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Hong LX, Sun L, Li C, Zhang RL, Zhao JS. Multiple Applications of a Novel Fluorescence Probe with Large Stokes Shift and Sensitivity for Rapid H 2S Detection. J Fluoresc 2023:10.1007/s10895-023-03377-y. [PMID: 37552376 DOI: 10.1007/s10895-023-03377-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Herein, a novel fluorescence probe Fla-DNP based on flavonol has been designed and synthesized for rapid, specific detection of H2S. With the addition of H2S, Fla-DNP triggered thiolysis and released Fla displaying the "turn-on" fluorescence response at 566 nm, which is consistent with the reaction site predicted by calculating Electrostatic potential and ADCH charges. As an easily available H2S probe, Fla-DNP has the advantages of high selectivity, anti-interference, low detection limit (0.834 μM), short response time (6 min), and large Stokes shift (124 nm). The sensing mechanism of H2S was determined by HRMS analysis and DFT calculation. Moreover, Fla-DNP processes a wide range of multiple applications, including the detection of H2S in environmental water samples with good recovery rates ranging from 89.6% to 102.0%, as well as tracking the production of H2S during food spoilage. Meanwhile, the probe exhibits superior biocompatibility and can not only be available used for H2S detection in living cells but be further designed as an H2S-activated CO photoreleaser, based on which it can be developed as a targeted anti-cancer drug. A novel fluorescence probe Fla-DNP was synthesized utilizing 4-dimethylaminobenzoxanthone fluorescent dye (Fla) as the fluorophore, 2, 4-dinitrobenzenether group (DNP) as the recognition group, which can rapidly respond to H2S with high selectivity, anti-interference, low detection limit (0.834 μM), short response time (6 min), and large Stokes shift (124 nm) characteristics. The practical applications of Fla-DNP were further explored in water, foodstuffs samples and living cells. It is reflected that Fla-DNP can not only track H2S in complex environment water, but also can detect H2S produced during foodstuffs spoilage to monitor food freshness. More importantly, Fla-DNP can be available used for H2S detection in living cells and utilize the properties of the photoinduced release of CO from flavonols to be designed as a bifunctional platform for H2S detection and CO release. It is demonstrated that H2S-activated CO photoreleaser Fla-DNP has promise for development as an anti-cancer drug.
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Affiliation(s)
- Lai-Xin Hong
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, Xi'an, Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Le Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, Xi'an, Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Cong Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, Xi'an, Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Rong-Lan Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, Xi'an, Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China.
| | - Jian-She Zhao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, Xi'an, Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi, 710069, People's Republic of China
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2
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Hempel T, Elez K, Krüger N, Raich L, Shrimp JH, Danov O, Jonigk D, Braun A, Shen M, Hall MD, Pöhlmann S, Hoffmann M, Noé F. Synergistic inhibition of SARS-CoV-2 cell entry by otamixaban and covalent protease inhibitors: pre-clinical assessment of pharmacological and molecular properties. Chem Sci 2021; 12:12600-12609. [PMID: 34703545 PMCID: PMC8494051 DOI: 10.1039/d1sc01494c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/20/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2, the cause of the COVID-19 pandemic, exploits host cell proteins for viral entry into human lung cells. One of them, the protease TMPRSS2, is required to activate the viral spike protein (S). Even though two inhibitors, camostat and nafamostat, are known to inhibit TMPRSS2 and block cell entry of SARS-CoV-2, finding further potent therapeutic options is still an important task. In this study, we report that a late-stage drug candidate, otamixaban, inhibits SARS-CoV-2 cell entry. We show that otamixaban suppresses TMPRSS2 activity and SARS-CoV-2 infection of a human lung cell line, although with lower potency than camostat or nafamostat. In contrast, otamixaban inhibits SARS-CoV-2 infection of precision cut lung slices with the same potency as camostat. Furthermore, we report that otamixaban's potency can be significantly enhanced by (sub-) nanomolar nafamostat or camostat supplementation. Dominant molecular TMPRSS2-otamixaban interactions are assessed by extensive 109 μs of atomistic molecular dynamics simulations. Our findings suggest that combinations of otamixaban with supplemental camostat or nafamostat are a promising option for the treatment of COVID-19.
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Affiliation(s)
- Tim Hempel
- Department of Mathematics and Computer Science, Freie Universität Berlin Berlin Germany
- Department of Physics, Freie Universität Berlin Berlin Germany
| | - Katarina Elez
- Department of Mathematics and Computer Science, Freie Universität Berlin Berlin Germany
| | - Nadine Krüger
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research Göttingen Germany
| | - Lluís Raich
- Department of Mathematics and Computer Science, Freie Universität Berlin Berlin Germany
| | - Jonathan H Shrimp
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville MD USA
| | - Olga Danov
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR) Hannover Germany
| | - Danny Jonigk
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR) Hannover Germany
- Institute of Pathology, Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Hannover Germany
| | - Armin Braun
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Member of Fraunhofer International Consortium for Anti-Infective Research (iCAIR) Hannover Germany
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville MD USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health Rockville MD USA
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research Göttingen Germany
- Faculty of Biology and Psychology, University Göttingen Göttingen Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center - Leibniz Institute for Primate Research Göttingen Germany
- Faculty of Biology and Psychology, University Göttingen Göttingen Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin Berlin Germany
- Department of Physics, Freie Universität Berlin Berlin Germany
- Department of Chemistry, Rice University Houston TX USA
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3
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Balusek C, Hwang H, Lau CH, Lundquist K, Hazel A, Pavlova A, Lynch DL, Reggio PH, Wang Y, Gumbart JC. Accelerating Membrane Simulations with Hydrogen Mass Repartitioning. J Chem Theory Comput 2019; 15:4673-4686. [PMID: 31265271 PMCID: PMC7271963 DOI: 10.1021/acs.jctc.9b00160] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The time step of atomistic molecular dynamics (MD) simulations is determined by the fastest motions in the system and is typically limited to 2 fs. An increasingly popular approach is to increase the mass of the hydrogen atoms to ∼3 amu and decrease the mass of the parent atom by an equivalent amount. This approach, known as hydrogen-mass repartitioning (HMR), permits time steps up to 4 fs with reasonable simulation stability. While HMR has been applied in many published studies to date, it has not been extensively tested for membrane-containing systems. Here, we compare the results of simulations of a variety of membranes and membrane-protein systems run using a 2 fs time step and a 4 fs time step with HMR. For pure membrane systems, we find almost no difference in structural properties, such as area-per-lipid, electron density profiles, and order parameters, although there are differences in kinetic properties such as the diffusion constant. Conductance through a porin in an applied field, partitioning of a small peptide, hydrogen-bond dynamics, and membrane mixing show very little dependence on HMR and the time step. We also tested a 9 Å cutoff as compared to the standard CHARMM cutoff of 12 Å, finding significant deviations in many properties tested. We conclude that HMR is a valid approach for membrane systems, but a 9 Å cutoff is not.
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Affiliation(s)
| | | | - Chun Hon Lau
- Department of Physics , The Chinese University of Hong Kong , Shatin, NT, Hong Kong , People's Republic of China
| | | | | | | | - Diane L Lynch
- Department of Chemistry and Biochemistry , University of North Carolina , Greensboro , North Carolina 27402 , United States
| | - Patricia H Reggio
- Department of Chemistry and Biochemistry , University of North Carolina , Greensboro , North Carolina 27402 , United States
| | - Yi Wang
- Department of Physics , The Chinese University of Hong Kong , Shatin, NT, Hong Kong , People's Republic of China
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4
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Pang YP. Low-mass molecular dynamics simulation for configurational sampling enhancement: More evidence and theoretical explanation. Biochem Biophys Rep 2015; 4:126-133. [PMID: 29124195 PMCID: PMC5668912 DOI: 10.1016/j.bbrep.2015.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/30/2015] [Accepted: 08/31/2015] [Indexed: 11/28/2022] Open
Abstract
It has been reported recently that classical, isothermal-isobaric molecular dynamics (NTP MD) simulations at a time step of 1.00 fs of the standard-mass time (Δt=1.00 fssmt) and a temperature of ≤340 K using uniformly reduced atomic masses by tenfold offers better configurational sampling than standard-mass NTP MD simulations at the same time step. However, it has long been reported that atomic masses can also be increased to improve configurational sampling because higher atomic masses permit the use of a longer time step. It is worth investigating whether standard-mass NTP MD simulations at Δt=2.00 or 3.16 fssmt can offer better or comparable configurational sampling than low-mass NTP MD simulations at Δt=1.00 fssmt. This article reports folding simulations of two β-hairpins showing that the configurational sampling efficiency of NTP MD simulations using atomic masses uniformly reduced by tenfold at Δt=1.00 fssmt is statistically equivalent to and better than those using standard masses at Δt=3.16 and 2.00 fssmt, respectively. The results confirm that, relative to those using standard masses at routine Δt=2.00 fssmt, the low-mass NTP MD simulations at Δt=1.00 fssmt are a simple and generic technique to enhance configurational sampling at temperatures of ≤340 K.
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Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic, Stabile 12-26, 200 First Street SW, Rochester, MN 55905, USA
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5
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Hopkins CW, Le Grand S, Walker RC, Roitberg AE. Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning. J Chem Theory Comput 2015; 11:1864-74. [PMID: 26574392 DOI: 10.1021/ct5010406] [Citation(s) in RCA: 709] [Impact Index Per Article: 78.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a potentially useful tool for accelerating molecular dynamics (MD) simulations. By repartitioning the mass of heavy atoms into the bonded hydrogen atoms, it is possible to slow the highest-frequency motions of the macromolecule under study, thus allowing the time step of the simulation to be increased by up to a factor of 2. In this communication, we investigate further how this mass repartitioning allows the simulation time step to be increased in a stable fashion without significantly increasing discretization error. To this end, we ran a set of simulations with different time steps and mass distributions on a three-residue peptide to get a comprehensive view of the effect of mass repartitioning and time step increase on a system whose accessible phase space is fully explored in a relatively short amount of time. We next studied a 129-residue protein, hen egg white lysozyme (HEWL), to verify that the observed behavior extends to a larger, more-realistic, system. Results for the protein include structural comparisons from MD trajectories, as well as comparisons of pKa calculations via constant-pH MD. We also calculated a potential of mean force (PMF) of a dihedral rotation for the MTS [(1-oxyl-2,2,5,5-tetramethyl-pyrroline-3-methyl)methanethiosulfonate] spin label via umbrella sampling with a set of regular MD trajectories, as well as a set of mass-repartitioned trajectories with a time step of 4 fs. Since no significant difference in kinetics or thermodynamics is observed by the use of fast HMR trajectories, further evidence is provided that long-time-step HMR MD simulations are a viable tool for accelerating MD simulations for molecules of biochemical interest.
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Affiliation(s)
- Chad W Hopkins
- Department of Physics, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States
| | - Scott Le Grand
- Amazon Web Services, 2201 Westlake Ave., Suite 500, Seattle, Washington 98121, United States
| | - Ross C Walker
- San Diego Supercomputer Center & Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, MC0505, La Jolla, California 92093-0505, United States
| | - Adrian E Roitberg
- Department of Chemistry, Quantum Theory Project, University of Florida , Gainesville, Florida 32611, United States
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6
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Gopal SM, Kuhn AB, Schäfer LV. Systematic evaluation of bundled SPC water for biomolecular simulations. Phys Chem Chem Phys 2015; 17:8393-406. [DOI: 10.1039/c4cp04784b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
How accurate is bundled SPC water as inner shell solvent for hybrid all-atom/coarse-grained simulations?
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Affiliation(s)
| | | | - Lars V. Schäfer
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- Germany
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7
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Lu C, Prada-Gracia D, Rao F. Structure and dynamics of water in crowded environments slows down peptide conformational changes. J Chem Phys 2014; 141:045101. [DOI: 10.1063/1.4891465] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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8
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Braun D, Boresch S, Steinhauser O. Transport and dielectric properties of water and the influence of coarse-graining: Comparing BMW, SPC/E, and TIP3P models. J Chem Phys 2014; 140:064107. [DOI: 10.1063/1.4864117] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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9
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Berezovska G, Prada-Gracia D, Mostarda S, Rao F. Accounting for the kinetics in order parameter analysis: lessons from theoretical models and a disordered peptide. J Chem Phys 2013. [PMID: 23181288 DOI: 10.1063/1.4764868] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular simulations as well as single molecule experiments have been widely analyzed in terms of order parameters, the latter representing candidate probes for the relevant degrees of freedom. Notwithstanding this approach is very intuitive, mounting evidence showed that such descriptions are inaccurate, leading to ambiguous definitions of states and wrong kinetics. To overcome these limitations a framework making use of order parameter fluctuations in conjunction with complex network analysis is investigated. Derived from recent advances in the analysis of single molecule time traces, this approach takes into account the fluctuations around each time point to distinguish between states that have similar values of the order parameter but different dynamics. Snapshots with similar fluctuations are used as nodes of a transition network, the clusterization of which into states provides accurate Markov-state-models of the system under study. Application of the methodology to theoretical models with a noisy order parameter as well as the dynamics of a disordered peptide illustrates the possibility to build accurate descriptions of molecular processes on the sole basis of order parameter time series without using any supplementary information.
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Affiliation(s)
- Ganna Berezovska
- Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany
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10
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Artemova S, Redon S. Adaptively restrained particle simulations. PHYSICAL REVIEW LETTERS 2012; 109:190201. [PMID: 23215362 DOI: 10.1103/physrevlett.109.190201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 06/22/2012] [Indexed: 06/01/2023]
Abstract
Interaction potentials used in particle simulations are typically written as a sum of terms which depend on just a few relative particle positions. Traditional simulation methods move all particles at each time step, and may thus spend a lot of time updating interparticle forces. In this Letter we introduce adaptively restrained particle simulations (ARPS) to speed up particle simulations by adaptively switching on and off positional degrees of freedom, while letting momenta evolve. We illustrate ARPS on several numerical experiments, including (a) a collision cascade example that demonstrates how ARPS make it possible to smoothly trade between precision and speed and (b) a polymer-in-solvent study that shows how one may efficiently determine static equilibrium properties with ARPS.
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Affiliation(s)
- Svetlana Artemova
- NANO-D, INRIA Grenoble-Rhone-Alpes, 38334 Saint Ismier Cedex, Montbonnot, France
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Villarreal MA, Oviedo OA, Leiva EPM. A Straightforward Approach for the Determination of the Maximum Time Step for the Simulation of Nanometric Metallic Systems. J Chem Theory Comput 2012; 8:1744-9. [DOI: 10.1021/ct300069d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Marcos A. Villarreal
- INFIQC, CONICET, Departamento de Matemática
y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba,
Argentina, X5000HUA
| | - Oscar A. Oviedo
- INFIQC, CONICET, Departamento de Matemática
y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba,
Argentina, X5000HUA
| | - Ezequiel P. M. Leiva
- INFIQC, CONICET, Departamento de Matemática
y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba,
Argentina, X5000HUA
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