1
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Chen W, Zhang Y, Qiang Q, Zou L, Zou P, Xu Y. Pinobanksin from peony seed husk: A flavonoid with the potential to inhibit the proliferation of SH-SY5Y. Food Sci Nutr 2024; 12:815-829. [PMID: 38370064 PMCID: PMC10867468 DOI: 10.1002/fsn3.3786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/14/2023] [Accepted: 10/08/2023] [Indexed: 02/20/2024] Open
Abstract
Pinobanksin, as one of the flavonoids, has powerful biological activities but has been under-recognized. In this study, we optimized the extraction method of phragmites from peony seed shells by using organic solvent extraction. The yield of PSMS was 10.54 ± 0.13% under the conditions of ethanol volume fraction 70%, extraction temperature 70°C, material-liquid ratio 1:25 g/mL, and extraction time 60 min; the optimized PSMS could be effectively separated in S-8 macroporous resin coupled with C18. The relative content of PSMS was increased from 0.42% in PSMS to 92.53% after C18 purification; the antioxidant activity test revealed that pinobanksin could exert antioxidant ability by binding catalase (CAT) enzyme. Second, it was found that pinobanksin could effectively inhibit the proliferation of SH-SY5Y cells, mainly by binding to BCL2-associated X (BAX), B-cell lymphoma-2 (BCL-2), and cyclin-dependent Kinase 4/6 (CDK4/6) to produce more hydrogen bonds to inhibit their activities. This study confirms the medicinal potential of pinobanksin and provides the basis for the proper understanding of pinobanksin and the development of related products.
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Affiliation(s)
- Wen‐Tao Chen
- School of Biological and Food EngineeringChangzhou UniversityChangzhouJiangsuChina
| | - Ying‐Yang Zhang
- School of Biological and Food EngineeringChangzhou UniversityChangzhouJiangsuChina
| | - Qiang Qiang
- Changzhou Wujin No. 3 People's HospitalChangzhouJiangsuChina
| | - Lin‐Ling Zou
- School of Biological and Food EngineeringChangzhou UniversityChangzhouJiangsuChina
| | - Ping Zou
- School of Biological and Food EngineeringChangzhou UniversityChangzhouJiangsuChina
| | - Ying Xu
- School of Biological and Food EngineeringChangzhou UniversityChangzhouJiangsuChina
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2
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Jacobsen L, Lydersen L, Khandelia H. ATP-Bound State of the Uncoupling Protein 1 (UCP1) from Molecular Simulations. J Phys Chem B 2023; 127:9685-9696. [PMID: 37921649 DOI: 10.1021/acs.jpcb.3c03473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The uncoupling protein 1 (UCP1) dissipates the transmembrane (TM) proton gradient in the inner mitochondrial membrane (IMM) by leaking protons across the membrane and producing heat in the process. Such a nonshivering production of heat in the brown adipose tissue can combat obesity-related diseases. UCP1-associated proton leak is activated by free fatty acids and inhibited by purine nucleotides. The mechanism of proton leak and the binding sites of the activators (fatty acids) remain unknown, while the binding site of the inhibitors (nucleotides) was described recently. Using molecular dynamics simulations, we generated a conformational ensemble of UCP1. Using metadynamics-based free energy calculations, we obtained the most likely ATP-bound conformation of UCP1. Our conformational ensemble provides a molecular basis for a breadth of prior biochemical data available for UCP1. Based on the simulations, we make the following testable predictions about the mechanisms of activation of proton leak and proton leak inhibition by ATP: (1) R277 plays the dual role of stabilizing ATP at the binding site for inhibition and acting as a proton surrogate for D28 in the absence of a proton during proton transport, (2) the binding of ATP to UCP1 is mediated by residues R84, R92, R183, and S88, (3) R92 shuttles ATP from the E191-R92 gate in the intermembrane space to the nucleotide binding site and serves to increase ATP affinity, (4) ATP can inhibit proton leak by controlling the ionization states of matrix facing lysine residues such as K269 and K56, and (5) fatty acids can bind to UCP1 from the IMM either via the cavity between TM1 and TM2 or between TM5 and TM6. Our simulations set the platform for future investigations into the proton transport and inhibition mechanisms of UCP1.
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Affiliation(s)
- Luise Jacobsen
- PhyLife: Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Laura Lydersen
- PhyLife: Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Himanshu Khandelia
- PhyLife: Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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3
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Zhang L, Yao L, Zhao F, Yu A, Zhou Y, Wen Q, Wang J, Zheng T, Chen P. Protein and Peptide-Based Nanotechnology for Enhancing Stability, Bioactivity, and Delivery of Anthocyanins. Adv Healthc Mater 2023; 12:e2300473. [PMID: 37537383 DOI: 10.1002/adhm.202300473] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/18/2023] [Indexed: 08/05/2023]
Abstract
Anthocyanin, a unique natural polyphenol, is abundant in plants and widely utilized in biomedicine, cosmetics, and the food industry due to its excellent antioxidant, anticancer, antiaging, antimicrobial, and anti-inflammatory properties. However, the degradation of anthocyanin in an extreme environment, such as alkali pH, high temperatures, and metal ions, limits its physiochemical stabilities and bioavailabilities. Encapsulation and combining anthocyanin with biomaterials could efficiently stabilize anthocyanin for protection. Promisingly, natural or artificially designed proteins and peptides with favorable stabilities, excellent biocapacity, and wide sources are potential candidates to stabilize anthocyanin. This review focuses on recent progress, strategies, and perspectives on protein and peptide for anthocyanin functionalization and delivery, i.e., formulation technologies, physicochemical stability enhancement, cellular uptake, bioavailabilities, and biological activities development. Interestingly, due to the simplicity and diversity of peptide structure, the interaction mechanisms between peptide and anthocyanin could be illustrated. This work sheds light on the mechanism of protein/peptide-anthocyanin nanoparticle construction and expands on potential applications of anthocyanin in nutrition and biomedicine.
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Affiliation(s)
- Lei Zhang
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L3G1, Canada
| | - Liang Yao
- College of Biotechnology, Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Feng Zhao
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L3G1, Canada
| | - Alice Yu
- Schulich School of Medicine and Dentistry, Western University, Ontario, N6A 3K7, Canada
| | - Yueru Zhou
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L3G1, Canada
| | - Qingmei Wen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Jun Wang
- College of Biotechnology, Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Tao Zheng
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Pu Chen
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L3G1, Canada
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4
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Computational insight into stability-enhanced systems of anthocyanin with protein/peptide. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 6:100168. [PMID: 36923156 PMCID: PMC10009195 DOI: 10.1016/j.fochms.2023.100168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/24/2022] [Accepted: 02/18/2023] [Indexed: 02/24/2023]
Abstract
Anthocyanins, which belong to the flavonoid group, are commonly found in the organs of plants native to South and Central America. However, these pigments are unstable under conditions of varying pH, heat, etc., which limits their potential applications. One method for preserving the stability of anthocyanins is through encapsulation using proteins or peptides. Nevertheless, the complex and diverse structure of these molecules, as well as the limitation of experimental technologies, have hindered a comprehensive understanding of the encapsulation processes and the mechanisms by which stability is enhanced. To address these challenges, computational methods, such as molecular docking and molecular dynamics simulation have been used to study the binding affinity and dynamics of interactions between proteins/peptides and anthocyanins. This review summarizes the mechanisms of interaction between these systems, based on computational approaches, and highlights the role of proteins and peptides in the stability enhancement of anthocyanins. It also discusses the current limitations of these methods and suggests possible solutions.
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5
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Alizadeh Sahraei A, Azizi D, Mokarizadeh AH, Boffito DC, Larachi F. Emerging Trends of Computational Chemistry and Molecular Modeling in Froth Flotation: A Review. ACS ENGINEERING AU 2023; 3:128-164. [PMID: 37362006 PMCID: PMC10288516 DOI: 10.1021/acsengineeringau.2c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 06/28/2023]
Abstract
Froth flotation is the most versatile process in mineral beneficiation, extensively used to concentrate a wide range of minerals. This process comprises mixtures of more or less liberated minerals, water, air, and various chemical reagents, involving a series of intermingled multiphase physical and chemical phenomena in the aqueous environment. Today's main challenge facing the froth flotation process is to gain atomic-level insights into the properties of its inherent phenomena governing the process performance. While it is often challenging to determine these phenomena via trial-and-error experimentations, molecular modeling approaches not only elicit a deeper understanding of froth flotation but can also assist experimental studies in saving time and budget. Thanks to the rapid development of computer science and advances in high-performance computing (HPC) infrastructures, theoretical/computational chemistry has now matured enough to successfully and gainfully apply to tackle the challenges of complex systems. In mineral processing, however, advanced applications of computational chemistry are increasingly gaining ground and demonstrating merit in addressing these challenges. Accordingly, this contribution aims to encourage mineral scientists, especially those interested in rational reagent design, to become familiarized with the necessary concepts of molecular modeling and to apply similar strategies when studying and tailoring properties at the molecular level. This review also strives to deliver the state-of-the-art integration and application of molecular modeling in froth flotation studies to assist either active researchers in this field to disclose new directions for future research or newcomers to the field to initiate innovative works.
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Affiliation(s)
- Abolfazl Alizadeh Sahraei
- Department
of Chemical Engineering, Université
Laval, 1065 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada
| | - Dariush Azizi
- Department
of Chemical Engineering, École Polytechnique
de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal H3T 1J4, Canada
| | - Abdol Hadi Mokarizadeh
- School
of Polymer Science and Polymer Engineering, University of Akron, Akron, Ohio 44325, United States
| | - Daria Camilla Boffito
- Department
of Chemical Engineering, École Polytechnique
de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal H3T 1J4, Canada
| | - Faïçal Larachi
- Department
of Chemical Engineering, Université
Laval, 1065 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada
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6
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Sami S, Marrink SJ. Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations. J Chem Theory Comput 2023. [PMID: 37327401 DOI: 10.1021/acs.jctc.2c01186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Chemical reactions are ubiquitous in both materials and the biophysical sciences. While coarse-grained (CG) molecular dynamics simulations are often needed to study the spatiotemporal scales present in these fields, chemical reactivity has not been explored thoroughly in CG models. In this work, a new approach to model chemical reactivity is presented for the widely used Martini CG Martini model. Employing tabulated potentials with a single extra particle for the angle dependence, the model provides a generic framework for capturing bonded topology changes using nonbonded interactions. As a first example application, the reactive model is used to study the macrocycle formation of benzene-1,3-dithiol molecules through the formation of disulfide bonds. We show that starting from monomers, macrocycles with sizes in agreement with experimental results are obtained using reactive Martini. Overall, our reactive Martini framework is general and can be easily extended to other systems. All of the required scripts and tutorials to explain its use are provided online.
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Affiliation(s)
- Selim Sami
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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7
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Bosia F, Zheng P, Vaucher A, Weymuth T, Dral PO, Reiher M. Ultra-fast semi-empirical quantum chemistry for high-throughput computational campaigns with Sparrow. J Chem Phys 2023; 158:054118. [PMID: 36754821 DOI: 10.1063/5.0136404] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Semi-empirical quantum chemical approaches are known to compromise accuracy for the feasibility of calculations on huge molecules. However, the need for ultrafast calculations in interactive quantum mechanical studies, high-throughput virtual screening, and data-driven machine learning has shifted the emphasis toward calculation runtimes recently. This comes with new constraints for the software implementation as many fast calculations would suffer from a large overhead of the manual setup and other procedures that are comparatively fast when studying a single molecular structure, but which become prohibitively slow for high-throughput demands. In this work, we discuss the effect of various well-established semi-empirical approximations on calculation speed and relate this to data transfer rates from the raw-data source computer to the results of the visualization front end. For the former, we consider desktop computers, local high performance computing, and remote cloud services in order to elucidate the effect on interactive calculations, for web and cloud interfaces in local applications, and in world-wide interactive virtual sessions. The models discussed in this work have been implemented into our open-source software SCINE Sparrow.
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Affiliation(s)
- Francesco Bosia
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Peikun Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Alain Vaucher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Thomas Weymuth
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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8
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Alaghemandi M, Salehi L, Samolis P, Trachtenberg BT, Turnali A, Sander MY, Sharifzadeh S. Atomic understanding of structural deformations upon ablation of graphene. NANO SELECT 2021. [DOI: 10.1002/nano.202000248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Mohammad Alaghemandi
- Department of Electrical and Computer Engineering Boston University Boston Massachusetts USA
| | - Leili Salehi
- Department of Electrical and Computer Engineering Boston University Boston Massachusetts USA
| | - Panagis Samolis
- Department of Electrical and Computer Engineering Boston University Boston Massachusetts USA
| | | | - Ahmet Turnali
- Department of Electrical and Computer Engineering Boston University Boston Massachusetts USA
| | - Michelle Y. Sander
- Department of Electrical and Computer Engineering Boston University Boston Massachusetts USA
- Division of Materials Science and Engineering Boston University Boston Massachusetts USA
- Department of Biomedical Engineering Boston University Boston Massachusetts USA
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering Boston University Boston Massachusetts USA
- Division of Materials Science and Engineering Boston University Boston Massachusetts USA
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9
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Pezeshkian W, Marrink SJ. Simulating realistic membrane shapes. Curr Opin Cell Biol 2021; 71:103-111. [PMID: 33721706 DOI: 10.1016/j.ceb.2021.02.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
Abstract
Biological membranes exhibit diversity in their shapes and complexity in chemical compositions that are linked to many cellular functions. These two central features of biomembranes have been the subject of numerous simulation studies, using a diverse range of computational techniques. Currently, the field is able to capture this complexity at increasing levels of realism and connect the microscopic view on protein-lipid interactions to cellular morphologies at the level of entire organelles. Here we highlight recent advances in this topic, identify current bottlenecks, and sketch possible ways ahead.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
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10
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Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation. Nat Commun 2020; 11:5713. [PMID: 33177517 PMCID: PMC7658983 DOI: 10.1038/s41467-020-19497-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022] Open
Abstract
Combustion is a complex chemical system which involves thousands of chemical reactions and generates hundreds of molecular species and radicals during the process. In this work, a neural network-based molecular dynamics (MD) simulation is carried out to simulate the benchmark combustion of methane. During MD simulation, detailed reaction processes leading to the creation of specific molecular species including various intermediate radicals and the products are intimately revealed and characterized. Overall, a total of 798 different chemical reactions were recorded and some new chemical reaction pathways were discovered. We believe that the present work heralds the dawn of a new era in which neural network-based reactive MD simulation can be practically applied to simulating important complex reaction systems at ab initio level, which provides atomic-level understanding of chemical reaction processes as well as discovery of new reaction pathways at an unprecedented level of detail beyond what laboratory experiments could accomplish. Gaining insights into combustion processes is challenging due to the complex reactions involved. The present work proposes a neural network potential model trained to ab initio data that enables to simulate the combustion of methane by predicting reactants, products and reaction intermediates.
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11
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Gissinger JR, Jensen BD, Wise KE. REACTER: A Heuristic Method for Reactive Molecular Dynamics. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c02012] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacob R. Gissinger
- Advanced Materials and Processing Branch, NASA Langley Research Center, Hampton, Virginia 23681, United States
| | - Benjamin D. Jensen
- Advanced Materials and Processing Branch, NASA Langley Research Center, Hampton, Virginia 23681, United States
| | - Kristopher E. Wise
- Advanced Materials and Processing Branch, NASA Langley Research Center, Hampton, Virginia 23681, United States
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12
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Rice BM, Mattson WD, Larentzos JP, Byrd EFC. Heuristics for chemical species identification in dense systems. J Chem Phys 2020; 153:064102. [DOI: 10.1063/5.0015664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Betsy M. Rice
- US Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, Maryland 21005, USA
| | - William D. Mattson
- US Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, Maryland 21005, USA
| | - James P. Larentzos
- US Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, Maryland 21005, USA
| | - Edward F. C. Byrd
- US Army CCDC Army Research Laboratory, Aberdeen Proving Ground, Aberdeen, Maryland 21005, USA
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13
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Young JM, Mondal A, Barckholtz TA, Kiss G, Koziol L, Panagiotopoulos AZ. Predicting chemical reaction equilibria in molten carbonate fuel cells via molecular simulations. AIChE J 2020. [DOI: 10.1002/aic.16988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jeffrey M. Young
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | - Anirban Mondal
- Department of Chemical and Biological Engineering Princeton University Princeton New Jersey USA
| | | | - Gabor Kiss
- ExxonMobil Research and Engineering Annandale New Jersey USA
| | - Lucas Koziol
- ExxonMobil Research and Engineering Annandale New Jersey USA
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14
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Lindsey RK, Goldman N, Fried LE, Bastea S. Many-body reactive force field development for carbon condensation in C/O systems under extreme conditions. J Chem Phys 2020; 153:054103. [DOI: 10.1063/5.0012840] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Rebecca K. Lindsey
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Nir Goldman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
- Department of Chemical Engineering, University of California, Davis, California 95616, USA
| | - Laurence E. Fried
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Sorin Bastea
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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15
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Capelli R, Lyu W, Bolnykh V, Meloni S, Olsen JMH, Rothlisberger U, Parrinello M, Carloni P. Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study. J Phys Chem Lett 2020; 11:6373-6381. [PMID: 32672983 DOI: 10.1021/acs.jpclett.0c00999] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The koff values of ligands unbinding to proteins are key parameters for drug discovery. Their predictions based on molecular simulation may under- or overestimate experiment in a system- and/or technique-dependent way. Here we use an established method-infrequent metadynamics, based on the AMBER force field-to compute the koff of the ligand iperoxo (in clinical use) targeting the muscarinic receptor M2. The ligand charges are calculated by either (i) the Amber standard procedure or (ii) B3LYP-DFT. The calculations using (i) turn out not to provide a reasonable estimation of the transition-state free energy. Those using (ii) differ from experiment by 2 orders of magnitude. On the basis of B3LYP DFT QM/MM simulations, we suggest that the observed discrepancy in (ii) arises, at least in part, from the lack of electronic polarization and/or charge transfer in biomolecular force fields. These issues might be present in other systems, such as DNA-protein complexes.
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Affiliation(s)
- Riccardo Capelli
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
- JARA-HPC, Forschungszentrum Jülich, D-54245 Jülich, Germany
| | - Wenping Lyu
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
| | - Viacheslav Bolnykh
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Simone Meloni
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Luigi Borsari 46, I-44121, Ferrara, Italy
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zürich, c/o USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Ticino, Switzerland
- Facoltà di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana (USI), Via Giuseppe Buffi 13, CH-6900, Lugano, Ticino, Switzerland
- Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Paolo Carloni
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
- JARA-Institute INM-11: Molecular Neuroscience and Neuroimaging, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
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16
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Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review. Catalysts 2020. [DOI: 10.3390/catal10060691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.
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17
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Käser S, Unke OT, Meuwly M. Isomerization and decomposition reactions of acetaldehyde relevant to atmospheric processes from dynamics simulations on neural network-based potential energy surfaces. J Chem Phys 2020; 152:214304. [DOI: 10.1063/5.0008223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Oliver T. Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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18
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Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk. J Phys Chem B 2019; 123:9846-9861. [PMID: 31647873 DOI: 10.1021/acs.jpcb.9b03258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular mechanics with proton transfer (MMPT) force field is combined with multistate adiabatic reactive molecular dynamics (MS-ARMD) to describe proton transport in the condensed phase. Parametrization for small protonated water clusters based on electronic structure calculations at the MP2/6-311+G(2d,2p) level of theory and refinement by comparing with infrared spectra for a protonated water tetramer yields a force field which faithfully describes the minimum energy structures of small protonated water clusters. In protonated water clusters up to (H2O)100H+, the proton hopping rate is around 100 hops/ns. This rate converges for 21 ≤ n ≤ 31, and no further speedup in bulk water is found. This indicates that bulklike behavior requires the solvation of a Zundel motif by ∼25 water molecules, which corresponds to the second solvation sphere. For smaller cluster sizes, the number of available states (i.e., the number of proton acceptors) is too small and slows down proton-transfer rates. The cluster simulations confirm that the excess proton is typically located on the surface. The free-energy surface as a function of the weights of the two lowest states and a configurational parameter suggests that the "special pair" plays a central role in rapid proton transport. The barriers between this minimum-energy structure and the Zundel and Eigen minima are sufficiently low (∼1 kcal/mol, consistent with recent experiments and commensurate with a hopping rate of ∼100/ns or 1 every 10 ps), leading to a highly dynamic environment. These findings are also consistent with recent experiments which find that Zundel-type hydration geometries are prevalent in bulk water.
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19
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Rivero U, Unke OT, Meuwly M, Willitsch S. Reactive atomistic simulations of Diels-Alder reactions: The importance of molecular rotations. J Chem Phys 2019; 151:104301. [DOI: 10.1063/1.5114981] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Uxía Rivero
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Oliver T. Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Stefan Willitsch
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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20
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Unke OT, Brickel S, Meuwly M. Sampling reactive regions in phase space by following the minimum dynamic path. J Chem Phys 2019; 150:074107. [DOI: 10.1063/1.5082885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Oliver T. Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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21
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Simm GN, Vaucher AC, Reiher M. Exploration of Reaction Pathways and Chemical Transformation Networks. J Phys Chem A 2018; 123:385-399. [DOI: 10.1021/acs.jpca.8b10007] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gregor N. Simm
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Alain C. Vaucher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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