensil in the growing toolbox of protein nanomechanics.
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121
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Chen J, Liu X, Chen J. Atomistic Peptide Folding Simulations Reveal Interplay of Entropy and Long-Range Interactions in Folding Cooperativity. Sci Rep 2018; 8:13668. [PMID: 30209295 PMCID: PMC6135771 DOI: 10.1038/s41598-018-32028-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/30/2018] [Indexed: 11/23/2022] Open
Abstract
Understanding how proteins fold has remained a problem of great interest in biophysical research. Atomistic computer simulations using physics-based force fields can provide important insights on the interplay of different interactions and energetics and their roles in governing the folding thermodynamics and mechanism. In particular, generalized Born (GB)-based implicit solvent force fields can be optimized to provide an appropriate balance between solvation and intramolecular interactions and successfully recapitulate experimental conformational equilibria for a set of helical and β-hairpin peptides. Here, we further demonstrate that key thermodynamic properties and their temperature dependence obtained from replica exchange molecular dynamics simulations of these peptides are in quantitative agreement with experimental results. Useful lessons can be learned on how the interplay of entropy and sequentially long-range interactions governs the mechanism and cooperativity of folding. These results highlight the great potential of high-quality implicit solvent force fields for studying protein folding and large-scale conformational transitions.
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Affiliation(s)
- Jianlin Chen
- Department of Hematology, The Central Hospital of Taizhou, Taizhou, Zhejiang, 318000, P.R. China
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA. .,Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA.
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Ramesh K, Lama D, Tan KW, Nguyen VS, Chew FT, Verma CS, Mok YK. Homologous Lympho-Epithelial Kazal-type Inhibitor Domains Delay Blood Coagulation by Inhibiting Factor X and XI with Differential Specificity. Structure 2018; 26:1178-1186.e3. [PMID: 30017565 DOI: 10.1016/j.str.2018.05.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/30/2018] [Accepted: 05/29/2018] [Indexed: 10/28/2022]
Abstract
Despite being initially identified in the blood filtrate, LEKTI is a 15-domain Kazal-type inhibitor mostly known in the regulation of skin desquamation. In the current study, screening of serine proteases in blood coagulation cascade showed that LEKTI domain 4 has inhibitory activity toward only FXIa, whereas LEKTI domain 6 inhibits both FXIa and FXaB (bovine FXa). Nuclear magnetic resonance structural and dynamic experiments plus molecular dynamics simulation revealed that LEKTI domain 4 has enhanced backbone flexibility at the reactive-site loop. A model of the LEKTI-protease complex revealed that FXaB has a narrower S4 pocket compared with FXIa and hence prefers only small side-chain residues at the P4 position, such as Ala in LEKTI domain 6. Mutational studies combined with a molecular complex model suggest that both a more flexible reactive-site loop and a bulky residue at the P4 position make LEKTI domain 4 a weaker but highly selective inhibitor of FXIa.
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Affiliation(s)
- Karthik Ramesh
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Dilraj Lama
- Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Kang Wei Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Van Sang Nguyen
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore
| | - Chandra S Verma
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; Bioinformatics Institute, A(∗)STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore; School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore.
| | - Yu Keung Mok
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore.
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123
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Wang Y, Lin W, Wu N, He X, Wang J, Feng Z, Xie XQ. An insight into paracetamol and its metabolites using molecular docking and molecular dynamics simulation. J Mol Model 2018; 24:243. [PMID: 30121710 PMCID: PMC6733030 DOI: 10.1007/s00894-018-3790-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
Abstract
Paracetamol is a relatively safe analgesia/antipyretic drug without the risks of addiction, dependence, tolerance, and withdrawal when used alone. However, when administrated in an opioid/paracetamol combination product, which often contains a large quantity of paracetamol, it can be potentially dangerous due to the risk of hepatotoxicity. Paracetamol is known to be metabolized into N-(4-hydroxyphenyl)-arachidonamide (AM404) via fatty acid amide hydrolase (FAAH) and into N-acetyl-p-benzoquinone imine (NAPQI) via cytochrome P450 (CYP) enzymes. However, the underlying mechanism of paracetamol is still unclear. In addition, paracetamol has the potential to interact with other drugs that are also involved with CYP family enzymes (inducer/inhibitor/substrate), an example being illicit drugs. In our present work, we looked into the relationship between paracetamol and its metabolites (AM404 and NAPQI) using molecular docking and molecular dynamics (MD) simulations. We first carried out a series of molecular docking studies between paracetamol/AM404/NAQPI and their reported targets, including CYP 2E1, FAAH, TRPA1, CB1, and TRPV1. Subsequently, we performed MD simulations and energy decomposition for CB1-AM404, TRPV1-AM404, and TRPV1-NAPQI for further investigation of the dynamics interactions. Finally, we summarized and discussed the reported drug-drug interactions between paracetamol and central nervous system drugs, especially illicit drugs. Overall, we are able to provide new insights into the structural and functional roles of paracetamol and its metabolites that can inform the potential prevention and treatment of paracetamol overdose. Graphical abstract Paracetamol and its metabolites.
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Affiliation(s)
- Yuanqiang Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing, 400054, China
- Chongqing Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing, 400054, China
| | - Weiwei Lin
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nan Wu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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124
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Shao Q, Zhu W. The effects of implicit modeling of nonpolar solvation on protein folding simulations. Phys Chem Chem Phys 2018; 20:18410-18419. [PMID: 29946610 DOI: 10.1039/c8cp03156h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Implicit solvent models, in which the polar and nonpolar solvation free-energies of solute molecules are treated separately, have been widely adopted for molecular dynamics simulation of protein folding. While the development of the implicit models is mainly focused on the methodological improvement and key parameter optimization for polar solvation, nonpolar solvation has been either ignored or described by a simplistic surface area (SA) model. In this work, we performed the folding simulations of multiple β-hairpin and α-helical proteins with varied surface tension coefficients embedded in the SA model to clearly demonstrate the effects of nonpolar solvation treated by a popular SA model on protein folding. The results indicate that the change in the surface tension coefficient does not alter the ability of implicit solvent simulations to reproduce a protein native structure but indeed controls the components of the equilibrium conformational ensemble and modifies the energetic characterization of the folding transition pathway. The suitably set surface tension coefficient can yield explicit solvent simulations and/or experimentally suggested folding mechanism of protein. In addition, the implicit treatment of both polar and nonpolar components of solvation free-energy contributes to the overestimation of the secondary structure in implicit solvent simulations.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
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125
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Sun X, Yan X, Zhuo W, Gu J, Zuo K, Liu W, Liang L, Gan Y, He G, Wan H, Gou X, Shi H, Hu J. PD-L1 Nanobody Competitively Inhibits the Formation of the PD-1/PD-L1 Complex: Comparative Molecular Dynamics Simulations. Int J Mol Sci 2018; 19:E1984. [PMID: 29986511 PMCID: PMC6073277 DOI: 10.3390/ijms19071984] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 12/22/2022] Open
Abstract
The anti-PD-L1 monoclonal antibody (mAb) targeting PD-1/PD-L1 immune checkpoint has achieved outstanding results in clinical application and has become one of the most popular anti-cancer drugs. The mechanism of molecular recognition and inhibition of PD-L1 mAbs is not yet clear, which hinders the subsequent antibody design and modification. In this work, the trajectories of PD-1/PD-L1 and nanobody/PD-L1 complexes were obtained via comparative molecular dynamics simulations. Then, a series of physicochemical parameters including hydrogen bond, dihedral angle distribution, pKa value and binding free energy, and so forth, were all comparatively analyzed to investigate the recognition difference between PD-L1 and PD-1 and nanobody. Both LR113 (the amino acid residues in PD-L1 are represented by the lower left sign of L) and LR125 residues of PD-L1 undergo significant conformational change after association with mAbs, which dominates a strong electrostatic interaction. Solvation effect analysis revealed that solvent-water enhanced molecular recognition between PD-L1 and nanobody. By combining the analyses of the time-dependent root mean squared fluctuation (RMSF), free energy landscape, clustering and energy decomposition, the potential inhibition mechanism was proposed that the nanobody competitively and specifically bound to the β-sheet groups of PD-L1, reduced the PD-L1’s flexibility and finally blocked the formation of PD-1/PD-L1 complex. Based on the simulation results, site-directed mutagenesis of ND99 (the amino acid residues in Nano are displayed by the lower left sign of N) and NQ116 in the nanobody may be beneficial for improving antibody activity. This work offers some structural guidance for the design and modification of anticancer mAbs based on the structure of the PD-1/PD-L1 complex.
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Affiliation(s)
- Xin Sun
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
| | - Xiao Yan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
| | - Wei Zhuo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Ke Zuo
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
| | - Wei Liu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
| | - Li Liang
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
| | - Ya Gan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
| | - Gang He
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
| | - Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaojun Gou
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
| | - Hubing Shi
- Laboratory of tumor targeted and immune therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China.
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Sainas S, Pippione AC, Lupino E, Giorgis M, Circosta P, Gaidano V, Goyal P, Bonanni D, Rolando B, Cignetti A, Ducime A, Andersson M, Järvå M, Friemann R, Piccinini M, Ramondetti C, Buccinnà B, Al-Karadaghi S, Boschi D, Saglio G, Lolli ML. Targeting Myeloid Differentiation Using Potent 2-Hydroxypyrazolo[1,5-a]pyridine Scaffold-Based Human Dihydroorotate Dehydrogenase Inhibitors. J Med Chem 2018; 61:6034-6055. [DOI: 10.1021/acs.jmedchem.8b00373] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
| | | | | | | | - Paola Circosta
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
- Molecular Biotechnology Center, Turin 10126, Italy
| | - Valentina Gaidano
- Department of Clinical and Biological Sciences, University of Turin, Turin 10043, Italy
- Mauriziano Hospital S.C.D.U. Hematology, Turin 10128, Italy
| | - Parveen Goyal
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE 405, Sweden
| | | | | | - Alessandro Cignetti
- Department of Clinical and Biological Sciences, University of Turin, Turin 10043, Italy
- Mauriziano Hospital S.C.D.U. Hematology, Turin 10128, Italy
| | | | - Mikael Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE 405, Sweden
| | - Michael Järvå
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE 405, Sweden
| | | | | | | | - Salam Al-Karadaghi
- Department of Biochemistry and Structural Biology, Lund University, Lund 221 00, Sweden
| | | | - Giuseppe Saglio
- Department of Clinical and Biological Sciences, University of Turin, Turin 10043, Italy
- Mauriziano Hospital S.C.D.U. Hematology, Turin 10128, Italy
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127
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Liu JL, Eisenberg B. Poisson-Fermi modeling of ion activities in aqueous single and mixed electrolyte solutions at variable temperature. J Chem Phys 2018; 148:054501. [PMID: 29421887 DOI: 10.1063/1.5021508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The combinatorial explosion of empirical parameters in tens of thousands presents a tremendous challenge for extended Debye-Hückel models to calculate activity coefficients of aqueous mixtures of the most important salts in chemistry. The explosion of parameters originates from the phenomenological extension of the Debye-Hückel theory that does not take steric and correlation effects of ions and water into account. By contrast, the Poisson-Fermi theory developed in recent years treats ions and water molecules as nonuniform hard spheres of any size with interstitial voids and includes ion-water and ion-ion correlations. We present a Poisson-Fermi model and numerical methods for calculating the individual or mean activity coefficient of electrolyte solutions with any arbitrary number of ionic species in a large range of salt concentrations and temperatures. For each activity-concentration curve, we show that the Poisson-Fermi model requires only three unchanging parameters at most to well fit the corresponding experimental data. The three parameters are associated with the Born radius of the solvation energy of an ion in electrolyte solution that changes with salt concentrations in a highly nonlinear manner.
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Affiliation(s)
- Jinn-Liang Liu
- Institute of Computational and Modeling Science, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Bob Eisenberg
- Department of Physiology and Biophysics, Rush University, Chicago, Illinois 60612, USA and Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
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128
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Xiao L, Luo R. Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid. J Chem Phys 2018; 147:214112. [PMID: 29221408 DOI: 10.1063/1.5016052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.
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Affiliation(s)
- Li Xiao
- Departments of Biomedical Engineering, University of California, Irvine, California 92697, USA
| | - Ray Luo
- Departments of Biomedical Engineering, University of California, Irvine, California 92697, USA
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129
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Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7480749. [PMID: 29967786 PMCID: PMC6008865 DOI: 10.1155/2018/7480749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/06/2018] [Indexed: 12/15/2022]
Abstract
Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR), i.e., the double mutant F87M/L110M (MT-TTR) and the triple mutant F87M/L110M/S117E (3M-TTR), in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets) appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
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130
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Role of the cell membrane interface in modulating production and uptake of Alzheimer's beta amyloid protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1639-1651. [PMID: 29572033 DOI: 10.1016/j.bbamem.2018.03.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 12/22/2022]
Abstract
The beta amyloid protein (Aβ) plays a central role in Alzheimer's disease (AD) pathogenesis and its interaction with cell membranes in known to promote mutually disruptive structural perturbations that contribute to amyloid deposition and neurodegeneration in the brain. In addition to protein aggregation at the membrane interface and disruption of membrane integrity, growing reports demonstrate an important role for the membrane in modulating Aβ production and uptake into cells. The aim of this review is to highlight and summarize recent literature that have contributed insight into the implications of altered membrane composition on amyloid precursor protein (APP) proteolysis, production of Aβ, its internalization in to cells via permeabilization and receptor mediated uptake. Here, we also review the various membrane model systems and experimental tools used for probing Aβ-membrane interactions to investigate the key mechanistic aspects underlying the accumulation and toxicity of Aβ in AD.
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131
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Bai Q, Pérez-Sánchez H, Shi Z, Li L, Shi D, Liu H, Yao X. Computational studies on horseshoe shape pocket of human orexin receptor type 2 and boat conformation of suvorexant by molecular dynamics simulations. Chem Biol Drug Des 2018; 92:1221-1231. [PMID: 29450984 DOI: 10.1111/cbdd.13181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/08/2017] [Accepted: 11/11/2017] [Indexed: 12/29/2022]
Abstract
The FDA approved drug suvorexant binds to the horseshoe shape pocket of OX2 R with the boat conformation. The horseshoe shape pocket plays an important role on the biological activity of OX2 R in the cell membrane. To study the binding mechanism between the horseshoe shape pocket of OX2 R and boat conformation of suvorexant, the crystal structures of wild type and N324A mutant of OX2 R in complex with antagonist suvorexant are chosen to perform molecular dynamics (MD) simulations, QM/MM, and MMGBSA calculations. By comparison with the wild type of OX2 R, the results show the 1,2,3-triazole and p-toluamide groups of suvorexant are changed in the N324A mutant of OX2 R during 200 ns MD simulations. The QM/MM and weak interaction analysis are employed to calculate the non-covalent bonds interaction between suvorexant and key residues in the wild type and N324A mutant of OX2 R. The MMGBSA calculations indicate the entropy energy is an important influence factor for suvorexant affinity in the distorted horseshoe shape pocket of OX2 R. Our results not only show the horseshoe shape pocket of OX2 R is the necessary conformation for the binding of antagonist suvorexant, but also give the important sites and structural features for antagonist design of OX2 R.
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Affiliation(s)
- Qifeng Bai
- Key Lab of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Horacio Pérez-Sánchez
- Computer Science Department, Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
| | - Zhuoyu Shi
- Key Lab of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Lanlan Li
- Department of Chemistry, Lanzhou University, Lanzhou, Gansu, China
| | - Danfeng Shi
- Department of Chemistry, Lanzhou University, Lanzhou, Gansu, China
| | - Huanxiang Liu
- Key Lab of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaojun Yao
- Key Lab of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu, China.,Department of Chemistry, Lanzhou University, Lanzhou, Gansu, China
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132
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Zhang K, Keane SC, Su Z, Irobalieva RN, Chen M, Van V, Sciandra CA, Marchant J, Heng X, Schmid MF, Case DA, Ludtke SJ, Summers MF, Chiu W. Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach. Structure 2018; 26:490-498.e3. [PMID: 29398526 PMCID: PMC5842133 DOI: 10.1016/j.str.2018.01.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/12/2017] [Accepted: 01/03/2018] [Indexed: 02/01/2023]
Abstract
Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS]2; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs.
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Affiliation(s)
- Kaiming Zhang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah C Keane
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Zhaoming Su
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rossitza N Irobalieva
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muyuan Chen
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Verna Van
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Carly A Sciandra
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Jan Marchant
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Case
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Michael F Summers
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA.
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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133
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Ji N, Liu T, Xu J, Shen LQ, Lu B. A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins. Int J Mol Sci 2018; 19:ijms19030695. [PMID: 29495644 PMCID: PMC5877556 DOI: 10.3390/ijms19030695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 02/08/2018] [Accepted: 02/26/2018] [Indexed: 12/03/2022] Open
Abstract
Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson–Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the z-axis; and (3) add a non-polar solvation energy term to complete the estimation of the total solvation energy of a membrane protein. A mesh resolution of about 0.25 Å (cubic grid space)/0.36 Å (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations.
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Affiliation(s)
- Nan Ji
- LSEC, National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Tiantian Liu
- CAEP Software Center for High Performance Numerical Simulation, Beijing 100088, China.
| | - Jingjie Xu
- School of Mathematical Sciences, University of Science and Technology of China, Hefei 230026, China.
| | - Longzhu Q Shen
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
| | - Benzhuo Lu
- LSEC, National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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134
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Izadi S, Harris RC, Fenley MO, Onufriev AV. Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies. J Chem Theory Comput 2018; 14:1656-1670. [PMID: 29378399 DOI: 10.1021/acs.jctc.7b00886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The need for accurate yet efficient representation of the aqueous environment in biomolecular modeling has led to the development of a variety of generalized Born (GB) implicit solvent models. While many studies have focused on the accuracy of available GB models in predicting solvation free energies, a systematic assessment of the quality of these models in binding free energy calculations, crucial for rational drug design, has not been undertaken. Here, we evaluate the accuracies of eight common GB flavors (GB-HCT, GB-OBC, GB-neck2, GBNSR6, GBSW, GBMV1, GBMV2, and GBMV3), available in major molecular dynamics packages, in predicting the electrostatic binding free energies ( ΔΔ Gel) for a diverse set of 60 biomolecular complexes belonging to four main classes: protein-protein, protein-drug, RNA-peptide, and small complexes. The GB flavors are examined in terms of their ability to reproduce the results from the Poisson-Boltzmann (PB) model, commonly used as accuracy reference in this context. We show that the agreement with the PB of ΔΔ Gel estimates varies widely between different GB models and also across different types of biomolecular complexes, with R2 correlations ranging from 0.3772 to 0.9986. A surface-based "R6" GB model recently implemented in AMBER shows the closest overall agreement with reference PB ( R2 = 0.9949, RMSD = 8.75 kcal/mol). The RNA-peptide and protein-drug complex sets appear to be most challenging for all but one model, as indicated by the large deviations from the PB in ΔΔ Gel. Small neutral complexes present the least challenge for most of the GB models tested. The quantitative demonstration of the strengths and weaknesses of the GB models across the diverse complex types provided here can be used as a guide for practical computations and future development efforts.
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Affiliation(s)
- Saeed Izadi
- Early Stage Pharmaceutical Development , Genentech Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Robert C Harris
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , Maryland 21201 , United States
| | - Marcia O Fenley
- Institute of Molecular Biophysics , Florida State University , Tallahassee , Florida 32306-3408 , United States
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135
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Ricci CG, Li B, Cheng LT, Dzubiella J, McCammon JA. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly. Front Mol Biosci 2018; 5:13. [PMID: 29484300 PMCID: PMC5816062 DOI: 10.3389/fmolb.2018.00013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/26/2018] [Indexed: 01/12/2023] Open
Abstract
Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes.
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Affiliation(s)
- Clarisse Gravina Ricci
- Department of Pharmacology and Department of Chemistry and Biochemistry, National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA, United States
| | - Bo Li
- Department of Mathematics, University of California, San Diego, La Jolla, CA, United States.,Quantitative Biology Graduate Program, University of California, San Diego, La Jolla, CA, United States
| | - Li-Tien Cheng
- Department of Mathematics, University of California, San Diego, La Jolla, CA, United States
| | - Joachim Dzubiella
- Institut für Physik, Humboldt-Universität zu Berlin, Berlin, Germany.,Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - J Andrew McCammon
- Department of Pharmacology and Department of Chemistry and Biochemistry, National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA, United States
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136
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Experimental and theoretical studies on tautomeric structures of a newly synthesized 2,2′(hydrazine-1,2-diylidenebis(propan-1-yl-1-ylidene))diphenol. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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137
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 454] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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138
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Ler LD, Ghosh S, Chai X, Thike AA, Heng HL, Siew EY, Dey S, Koh LK, Lim JQ, Lim WK, Myint SS, Loh JL, Ong P, Sam XX, Huang D, Lim T, Tan PH, Nagarajan S, Cheng CWS, Ho H, Ng LG, Yuen J, Lin PH, Chuang CK, Chang YH, Weng WH, Rozen SG, Tan P, Creasy CL, Pang ST, McCabe MT, Poon SL, Teh BT. Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2. Sci Transl Med 2017; 9:9/378/eaai8312. [PMID: 28228601 DOI: 10.1126/scitranslmed.aai8312] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/02/2017] [Indexed: 12/12/2022]
Abstract
Trithorax-like group complex containing KDM6A acts antagonistically to Polycomb-repressive complex 2 (PRC2) containing EZH2 in maintaining the dynamics of the repression and activation of gene expression through H3K27 methylation. In urothelial bladder carcinoma, KDM6A (a H3K27 demethylase) is frequently mutated, but its functional consequences and therapeutic targetability remain unknown. About 70% of KDM6A mutations resulted in a total loss of expression and a consequent loss of demethylase function in this cancer type. Further transcriptome analysis found multiple deregulated pathways, especially PRC2/EZH2, in KDM6A-mutated urothelial bladder carcinoma. Chromatin immunoprecipitation sequencing analysis revealed enrichment of H3K27me3 at specific loci in KDM6A-null cells, including PRC2/EZH2 and their downstream targets. Consequently, we targeted EZH2 (an H3K27 methylase) and demonstrated that KDM6A-null urothelial bladder carcinoma cell lines were sensitive to EZH2 inhibition. Loss- and gain-of-function assays confirmed that cells with loss of KDM6A are vulnerable to EZH2. IGFBP3, a direct KDM6A/EZH2/H3K27me3 target, was up-regulated by EZH2 inhibition and contributed to the observed EZH2-dependent growth suppression in KDM6A-null cell lines. EZH2 inhibition delayed tumor onset in KDM6A-null cells and caused regression of KDM6A-null bladder tumors in both patient-derived and cell line xenograft models. In summary, our study demonstrates that inactivating mutations of KDM6A, which are common in urothelial bladder carcinoma, are potentially targetable by inhibiting EZH2.
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Affiliation(s)
- Lian Dee Ler
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, 28 Medical Drive, Singapore 117456, Singapore
| | - Sujoy Ghosh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Xiaoran Chai
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Aye Aye Thike
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Hong Lee Heng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Ee Yan Siew
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Sucharita Dey
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore
| | - Liang Kai Koh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jing Quan Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Weng Khong Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Swe Swe Myint
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jia Liang Loh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Pauline Ong
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Xin Xiu Sam
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Dachuan Huang
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Tony Lim
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Puay Hoon Tan
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Sanjanaa Nagarajan
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | | | - Henry Ho
- Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Lay Guat Ng
- Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - John Yuen
- Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Po-Hung Lin
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan
| | - Cheng-Keng Chuang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan
| | - Ying-Hsu Chang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan
| | - Wen-Hui Weng
- Department of Chemical Engineering and Biotechnology and Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Steven G Rozen
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore.,Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore.,Genome Institute of Singapore, 60 Biopolis Street Genome, Singapore 138672, Singapore
| | - Caretha L Creasy
- Cancer Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - See-Tong Pang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan.
| | - Michael T McCabe
- Cancer Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.
| | - Song Ling Poon
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore. .,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore. .,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, #07-18, Singapore 138673, Singapore
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139
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Xiao T, Song X. A molecular Debye-Hückel theory of solvation in polar fluids: An extension of the Born model. J Chem Phys 2017; 147:214502. [DOI: 10.1063/1.4998255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Tiejun Xiao
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, Guiyang 550018, People’s Republic of China and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Xueyu Song
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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140
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Wang C, Ren P, Luo R. Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling. J Phys Chem B 2017; 121:11169-11179. [PMID: 29164898 DOI: 10.1021/acs.jpcb.7b09616] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solvent-mediated electrostatic interactions were well recognized to be important in the structure and function of molecular systems. Ionic interaction is an important component in electrostatic interactions, especially in highly charged molecules, such as nucleic acids. Here, we focus on the quality of the widely used Poisson-Boltzmann surface area (PBSA) continuum models in modeling ionic interactions by comparing with both explicit solvent simulations and the experiment. In this work, the molality-dependent chemical potentials for sodium chloride (NaCl) electrolyte were first simulated in the SPC/E explicit solvent. Our high-quality simulation agrees well with both the previous study and the experiment. Given the free-energy simulations in SPC/E as the benchmark, we used the same sets of snapshots collected in the SPC/E solvent model for PBSA free-energy calculations in the hope to achieve the maximum consistency between the two solvent models. Our comparative analysis shows that the molality-dependent chemical potentials of NaCl were reproduced well with both linear PB and nonlinear PB methods, although nonlinear PB agrees better with SPC/E and the experiment. Our free-energy simulations also show that the presence of salt increases the hydrophobic effect in a nonlinear fashion, in qualitative agreement with previous theoretical studies of Onsager and Samaras. However, the lack of molality-dependency in the nonelectrostatics continuum models dramatically reduces the overall quality of PBSA methods in modeling salt-dependent energetics. These analyses point to further improvements needed for more robust modeling of solvent-mediated interactions by the continuum solvation frameworks.
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Affiliation(s)
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas , Austin, Texas 78712, United States
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141
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Onufriev AV, Izadi S. Water models for biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1347] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alexey V. Onufriev
- Department of Physics; Virginia Tech; Blacksburg VA USA
- Department of Computer Science; Virginia Tech; Blacksburg VA USA
- Center for Soft Matter and Biological Physics; Virginia Tech; Blacksburg VA USA
| | - Saeed Izadi
- Early Stage Pharmaceutical Development; Genentech Inc.; South San Francisco, CA USA
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142
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Wang B, Wang C, Wu K, Wei G. Breaking the polar‐nonpolar division in solvation free energy prediction. J Comput Chem 2017; 39:217-233. [DOI: 10.1002/jcc.25107] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/02/2017] [Accepted: 10/22/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Bao Wang
- Department of MathematicsMichigan State University Michigan48824
| | - Chengzhang Wang
- School of Statistics and MathematicsCentral University of Finance and EconomicsBeijing100081 China
| | - Kedi Wu
- Department of MathematicsMichigan State University Michigan48824
| | - Guo‐Wei Wei
- Department of MathematicsMichigan State University Michigan48824
- Department of Electrical and ComputerEngineering Michigan State University Michigan48824
- Department of Biochemistry and MolecularBiology Michigan State UniversityMichigan48824
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143
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Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Computational revelation of binding mechanisms of inhibitors to endocellular protein tyrosine phosphatase 1B using molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:3636-3650. [DOI: 10.1080/07391102.2017.1394221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
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144
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Eisenberg B, Oriols X, Ferry D. Dynamics of Current, Charge and Mass. COMPUTATIONAL AND MATHEMATICAL BIOPHYSICS 2017. [DOI: 10.1515/mlbmb-2017-0006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract Electricity plays a special role in our lives and life. The dynamics of electrons allow light to flow through a vacuum. The equations of electron dynamics are nearly exact and apply from nuclear particles to stars. These Maxwell equations include a special term, the displacement current (of a vacuum). The displacement current allows electrical signals to propagate through space. Displacement current guarantees that current is exactly conserved from inside atoms to between stars, as long as current is defined as the entire source of the curl of the magnetic field, as Maxwell did.We show that the Bohm formulation of quantum mechanics allows the easy definition of the total current, and its conservation, without the dificulties implicit in the orthodox quantum theory. The orthodox theory neglects the reality of magnitudes, like the currents, during times that they are not being explicitly measured.We show how conservation of current can be derived without mention of the polarization or dielectric properties of matter. We point out that displacement current is handled correctly in electrical engineering by ‘stray capacitances’, although it is rarely discussed explicitly. Matter does not behave as physicists of the 1800’s thought it did. They could only measure on a time scale of seconds and tried to explain dielectric properties and polarization with a single dielectric constant, a real positive number independent of everything. Matter and thus charge moves in enormously complicated ways that cannot be described by a single dielectric constant,when studied on time scales important today for electronic technology and molecular biology. When classical theories could not explain complex charge movements, constants in equations were allowed to vary in solutions of those equations, in a way not justified by mathematics, with predictable consequences. Life occurs in ionic solutions where charge is moved by forces not mentioned or described in the Maxwell equations, like convection and diffusion. These movements and forces produce crucial currents that cannot be described as classical conduction or classical polarization. Derivations of conservation of current involve oversimplified treatments of dielectrics and polarization in nearly every textbook. Because real dielectrics do not behave in that simple way-not even approximately-classical derivations of conservation of current are often distrusted or even ignored. We show that current is conserved inside atoms. We show that current is conserved exactly in any material no matter how complex are the properties of dielectric, polarization, or conduction currents. Electricity has a special role because conservation of current is a universal law.Most models of chemical reactions do not conserve current and need to be changed to do so. On the macroscopic scale of life, conservation of current necessarily links far spread boundaries to each other, correlating inputs and outputs, and thereby creating devices.We suspect that correlations created by displacement current link all scales and allow atoms to control the machines and organisms of life. Conservation of current has a special role in our lives and life, as well as in physics. We believe models, simulations, and computations should conserve current on all scales, as accurately as possible, because physics conserves current that way. We believe models will be much more successful if they conserve current at every level of resolution, the way physics does.We surely need successful models as we try to control macroscopic functions by atomic interventions, in technology, life, and medicine. Maxwell’s displacement current lets us see stars. We hope it will help us see how atoms control life.
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Affiliation(s)
- Bob Eisenberg
- 1Department of Applied Mathematics, Illinois Institute of Technology, Illinois,USA
- 2Department of Physiology and Biophysics, Rush University, USA
| | - Xavier Oriols
- 3Departament d’Enginyeria Electrònica, Universitat Autònoma de Barcelona, Spain
| | - David Ferry
- 4School of Electrical, Computer, and Energy Engineering, Arizona State University, USA
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145
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Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei GW, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci 2017; 27:112-128. [PMID: 28836357 DOI: 10.1002/pro.3280] [Citation(s) in RCA: 1183] [Impact Index Per Article: 169.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/11/2022]
Abstract
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.
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Affiliation(s)
| | - Dave Engel
- Pacific Northwest National Laboratory, Richland, Washington
| | - Keith Star
- Pacific Northwest National Laboratory, Richland, Washington
| | - Kyle Monson
- Pacific Northwest National Laboratory, Richland, Washington
| | - Juan Brandi
- Pacific Northwest National Laboratory, Richland, Washington
| | | | | | | | - Jiahui Chen
- Southern Methodist University, Dallas, Texas
| | - Karina Liles
- Pacific Northwest National Laboratory, Richland, Washington
| | - Minju Chun
- Pacific Northwest National Laboratory, Richland, Washington
| | - Peter Li
- Pacific Northwest National Laboratory, Richland, Washington
| | | | | | - Robert Konecny
- University of California San Diego, San Diego, California
| | - David R Koes
- University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | - Weihua Geng
- Southern Methodist University, Dallas, Texas
| | | | - Guo-Wei Wei
- Michigan State University, East Lansing, Michigan
| | | | | | - Nathan A Baker
- Pacific Northwest National Laboratory, Richland, Washington.,Brown University, Providence, Rhode Island
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146
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Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšič M, Dill KA. How Water's Properties Are Encoded in Its Molecular Structure and Energies. Chem Rev 2017; 117:12385-12414. [PMID: 28949513 PMCID: PMC5639468 DOI: 10.1021/acs.chemrev.7b00259] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 11/29/2022]
Abstract
How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties.
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Affiliation(s)
- Emiliano Brini
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Christopher J. Fennell
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Marivi Fernandez-Serra
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Barbara Hribar-Lee
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, SI-1000 Ljubljana, Slovenia
| | - Miha Lukšič
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Večna
pot 113, SI-1000 Ljubljana, Slovenia
| | - Ken A. Dill
- Laufer
Center for Physical and Quantitative Biology, Department of Physics and Astronomy, and Department of
Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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147
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Gygli G, Lucas MF, Guallar V, van Berkel WJH. The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths. PLoS Comput Biol 2017; 13:e1005787. [PMID: 28985219 PMCID: PMC5646868 DOI: 10.1371/journal.pcbi.1005787] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/18/2017] [Accepted: 09/21/2017] [Indexed: 01/03/2023] Open
Abstract
Vanillyl alcohol oxidase (VAO) is a homo-octameric flavoenzyme belonging to the VAO/PCMH family. Each VAO subunit consists of two domains, the FAD-binding and the cap domain. VAO catalyses, among other reactions, the two-step conversion of p-creosol (2-methoxy-4-methylphenol) to vanillin (4-hydroxy-3-methoxybenzaldehyde). To elucidate how different ligands enter and exit the secluded active site, Monte Carlo based simulations have been performed. One entry/exit path via the subunit interface and two additional exit paths have been identified for phenolic ligands, all leading to the si side of FAD. We argue that the entry/exit path is the most probable route for these ligands. A fourth path leading to the re side of FAD has been found for the co-ligands dioxygen and hydrogen peroxide. Based on binding energies and on the behaviour of ligands in these four paths, we propose a sequence of events for ligand and co-ligand migration during catalysis. We have also identified two residues, His466 and Tyr503, which could act as concierges of the active site for phenolic ligands, as well as two other residues, Tyr51 and Tyr408, which could act as a gateway to the re side of FAD for dioxygen. Most of the residues in the four paths are also present in VAO’s closest relatives, eugenol oxidase and p-cresol methylhydroxylase. Key path residues show movements in our simulations that correspond well to conformations observed in crystal structures of these enzymes. Preservation of other path residues can be linked to the electron acceptor specificity and oligomerisation state of the three enzymes. This study is the first comprehensive overview of ligand and co-ligand migration in a member of the VAO/PCMH family, and provides a proof of concept for the use of an unbiased method to sample this process. Enzymes are bionanomachines, which speed up chemical reactions in organisms. To understand how they achieve that, we need to study their mechanisms. Computational enzymology can show us what happens in the enzyme’s active site during a reaction. But molecules need first to reach the active site before a reaction can start. The process of substrate entry and product exit to the active site is often neglected when studying enzymes. However, these two events are of fundamental importance to the proper functioning of any enzyme. We are interested in these dynamic processes to complete our understanding of the mode of action of enzymes. In our work, we have studied substrate and product migration in vanillyl alcohol oxidase. This enzyme can produce the flavour vanillin and enantiopure alcohols, but also catalyses other reactions. The named products are of interest to the flavour- and fine-chemical industries.
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Affiliation(s)
- Gudrun Gygli
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, WE Wageningen, The Netherlands
| | - Maria Fátima Lucas
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona, Spain
| | - Victor Guallar
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Spain
| | - Willem J. H. van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, WE Wageningen, The Netherlands
- * E-mail:
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148
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Pillong M, Hiss JA, Schneider P, Lin YC, Posselt G, Pfeiffer B, Blatter M, Müller AT, Bachler S, Neuhaus CS, Dittrich PS, Altmann KH, Wessler S, Schneider G. Rational Design of Membrane-Pore-Forming Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1701316. [PMID: 28799716 DOI: 10.1002/smll.201701316] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/29/2017] [Indexed: 06/07/2023]
Abstract
Specific interactions of peptides with lipid membranes are essential for cellular communication and constitute a central aspect of the innate host defense against pathogens. A computational method for generating innovative membrane-pore-forming peptides inspired by natural templates is presented. Peptide representation in terms of sequence- and topology-dependent hydrophobic moments is introduced. This design concept proves to be appropriate for the de novo generation of first-in-class membrane-active peptides with the anticipated mode of action. The designed peptides outperform the natural template in terms of their antibacterial activity. They form a kinked helical structure and self-assemble in the membrane by an entropy-driven mechanism to form dynamically growing pores that are dependent on the lipid composition. The results of this study demonstrate the unique potential of natural template-based peptide design for chemical biology and medicinal chemistry.
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Affiliation(s)
- Max Pillong
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Jan A Hiss
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Yen-Chu Lin
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Gernot Posselt
- Department of Molecular Biology, University of Salzburg, 5020, Salzburg, Austria
| | - Bernhard Pfeiffer
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Markus Blatter
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Alex T Müller
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Simon Bachler
- Department of Biosystems Science and Engineering, ETH Zurich, 8093, Zurich, Switzerland
| | - Claudia S Neuhaus
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, 8093, Zurich, Switzerland
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Silja Wessler
- Department of Molecular Biology, University of Salzburg, 5020, Salzburg, Austria
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
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149
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Izairi R, Kamberaj H. Comparison Study of Polar and Nonpolar Contributions to Solvation Free Energy. J Chem Inf Model 2017; 57:2539-2553. [PMID: 28880080 DOI: 10.1021/acs.jcim.7b00368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we compared the contributions of polar and nonpolar interactions to the solvation free energy of a solute in solvent, which is decomposed into four different terms based on the nature of interactions: (i) electrostatic solvation free energy term counting for the work done to move solute charges from fixed points in some reference environment to their configuration positions in solvent; (ii) solute-solvent van der Waals dispersion interactions; (iii) change on solvent-solvent interactions and solvent entropy due to reorganization of solvent around solute cavity in solvent; and (iv) compensation of electrostatic forces acting on the dielectric surface boundary between solvent and solute. We compared these contributions to each other for a data set of 573 proteins, which were prepared using CHARMM22 and AMBER force fields. In addition, we compared the calculated with experimental hydration free energies for a data set of 642 small molecules, which were prepared using the general AMBER force field. Our results indicated the significance of each term to the total solvation free energy.
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Affiliation(s)
- Redona Izairi
- Department of Physics, Faculty of Mathematics and Natural Sciences, State University of Tetovo , Street Ilinden, 1200, Tetovo, Republic of Macedonia
| | - Hiqmet Kamberaj
- Department of Computer Engineering, Faculty of Engineering, International Balkan University , Tashko Karadza, 11A, 1000, Skopje, Republic of Macedonia
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150
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Marchand JR, Dalle Vedove A, Lolli G, Caflisch A. Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. J Chem Inf Model 2017; 57:2584-2597. [PMID: 28862840 DOI: 10.1021/acs.jcim.7b00336] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The high-throughput docking protocol called ALTA-VS (anchor-based library tailoring approach for virtual screening) was developed in 2005 for the efficient in silico screening of large libraries of compounds by preselection of only those molecules that have optimal fragments (anchors) for the protein target. Here we present an updated version of ALTA-VS with a broader range of potential applications. The evaluation of binding energy makes use of a classical force field with implicit solvent in the continuum dielectric approximation. In about 2 days per protein target on a 96-core compute cluster (equipped with Xeon E3-1280 quad core processors at 2.5 GHz), the screening of a library of nearly 77 000 diverse molecules with the updated ALTA-VS protocol has resulted in the identification of 19, 3, 3, and 2 μM inhibitors of the human bromodomains ATAD2, BAZ2B, BRD4(1), and CREBBP, respectively. The success ratio (i.e., number of actives in a competition binding assay in vitro divided by the number of compounds tested) ranges from 8% to 13% in dose-response measurements. The poses predicted by fragment-based docking for the three ligands of the BAZ2B bromodomain were confirmed by protein X-ray crystallography.
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Affiliation(s)
- Jean-Rémy Marchand
- Department of Biochemistry, University of Zürich , CH-8057, Zürich, Switzerland
| | | | - Graziano Lolli
- Centre for Integrative Biology, University of Trento , I-38123, Povo, Italy
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich , CH-8057, Zürich, Switzerland
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