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Fusè M, Mazzeo G, Ghidinelli S, Evidente A, Abbate S, Longhi G. Experimental and theoretical aspects of magnetic circular dichroism and magnetic circularly polarized luminescence in the UV, visible and IR ranges: A review. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124583. [PMID: 38850611 DOI: 10.1016/j.saa.2024.124583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/21/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
A historical sketch of the MCD (magnetic circular dichroism) spectroscopy is reported in its experimental and theoretical aspects. MCPL (magnetic circularly polarized luminescence) is also considered. The main studies are presented encompassing porphyrinoid systems, aggregates and materials, as well as simple organic molecules useful for the advancement of the interpretation. The MCD of chiral systems is discussed with special attention to new studies of natural products with potential pharmaceutical valence, including Amaryllidaceae alkaloids and related isocarbostyrils. Finally, the vibrational form of MCD, called MVCD, which is recorded in the IR part of the spectrum is also discussed. A final brief note on perspectives is given.
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Affiliation(s)
- Marco Fusè
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Giuseppe Mazzeo
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Simone Ghidinelli
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Antonio Evidente
- Institute of Sciences of Food Production, National Research Council, Via Amendola 122/O, 70185 Bari, Italy
| | - Sergio Abbate
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy; Istituto Nazionale di Ottica, INO-CNR, Research Unit of Brescia, c/o CSMT, Via Branze 35, 25123 Brescia, Italy
| | - Giovanna Longhi
- Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy; Istituto Nazionale di Ottica, INO-CNR, Research Unit of Brescia, c/o CSMT, Via Branze 35, 25123 Brescia, Italy
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152
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Denjean AEF, Rio J, Ciofini I, Perrin MEL, Payard PA. Computed versus experimental energy barriers in solution: Influence of the type of the density functional approximation. J Comput Chem 2024; 45:2284-2293. [PMID: 38847601 DOI: 10.1002/jcc.27436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 08/15/2024]
Abstract
Mechanistic investigations at the density functional theory level of organic and organometallic reactions in solution are now broadly accessible and routinely implemented to complement experimental investigations. The selection of an appropriate functional among the plethora of developed ones is the first challenge on the way to reliable energy barrier calculations. To provide guidelines for the choice of an initial and reliable computational level, the performances of commonly used non-empirical (PBE, PBE0, PBE0-DH) and empirical density functionals (BLYP, B3LYP, B2PLYP) were evaluated relative to experimental activation enthalpies. Most reactivity databases to assess density functional performances are primarily based on high level calculations, here a set of experimental activation enthalpies of organic and organometallic reactions performed in solution were selected from the literature. As a general trend, the non-empirical functionals outperform the empirical ones. The most accurate energy barriers are obtained with hybrid PBE0 and double-hybrid PBE0-DH density functionals, both providing similar performance. Regardless of the functional under consideration, the addition of the GD3-BJ empirical dispersion correction does not enhance the accuracy of computed energy barriers.
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Affiliation(s)
- Aurore E F Denjean
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
| | - Jordan Rio
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
| | - Ilaria Ciofini
- i-CLeHS (UMR 8060), CNRS Chimie Paris-Tech-PSL, Université Paris Sciences et Lettres, Paris, France
| | - Marie-Eve L Perrin
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
| | - Pierre-Adrien Payard
- Universite Claude Bernard Lyon I, CNRS, CPE-Lyon, INSA-Lyon, UMR 5246, ICBMS Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, Villeurbanne, France
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153
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Zhang S, Jiang DE, Zhou N, Tang J, Zhang K, Li Y, Hu J, Peng C, Liu H, Yang B, Yao Y. Ionic liquids intercalation in titanium carbide MXenes: A first-principles investigation. J Comput Chem 2024; 45:2294-2307. [PMID: 38847556 DOI: 10.1002/jcc.27444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/24/2024] [Accepted: 05/23/2024] [Indexed: 08/15/2024]
Abstract
Herein, we present a density functional theory with dispersion correction (DFT-D) calculations that focus on the intercalation of ionic liquids (ILs) electrolytes into the two-dimensional (2D) Ti3C2Tx MXenes. These ILs include the cation 1-ethyl-3-methylimidazolium (Emim+), accompanied by three distinct anions: bis(trifluoromethylsulfonyl)imide (TFSA-), (fluorosulfonyl)imide (FSA-) and fluorosulfonyl(trifluoromethanesulfonyl)imide (FTFSA-). By altering the surface termination elements, we explore the intricate geometries of IL intercalation in neutral, negative, and positive pore systems. Accurate estimation of charge transfer is achieved through five population analysis models, such as Hirshfeld, Hirshfeld-I, DDEC6 (density derived electrostatic and chemical), Bader, and VDD (voronoi deformation density) charges. In this work, we recommend the DDEC6 and Hirshfeld-I charge models, as they offer moderate values and exhibit reasonable trends. The investigation, aimed at visualizing non-covalent interactions, elucidates the role of cation-MXene and anion-MXene interactions in governing the intercalation phenomenon of ionic liquids within MXenes. The magnitude of this role depends on two factors: the specific arrangement of the cation, and the nature of the anionic species involved in the process.
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Affiliation(s)
- Shaoze Zhang
- National Engineering Research Center of Vacuum Metallurgy, Kunming University of Science and Technology, Kunming, China
- Engineering Laboratory for Advanced Battery and Materials of Yunnan Province, Kunming University of Science and Technology, Kunming, China
| | - De-En Jiang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Nan Zhou
- National Engineering Research Center of Vacuum Metallurgy, Kunming University of Science and Technology, Kunming, China
- Engineering Laboratory for Advanced Battery and Materials of Yunnan Province, Kunming University of Science and Technology, Kunming, China
| | - Jiaxing Tang
- National Engineering Research Center of Vacuum Metallurgy, Kunming University of Science and Technology, Kunming, China
- Engineering Laboratory for Advanced Battery and Materials of Yunnan Province, Kunming University of Science and Technology, Kunming, China
| | - Keyu Zhang
- National Engineering Research Center of Vacuum Metallurgy, Kunming University of Science and Technology, Kunming, China
- Engineering Laboratory for Advanced Battery and Materials of Yunnan Province, Kunming University of Science and Technology, Kunming, China
| | - Yin Li
- National Engineering Research Center of Vacuum Metallurgy, Kunming University of Science and Technology, Kunming, China
- Engineering Laboratory for Advanced Battery and Materials of Yunnan Province, Kunming University of Science and Technology, Kunming, China
| | - Junxian Hu
- National Engineering Research Center of Vacuum Metallurgy, Kunming University of Science and Technology, Kunming, China
- Engineering Laboratory for Advanced Battery and Materials of Yunnan Province, Kunming University of Science and Technology, Kunming, China
| | - Changjun Peng
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Honglai Liu
- Key Laboratory for Advanced Materials and School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Bin Yang
- National Engineering Research Center of Vacuum Metallurgy, Kunming University of Science and Technology, Kunming, China
- Engineering Laboratory for Advanced Battery and Materials of Yunnan Province, Kunming University of Science and Technology, Kunming, China
| | - Yaochun Yao
- National Engineering Research Center of Vacuum Metallurgy, Kunming University of Science and Technology, Kunming, China
- Engineering Laboratory for Advanced Battery and Materials of Yunnan Province, Kunming University of Science and Technology, Kunming, China
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154
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Lembo A, Molinaro A, De Castro C, Berti F, Biagini M. Impact of glycosylation on viral vaccines. Carbohydr Polym 2024; 342:122402. [PMID: 39048237 DOI: 10.1016/j.carbpol.2024.122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
Glycosylation is the most prominent modification important for vaccines and its specific pattern depends on several factors that need to be considered when developing a new biopharmaceutical. Tailor-made glycosylation can be exploited to develop more effective and safer vaccines; for this reason, a deep understanding of both glycoengineering strategies and glycans structures and functions is required. In this review we discuss the recent advances concerning glycoprotein expression systems and the explanation of glycans immunomodulation mechanisms. Furthermore, we highlight how glycans tune the immunological properties among different vaccines platforms (whole virus, recombinant protein, nucleic acid), also comparing commercially available formulations and describing the state-of-the-art analytical technologies for glycosylation analysis. The whole review stresses the aspect of glycoprotein glycans as a potential tool to overcome nowadays medical needs in vaccine field.
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Affiliation(s)
- Antonio Lembo
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy; GSK, Siena, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.
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155
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Krupová M, Leszczenko P, Sierka E, Hamplová SE, Klepetářová B, Pelc R, Andrushchenko V. Vibrational circular dichroism of adenosine crystals. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124381. [PMID: 38838602 DOI: 10.1016/j.saa.2024.124381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024]
Abstract
Adenosine is one of the building blocks of nucleic acids and other biologically important molecules. Spectroscopic methods have been among the most utilized techniques to study adenosine and its derivatives. However, most of them deal with adenosine in solution. Here, we present the first vibrational circular dichroism (VCD) spectroscopic study of adenosine crystals in solid state. Highly regular arrangement of adenosine molecules in a crystal resulted in a strongly enhanced supramolecular VCD signal originating from long-range coupling of vibrations. The data suggested that adenosine crystals, in contrast to guanosine ones, do not imbibe atmospheric water. Relatively large dimensions of the adenosine crystals resulted in scattering and substantial orientational artifacts affecting the spectra. Several strategies for tackling the artifacts have been proposed and tested. Atypical features in IR absorption spectra of crystalline adenosine (e.g., extremely low absorption in mid-IR spectral range) were observed and attributed to refractive properties of adenosine crystals.
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Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic; Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Patrycja Leszczenko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic; Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Ewa Sierka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic; Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Sára Emma Hamplová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Radek Pelc
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic; Third Faculty of Medicine, Charles University, Ruská 87, 10000 Prague, Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
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156
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Wang K, Zhao J, Guo J, Chen S, Zhao Y, Chen J, Wang Y, Liu L, Wang C, Liu Z. Magnetic properties of CrMnGe n (n = 3-20) clusters. J Comput Chem 2024; 45:2318-2324. [PMID: 38872590 DOI: 10.1002/jcc.27448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/19/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024]
Abstract
Due to the potential applications in next-generation micro/nano electronic devices and functional materials, magnetic germanium (Ge)-based clusters are receiving increasing attention. In this work, we reported the structures, electronic and magnetic properties of CrMnGen with sizes n = 3-20. Transition metals (TMs) of Cr and Mn tend to stay together and be surrounded by Ge atoms. Small sized clusters with n ≤ 8 prefer to adopt bipyramid-based structures as the motifs with the excess Ge atoms absorbed on the surface. Starting from n = 9, the structure with one TM atom interior appears and persists until n = 16, and for larger sizes n = 17-20, the two TM atoms are full-encapsulated by Ge atoms to form endohedral structures. The Hirshfeld population analyses show that Cr atom always acts as the electron donor, while Mn atom is always the acceptor except for sizes 3 and 6. The average binding energies of these clusters increase with cluster size n, sharing a very similar trend as that of CrMnSin (n = 4-20) clusters, which indicates that it is favorable to form large-sized clusters. CrMnGen (n = 6, 13, 16, 19, and 20) clusters prefer to exhibit ferromagnetic Cr-Mn coupling, while the remaining clusters are ferrimagnetic.
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Affiliation(s)
- Kai Wang
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
| | - Jun Zhao
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
| | - Junji Guo
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
| | - Shanbao Chen
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
| | - Yapeng Zhao
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
| | - Jiaye Chen
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
| | - Yarui Wang
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
| | - Le Liu
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
| | - Chaoyong Wang
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
| | - Zhiqing Liu
- Henan Engineering Research Centre of Building-Photovoltaics, School of Mathematics and Physics, Henan University of Urban Construction, Pingdingshan, China
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157
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Abdollahi-Najafabadi M, Farhadian S, Shareghi B, Asgharzadeh S. The investigation of the interaction determination between carbendazim and elastase, using both in vitro and in silico methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124586. [PMID: 38833886 DOI: 10.1016/j.saa.2024.124586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 05/28/2024] [Accepted: 06/01/2024] [Indexed: 06/06/2024]
Abstract
Pesticides, including fungicides, are one of the important groups of environmental toxins that affect human and animal health. Studies have shown that these compounds are considered chemical pollutants. Carbendazim is a systemic fungicide. Unfortunately, excessive use of carbendazim has caused environmental pollution all over the world. In this study, the effect of carbendazim on the enzyme elastase (secreted from the endocrine gland of the pancreas) has been investigated. In a study, the performance and reaction of carbendazim with elastase were investigated using spectroscopic techniques. The stability and structure of elastase enzymes were studied under the influence of carbendazim. The results of fluorescence emission and UV-visible absorption spectrum showed that in the presence of carbendazim, there is an increase in UV-Vis absorption and a decrease in the intensity of the intrinsic fluorescence emission in the protein spectrum. Additionally, a decrease in the thermal stability of elastase was observed in the presence of carbendazim. The stability and structure of elastase enzyme were investigated in the presence of carbendazim. The results revealed that the UV-Vis absorption increased due to the presence of carbendazim, as indicated by the hyperchromic spectrum at 220 and 280 nm peaks. Additionally, the intrinsic fluorescence emission in the protein spectrum decreased with increasing carbendazim concentration at three different temperatures (298, 303, and 313 K). Moreover, the study demonstrated that the TM decreased from 2.59 to 4.58 with the increase of carbendazim, suggesting a decrease in the stability of the elastase structure in response to the elevated carbendazim concentration. According to the results of the research, the interaction between elastase and carbendazim has occurred, and changes have been made in the enzyme under the influence of carbendazim. The formation of the complex between elastase and carbendazim was consistent with the results obtained from molecular simulation and confirmed the thermodynamic data.
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Affiliation(s)
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sanaz Asgharzadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box 115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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158
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Su J, Yang X, Xu H, Pei Y, Liu QS, Zhou Q, Jiang G. Screening (ant)agonistic activities of xenobiotics on the retinoic acid receptor alpha (RARα) using in vitro and in silico analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174717. [PMID: 38997027 DOI: 10.1016/j.scitotenv.2024.174717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/07/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Retinoic acid receptors (RARs) are known as crucial endocrine receptors that could mediate a broad diversity of biological processes. However, the data on endocrine disrupting effects of emerging chemicals by targeting RAR (ant)agonism are far from sufficient. Herein, we investigated the RARα agonistic or antagonistic activities for 75 emerging chemicals of concern, and explored their interactions with this receptor. A recombinant two-hybrid yeast assay was used to examine the RARα activities of the test chemicals, wherein 7 showed effects of RARα agonism and 54 exerted potentials of RARα antagonism. The representative chemicals with RARα agonistic activities, i.e. 4-hydroxylphenol (4-HP) and bisphenol AF (BPAF), significantly increased the mRNA levels of CRABP2 and CYP26A1, while 4 select chemicals with RARα antagonistic potentials, including bisphenol A (BPA), tetrabromobisphenol A (TBBPA), 4-tert-octylphenol (4-t-OP), and 4-n-nonylphenol (4-n-NP), conversely decreased the transcriptional levels of the test genes. The in silico molecular docking analysis using 3 different approaches further confirmed the substantial binding between the chemicals with RARα activities and this nuclear receptor protein. This work highlights the promising strategy for screening endocrine-disrupting effects of emerging chemicals of concern by targeting RARα (ant)agonism.
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Affiliation(s)
- Jiahui Su
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxi Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Hanqing Xu
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Wenzhou University, Wenzhou 325035, China
| | - Yao Pei
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian S Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qunfang Zhou
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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159
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Liao M, Gong H, Shen K, Wang Z, Li R, Campana M, Hu X, Lu JR. Unlocking roles of cationic and aromatic residues in peptide amphiphiles in treating drug-resistant gram-positive pathogens. J Colloid Interface Sci 2024; 672:209-223. [PMID: 38838629 DOI: 10.1016/j.jcis.2024.05.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
Multidrug resistance (MDR) is a rising threat to global health because the number of essential antibiotics used for treating MDR infections is increasingly compromised. In this work we report a group of new amphiphilic peptides (AMPs) derived from the well-studied G3 (G(IIKK)3I-NH2) to fight infections from Gram-positive bacteria including susceptible Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA), focusing on membrane interactions. Time-dependent killing experiments revealed that substitutions of II by WW (GWK), II by FF (GFK) and KK by RR (GIR) resulted in improved bactericidal efficiencies compared to G3 (GIK) on both S. aureus and MRSA, with the order of GWK > GIR > GFK > GIK. Electronic microscopy imaging revealed structural disruptions of AMP binding to bacterial cell walls. Fluorescence assays including AMP binding to anionic lipoteichoic acids (LTA) in cell-free and cell systems indicated concentration and time-dependent membrane destabilization associated with bacterial killing. Furthermore, AMP's binding to anionic plasma membrane via similar fluorescence assays revealed a different extent of membrane depolarization and leakage. These observations were supported by the penetration of AMPs into the LTA barrier and the subsequent structural compromise to the cytoplasmic membrane as revealed from SANS (small angle neutron scattering). Both experiments and molecular dynamics (MD) simulations revealed that GWK and GIR could make the membrane more rigid but less effective in diffusive efficiency than GIK and GFK through forming intramembrane peptide nanoaggregates associated with hydrophobic mismatch and formation of fluidic and rigid patches. The reported peptide-aggregate-induced phase-separation emerged as a crucial factor in accelerated membrane disintegration and fast bacterial killing. This work has demonstrated the importance of membrane interactions to the development of more effective AMPs and the relevance of the approaches as reported in assisting this area of research.
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Affiliation(s)
- Mingrui Liao
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Haoning Gong
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Kangcheng Shen
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Ziwei Wang
- National Graphene Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Renzhi Li
- Department of Materials, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Mario Campana
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, UK
| | - Xuzhi Hu
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Jian R Lu
- Biological Physics Laboratory, Department of Physics and Astronomy, School of Natural Science, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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160
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Li H, Jin X, Owens G, Chen Z. Reconstructing the electron and spin structures of nanoscale iron sulfide through a biosurfactant layer towards radical-nonradical co-dominant regime. J Colloid Interface Sci 2024; 672:299-310. [PMID: 38843682 DOI: 10.1016/j.jcis.2024.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/22/2024] [Accepted: 06/03/2024] [Indexed: 07/07/2024]
Abstract
Radical-nonradical co-dominant pathways have become a hot topic in advanced oxidation, but achieving this on transition metal sulfides (TMS) remains challenging because their inherently higher electron and spin densities always induce radicals rather than nonradicals. Herein, a biosurfactant layer (BLR) was introduced to redistribute the electron and spin structure of nanoscale iron sulfide (FeS), which allowed both radical and nonradical to co-dominate the catalytic reaction. The resulting BLR-encased FeS hybrid (BLR@FeS) exhibited satisfactory removal efficiency (98.5 %) for hydrogen peroxide (H2O2) activation, outperforming both the constituent components [FeS (70.9 %) and BLR (86.2 %)]. Advanced characterizations showed that C, O, N-related sites (-CO and -NC) in BLR attracted electrons in FeS due to their strong electronegativity and electron-withdrawing capacity, which not only decreased electron density in FeS, but also resulted in a shift of the Fe/S sites from the high-spin to the medium-spin state. The reaction routes established by the BLR@FeS/H2O2 system maintained desirable stability against environmental interferences such as common inorganic anions, humic acid and changes in pH. Our study provides a state-of-the-art, molecule-level understanding of tunable co-dominant pathways and expands the targeted applications in the field of advanced oxidation.
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Affiliation(s)
- Heng Li
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental and Resource Sciences, Fujian Normal University, Fuzhou 350117, Fujian Province, China
| | - Xiaoying Jin
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental and Resource Sciences, Fujian Normal University, Fuzhou 350117, Fujian Province, China.
| | - Gary Owens
- Environmental Contaminants Group, Future Industries Institute, University of South Australian, Mawson Lakes, SA, 5095, Australia
| | - Zuliang Chen
- Fujian Key Laboratory of Pollution Control and Resource Reuse, School of Environmental and Resource Sciences, Fujian Normal University, Fuzhou 350117, Fujian Province, China.
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161
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Xu J, Yang W, Liu Y. An innovative carbon dots polarity probe based on intramolecular charge-transfer for visual monitoring of the total polar materials in frying oil. Food Chem 2024; 455:139770. [PMID: 38823139 DOI: 10.1016/j.foodchem.2024.139770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/09/2024] [Accepted: 05/19/2024] [Indexed: 06/03/2024]
Abstract
The presence of Total Polar Materials (TPM) in edible oils is a crucial indicator for assessing oil quality. It is of paramount importance to develop a rapid and dependable technique for monitoring polarity in frying oil. Sensitive polarity responsive fluorescence carbon dots (F-CDs) were synthesized by using p-phenylenediamine as precursors and 2-formylphenylboronic acid pinacol ester (2-FAPE) as a post-modifier. The construction of the fluorescent probe F-CDs involved a strong intramolecular charge-transfer (ICT) mechanism, with 2-FAPE serving as the electron-withdrawing fluorophore and the π-conjugated structure acting as a potent electron-donating group. A strong linear relationship was observed between the emission wavelength and the TPM value of frying oil within a range of 11% to 30%. Notably, the fluorescence color of the probe transitioned from blue to yellow under UV light at 365 nm as the TMP value increased. This study expands the range of sensing applications for CDs in food safety.
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Affiliation(s)
- Jiangbin Xu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China
| | - Wei Yang
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China; Future Food (Bai Ma) Research Institute, 111 Baima Road, Nanjing 211200, Jiangsu, People's Republic of China.
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162
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Qin Y, Zhou RR, Liu H, Shi SY, Zhang SH. New insights into the chemistry and anticancer activity of Ophiocordyceps xuefengensis. J Pharm Biomed Anal 2024; 249:116345. [PMID: 38986348 DOI: 10.1016/j.jpba.2024.116345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/25/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Ophiocordyceps xuefengensis (O. xuefengensis), the sister taxon of Ophiocordyceps sinensis (O. sinensis), is consumed as a "tonic food" due to its health benefits. However, little is known regarding the chemistry and bioactivity of O. xuefengensis. In this study, we characterized 80 indole-based alkaloids in the ethyl acetate fraction of O. xuefengensis by high performance liquid chromatography-quadrupole time of flight mass spectrometry (HPLC-Q-TOF-MS/MS), of which 54 indole-based alkaloids were identified as possibly new compounds. Furthermore, 29 of these compounds were established as potential anti-cancer compounds by ligand fishing combined with HPLC-Q-TOF-MS/MS. Moreover, molecular docking identified the NH- and OH- groups of these compounds as the key active groups. The present study has expanded the knowledge on the characteristic indole-based alkaloids and anti-cancer activity of O. xuefengensis.
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Affiliation(s)
- You Qin
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha 410013, PR China
| | - Rong-Rong Zhou
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha 410013, PR China; Hunan Academy of Chinese Medicine Affiliated Hospital, Changsha 410013, PR China
| | - Hao Liu
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha 410013, PR China
| | - Shu-Yun Shi
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China.
| | - Shui-Han Zhang
- Institute of Chinese Medicine Resources, Hunan Academy of Chinese Medicine, Changsha 410013, PR China.
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163
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Li D, Zhang XY, Xie JF, Chen JJ, Zhao QB, Liu L, Wang WK, Li WW, Yu HQ. Ultrathin cobalt-based nanosheets containing surface oxygen promoted near-complete nitrate removal. J Colloid Interface Sci 2024; 672:383-391. [PMID: 38848622 DOI: 10.1016/j.jcis.2024.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Electrocatalytic nitrate removal offers a sustainable approach to alleviate nitrate pollution and to boost the anthropogenic nitrogen cycle, but it still suffers from limited removal efficiency at high rates, especially at low levels of nitrate. Herein, we report the near-complete removal of low-level nitrate (10-200 ppm) within 2 h using ultrathin cobalt-based nanosheets (CoNS) containing surface oxygen, which was fabricated from in-situ electrochemical reconstruction of conventional nanosheets. The average nitrate removal of 99.7 % with ammonia selectivity of 98.2 % in 9 cyclic runs ranked in the best of reported catalysts. Powered by a solar cell under the winter sun, the full-cell nitrate electrolysis system, equipped with ultrathin CoNS, achieved 100 % nitrogen gas selectivity and 99.6 % total nitrogen removal. The in-situ Fourier Transform Infrared included experiments and theoretical computations revealed that in-situ electrochemical reconstruction not only increased electrochemical active surface area but also constructed surface oxygen in active sites, leading to enhanced stabilization of nitrate adsorption in a symmetry breaking configuration and charge transfer, contributing to near-complete nitrate removal on ultrathin CoNS. This work provides a strategy to design ultrathin nanocatalysts for nitrate removal.
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Affiliation(s)
- Ding Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Yu Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Jia-Fang Xie
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China; Research Center of Urban Carbon Neutrality, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Jie-Jie Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Quan-Bao Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Kang Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Technology, University of Science and Technology of China, Hefei 230026, China.
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164
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Kumar P, Purohit R. Driving forces and large scale affinity calculations for piperine/γ-cyclodxetrin complexes: Mechanistic insights from umbrella sampling simulation and DFT calculations. Carbohydr Polym 2024; 342:122350. [PMID: 39048216 DOI: 10.1016/j.carbpol.2024.122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/13/2024] [Accepted: 05/29/2024] [Indexed: 07/27/2024]
Abstract
Piperine (PiP), a bioactive molecule, exhibits numerous health benefits and is frequently employed as a co-delivery agent with various phytomedicines (e.g., curcumin) to enhance their bioavailability. This is attributed to PiP's inhibitory activity against drug-metabolizing proteins, notably CYP3A4. Nevertheless, PiP encounters solubility challenges addressed in this study using cyclodextrins (CDs). Specifically, γ-CD and its derivatives, Hydroxypropyl-γ-CD (HP-γ-CD), and Octakis (6-O-sulfo)-γ-CD (Octakis-S-γ-CD), were employed to form supramolecular complexes with PiP. The conformational space of the complexes was assessed through 1 μs molecular dynamics simulations and umbrella sampling. Additionally, quantum mechanical calculations using wB97X-D dispersion-corrected DFT functional and 6-311 + G(d,p) basis set were conducted on the complexes to examine the thermodynamics and kinetic stability. Results indicated that Octakis-S-γ-CD exhibits superior host capabilities for PiP, with the most favorable complexation energy (-457.05 kJ/mol), followed by HP-γ-CD (-249.16 kJ/mol). Furthermore, two conformations of the Octakis-S-γ-CD/PiP complex were explored to elucidate the optimal binding orientation of PiP within the binding pocket of Octakis-S-γ-CD. Supramolecular chemistry relies significantly on non-covalent interactions. Therefore, our investigation extensively explores the critical atoms involved in these interactions, elucidating the influence of substituted groups on the stability of inclusion complexes. This comprehensive analysis contributes to emphasizing the γ-CD derivatives with improved host capacity.
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Affiliation(s)
- Pramod Kumar
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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165
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Stuyver T. TS-tools: Rapid and automated localization of transition states based on a textual reaction SMILES input. J Comput Chem 2024; 45:2308-2317. [PMID: 38850166 DOI: 10.1002/jcc.27374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/08/2024] [Accepted: 03/20/2024] [Indexed: 06/10/2024]
Abstract
Here, TS-tools is presented, a Python package facilitating the automated localization of transition states (TS) based on a textual reaction SMILES input. TS searches can either be performed at xTB or DFT level of theory, with the former yielding guesses at marginal computational cost, and the latter directly yielding accurate structures at greater expense. On a benchmarking dataset of mono- and bimolecular reactions, TS-tools reaches an excellent success rate of 95% already at xTB level of theory. For tri- and multimolecular reaction pathways - which are typically not benchmarked when developing new automated TS search approaches, yet are relevant for various types of reactivity, cf. solvent- and autocatalysis and enzymatic reactivity - TS-tools retains its ability to identify TS geometries, though a DFT treatment becomes essential in many cases. Throughout the presented applications, a particular emphasis is placed on solvation-induced mechanistic changes, another issue that received limited attention in the automated TS search literature so far.
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Affiliation(s)
- Thijs Stuyver
- Ecole Nationale Supérieure de Chimie de Paris, Université PSL, CNRS, Institute of Chemistry for Life and Health Sciences, Paris, France
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166
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Song H, Jiang P, Tang H, Wang Z, Ge X, Li X, He F, Guo S, Tian G, Qi Y, Hu S, Liu R. Nanoplastics composite norfloxacin induced changes in conformation and function of lysozyme and differential effects of co-exposure contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174688. [PMID: 38992361 DOI: 10.1016/j.scitotenv.2024.174688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
The concurrent environmental contamination by nanoplastics (NPs) and norfloxacin (NOR) is a burgeoning concern, with significant accumulations in various ecosystems and potential ingress into the human body via the food chain, posing threats to both public health and ecological balance. Despite the gravity of the situation, studies on the co-exposure contamination effects of these substances are limited. Moreover, the response mechanisms of key functional proteins to these pollutants are yet to be fully elucidated. In this work, we conducted a comprehensive assessment of the interaction mechanisms of NPs and NOR with lysozyme under both single and co-exposure condition, utilizing dynamic light scattering, ζ-potential measurements, multi-spectroscopy methods, enzyme activity assays and molecular docking, to obtain a relationship between the compound effects of NPs and NOR. Our results indicate that NPs adsorb NOR on their surface, forming more stable aggregates. These aggregates influence the conformation, secondary structure (α-Helix ratio decreased by 3.1 %) and amino acid residue microenvironment of lysozyme. And changes in structure affect the activity of lysozyme (reduced by 39.9 %) with the influence of composited pollutants exerting stronger changes. Molecular simulation indicated the key residues Asp 52 for protein function located near the docking site, suggesting pollutants preferentially binds to the active center of lysozyme. Through this study, we have found the effect of increased toxicity on lysozyme under the compounded conditions of NPs and NOR, confirming that the increased molecular toxicity of NPs and NOR is predominantly realized through the increase in particle size and stability of the aggregates under weak interactions, as well as induction of protein structural looseness. This study proposes a molecular perspective on the differential effects and mechanisms of NPs-NOR composite pollution, providing new insights into the assessment of in vitro responses to composite pollutant exposure.
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Affiliation(s)
- Hengyu Song
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Pin Jiang
- Yanzhou District branch of Jining Ecological Environment Bureau, No. 159, Wenhua East Road, Yanzhou District, Jining City, Shandong Province 272100, PR China
| | - Houquan Tang
- Jinan Ecological and Environmental Monitoring Center, Jinan City, Shandong Province 250104, China
| | - Zaifeng Wang
- Jinan Ecological and Environmental Monitoring Center, Jinan City, Shandong Province 250104, China
| | - Xuan Ge
- Jinan Ecological and Environmental Monitoring Center, Jinan City, Shandong Province 250104, China
| | - Xiangxiang Li
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Falin He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Shuqi Guo
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Guang Tian
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Yuntao Qi
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Shaoyang Hu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
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167
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Tognetti V, Joubert L. Exchange-correlation effects in interatomic energies for pure density functionals and their application to the molecular energy prediction. J Comput Chem 2024; 45:2270-2283. [PMID: 38847367 DOI: 10.1002/jcc.27431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/02/2024] [Accepted: 04/28/2024] [Indexed: 08/15/2024]
Abstract
In this proof-of-concept paper, we show how exchange-correlation effects can be simply recovered for interatomic energies within the interacting quantum atoms decomposition when local, gradient generalized, or meta-gradient generalized approximations are used in density functional theory (DFT) calculations. We also demonstrate how inhomogeneity and non-local effects can be introduced even from a pure local scheme, without resorting to any orbital information. Finally, we provide numerical evidence on a database of selected energetic molecules that this decomposition scheme can be efficiently used to build accurate models for the prediction of molecular energies from an initial "cheap" DFT calculation.
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Affiliation(s)
- Vincent Tognetti
- University of Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie University, Rouen, France
| | - Laurent Joubert
- University of Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie University, Rouen, France
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168
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Razali NSM, Ikhwanuddin M, Maulidiani M, Gooderham NJ, Alam M, Kadir NHA. Ecotoxicological impact of heavy metals on wild mud crabs (Scylla olivacea) in Malaysia: An integrative approach of omics, molecular docking and human risk assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174210. [PMID: 38914323 DOI: 10.1016/j.scitotenv.2024.174210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Mud crab, one of the aquatic organisms found in estuary areas, has become a significant economic source of seafood for communities due to its delectable taste. However, they face the threat of heavy metal contamination, which may adversely affect their biological traits. This study explored the comparison of the mud crabs collected from Setiu Wetland as a reference site, while Kuala Sepetang is an area that contains a higher concentration of heavy metals than Setiu Wetlands. Heavy metal levels were quantified using inductively coupled plasma mass spectrometry (ICP-MS), while proteomes were assessed using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and 1H nuclear magnetic resonance (NMR)-based metabolomics, respectively. Heavy metal contamination affects the proteome, metabolome, and putative molecular targets in mud crabs (Scylla olivacea), leading to oxidative stress. Mud crabs collected from the metal-polluted area of Kuala Sepetang in Perak had considerably elevated concentrations of nickel (Ni), copper (Cu), zinc (Zn), lead (Pb), chromium (Cr), and cadmium (Cd) in comparison to the reference site of Setiu Wetlands in Terengganu. The proteome analysis revealed an upregulation of the stress-response protein Hsp70, which triggered superoxide dismutase (SOD) and increased arginine kinase expression (5.47 fold) in the muscle tissue, results in the alteration of metabolite regulation in the mud crab from Kuala Sepetang. Additionally, in the muscle tissues of mud crabs obtained from Kuala Sepetang, uncharacterized myosin-tail 1 domain proteins and sarcoplasmic calcium-binding proteins were downregulated. The metabolomic investigation identified changes in metabolites associated with energy metabolism and osmoregulation. Exploration of docking analysis suggests potential connections between methylarsonic acid and essential proteins in mud crabs. These findings suggest that the presence of heavy metals disrupts physiological processes and highlights potential molecular targets that warrant further investigation.
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Affiliation(s)
- Nur Syafinaz Mohd Razali
- Faculty of Science and Environmental Marine, Universiti Malaysia Terengganu, 21030, Terengganu, Malaysia
| | - Mhd Ikhwanuddin
- Higher Institution Center of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - M Maulidiani
- Faculty of Science and Environmental Marine, Universiti Malaysia Terengganu, 21030, Terengganu, Malaysia
| | - Nigel J Gooderham
- Department of Metabolism, Digestion, Reproduction, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| | - Mahboob Alam
- Department of Safety Engineering, Dongguk University, 123 Dongdae-ro, Gyeongju-si, Gyeongbuk 780714, Republic of Korea.
| | - Nurul Huda Abd Kadir
- Faculty of Science and Environmental Marine, Universiti Malaysia Terengganu, 21030, Terengganu, Malaysia; RIG BIOSES, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
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169
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Kim S, Ko S, Kim M, Jang Y, Hyun J. Cryo-EM structure of orf virus scaffolding protein orfv075. Biochem Biophys Res Commun 2024; 728:150334. [PMID: 38968773 DOI: 10.1016/j.bbrc.2024.150334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
Capsid-like poxvirus scaffold proteins self-assemble into semi-regular lattice that govern the formation of spherical immature virus particles. The scaffolding is a critical step in virus morphogenesis as exemplified by the drug rifampicin that impairs the recruitment of scaffold onto the viral membrane in vaccinia virus (VACV). Here we report cryo-electron microscopy structure of scaffolding protein Orfv075 of orf virus (ORFV) that causes smallpox-like diseases in sheep, goats and occasionally humans via zoonotic infection. We demonstrate that the regions that are involved in intertrimeric interactions for scaffold assembly are largely conserved in comparison to its VACV orthologue protein D13 whose intermediate assembly structures have been previously characterized. By contrast, less conserved regions are located away from these interfaces, indicating both viruses share similar assembly mechanisms. We also show that the phenylalanine-rich binding site of rifampicin in D13 is conserved in Orfv075, and molecular docking simulation confirms similar binding modes. Our study provides structural basis of scaffolding protein as a target for anti-poxvirus treatment across wide range of poxvirus genera.
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Affiliation(s)
- Seungmi Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sumin Ko
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Minjae Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yeontae Jang
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaekyung Hyun
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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170
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Nguyen LH, Truong TN. Nature of partial sigma bond. J Comput Chem 2024; 45:2251-2264. [PMID: 38838302 DOI: 10.1002/jcc.27445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/07/2024]
Abstract
This study investigates the formation of partial sigma (σ) covalent bonds in experimentally synthesizable biradicals formed from hydrogenated and fluorinated C8, C20, and C60 cage structures, by assessing their stability, geometry, and bonding character in singlet and triplet states using restricted B3LYP-D3/6-31+G(d,p) theory, natural bond orbital (NBO) analysis, and complete active space self-consistent field (CASSCF) method. The results show that these partial σCC bonds have Wiberg bond orders of 0.38 to 0.48 and bond lengths ranging from 2.62 Å to 5.93 Å. Cage size influences the characteristics of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), with electrons favoring more antibonding orbitals in smaller cages where electrons reside more on the exterior of the cage and favoring bonding orbitals in larger ones where electrons are more in the interior. Fluorination enhances electron density on bonding orbitals. The analysis further clarified that the differentiation between antibonding and bonding features of HOMOs and LUMOs extends beyond merely electron transfer from s- to p-atomic orbitals, also noting possible interactions of the same symmetry repel. The study also introduces hyperconjugation from α-position CH bonds as a factor in stabilizing partial σ-bond formation. The results also caution against the use of broken symmetry methodology in unrestricted SCF wavefunctions for biradicals, such as those in this study as it may cause large spin contamination and thus errors in the calculated electronic properties results.
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Affiliation(s)
- Lam H Nguyen
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Thanh N Truong
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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171
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Zhou L, Qi Z, Wang X, Li Z, Feng W, Wang N, Li X, Ning X, Xing Y, Jiang X, Xu Z, Zhao Q. Discovery of a novel Xanthone derivative P24 for anti-AD via targeting sTGFBR3. Eur J Med Chem 2024; 276:116729. [PMID: 39088998 DOI: 10.1016/j.ejmech.2024.116729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
Soluble transforming growth factor beta receptor 3 (sTGFBR3) antagonist is a new focus in the research and development of Alzheimer's disease (AD) drugs. Our previous studies have identified sTGFBR3 as a promising new target for AD, with few targeted antagonists identified. In this study, we performed structural modeling of sTGFBR3 using AlphaFold2, followed by high-throughput virtual screening and surface plasmon resonance assays. which collectively identified Xanthone as potential compounds for targeting sTGFBR3. After optimizing the sTGFBR3-Xanthone complex using molecular dynamics (MD) simulations, we prepared a series of novel Xanthone derivatives and evaluated their anti-inflammatory activity, toxicity, and structure-activity relationship in BV2 cell model induced by lipopolysaccharides (LPS) or APP/PS1/tau mouse brain extract (BE). Several derivatives with the most potent anti-inflammatory activity were tested for blood-brain barrier permeability and sTGFBR3 affinity. Derivative P24, selected for its superior properties, was further evaluated in vitro. The results indicated that P24 increased the activation of TGF-β signaling and decreased the activation of IκBα/NF-κB signaling by targeting sTGFBR3, thereby regulating the inflammation-phagocytosis balance in microglia. Moreover, the low acute toxicity, long half-life, and low plasma clearance of P24 suggest that it can be sustained in vivo. This property may render P24 a more effective treatment modality for chronic diseases, particularly AD. The study demonstrates P24 serve as potential novel candidates for the treatment of AD via antagonizing sTGFBR3.
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Affiliation(s)
- Lijun Zhou
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China; Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Zhentong Qi
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xinpeng Wang
- Department of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China
| | - Zhenshu Li
- Department of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China
| | - Wenzhen Feng
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Nan Wang
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xinzhu Li
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xinyue Ning
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Yu Xing
- Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xiaowen Jiang
- School of Traditional Chinese Medicine, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Zihua Xu
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China; Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Qingchun Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China; Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.
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Sklenář A, Růžičková L, Schrenková V, Bednárová L, Pazderková M, Chatziadi A, Zmeškalová Skořepová E, Šoóš M, Kaminský J. Solid-state vibrational circular dichroism for pharmaceutical applications: Polymorphs and cocrystal of sofosbuvir. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124478. [PMID: 38788502 DOI: 10.1016/j.saa.2024.124478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024]
Abstract
X-ray diffraction is a commonly used technique in the pharmaceutical industry for the determination of the atomic and molecular structure of crystals. However, it is costly, sometimes time-consuming, and it requires a considerable degree of expertise. Vibrational circular dichroism (VCD) spectroscopy resolves these limitations, while also exhibiting substantial sensitivity to subtle modifications in the conformation and molecular packaging in the solid state. This study showcases VCD's ability to differentiate between various crystal structures of the same molecule (polymorphs, cocrystals). We examined the most effective approach for producing high-quality spectra and unveiled the intricate link between structure and spectrum via quantum-chemical computations. We rigorously assessed, using alanine as a model compound, multiple experimental conditions on the resulting VCD spectra, with the aim of proposing an optimal and efficient procedure. The proposed approach, which yields reliable, reproducible, and artifact-free results with maximal signal-to-noise ratio, was then validated using a set comprising of three amino acids (serine, alanine, tyrosine), one hydroxy acid (tartaric acid), and a monosaccharide (ribose) to mimic active pharmaceutical components. Finally, the optimized approach was applied to distinguish three polymorphs of the antiviral drug sofosbuvir and its cocrystal with piperazine. Our results indicate that solid-state VCD is a prompt, cost-effective, and easy-to-use technique to identify crystal structures, demonstrating potential for application in pharmaceuticals. We also adapted the cluster and transfer approach to calculate the spectral properties of molecules in a periodic crystal environment. Our findings demonstrate that this approach reliably produces solid-state VCD spectra of model compounds. Although for large molecules with many atoms per unit cell, such as sofosbuvir, this approach has to be simplified and provides only a qualitative match, spectral calculations, and energy analysis helped us to decipher the observed differences in the experimental spectra of sofosbuvir.
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Affiliation(s)
- Adam Sklenář
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic; University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic
| | - Lucie Růžičková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic; Imperial College London, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, UK
| | - Věra Schrenková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic
| | - Argyro Chatziadi
- University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic
| | - Eliška Zmeškalová Skořepová
- University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic; Institute of Physics of the CAS, Na Slovance 1999/2, Prague 182 21, Czech Republic
| | - Miroslav Šoóš
- University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám.2, Prague 166 10, Czech Republic.
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173
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Trojniak AE, Dang VQ, Czekner KM, Russo RJ, Mather LM, Stahl EL, Cameron MD, Bohn LM, Aubé J. Synthesis and evaluation of 3,4,5-trisubstituted triazoles as G protein-biased kappa opioid receptor agonists. Eur J Med Chem 2024; 276:116627. [PMID: 38971050 PMCID: PMC11316643 DOI: 10.1016/j.ejmech.2024.116627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 07/08/2024]
Abstract
Kappa opioid receptor (KOR) agonists represent promising therapeutics for pain relief due to their analgesic properties along with lower abuse potential than opioids that act at the mu opioid receptor. However, typical KOR agonists produce sedation and dysphoria. Previous studies have shown that G protein signaling-biased KOR agonists may present a means to untangle the desired analgesic properties from undesired side effects. In this paper, we report a new series of G protein signaling-biased KOR agonists entailing -S- → -CH2- replacement in a previously reported KOR agonist, triazole 1.1. With an optimized carbon linker in hand, further development of the scaffold was undertaken to investigate the appendages of the triazole core. The structure-activity relationship study of this series is described, including several analogues that display enhanced potency while maintaining G protein-signaling bias compared to triazole 1.1.
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Affiliation(s)
- Ashley E Trojniak
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7363, USA
| | - Vuong Q Dang
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Kerri M Czekner
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL, 33458, USA; The Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, Jupiter, FL, 33458, USA
| | - Robin J Russo
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL, 33458, USA; The Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, Jupiter, FL, 33458, USA
| | - Lilyan M Mather
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7363, USA
| | - Edward L Stahl
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Michael D Cameron
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Laura M Bohn
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 130 Scripps Way, Jupiter, FL, 33458, USA; The Skaggs Graduate School of Chemical and Biological Sciences at Scripps Research, Jupiter, FL, 33458, USA
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7363, USA.
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174
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Sannino GV, Pecoraro A, Veneri PD, Pavone M, Muñoz-García AB. Effective prediction of SnO 2 conduction band edge potential: The key role of surface oxygen vacancies. J Comput Chem 2024; 45:2198-2203. [PMID: 38795374 DOI: 10.1002/jcc.27434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/27/2024]
Abstract
Several theoretical studies at different levels of theory have attempted to calculate the absolute position of the SnO2 conduction band, whose knowledge is key for its effective application in optoelectronic devices such us, for example, perovskite solar cells. However, the predicted band edges fall outside the experimentally measured range. In this work, we introduce a computational scheme designed to calculate the conduction band minimum values of SnO2, yielding results aligned with experiments. Our analysis points out the fundamental role of encompassing surface oxygen vacancies to properly describe the electronic profile of this material. We explore the impact of both bridge and in-plane oxygen vacancy defects on the structural and electronic properties of SnO2, explaining from an atomistic perspective the experimental observables. The results underscore the importance of simulating both types of defects to accurately predict SnO2 features and provide new fundamental insights that can guide future studies concerning design and optimization of SnO2-based materials and functional interfaces.
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Affiliation(s)
| | - Adriana Pecoraro
- Department of Physics "E. Pancini", University of Naples Federico II, Naples, Italy
| | - Paola Delli Veneri
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Portici, Italy
| | - Michele Pavone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
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175
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Papadopoulos MGE, Perhal AF, Medel-Lacruz B, Ladurner A, Selent J, Dirsch VM, Kolb P. Discovery and characterization of small-molecule TGR5 ligands with agonistic activity. Eur J Med Chem 2024; 276:116616. [PMID: 38996653 DOI: 10.1016/j.ejmech.2024.116616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/15/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024]
Abstract
The Takeda G protein-coupled receptor 5 (TGR5) is activated endogenously by primary and secondary bile acids. This receptor is considered a candidate target for addressing inflammatory and metabolic disorders. We have targeted TGR5 with structure-based methods for ligand finding using the recently solved experimental structures, as well as structures obtained from molecular dynamics simulations. Through addressing the orthosteric as well as a putative allosteric site, we identified agonists and positive allosteric modulators. While the predicted binding locations were not in line with their efficacy, our work contributes activating small-molecule ligands that we have thoroughly characterized in vitro.
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Affiliation(s)
| | - Alexander F Perhal
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Brian Medel-Lacruz
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Pompeu Fabra University (UPF), Barcelona, Spain
| | - Angela Ladurner
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Pompeu Fabra University (UPF), Barcelona, Spain
| | - Verena M Dirsch
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, University of Marburg, Marburg, Germany.
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176
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Ren F, Wu X, Liu G, Ding Y. Fluorescent response mechanism based on ESIPT and TICT of novel probe H 2Q JI: A TD-DFT investigation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124383. [PMID: 38772177 DOI: 10.1016/j.saa.2024.124383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/23/2024]
Abstract
Recently, synthesized N-linked-disalicylaldehyde H2QJI probes have been used to detect heavy metal ions in the experiment conveniently. Nevertheless, there needs to be a more in-depth examination of the excited state intramolecular proton transfer (ESIPT) mechanism and photophysical properties of the probe. This work remedied it based on quantum chemistry calculations. We contained due hydrogen bond (O1-H2 ⋯ N3 and O4-H5 ⋯ O6) and then analyzed bond parameters, IR vibration spectra, and non-covalent interaction. The bond strength is enhanced under photoexcitation, and the former is significantly stronger. The calculated electron spectra are in agreement with the experimental values. The results of the S0 and S1 potential energy curves and IRC calculations also confirm the unique ESIPT behavior, which isan excited stated stepwise double proton transfer. The fluorescence, internal conversion, and intersystem crossing rate of KD molecules (twisted-, double proton transfer) were calculated respectively to reveal the radiative and non-radiative pathways. It proved that the corresponding spectra are not obtained since the electrons are mainly deactivated by the ISC (S1->T1). Furthermore, the interfragment charge transfer (IFCT) approach indicates that the molecule possesses twisted intramolecular charge transfer (TICT) characteristics, which lead to the quenching of fluorescence introduction.
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Affiliation(s)
- Fangyu Ren
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Xiaoxue Wu
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Guoqing Liu
- School of Physics, Liaoning University, Shenyang 110036, PR China
| | - Yong Ding
- School of Physics, Liaoning University, Shenyang 110036, PR China.
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177
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Sugisaki K, Nakano T, Mochizuki Y. Size-consistency and orbital-invariance issues revealed by VQE-UCCSD calculations with the FMO scheme. J Comput Chem 2024; 45:2204-2213. [PMID: 38795375 DOI: 10.1002/jcc.27438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/27/2024]
Abstract
The fragment molecular orbital (FMO) scheme is one of the popular fragmentation-based methods and has the potential advantage of making the circuit shallow for quantum chemical calculations on quantum computers. In this study, we used a GPU-accelerated quantum simulator (cuQuantum) to perform the electron correlation part of the FMO calculation as unitary coupled-cluster singles and doubles (UCCSD) with the variational quantum eigensolver (VQE) for hydrogen-bonded (FH) 3 and (FH) 2 -H 2 O systems with the STO-3G basis set. VQE-UCCSD calculations were performed using both canonical and localized MO sets, and the results were examined from the point of view of size-consistency and orbital-invariance affected by the Trotter error. It was found that the use of localized MO leads to better results, especially for (FH) 2 -H 2 O. The GPU acceleration was substantial for the simulations with larger numbers of qubits, and was about a factor of 6.7-7.7 for 18 qubit systems.
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Affiliation(s)
- Kenji Sugisaki
- Graduate School of Science and Technology, Keio University, Kawasaki, Japan
- Quantum Computing Center, Keio University, Yokohama, Japan
- Centre for Quantum Engineering, Research and Education, TCG Centres for Research and Education in Science and Technology, Kolkata, India
| | - Tatsuya Nakano
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Toshima-ku, Japan
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Japan
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178
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Kummur KN, Panda SM, Patil MB, Tripathy U, Sidarai AH. Revealing the interaction mechanism between bovine serum albumin (BSA) and a fluorescent coumarin derivative: A multispectroscopic and in silico approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124466. [PMID: 38761474 DOI: 10.1016/j.saa.2024.124466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/05/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
The interaction of biomacromolecules with each other or with the ligands is essential for biological activity. In this context, the molecular recognition of bovine serum albumin (BSA) with 4-(Benzo[1,3]dioxol-5-yloxymethyl)-7-hydroxy-chromen-2-one (4BHC) is explored using multispectroscopic and computational techniques. UV-Vis spectroscopy helped in predicting the conformational variations in BSA. Using fluorescence spectroscopy, the quenching behaviour of the fluorophore upon interaction with the ligand is examined, which is found to be a static type of quenching; fluorescence lifetime studies further verify this. The binding constant is discovered to be in the range of 104 M-1, which indicates the moderate type of association that results in reversible binding, where the transport and release of ligands in the target tissue takes place. Fourier-transform infrared spectroscopy (FT-IR) measurements validate the secondary structure conformational changes of BSA after complexing with 4BHC. The thermodynamic factors obtained through temperature-dependent fluorescence studies suggest that the dominant kind of interaction force is hydrophobic in nature, and the interaction process is spontaneous. The alterations in the surrounding microenvironment of the binding site and conformational shifts in the structure of the protein are studied through 3D fluorescence and synchronous fluorescence studies. Molecular docking and molecular dynamics (MD) simulations agree with experimental results and explain the structural stability throughout the discussion. The outcomes might have possible applications in the field of pharmacodynamics and pharmacokinetics.
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Affiliation(s)
- Kavyashree Nagappa Kummur
- Department of Studies in Physics, Karnatak University, Pavatenagar, Dharwad, 580003, Karnataka, India
| | - Smita Manjari Panda
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India
| | | | - Umakanta Tripathy
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, Jharkhand, India.
| | - Ashok H Sidarai
- Department of Studies in Physics, Karnatak University, Pavatenagar, Dharwad, 580003, Karnataka, India.
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179
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Petrus E, Buils J, Garay-Ruiz D, Segado-Centellas M, Bo C. POMSimulator: An open-source tool for predicting the aqueous speciation and self-assembly mechanisms of polyoxometalates. J Comput Chem 2024; 45:2242-2250. [PMID: 38826122 DOI: 10.1002/jcc.27389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 06/04/2024]
Abstract
Elucidating the speciation (in terms of concentration versus pH) and understanding the formation mechanisms of polyoxometalates remains a significant challenge, both in experimental and computational domains. POMSimulator is a new methodology that tackles this problem from a purely computational perspective. The methodology uses results from quantum mechanics based methods to automatically set up the chemical reaction network, and to build speciation models. As a result, it becomes possible to predict speciation and phase diagrams, as well as to derive new insights into the formation mechanisms of large molecular clusters. In this work we present the main features of the first open-source version of the software. Since the first report [Chem. Sci. 2020, 11, 8448-8456], POMSimulator has undergone several improvements to keep up with the growing challenges that were tackled. After four years of research, we recognize that the source code is sufficiently stable to share a polished and user-friendly version. The Python code, manual, examples, and install instructions can be found at https://github.com/petrusen/pomsimulator.
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Affiliation(s)
- Enric Petrus
- Department of Environmental Chemistry, EAWAG: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jordi Buils
- Institute of Chemical Research of Catalonia (ICIQ), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Diego Garay-Ruiz
- Institute of Chemical Research of Catalonia (ICIQ), Tarragona, Spain
| | - Mireia Segado-Centellas
- Institute of Chemical Research of Catalonia (ICIQ), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
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180
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Arunachalam K, Matchado MS, Damazo AS, Cardoso CAL, Castro TLAD, Baranoski A, Neves SCD, Martins DTDO, Nascimento VAD, Oliveira RJ. Casearia sylvestris var. lingua (Càmbess.) Eichler leaves aqueous extract improves colon inflammation through mucogenic, antioxidant and anti-inflammatory actions in TNBS- induced IBD rats. JOURNAL OF ETHNOPHARMACOLOGY 2024; 332:118393. [PMID: 38801913 DOI: 10.1016/j.jep.2024.118393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Casearia sylvestris var. lingua (Cambess.) Eichler, a member of the Salicaceae family, holds a prominent place in traditional medicine across various cultures due to its versatile therapeutic properties. Historically, indigenous communities have utilized different parts of the plant, including leaves, bark, and roots, to address a wide array of health conditions. Traditional uses of C. sylvestris var. lingua encompasses the treatment of gastrointestinal disorders, respiratory infections, wound healing, inflammation, and stomach ulcers. Pharmacological studies have demonstrated the plant's antimicrobial, anti-inflammatory, antioxidant, analgesic, gastroprotective, and immunomodulatory effects. This signifies the first scientific validation report for C. sylvestris var. lingua regarding its effectiveness against ulcerative colitis. The report aims to affirm the traditional use of this plant through pre-clinical experiments. AIM OF THE RESEARCH This work uses an aqueous extract from C. sylvestris var. lingua leaves (AECs) to evaluate the acute anti-ulcerative colitis efficacy in rat and HT-29 (human colorectal cancer cell line) models. METHODS To determine the secondary metabolites of AECs, liquid chromatography with a diode array detector (LC-DAD) study was carried out. 2,4,6-trinitrobenzenesulfonic acid (TNBS, 30 mg/0.25 mL EtOH 30% v/v) was used as an enema to cause acute colitis. Three days were spent giving the C. sylvestris var. lingua extract orally by gavage at dosages of 3, 30, and 300 mg/kg. The same route was used to deliver distilled water to the vehicle and naïve groups. After the animals were sacrificed on the fourth day, intestinal tissues were taken for histological examination and evaluation of biochemical tests such as those measuring superoxide dismutase (SOD), reduced glutathione (GSH), catalase (CAT), malondialdehyde (MDA), nitrite/nitrate, myeloperoxidase (MPO) activity. Additionally, interleukin 1 beta (IL-1β), tumor necrosis factor alpha (TNF-α), and interleukin 10 (IL-10), were conducted on the intestinal tissues. Additionally, an MTT assay was used to evaluate the effect of AECs on the viability of HT-29 cells. Additionally, a molecular docking study was carried out to compare some potential target proteins with identified chemicals found in AECs. RESULTS LC-DAD analysis identified five compounds (caffeic acid, ellagic acid, ferulic acid, gallic acid, and quercetin) in AECs. Pre-administration of AECs (3; 30; 300 mg/kg) and mesalazine (500 mg/kg) reduced macroscopic scores (55%, 47%, 45%, and 52%, p < 0.001) and ulcerated areas (70.3%, 70.5%, 57%, and 56%, p < 0.001), respectively. It also increased SOD, GSH, and CAT activities (p < 0.01), while decreasing MDA (p < 0.001), nitrite/nitrate (p < 0.05), and MPO (p < 0.001) activities compared to the colitis group. Concerning inflammatory markers, significant modulations were observed: AECs (3, 30, and 300 mg/kg) lowered levels of IL-1β and TNF-α (p < 0.001) and increased IL-10 levels (p < 0.001) compared to the colitis groups. The viability of HT-29 cells was suppressed by AECs with an IC50 of 195.90 ± 0.01 μg/mL (48 h). During the molecular docking analysis, quercetin, gallic acid, ferulic acid, caffeic acid, and ellagic acid demonstrated consistent binding affinities, forming stable interactions with the 3w3l (TLR8) and the 3ds6 (MAPK14) complexes. CONCLUSION These results imply that the intestinal mucogenic, anti-inflammatory, and antioxidant properties of the C. sylvestris var. lingua leaf extract may be involved in its therapeutic actions for ulcerative colitis. The results of the in silico study point to the possibility of quercetin and ellagic acid interacting with P38 and TLR8, respectively, in a beneficial way.
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Affiliation(s)
- Karuppusamy Arunachalam
- Center for Studies in Stem Cells, Cell Therapy and Toxicological Genetics (CeTroGen), Federal University of Mato Grosso Do Sul (UFMS), Campo Grande, 79070-900, MS, Brazil; Postgraduate Program in Health and Development of the Midwest Region, School of Medicine (FAMED), Federal University of Mato Grosso Do Sul (UFMS), Campo Grande, 79070-900, MS, Brazil.
| | - Monica Steffi Matchado
- Ganga Orthopaedic Research & Education Foundation (GOREF), Coimbatore, Tamil Nadu, India.
| | - Amilcar Sabino Damazo
- Histology Laboratory, Department of Basic Sciences in Health, Faculty of Medicine, Federal University of Mato Grosso (UFMT), Cuiabá, MT, Brazil.
| | - Claudia Andrea Lima Cardoso
- Postgraduate Program in Natural Resources, State University of Mato Grosso Do Sul, Cidade Universitária de Dourados, Rodovia Itahum, Km 12, Dourados, MS, 79804-970, Brazil.
| | - Thiago Luis Aguayo de Castro
- Postgraduate Program in Natural Resources, State University of Mato Grosso Do Sul, Cidade Universitária de Dourados, Rodovia Itahum, Km 12, Dourados, MS, 79804-970, Brazil.
| | - Adrivanio Baranoski
- Center for Studies in Stem Cells, Cell Therapy and Toxicological Genetics (CeTroGen), Federal University of Mato Grosso Do Sul (UFMS), Campo Grande, 79070-900, MS, Brazil.
| | - Silvia Cordeiro das Neves
- Center for Studies in Stem Cells, Cell Therapy and Toxicological Genetics (CeTroGen), Federal University of Mato Grosso Do Sul (UFMS), Campo Grande, 79070-900, MS, Brazil.
| | | | - Valter Aragão do Nascimento
- Postgraduate Program in Health and Development of the Midwest Region, School of Medicine (FAMED), Federal University of Mato Grosso Do Sul (UFMS), Campo Grande, 79070-900, MS, Brazil.
| | - Rodrigo Juliano Oliveira
- Center for Studies in Stem Cells, Cell Therapy and Toxicological Genetics (CeTroGen), Federal University of Mato Grosso Do Sul (UFMS), Campo Grande, 79070-900, MS, Brazil; Postgraduate Program in Health and Development of the Midwest Region, School of Medicine (FAMED), Federal University of Mato Grosso Do Sul (UFMS), Campo Grande, 79070-900, MS, Brazil.
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Zahirović A, Fetahović S, Feizi-Dehnayebi M, Višnjevac A, Bešta-Gajević R, Kozarić A, Martić L, Topčagić A, Roca S. Dual Antimicrobial-Anticancer Potential, Hydrolysis, and DNA/BSA Binding Affinity of a Novel Water-Soluble Ruthenium-Arene Ethylenediamine Schiff base (RAES) Organometallic. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124528. [PMID: 38801789 DOI: 10.1016/j.saa.2024.124528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
The need for a systematic approach in developing new metal-based drugs with dual anticancer-antimicrobial properties is emphasized by the vulnerability of cancer patients to bacterial infections. In this context, a novel organometallic assembly was designed, featuring ruthenium(II) coordination with p-cymene, one chlorido ligand, and a bidentate neutral Schiff base derived from 4-methoxybenzaldehyde and N,N-dimethylethylenediamine. The compound was extensively characterized in both solid-state and solution, employing single crystal X-ray diffraction, nuclear magnetic resonance, infrared, ultraviolet-visible spectroscopy, and density functional theory, alongside Hirshfeld surface analysis. The hydrolysis kinetic was thoroughly investigated, revealing the important role of the chloro-aqua equilibrium in the dynamics of binding with deoxyribonucleic acid and bovine serum albumin. Notably, the aqua species exhibited a pronounced affinity for deoxyribonucleic acid, engaging through electrostatic and hydrogen bonding interactions, while the chloro species demonstrated groove-binding properties. Interaction with albumin revealed distinct binding mechanisms. The aqua species displayed covalent binding, contrasting with the ligand-like van der Waals interactions and hydrogen bonding observed with the chloro specie. Molecular docking studies highlighted site-specific interactions with biomolecular targets. Remarkably, the compound exhibited wide spectrum moderate antimicrobial activity against Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans, coupled with low micromolar cytotoxic activity against human colorectal adenocarcinoma cells and significant activity against human leukemic monocyte lymphoma cells. The presented findings encourage further development of this compound, promising avenues for its evolution into a versatile therapeutic agent targeting both infectious diseases and cancer.
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Affiliation(s)
- Adnan Zahirović
- Laboratory for Inorganic and Bioinorganic Chemistry, Department of Chemistry, Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina.
| | - Selma Fetahović
- Laboratory for Inorganic and Bioinorganic Chemistry, Department of Chemistry, Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | - Aleksandar Višnjevac
- Laboratory for Chemical and Biological Crystallography, Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Renata Bešta-Gajević
- Department of Biology, Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Amina Kozarić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Lora Martić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Anela Topčagić
- Laboratory for Inorganic and Bioinorganic Chemistry, Department of Chemistry, Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Sunčica Roca
- NMR Centre, Ruđer Bošković Institute, Zagreb, Croatia.
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182
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Tang L, Wang D, Chang H, Liu Z, Zhang X, Feng X, Han L. Treating ischemic stroke by improving vascular structure and promoting angiogenesis using Taohong Siwu Decoction: An integrative pharmacology strategy. JOURNAL OF ETHNOPHARMACOLOGY 2024; 332:118372. [PMID: 38777084 DOI: 10.1016/j.jep.2024.118372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Neovessels represent a crucial therapeutic target and strategy for repairing ischemic tissue. Taohong Siwu Decoction (THSWD) exhibits potential in promoting angiogenesis to address ischemic stroke (IS). However, its impact on neovessel structure and function, alongside the underlying molecular mechanisms, remains elusive. AIM OF THE STUDY Our aim is to investigate the protective effects of THSWD on neovessel structure and function, as well as the associated molecular mechanisms, utilizing an integrative pharmacological approach. MATERIALS AND METHODS We initially employed behavioral tests, 2,3,5-triphenyltetrazolium chloride (TTC) staining, Haematoxylin-eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), Laser Doppler flowmetry (LDF), Evans blue staining, and immunofluorescence to evaluate the protective effects of THSWD on neovascular structure and function in middle cerebral artery occlusion/reperfusion (MCAO/R) rats. Subsequently, we utilized network pharmacology, metabolomics, and experimental validation to elucidate the underlying molecular mechanisms of THSWD in enhancing neovascular structure and function. RESULT In addition to significantly reducing neurological deficits and cerebral infarct volume, THSWD mitigated pathological damage, blood-brain barrier (BBB) leakage, and cerebral blood flow disruption. Moreover, it preserved neovascular structure and stimulated angiogenesis. THSWD demonstrated potential in ameliorating cerebral microvascular metabolic disturbances including lipoic acid metabolism, fructose and mannose metabolism, purine metabolism, and ether lipid metabolism. Consequently, it exhibited multifaceted therapeutic effects, encompassing anti-inflammatory, antioxidant, energy metabolism modulation, and antiplatelet aggregation properties. CONCLUSION THSWD exhibited protective effects on cerebral vascular structure and function and facilitated angiogenesis by rectifying cerebral microvascular metabolic disturbances in MCAO/R rats. Furthermore, integrated pharmacology offers a promising approach for studying the intricate traditional Chinese medicine (TCM) system in IS treatment.
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Affiliation(s)
- Linfeng Tang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Dandan Wang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Hao Chang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Zhuqing Liu
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Xueting Zhang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Xuefeng Feng
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230031, China
| | - Lan Han
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China; MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, 230012, China.
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183
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Jena S, Gonzalez G, Vítek D, Kvasnicová M, Štěpánková Š, Strnad M, Voller J, Chanda K. Novel neuroprotective 5,6-dihydropyrido[2',1':2,3]imidazo[4,5-c]quinoline derivatives acting through cholinesterase inhibition and CB2 signaling modulation. Eur J Med Chem 2024; 276:116592. [PMID: 39013357 DOI: 10.1016/j.ejmech.2024.116592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 07/18/2024]
Abstract
A novel group of 5,6-dihydropyrido [2',1':2,3]imidazo [4,5-c]quinolines was prepared via a microwave assisted one-pot telescopic approach. The synthetic sequence involves the formation of an amine precursor of imidazo [1,2-a]pyridine via condensation and reduction under microwave irradiation. Subsequently, the Pictet-Spengler cyclisation reaction occurs with ketones (cyclic or acyclic) to obtain substituted 5,6-dihydropyrido [2',1':2,3]imidazo [4,5-c]quinolines in excellent yields. The compounds were tested as neuroprotective agents. Observed protection of neuron-like cells, SH-SY5Y differentiated with ATRA, in Parkinson's and Huntington's disease models inspired further mechanistic studies of protective activity against damage induced by 1-methyl-4-phenylpyridinium (MPP+), a compound causing Parkinson's disease. The novel compounds exhibit similar or higher potency than ebselen, an established drug with antioxidant activity, in the cells against MPP + -induced total cellular superoxide production and cell death. However, they exhibit a significantly higher capacity to reduce mitochondrial superoxide and preserve mitochondrial membrane potential. We also observed marked differences between a selected derivative and ebselen in terms of normalizing MPP + -induced phosphorylation of Akt and ERK1/2. The cytoprotective activity was abrogated when signaling through cannabinoid receptor CB2 was blocked. The compounds also inhibit both acetylcholine and butyrylcholine esterases. Overall the data show that novel 5,6-dihydropyrido [2',1':2,3]imidazo [4,5-c]quinoline have a broad cytoprotective activity which is mediated by several mechanisms including mitoprotection.
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Affiliation(s)
- Sushovan Jena
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Gabriel Gonzalez
- Department of Experimental Biology, Palacky University Olomouc, Faculty of Science, Šlechtitelů 27, 78371, Olomouc, Czech Republic; Department of Neurology, University Hospital in Olomouc, I. P. Pavlova 6, 77520, Olomouc, Czech Republic
| | - Dominik Vítek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 5, 77515, Olomouc, Czech Republic
| | - Marie Kvasnicová
- Department of Experimental Biology, Palacky University Olomouc, Faculty of Science, Šlechtitelů 27, 78371, Olomouc, Czech Republic; Laboratory of Growth Regulators, Faculty of Science, Palacký University Olomouc, and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Šárka Štěpánková
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 53210, Pardubice, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Palacký University Olomouc, and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Jiří Voller
- Department of Experimental Biology, Palacky University Olomouc, Faculty of Science, Šlechtitelů 27, 78371, Olomouc, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 5, 77515, Olomouc, Czech Republic.
| | - Kaushik Chanda
- Department of Chemistry, Rabindranath Tagore University, Hojai, Assam, 782435, India.
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184
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Sanz-Villafruela J, Bermejo-Casadesus C, Zafon E, Martínez-Alonso M, Durá G, Heras A, Soriano-Díaz I, Giussani A, Ortí E, Tebar F, Espino G, Massaguer A. Insights into the anticancer photodynamic activity of Ir(III) and Ru(II) polypyridyl complexes bearing β-carboline ligands. Eur J Med Chem 2024; 276:116618. [PMID: 38972079 DOI: 10.1016/j.ejmech.2024.116618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/31/2024] [Accepted: 06/22/2024] [Indexed: 07/09/2024]
Abstract
Ir(III) and Ru(II) polypyridyl complexes are promising photosensitizers (PSs) for photodynamic therapy (PDT) due to their outstanding photophysical properties. Herein, one series of cyclometallated Ir(III) complexes and two series of Ru(II) polypyridyl derivatives bearing three different thiazolyl-β-carboline N^N' ligands have been synthesized, aiming to evaluate the impact of the different metal fragments ([Ir(C^N)2]+ or [Ru(N^N)2]2+) and N^N' ligands on the photophysical and biological properties. All the compounds exhibit remarkable photostability under blue-light irradiation and are emissive (605 < λem < 720 nm), with the Ru(II) derivatives displaying higher photoluminescence quantum yields and longer excited state lifetimes. The Ir PSs display pKa values between 5.9 and 7.9, whereas their Ru counterparts are less acidic (pKa > 9.3). The presence of the deprotonated form in the Ir-PSs favours the generation of reactive oxygen species (ROS) since, according to theoretical calculations, it features a low-lying ligand-centered triplet excited state (T1 = 3LC) with a long lifetime. All compounds have demonstrated anticancer activity. Ir(III) complexes 1-3 exhibit the highest cytotoxicity in dark conditions, comparable to cisplatin. Their activity is notably enhanced by blue-light irradiation, resulting in nanomolar IC50 values and phototoxicity indexes (PIs) between 70 and 201 in different cancer cell lines. The Ir(III) PSs are also activated by green (with PI between 16 and 19.2) and red light in the case of complex 3 (PI = 8.5). Their antitumor efficacy is confirmed by clonogenic assays and using spheroid models. The Ir(III) complexes rapidly enter cells, accumulating in mitochondria and lysosomes. Upon photoactivation, they generate ROS, leading to mitochondrial dysfunction and lysosomal damage and ultimately cell apoptosis. Additionally, they inhibit cancer cell migration, a crucial step in metastasis. In contrast, Ru(II) complex 6 exhibits moderate mitochondrial activity. Overall, Ir(III) complexes 1-3 show potential for selective light-controlled cancer treatment, providing an alternative mechanism to chemotherapy and the ability to inhibit lethal cancer cell dissemination.
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Affiliation(s)
- Juan Sanz-Villafruela
- Universidad de Burgos, Departamento de Química, Facultad de Ciencias, Plaza Misael Bañuelos S/n, 09001, Burgos, Spain
| | - Cristina Bermejo-Casadesus
- Universitat de Girona, Departament de Biologia, Facultat de Ciències, Maria Aurelia Capmany 40, 17003, Girona, Spain
| | - Elisenda Zafon
- Universitat de Girona, Departament de Biologia, Facultat de Ciències, Maria Aurelia Capmany 40, 17003, Girona, Spain
| | - Marta Martínez-Alonso
- Universidad de Burgos, Departamento de Química, Facultad de Ciencias, Plaza Misael Bañuelos S/n, 09001, Burgos, Spain
| | - Gema Durá
- Universidad de Castilla-La Mancha, Departamento de Química Inorgánica, Orgánica y Bioquímica. Facultad de Químicas, Avda. Camilo J. Cela 10, 13071, Ciudad Real, Spain
| | - Aranzazu Heras
- Universidad de Burgos, Departamento de Química, Facultad de Ciencias, Plaza Misael Bañuelos S/n, 09001, Burgos, Spain
| | - Iván Soriano-Díaz
- Instituto de Ciencia Molecular, Universidad de Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
| | - Angelo Giussani
- Instituto de Ciencia Molecular, Universidad de Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
| | - Enrique Ortí
- Instituto de Ciencia Molecular, Universidad de Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.
| | - Francesc Tebar
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, 08036, Barcelona, Spain.
| | - Gustavo Espino
- Universidad de Burgos, Departamento de Química, Facultad de Ciencias, Plaza Misael Bañuelos S/n, 09001, Burgos, Spain.
| | - Anna Massaguer
- Universitat de Girona, Departament de Biologia, Facultat de Ciències, Maria Aurelia Capmany 40, 17003, Girona, Spain.
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185
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Borude AS, Deshmukh SR, Tiwari SV, Kumar SH, Thopate SR. Design and synthesis of novel Thiazolo[5,4-b]pyridine derivatives as potent and selective EGFR-TK inhibitors targeting resistance Mutations in non-small cell lung cancer. Eur J Med Chem 2024; 276:116727. [PMID: 39094428 DOI: 10.1016/j.ejmech.2024.116727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/22/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024]
Abstract
A novel series of substituted thiazolo[5,4-b]pyridine analogues were rationally designed and synthesized via a multi-step synthetic pathway, including Suzuki cross-coupling reaction. The anticancer activity of all forty-five synthesized derivatives was evaluated against HCC827, H1975, and A549 cancer cell lines utilizing the standard MTT assay. A significant number of the thiazolo[5,4-b]pyridine derivatives exhibited potent anticancer activity. Notably, compounds 10b, 10c, 10h, 10i, and 10k emerged as the most promising anticancer agents. The lead compound, N-(3-(6-(2-aminopyrimidin-5-yl)thiazolo[5,4-b]pyridin-2-yl)-2-methylphenyl)-2,5-difluorobenzenesulfonamide (10k), displayed remarkable potency with IC50 values of 0.010 μM, 0.08 μM, and 0.82 μM against the HCC827, NCI-H1975 and A-549 cancer cell lines, respectively, which were comparable to the clinically approved drug Osimertinib. Importantly, the potent derivatives 10b, 10c, 10h, 10i, and 10k exhibited selective cytotoxicity towards cancer cells and showing no toxicity against the normal BEAS-2B cell line at concentrations exceeding 35 μM. Mechanistic studies revealed that the active compound 10k acts as an EGFR-TK autophosphorylation inhibitor in HCC827 cells. Furthermore, apoptosis assays demonstrated that compound 10k induced substantial early apoptosis (31.9 %) and late apoptosis (8.8 %) in cancer cells, in contrast to the control condition exhibiting only 2.0 % early and 1.6 % late apoptosis. Molecular docking simulations of the synthesized compounds revealed that they formed essential hinge interactions and established hydrogen bonding with Cys797, indicating potential target engagement. These findings highlight the potential of the synthesized thiazolo [(Woodburn, 1999; Zigrossi et al., 2022) 5,45,4-b]pyridine derivatives as promising anticancer agents, warranting further investigation for the development of novel targeted therapies against non-small cell lung cancer.
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Affiliation(s)
- Avinash S Borude
- Department of Chemistry, Radhabai Kale Mahila Mahavidyalay, Ahmednagar, Maharashtra, 414001, India
| | - Santosh R Deshmukh
- Department of Chemistry, Ahmednagar College, Ahmednagar, Maharashtra, 414001, India.
| | - Shailee V Tiwari
- Department of Pharmaceutical Chemistry, Shri Ramkrishna Paramhans College of Pharmacy, Hasnapur, Parbhani, Maharashtra, 431401, India
| | - S Hemant Kumar
- thinkMolecular Technologies Pvt. Ltd, Bangalore, 560102, India
| | - Shankar R Thopate
- Department of Chemistry, Radhabai Kale Mahila Mahavidyalay, Ahmednagar, Maharashtra, 414001, India.
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186
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Purtscher FRS, Hofer TS. Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds III: QM/MM MD simulations of solid-state systems at the example of layered carbon structures. J Comput Chem 2024; 45:2186-2197. [PMID: 38795379 DOI: 10.1002/jcc.27428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/27/2024]
Abstract
The previously introduced workflow to achieve an energetically and structurally optimized description of frontier bonds in quantum mechanical/molecular mechanics (QM/MM)-type applications was extended into the regime of computational material sciences at the example of a layered carbon model systems. Optimized QM/MM link bond parameters at HSEsol/6-311G(d,p) and self-consistent density functional tight binding (SCC-DFTB) were derived for graphitic systems, enabling detailed investigation of specific structure motifs occurring in graphene-derived structures v i a quantum-chemical calculations. Exemplary molecular dynamics (MD) simulations in the isochoric-isothermic (NVT) ensemble were carried out to study the intercalation of lithium and the properties of the Stone-Thrower-Wales defect. The diffusivity of lithium as well as hydrogen and proton adsorption on a defective graphene surface served as additional example. The results of the QM/MM MD simulations provide detailed insight into the applicability of the employed link-bond strategy when studying intercalation and adsorption properties of graphitic materials.
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Affiliation(s)
- Felix R S Purtscher
- Institute of General, Inorganic and Theoretical Chemistry Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck, Austria
| | - Thomas S Hofer
- Institute of General, Inorganic and Theoretical Chemistry Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck, Austria
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187
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Lusardi M, Belvedere R, Petrella A, Iervasi E, Ponassi M, Brullo C, Spallarossa A. Novel tetrasubstituted 5-Arylamino pyrazoles able to interfere with angiogenesis and Ca 2+ mobilization. Eur J Med Chem 2024; 276:116715. [PMID: 39083983 DOI: 10.1016/j.ejmech.2024.116715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
In the last years, 5-pyrazolyl ureas and 5-aminopyrazoles have been investigated for their antiangiogenetic properties and their potential interaction with the ubiquitous Ca2+ binding protein Calreticulin. Based on the structure of the active compounds I and GeGe-3, novel 5-arylamino pyrazoles 2 and 3 were synthesized through a stepwise procedure. In MTT assays, all the new derivatives proved to be non-cytotoxic against eight different tumor cell lines, normal fibroblasts, and endothelial cells. Furthermore, selected derivatives showed relevant antiangiogenetic properties, resulting more effective than reference molecules I and GeGe-3 in inhibiting HUVEC endothelial tube formation. 5-Arylamino pyrazoles 2a and 2d were identified as the most interesting compounds and significantly prevented tube formation of tumor secretome-stimulated HUVEC. Furthermore, the two compounds inhibited HUVEC migration in wound healing assay and altered cell invasion capability. Additionally, 2a and 2d strongly affected Ca2+ mobilization and cytoskeletal organization of HUVEC cells, being as active as the reference compound GeGe-3. Differently from previous studies, molecular docking simulations suggested a poor affinity of 2a towards Calreticulin, one of the interacting partners of the lead compound GeGe-3. Collectively, this new amino-pyrazole library further extends the structure-activity relationships of the previously prepared derivatives and confirmed the biological attractiveness of this chemical scaffold as antiangiogenetic agents.
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Affiliation(s)
- Matteo Lusardi
- Department of Pharmacy, Section of Medicinal Chemistry, University of Genoa, Viale Benedetto XV 3, I-16132, Genova, Italy
| | - Raffaella Belvedere
- Department of Pharmacy, University of Salerno, Viale Giovanni Paolo II, 84084, Salerno, Italy
| | - Antonello Petrella
- Department of Pharmacy, University of Salerno, Viale Giovanni Paolo II, 84084, Salerno, Italy
| | - Erika Iervasi
- IRCCS Ospedale Policlinico San Martino, Proteomics and Mass Spectrometry Unit, Largo. R. Benzi, 10, 16132, Genova, Italy
| | - Marco Ponassi
- IRCCS Ospedale Policlinico San Martino, Proteomics and Mass Spectrometry Unit, Largo. R. Benzi, 10, 16132, Genova, Italy
| | - Chiara Brullo
- Department of Pharmacy, Section of Medicinal Chemistry, University of Genoa, Viale Benedetto XV 3, I-16132, Genova, Italy
| | - Andrea Spallarossa
- Department of Pharmacy, Section of Medicinal Chemistry, University of Genoa, Viale Benedetto XV 3, I-16132, Genova, Italy.
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188
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Zhao X, Chai Z, Wang J, Hou D, Li B, Zhang L, Huang W. Assessment on malvidin-3-glucoside interaction with TLR4 via multi-spectroscopic analysis and molecular docking. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124460. [PMID: 38761477 DOI: 10.1016/j.saa.2024.124460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/31/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
As one innate immune pattern recognition receptor, Toll-like receptor 4 (TLR4) recently has been considered as a critical player in glucolipid metabolism. Blueberries contain high level of anthocyanins, especially malvidin-3-glucoside (Mv-3-glc), which contribute the anti-inflammatory, hypoglycemic, and hypolipidemic effects. It is speculated that Mv-3-glc is able to possess these functions by binding to TLR4. Here, the noncovalent interactions of Mv-3-glc and TLR4 was explored through multi-techniques including fluorescence and ultraviolet-visible (UV-Vis) absorption spectroscopy, as well as molecular docking. The results demonstrated that Mv-3-glc was able to quench TLR4 intrinsic fluorescence effectively. A stable complex was formed spontaneously and the reaction was exothermic. The degree of binding of Mv-3-glc to TLR4 showed a strong dependence on the chemical concentration, temperature, and pH values. The negative signs for enthalpy (ΔH = -69.1 ± 10.8 kJ/mol) and entropy (ΔS = -105.0 ± 12.3 J/mol/K) from the interaction of the Mv-3-glc and TLR4 shows that the major driving forces are the hydrogen bonding and van der Waals' force, which is consistent with the molecular docking results. In addition, molecular docking predicted that the active center with specific amino acid residues, Phe126, Ser127, Leu54, Ile153, and Tyr131 was responsible for the site of Mv-3-glc binding to TLR4/myeloid differentiation protein-2 (MD-2). These findings confirmed that Mv-3-glc could bind to TLR4, which would be beneficial to understand the target therapeutic effects of blueberry anthocyanins on TLR4 in regulating glucolipid metabolism.
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Affiliation(s)
- Xingyu Zhao
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China.
| | - Zhi Chai
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China.
| | - Jing Wang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China.
| | - Dongjie Hou
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China.
| | - Bin Li
- College of Food Science, Shenyang Agricultural University, Liaoning 110866, PR China.
| | - Lixia Zhang
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China.
| | - Wuyang Huang
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China; College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, PR China.
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189
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Crescenzi O, Graziano G. The interaction of thiocyanate with peptides-A computational study. J Comput Chem 2024; 45:2214-2231. [PMID: 38795315 DOI: 10.1002/jcc.27440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/27/2024]
Abstract
According to the Hofmeister series, thiocyanate is the strongest "salting in" anion. In fact, it has a strong denaturant activity against the native state of globular proteins. A molecular level rationalization of the Hofmeister series is still missing, and therefore the denaturant activity of thiocyanate also awaits a robust explanation. In the last years, different types of experimental studies have shown that thiocyanate is capable to directly interact with both polar and nonpolar groups of polypeptide chains. This finding has been scrutinized via a careful computational procedure based on density functional theory approaches. The results indicate that thiocyanate is able to make H-bonds via both the nitrogen and sulfur atom, and to make strong van der Waals interactions with almost all the groups of polypeptide chains, regardless of their polarity.
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Affiliation(s)
- Orlando Crescenzi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Benevento, Italy
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Zhang K, Liu H, Cai L, Fan J, Lin L, Wang CK, Li J. Theoretical insights on highly efficient X-shaped near-infrared thermal activation delayed fluorescence emitter. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124500. [PMID: 38795526 DOI: 10.1016/j.saa.2024.124500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/29/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
The near-infrared (NIR) thermally activated delayed fluorescence (TADF) molecules hold practical application value in various fields, including biological imaging, anti-counterfeiting, sensors, telemedicine, photomicrography, and night vision display. These molecules have emerged as a significant development direction in organic electroluminescent devices, offering exciting possibilities for future technological advancements. Despite the remarkable potential of NIR-TADF molecules in various applications, the development of molecules that exhibit both long-wavelength emission and high efficiency remains a significant challenge. Herein, based on T-type and Y-type TADF molecules BCN-TPA and ECN-TPA, a novel X-type TADF molecule X-ECN-TPA is theoretically designed through a molecular fusion strategy. Utilizing first-principles calculations and the thermal vibration correlation function (TVCF) method, the photophysical properties and luminescent mechanisms of these three molecules in both solvent and solid (doped films) are revealed. A comparison of the luminescent properties of isomeric BCN-TPA and ECN-TPA shows that the enhanced luminescence efficiency of BCN-TPA in the solid states is attributed to higher radiative rates and lower non-radiative rates. Furthermore, compared to BCN-TPA and ECN-TPA, X-ECN-TPA exhibits significant conjugation extension, resulting in a pronounced redshift, reaching 831 nm and 813 nm in solvent and solid states, respectively. Importantly, molecular fusion significantly increases the transition dipole moment density between the donor and acceptor, leading to a substantial increase in radiative transition rates. Additionally, molecular fusion effectively reduces the energy gap between the first singlet excited state (S1) and the first triplet excited state (T1), facilitating the improvement of the reverse intersystem crossing (RISC) process. In addition, the calculation of Marcus formula shows that the triplet energy transfer from CBP to BCN-TPA, ECN-TPA and X-ECN-TPA is very effective. This work not only designs a novel efficient NIR-TADF molecule but also proposes a strategy for designing efficient NIR-TADF molecules. This principle offers unique insights for optimizing traditional molecular frameworks, opening up new possibilities for future advancements.
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Affiliation(s)
- Kai Zhang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, China.
| | - Huanling Liu
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China
| | - Lei Cai
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China
| | - Jianzhong Fan
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China
| | - Lili Lin
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China
| | - Chuan-Kui Wang
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, 250014 Jinan, China
| | - Jing Li
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, China.
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191
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Chi F, Cheng C, Zhang M, Su B, Hou Y, Bai G. Resveratrol targeting NRF2 disrupts the binding between KEAP1 and NRF2-DLG motif to ameliorate oxidative stress damage in mice pulmonary infection. JOURNAL OF ETHNOPHARMACOLOGY 2024; 332:118353. [PMID: 38762209 DOI: 10.1016/j.jep.2024.118353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The root of Polygonum cuspidatum Sieb. et Zucc (PC), known as 'Huzhang' in the Chinese Pharmacopoeia, has been traditionally employed for its anti-inflammatory, antiviral, antimicrobial, and other biological activities. Polydatin (PD) and its aglycone, resveratrol (RES), are key pharmacologically active components responsible for exerting anti-inflammatory and antioxidant effects. However, its specific targets and action mechanisms remain unclear. AIM OF THE STUDY The equilibrium of the KEAP1-NRF2 system serves as the primary protective response to oxidative and electrophilic stresses within the body, particularly in cases of acute lung injury caused by pathogenic microbial infection. In this study, the precise mechanisms by which RES alleviates oxidative stress damage in conjunction with NRF2 activators are discussed. MATERIALS AND METHODS The active components from PC were screened to evaluate their potential to inhibit reactive oxygen species (ROS) and activate antioxidant activity dependent on antioxidant response elements (ARE). RES was evaluated for its potential to alleviate the oxidative stress caused by pathogenic microbial infection. Functional probes were designed to study the RES distribution and identify its targets. A lipopolysaccharide (LPS)-induced oxidative injury model was used to evaluate the effects of RES on the KEAP1-NRF2/ARE pathway in RAW 264.7 cells. The interaction between RES and NRF2 was elucidated using drug-affinity responsive target stability (DARTS), cellular thermal shift assays (CETSA), co-immunoprecipitation (Co-IP), and microscale thermophoresis (MST) techniques. The key binding sites were predicted using molecular docking and validated in NRF2-knockdownand reconstructed cells. Finally, protective effects against pulmonary stress were verified in a mouse model of pathogenic infection. RESULTS The accumulation of RES in lung macrophages disrupted the binding between KEAP1 and NRF2, thereby preventing the ubiquitination degradation of NRF2 through its interaction with Ile28 on the NRF2-DLG motif. The activation of NRF2 resulted in the upregulation of nuclear transcription, enhances the expression of antioxidant genes dependent on ARE, suppresses ROS generation, and ameliorates oxidative damage both in vivo and in vitro. CONCLUSION These findings shed light on the potential of RES to mitigate oxidative stress damage caused by pathogenic microorganism-induced lung infections and facilitate the discovery of novel small molecule modulators targeting the KEAP1-NRF2 DLG motif interaction.
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Affiliation(s)
- Fuyun Chi
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Chuanjing Cheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Man Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Bo Su
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China
| | - Yuanyuan Hou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China.
| | - Gang Bai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300353, China.
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Trotta AM, Tomassi S, Di Maiolo G, Ieranò C, Vetrei C, D'Alterio C, Merlino F, Messere A, D'Aniello A, Del Bene A, Mazzarella V, Roggia M, Natale B, Cutolo R, Campagna E, Mottola S, Russo R, Chambery A, Benedetti R, Altucci L, Cosconati S, Scala S, Di Maro S. Disulfide bond replacement with non-reducible side chain to tail macrolactamization for the development of potent and selective CXCR4 peptide antagonists endowed with flanking binding sites. Eur J Med Chem 2024; 276:116669. [PMID: 39053189 DOI: 10.1016/j.ejmech.2024.116669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024]
Abstract
The present study describes a small library of peptides derived from a potent and selective CXCR4 antagonist (3), wherein the native disulfide bond is replaced using a side-chain to tail macrolactamization technique to vary ring size and amino acid composition. The peptides were preliminary assessed for their ability to interfere with the interaction between the receptor and anti-CXCR4 PE-conjugated antibody clone 12G5. Two promising candidates (13 and 17) were identified and further evaluated in a125I-CXCL12 competition binding assay, exhibiting IC50 in the low-nanomolar range. Furthermore, both candidates displayed high selectivity towards CXCR4 with respect to the cognate receptor CXCR7, ability to block CXCL12-dependent cancer cell migration, and receptor internalization, albeit at a higher concentration compared to 3. Molecular modeling studies on 13 and 17 produced a theoretical model that may serve as a guide for future modifications, aiding in the development of analogs with improved affinity. Finally, the study provides valuable insights into developing therapeutic agents targeting CXCR4-mediated processes, demonstrating the adaptability of our lead peptide 3 to alternative cyclization approaches and offering prospects for comprehensive investigations into the receptor region's interaction with its C-terminal region.
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Affiliation(s)
- Anna Maria Trotta
- Microenvironment Molecular Targets, Istituto Nazionale Tumori-IRCCS-Fondazione "G. Pascale", 80131 Naples, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Gaetana Di Maiolo
- Microenvironment Molecular Targets, Istituto Nazionale Tumori-IRCCS-Fondazione "G. Pascale", 80131 Naples, Italy
| | - Caterina Ieranò
- Microenvironment Molecular Targets, Istituto Nazionale Tumori-IRCCS-Fondazione "G. Pascale", 80131 Naples, Italy
| | - Cinzia Vetrei
- Microenvironment Molecular Targets, Istituto Nazionale Tumori-IRCCS-Fondazione "G. Pascale", 80131 Naples, Italy
| | - Crescenzo D'Alterio
- Microenvironment Molecular Targets, Istituto Nazionale Tumori-IRCCS-Fondazione "G. Pascale", 80131 Naples, Italy
| | - Francesco Merlino
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Antonia D'Aniello
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Michele Roggia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Benito Natale
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Roberto Cutolo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Erica Campagna
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Salvatore Mottola
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Rosaria Benedetti
- Department of Precision Medicine, University of Campania ''Luigi Vanvitelli'', Vico L. De Crecchio 7, 80138, Naples, Italy; Program of Medical Epigenetics, Vanvitelli Hospital, Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania ''Luigi Vanvitelli'', Vico L. De Crecchio 7, 80138, Naples, Italy; Program of Medical Epigenetics, Vanvitelli Hospital, Naples, Italy; Institute of Endocrinology and Oncology "Gaetano Salvatore" (IEOS), 80131, Naples, Italy; Biogem Institute of Molecular and Genetic Biology, 83031, Ariano Irpino, Italy
| | - Sandro Cosconati
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy.
| | - Stefania Scala
- Microenvironment Molecular Targets, Istituto Nazionale Tumori-IRCCS-Fondazione "G. Pascale", 80131 Naples, Italy.
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100, Caserta, Italy.
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Guha S, Talukdar D, Mandal GK, Mukherjee R, Ghosh S, Naskar R, Saha P, Murmu N, Das G. Crude extract of Ruellia tuberosa L. flower induces intracellular ROS, promotes DNA damage and apoptosis in triple negative breast cancer cells. JOURNAL OF ETHNOPHARMACOLOGY 2024; 332:118389. [PMID: 38821138 DOI: 10.1016/j.jep.2024.118389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Ruellia tuberosa L. (Acanthaceae) is a weed plant traditionally used in folklore medicine as a diuretic, anti-hypertensive, anti-pyretic, anti-cancerous, anti-diabetic, analgesic, and gastroprotective agent. It has been previously reported that R. tuberosa L. is enriched with various flavonoids, exhibiting significant cytotoxic potential in various cancer models but a detailed study concerning its molecular mechanism is yet to be explored. AIM OF THE STUDY Exploring and validating R. tuberosa L. flower methanolic extract (RTME) as an anti-cancerous agent as per traditional usage with special emphasis on multi-drug resistant human triple-negative breast cancer (TNBC) and investigating the possible signaling networks and regulatory pathways involved in it. MATERIALS AND METHODS In this study, RTME was prepared using methanol, and phytochemical analysis was performed through GC-MS. Then, the extract was tested for its anti-cancer potential through in-vitro cytotoxicity assay, clonogenic assay, wound healing assay, ROS generation assay, cell cycle arrest, apoptotic nuclear morphology study, cellular apoptosis study, mitochondrial membrane potential (MMP) alteration study, protein, and gene expressions alteration study. In addition, toxicological status was evaluated in female Balb/C mice, and to check the receptor-ligand interactions, in-silico molecular docking was also conducted. RESULTS Several phytochemicals were found within RTME through GC-MS, which have been already reported to act as ROS inductive, DNA damaging, cell cycle arresting, and apoptotic agents against cancer cells. Moreover, RTME was found to exhibit significant in-vitro cytotoxicity along with a reduction in colony formation, and inhibition of cell migratory potential. It also induced intracellular ROS, promoted G0/G1 cell cycle arrest, caused mitochondrial membrane potential (MMP) alteration, and promoted cell death. The Western blot and qRT-PCR data revealed that RTME promoted the intrinsic pathway of apoptosis. Furthermore, blood parameters and organ histology on female Balb/C mice disclosed the non-toxic nature of RTME. Finally, an in-silico molecular docking study displayed that the three identified lead phytochemicals in RTME show strong receptor-ligand interactions with the anti-apoptotic Bcl-2 and give a clue to the possible molecular mechanism of the RTME extract. CONCLUSIONS RTME is a potential source of several phytochemicals that have promising therapeutic potential against TNBC cells, and thus could further be utilized for anti-cancer drug development.
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Affiliation(s)
- Subhabrata Guha
- Department of Signal Transduction and Biogenic Amines, Chittaranjan National Cancer Institute, 37 S.P. Mukherjee Road, Kolkata, 700026, West Bengal, India; Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute, 37 S.P. Mukherjee Road, Kolkata, 700026, West Bengal, India.
| | - Debojit Talukdar
- Department of Signal Transduction and Biogenic Amines, Chittaranjan National Cancer Institute, 37 S.P. Mukherjee Road, Kolkata, 700026, West Bengal, India.
| | - Gautam Kumar Mandal
- IQ City Medical College Hospital, IQ City Road, Durgapur, 713206, West Bengal, India.
| | - Rimi Mukherjee
- Department of Signal Transduction and Biogenic Amines, Chittaranjan National Cancer Institute, 37 S.P. Mukherjee Road, Kolkata, 700026, West Bengal, India.
| | - Srestha Ghosh
- Department of Signal Transduction and Biogenic Amines, Chittaranjan National Cancer Institute, 37 S.P. Mukherjee Road, Kolkata, 700026, West Bengal, India.
| | - Rahul Naskar
- Department of Chemistry, Jadavpur University, Kolkata, 700032, West Bengal, India.
| | - Prosenjit Saha
- Department of Cancer Chemoprevention, Chittaranjan National Cancer Institute, 37 S.P. Mukherjee Road, Kolkata, 700026, West Bengal, India.
| | - Nabendu Murmu
- Department of Signal Transduction and Biogenic Amines, Chittaranjan National Cancer Institute, 37 S.P. Mukherjee Road, Kolkata, 700026, West Bengal, India.
| | - Gaurav Das
- Department of Signal Transduction and Biogenic Amines, Chittaranjan National Cancer Institute, 37 S.P. Mukherjee Road, Kolkata, 700026, West Bengal, India.
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194
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Luan J, Li Y, Yuan J, Wang Z, Shang X, Wang KP, Fang Y, Chen S, Hu ZQ. Simple cyclic chalcone dye with multiple optical functions: Piezochromism and lysosomes staining. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124485. [PMID: 38788510 DOI: 10.1016/j.saa.2024.124485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/16/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
Both artificially synthesized and naturally occurring cyclic chalcones have been widely studied for their excellent biological activities. However, research on its photophysical properties is still limited. In the present study, we designed and synthesized a small molecule fluorescent dye based on the ICT effect, using dimethylamino as the electron-donating group and carbonyl as the electron withdrawing group, and investigated its photophysical properties in depth. Although YB is a simple small molecule, it exhibits significant piezochromic properties. The fluorescence of YB can change from green to yellow through grinding. After solvent fumigation, the fluorescence reverts to green. Furthermore, YB was used successfully in the lysosomal targeting. This study expands the research on the photophysical properties of cyclic chalcone and give richness to application of cyclic chalcone compounds.
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Affiliation(s)
- Junyu Luan
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yahang Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jianhao Yuan
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zezhong Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xianzhao Shang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Kun-Peng Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Ying Fang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Shaojin Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Zhi-Qiang Hu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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195
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Voziyan P, Brown KL, Uppuganti S, Leser M, Rose KL, Nyman JS. A map of glycation and glycoxidation sites in collagen I of human cortical bone: Effects of sex and type 2 diabetes. Bone 2024; 187:117209. [PMID: 39047900 DOI: 10.1016/j.bone.2024.117209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
Complications of diabetes is a major health problem affecting multiple organs including bone, where the chronic disease increases the risk of fragility fractures. One hypothesis suggests a pathogenic role for hyperglycemia-induced modification of proteins, a.k.a. advanced glycation end products (AGEs), resulting in structural and functional damage to bone extracellular matrix (ECM). Evidence supporting this hypothesis has been limited by the lack of comprehensive information about the location of AGEs that accumulate in vivo at specific sites within the proteins of bone ECM. Analyzing extracts from cortical bone of cadaveric femurs by liquid chromatography tandem mass spectrometry, we generated a quantitative AGE map of human collagen I for male and female adult donors with and without diabetes. The map describes the chemical nature, sequence position, and levels of four major physiological AGEs, e.g. carboxymethyllysine, and an AGE precursor fructosyllysine within the collagen I triple-helical region. The important features of the map are: 1) high map reproducibility in the individual bone extracts, i.e. 20 male and 20 female donors; 2) localization of modifications to distinct clusters: 10 clusters containing 34 AGE sites in male donors and 9 clusters containing 28 sites in female donors; 3) significant increases in modification levels in diabetes at multiple sites: 26 out of 34 sites in males and in 17 out of 28 sites in females; and 4) generally higher modification levels in male vs. female donors. Moreover, the AGE levels at multiple individual sites correlated with total bone pentosidine levels in male but not in female donors. Molecular dynamics simulations and molecular modeling predicted significant impact of modifications on solvent exposure, charge distribution, and hydrophobicity of the triple helix as well as disruptions to the structure of collagen I fibril. In summary, the AGE map of collagen I revealed diabetes-induced, sex-specific non-enzymatic modifications at distinct triple helical sites that can disrupt collagen structure, thus proposing a specific mechanism of AGE contribution to diabetic complications in human bone.
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Affiliation(s)
- Paul Voziyan
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
| | - Kyle L Brown
- Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Sasidhar Uppuganti
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Micheal Leser
- Department of Biochemistry and Proteomics Core, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Kristie Lindsey Rose
- Department of Biochemistry and Proteomics Core, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeffry S Nyman
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA.
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196
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Palmero Casanova B, Albentosa González L, Maringer K, Sabariegos R, Mas A. A conserved role for AKT in the replication of emerging flaviviruses in vertebrates and vectors. Virus Res 2024; 348:199447. [PMID: 39117146 DOI: 10.1016/j.virusres.2024.199447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/11/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
One third of all emerging infectious diseases are vector-borne, with no licensed antiviral therapies available against any vector-borne viruses. Zika virus and Usutu virus are two emerging flaviviruses transmitted primarily by mosquitoes. These viruses modulate different host pathways, including the PI3K/AKT/mTOR pathway. Here, we report the effect on ZIKV and USUV replication of two AKT inhibitors, Miransertib (ARQ-092, allosteric inhibitor) and Capivasertib (AZD5363, competitive inhibitor) in different mammalian and mosquito cell lines. Miransertib showed a stronger inhibitory effect against ZIKV and USUV than Capivasertib in mammalian cells, while Capivasertib showed a stronger effect in mosquito cells. These findings indicate that AKT plays a conserved role in flavivirus infection, in both the vertebrate host and invertebrate vector. Nevertheless, the specific function of AKT may vary depending on the host species. These findings indicate that AKT may be playing a conserved role in flavivirus infection in both, the vertebrate host and the invertebrate vector. However, the specific function of AKT may vary depending on the host species. A better understanding of virus-host interactions is therefore required to develop new treatments to prevent human disease and new approaches to control transmission by insect vectors.
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Affiliation(s)
- Blanca Palmero Casanova
- Instituto de Investigación Biomédica de la UCLM (IB-UCLM), C/Almansa 14, 02008 Albacete, Spain
| | - Laura Albentosa González
- Instituto de Investigación Biomédica de la UCLM (IB-UCLM), C/Almansa 14, 02008 Albacete, Spain; Facultad de farmacia, Universidad de Castilla-La Mancha, Av. Dr. José María Sánchez Ibáñez, s/n, 02008 Albacete, Spain
| | - Kevin Maringer
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | - Rosario Sabariegos
- Instituto de Investigación Biomédica de la UCLM (IB-UCLM), C/Almansa 14, 02008 Albacete, Spain; Unidad asociada de Biomedicina UCLM-CSIC. Universidad de Castilla-La Mancha. C/Altagracia 50, 13071 Ciudad Real, Spain; Facultad de Medicina, Universidad de Castilla-La Mancha. C/Almansa 14, 02008 Albacete, Spain
| | - Antonio Mas
- Instituto de Investigación Biomédica de la UCLM (IB-UCLM), C/Almansa 14, 02008 Albacete, Spain; Facultad de farmacia, Universidad de Castilla-La Mancha, Av. Dr. José María Sánchez Ibáñez, s/n, 02008 Albacete, Spain; Unidad asociada de Biomedicina UCLM-CSIC. Universidad de Castilla-La Mancha. C/Altagracia 50, 13071 Ciudad Real, Spain.
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197
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Zhang Y, Lin H, Yu A, Wang X, Liu Y, Liu T, Zhao C, Mei R. Migration mechanism of atrazine in the simulated lake icing process at different freezing temperatures based on density function theory. J Environ Sci (China) 2024; 144:45-54. [PMID: 38802237 DOI: 10.1016/j.jes.2023.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/22/2023] [Accepted: 07/23/2023] [Indexed: 05/29/2024]
Abstract
Atrazine causes concern due to its resistant to biodegradation and could be accumulated in aquatic organisms, causing pollution in lakes. This study measured the concentration of atrazine in ice and the water under ice through a simulated icing experiment and calculated the distribution coefficient K to characterize its migration ability in the freezing process. Furthermore, density functional theory (DFT) calculations were employed to expatiate the migration law of atrazine during icing process. According to the results, it could release more energy into the environment when atrazine staying in water phase (-15.077 kcal/mol) than staying in ice phase (-14.388 kcal/mol), therefore it was beneficial for the migration of atrazine from ice to water. This explains that during the freezing process, the concentration of atrazine in the ice was lower than that in the water. Thermodynamic calculations indicated that when the temperature decreases from 268 to 248 K, the internal energy contribution of the compound of atrazine and ice molecule (water cluster) decreases at the same vibrational frequency, resulting in an increase in the free energy difference of the compound from -167.946 to -165.390 kcal/mol. This demonstrated the diminished migratory capacity of atrazine. This study revealed the environmental behavior of atrazine during lake freezing, which was beneficial for the management of atrazine and other pollutants during freezing and environmental protection.
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Affiliation(s)
- Yan Zhang
- School of Civil Engineering, Yantai University, Yantai 264005, China.
| | - Hao Lin
- School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Aixin Yu
- School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Xiaozhuang Wang
- School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Yucan Liu
- School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Tongshuai Liu
- School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Chen Zhao
- School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Rui Mei
- School of Civil Engineering, Yantai University, Yantai 264005, China
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198
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Kurakin S, Ivankov O, Dushanov E, Murugova T, Ermakova E, Efimov S, Mukhametzyanov T, Smerdova S, Klochkov V, Kuklin A, Kučerka N. Calcium ions do not influence the Aβ(25-35) triggered morphological changes of lipid membranes. Biophys Chem 2024; 313:107292. [PMID: 39018778 DOI: 10.1016/j.bpc.2024.107292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
We have studied the effect of calcium ions (Ca2+) at various concentrations on the structure of lipid vesicles in the presence of amyloid-beta peptide Aβ(25-35). In particular, we have investigated the influence of calcium ions on the formation of recently documented bicelle-like structures (BLSs) emerged as a result of Aβ(25-35) triggered membrane disintegration. First, we have shown by using small-angle X-ray and neutron scattering that peptide molecules rigidify the lipid bilayer of gel phase DPPC unilamellar vesicles (ULVs), while addition of the calcium ions to the system hinders this effect of Aβ(25-35). Secondly, the Aβ(25-35) demonstrates a critical peptide concentration at which the BLSs reorganize from ULVs due to heating and cooling the samples through the lipid main phase transition temperature (Tm). However, addition of calcium ions does not affect noticeably the Aβ-induced formation of BLSs and their structural parameters, though the changes in peptide's secondary structure, e.g. the increased α-helix fraction, has been registered by circular dichroism spectroscopy. Finally, according to 31P nuclear magnetic resonance (NMR) measurements, calcium ions do not affect the lipid-peptide arrangement in BLSs and their ability to align in the magnetic field of NMR spectrometer. The influences of various concentrations of calcium ions on the lipid-peptide interactions may prove biologically important because their local concentrations vary widely in in-vivo conditions. In the present work, calcium ions were investigated as a possible tool aimed at regulating the lipid-peptide interactions that demonstrated the disruptive effect of Aβ(25-35) on lipid membranes.
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Affiliation(s)
- Sergei Kurakin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia.
| | - Oleksandr Ivankov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Ermuhammad Dushanov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Department of Biophysics, Dubna State University, Universitetskaya 19, Dubna, Moscow Region 141982, Russia
| | - Tatiana Murugova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Elena Ermakova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Sergey Efimov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Timur Mukhametzyanov
- Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Svetlana Smerdova
- Kazan National Research Technological University, Karl Marx 68, Kazan 420015, Russia
| | - Vladimir Klochkov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Alexander Kuklin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Moscow Institute of Physics and Technology, Instytutskiy Pereulok 9, Dolgoprudny, Moscow Region 141701, Russia
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Odbojárov 10, Bratislava 832 32, Slovakia.
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199
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Hayashi D, Dennis EA. Differentiating human phospholipase A 2's activity toward phosphatidylinositol, phosphatidylinositol phosphate and phosphatidylinositol bisphosphate. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159527. [PMID: 38917952 DOI: 10.1016/j.bbalip.2024.159527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/02/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
Phospholipase A2's (PLA2's) constitute a superfamily of enzymes that hydrolyze the sn-2 fatty acyl chain on glycerophospholipids. We have previously reported that each PLA2 Type shows a unique substrate specificity for the molecular species it hydrolyzes, especially the acyl chain that is cleaved from the sn-2 position and to some extent the polar group. However, phosphatidylinositol (PI) and PI phosphates (PIPs) have not been as well studied as substrates as other phospholipids because the PIPs require adaptation of the standard analysis methods, but they are important in vivo. We determined the in vitro activity of the three major types of human PLA2's, namely the cytosolic (c), calcium-independent (i), and secreted (s) PLA2's toward PI, PI-4-phosphate (PI(4)P), and PI-4,5-bisphosphate (PI(4,5)P2). The in vitro assay revealed that Group IVA cPLA2 (GIVA cPLA2) showed relatively high activity toward PI and PI(4)P among the tested PLA2's; nevertheless, the highly hydrophilic headgroup disrupted the interaction between the lipid surface and the enzyme. GIVA cPLA2 and GVIA iPLA2 showed detectable activity toward PI(4,5)P2, but it appeared to be a poorer substrate for all of the PLA2's tested. Furthermore, molecular dynamics (MD) simulations demonstrated that Thr416 and Glu418 of GIVA cPLA2 contribute significantly to accommodating the hydrophilic head groups of PI and PI(4)P, which could explain some selectivity for PI and PI(4)P. These results indicated that GIVA cPLA2 can accommodate PI and PI(4)P in its active site and hydrolyze them, suggesting that the GIVA cPLA2 may best account for the PI and PIP hydrolysis in living cells.
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Affiliation(s)
- Daiki Hayashi
- Department of Applied Chemistry in Bioscience, Graduate School of Agricultural Science, Faculty of Agriculture, Kobe University, Kobe 657-8501, Japan; Department of Pharmacology and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Edward A Dennis
- Department of Pharmacology and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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200
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Wang X, Hao X, Yang Y, Jia S, Chen Y, Yang W, Luo Y, Xie Z, Gu Y, Wu Y, Zhang F, Li M, Wang Y, Shen X, Xu L. A phosphodiesterase CpdB in Yersinia pseudotuberculosis degrades CDNs to inhibit innate immune response. Vet Microbiol 2024; 297:110194. [PMID: 39084162 DOI: 10.1016/j.vetmic.2024.110194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 07/08/2024] [Accepted: 07/21/2024] [Indexed: 08/02/2024]
Abstract
Yersinia pseudotuberculosis (Yptb) is a pathogenic gram-negative bacterium that can colonize the intestines of different animals. Its infection leads to the activation of the host's innate immunity. Both host and bacterial-derived cyclic dinucleotides (CDNs) could activate the innate immune response of host cells. In bacteria, CDNs like c-di-AMP, c-di-GMP, or 3'3'-cGAMP can be hydrolyzed by different hydrolases. Recent studies showed that the degradation of those second messengers helps the pathogen evade immune detection. In this study, we identified a hydrolase, YPK_3776, namely CpdB in Yptb. CpdB is predicted to bind bacterial-derived c-di-AMP, c-di-GMP, 3'3'-cGAMP and host-derived 2'3'-cGAMP. Surprisingly, by using high-performance liquid chromatography (HPLC), we found that CpdB could only degrade bacterial-derived CDNs but not host-derived 2'3'-cGAMP. In addition, CpdB has 2'3'-cNMP activity. Consistently, the Yptb mutant lacking the cpdB gene exhibited a higher level of intracellular c-di-GMP. Furthermore, the ∆cpdB mutant elicited stronger innate immune responses during Yptb infection in macrophages, suggesting CpdB enables Yptb to evade host immune surveillance. Furthermore, CpdB inhibited the Yptb-induced innate immune response in a STING-dependent manner. Finally, we showed the ∆cpdB infection in mice model exhibited in lower bacterial burden, as compared to wild-type strain infection, indicating CpdB is important for bacterial survival in the host. Together, we identified a cyclic dinucleotide hydrolase CpdB in Yptb that could degrade bacterial-derived CDNs which help the pathogen to evade immune detection via the STING pathway.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinwei Hao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuqing Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Siyu Jia
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yating Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenguang Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Luo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhen Xie
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanchao Gu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuxuan Wu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fuhua Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengyuan Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Lei Xu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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