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Li T, Liu X, Wang Z, Liu C, Liu Y, Cui N, Meng F, Zhang W, Wang D, Xu Y, Zhu X, Guo C, Wang Y. Characterization and rational engineering of an alkaline-tolerant azoreductase derived from Roseibium sp. H3510 for enhanced decolorization of azo dyes. Int J Biol Macromol 2024; 280:135810. [PMID: 39322137 DOI: 10.1016/j.ijbiomac.2024.135810] [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: 08/16/2024] [Revised: 09/17/2024] [Accepted: 09/18/2024] [Indexed: 09/27/2024]
Abstract
rAzoR2326, an azoreductase derived from Roseibium sp. H3510, functions as an FMN-dependent homodimer utilizing NADH as cofactor. It demonstrated maximum activity at 45 °C and retained moderate activity above 50 °C, exhibiting stability from pH 7-10. Evolution and structure guided rational design of wild-type rAzoR2326 (WT) efficiently yielded 6 single-point mutants with improved thermostability and activity from a 22-variant library. Further combinatorial mutation led to mutant M20 with substantially enhanced thermostability (15-fold longer half-life at 50 °C) and activity (3.24-fold higher kcat/Km). M20 exhibited superior catalytic properties for decolorizing Allura Red compared to WT. Specifically, its decolorization capacity at pH 10.0 was 4.26-fold higher than WT. Additionally, M20 demonstrated remarkable thermostability, retaining 76.83 % decolorization activity for Allura Red after 120 min at 50 °C, whereas WT nearly lost all catalytic activity under the same conditions. Molecular dynamics simulations revealed the structural changes in M20, such as improved hydrogen bonding and a new C-H···π interaction, led to a more compact and rigid enzyme structure. This resulted in a more stable FMN-binding pocket and substrate tunnel, thereby improving the catalytic stability and activity of M20. Given its enhanced dye decolorization ability and alkaline tolerance, M20 shows promise as a biocatalyst for treating azo dye effluents.
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Affiliation(s)
- Tao Li
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Xinqi Liu
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Ziwei Wang
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Cong Liu
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Ning Cui
- Xinxiang Medical University Sanquan Medical College, Xinxiang 453003, PR China
| | - Fanling Meng
- Academic Affairs Office, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Wenbo Zhang
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Dandan Wang
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Yongtao Xu
- Henan Engineering Laboratory of Combinatorial Technique for Clinical & Biomedical Big Data, School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Xueyi Zhu
- Zhengzhou Feier Medical Laboratory Co., LTD, Zhengzhou 450099, PR China
| | - Changjiang Guo
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Yan Wang
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China.
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Chen X, Zhang X, Chen J, Wang M, Yang Y, An L, Liu Z, Song X, Yao L. Quantification of CH and NH/π-Stacking Interactions in Cells Using Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2024; 96:14354-14362. [PMID: 39177663 DOI: 10.1021/acs.analchem.4c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
π-Stacking, a type of noncovalent interactions involving aromatic residues, plays an important role in protein folding and function. In this work, an attempt has been made to measure CH/π and NH/π stacking interactions in a protein in Escherichia coli cells using a combined double-mutant cycle and nuclear magnetic resonance spectroscopy method. The results show that the CH/π and NH/π stacking interactions are generally weaker in cells than those in the buffer. The transient intermolecular noncovalent interactions between the protein and the complex cellular environment may compete with and thus weaken the stacking interactions in the protein. The weakening of stacking interactions can enhance the local conformational opening of proteins in E. coli cells. This is evident from the faster rates of amide hydrogen/deuterium exchange observed in cells than in the buffer, for residues that undergo local conformational opening. This study highlights the influence of the cellular environment on π-stacking and the conformational dynamics of proteins.
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Affiliation(s)
- Xiaoxu Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Xueying Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfei Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Mengting Wang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Liaoyuan An
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Zhijun Liu
- National Facility for Protein Science, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiangfei Song
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Lishan Yao
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
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Espinosa-Aguirre JJ, Camacho-Carranza R, Hernández-Ojeda SL, Cárdenas-Ávila RI, Santes-Palacios R. Apiole, an important constituent of parsley, is a mixed-type inhibitor of the CYP1A subfamily. Mutat Res 2024; 829:111881. [PMID: 39191149 DOI: 10.1016/j.mrfmmm.2024.111881] [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: 05/14/2024] [Revised: 07/18/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
Apiole (1-allyl-2,5-dimethoxy-3,4-methylenedioxybenzene) and parsley leaves ethanolic extract containing it inhibit the rat liver microsomal ethoxy- and methoxyresorufin-O-deacetylase activities associated with cytochrome P450 (CYP) 1A1 and 1A2, respectively. Cytochrome P4501A subfamily metabolizes environmental mutagens and several drugs, leading to the formation of mutagenic metabolites. Docking analysis showed that residue Phe123 within the active site of the CYP1A1 enzyme is bound to apiole through a π/π stacking of its benzene ring. In the case of 1A2, its Phe226 interacts with the dioxolane ring of apiole. Furthermore, apiole behaves as a mixed-type inhibitor of bacterial human recombinant CYP1A1. To explore one of the possible biological implications of this inhibitory effect, we tested the capacity of apiole and the parsley ethanolic extract to interfere with the mutagenicity of the promutagen 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) metabolized by CYP1A subfamily. As expected, both apiole and the plant extract reduced the number of revertant colonies of Salmonella typhimurium TA98 Ames strain after exposure to MeIQx, reaching a 78 % and 100 % reduction, respectively. Neither apiol nor parsley extract were mutagenic to the TA98 strain. We speculate that consuming apiole, a constituent of edible herbs, in conjunction with the utilization of pharmaceuticals metabolized by the CYP1A subfamily, may result in herb-drug interactions. Furthermore, the consumption of apiole by individuals who regularly ingest fresh vegetables may contribute to the low incidence of cancer observed in those who adhere to such a dietary regimen.
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Affiliation(s)
- J J Espinosa-Aguirre
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior sin Número, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - R Camacho-Carranza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior sin Número, Ciudad Universitaria, Ciudad de México 04510, Mexico.
| | - S L Hernández-Ojeda
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Exterior sin Número, Ciudad Universitaria, Ciudad de México 04510, Mexico
| | - R I Cárdenas-Ávila
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad de México 04510, Mexico
| | - R Santes-Palacios
- Laboratorio de Toxicología Genética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, Insurgentes Cuicuilco, Coyoacán, Ciudad de México C. P. 04530, Mexico
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Toma H, Tabata JI, Hirata K, Gregoire G, Fujii M, Ishiuchi SI. Micro Solvation Effect of Methanol on Excited-State Dynamics of Protonated Tryptophan and Dopamine. J Phys Chem A 2024; 128:6208-6215. [PMID: 39042432 DOI: 10.1021/acs.jpca.4c03178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The electronic and vibrational cryogenic ion spectroscopy of protonated tryptophan (TrpH+) and dopamine (DAH+) complexed with methanol has been recorded. These two biological chromophores exhibit ultrafast photochemistry due to excited-state proton transfer (ESPT). We have established the relationship between the structure of the complexes and their photodynamics and compared them with recent results obtained in hydrated complexes. For TrpH+, there is no substantial change between methanol and water complexes; ESPT is hindered by a single solvent molecule. In the DAH+(MeOH)1 complex, the most stable conformer adopts a structure that prevents the direct interaction of the ammonium group of the side chain with the catechol ring, thus blocking the ESPT reaction. Such a ring structure is indeed a very minor populated conformer in the single-hydrated complex. The change in conformal stability between water and methanol clusters is due to a weak CH-π attractive interaction of the methyl group of methanol with the catechol.
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Affiliation(s)
- Hideo Toma
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Jun-Ichi Tabata
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Keisuke Hirata
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama 226-8503, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Gilles Gregoire
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay F-91405, France
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama 226-8503, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Research and Development Initiative, Chuo University, Tokyo 112-8551, Japan
| | - Shun-Ichi Ishiuchi
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsu-ta-cho, Midori-ku, Yokohama 226-8503, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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5
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Malla S, Nyinawabera A, Neupane R, Pathak R, Lee D, Abou-Dahech M, Kumari S, Sinha S, Tang Y, Ray A, Ashby CR, Yang MQ, Babu RJ, Tiwari AK. Novel Thienopyrimidine-Hydrazinyl Compounds Induce DRP1-Mediated Non-Apoptotic Cell Death in Triple-Negative Breast Cancer Cells. Cancers (Basel) 2024; 16:2621. [PMID: 39123351 PMCID: PMC11311031 DOI: 10.3390/cancers16152621] [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: 06/14/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 08/12/2024] Open
Abstract
Apoptosis induction with taxanes or anthracyclines is the primary therapy for TNBC. Cancer cells can develop resistance to anticancer drugs, causing them to recur and metastasize. Therefore, non-apoptotic cell death inducers could be a potential treatment to circumvent apoptotic drug resistance. In this study, we discovered two novel compounds, TPH104c and TPH104m, which induced non-apoptotic cell death in TNBC cells. These lead compounds were 15- to 30-fold more selective in TNBC cell lines and significantly decreased the proliferation of TNBC cells compared to that of normal mammary epithelial cell lines. TPH104c and TPH104m induced a unique type of non-apoptotic cell death, characterized by the absence of cellular shrinkage and the absence of nuclear fragmentation and apoptotic blebs. Although TPH104c and TPH104m induced the loss of the mitochondrial membrane potential, TPH104c- and TPH104m-induced cell death did not increase the levels of cytochrome c and intracellular reactive oxygen species (ROS) and caspase activation, and cell death was not rescued by incubating cells with the pan-caspase inhibitor, carbobenzoxy-valyl-alanyl-aspartyl-[O-methyl]-fluoromethylketone (Z-VAD-FMK). Furthermore, TPH104c and TPH104m significantly downregulated the expression of the mitochondrial fission protein, DRP1, and their levels determined their cytotoxic efficacy. Overall, TPH104c and TPH104m induced non-apoptotic cell death, and further determination of their cell death mechanisms will aid in the development of new potent and efficacious anticancer drugs to treat TNBC.
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Affiliation(s)
- Saloni Malla
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA; (S.M.); (A.N.); (R.N.); (D.L.); (M.A.-D.); (S.K.)
| | - Angelique Nyinawabera
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA; (S.M.); (A.N.); (R.N.); (D.L.); (M.A.-D.); (S.K.)
| | - Rabin Neupane
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA; (S.M.); (A.N.); (R.N.); (D.L.); (M.A.-D.); (S.K.)
| | - Rajiv Pathak
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Donghyun Lee
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA; (S.M.); (A.N.); (R.N.); (D.L.); (M.A.-D.); (S.K.)
| | - Mariam Abou-Dahech
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA; (S.M.); (A.N.); (R.N.); (D.L.); (M.A.-D.); (S.K.)
| | - Shikha Kumari
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA; (S.M.); (A.N.); (R.N.); (D.L.); (M.A.-D.); (S.K.)
| | - Suman Sinha
- Institute of Pharmaceutical Research, GLA University, Mathura 281406, UP, India;
| | - Yuan Tang
- Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH 43606, USA;
| | - Aniruddha Ray
- Department of Physics, College of Math’s and Natural Sciences, University of Toledo, Toledo, OH 43606, USA;
| | - Charles R. Ashby
- Department of Pharmaceutical Sciences, College of Pharmacy, St. John’s University, Queens, NY 11439, USA;
| | - Mary Qu Yang
- MidSouth Bioinformatics Center and Joint Bioinformatics Graduate Program of University of Arkansas at Little Rock, University of Arkansas for Medical Sciences, Little Rock, AR 72204, USA;
| | - R. Jayachandra Babu
- Department of Drug Discovery & Development, Harrison School of Pharmacy, Auburn University, Auburn, AL 36849, USA;
| | - Amit K. Tiwari
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43614, USA; (S.M.); (A.N.); (R.N.); (D.L.); (M.A.-D.); (S.K.)
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
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6
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Wu Y, Zhang S, York DM, Wang L. Adsorption of Flavonoids in a Transcriptional Regulator TtgR: Relative Binding Free Energies and Intermolecular Interactions. J Phys Chem B 2024; 128:6529-6541. [PMID: 38935925 DOI: 10.1021/acs.jpcb.4c02303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Antimicrobial resistance in bacteria often arises from their ability to actively identify and expel toxic compounds. The bacterium strain Pseudomonas putida DOT-T1E utilizes its TtgABC efflux pump to confer robust resistance against antibiotics, flavonoids, and organic solvents. This resistance mechanism is intricately regulated at the transcriptional level by the TtgR protein. Through molecular dynamics and alchemical free energy simulations, we systematically examine the binding of seven flavonoids and their derivatives with the TtgR transcriptional regulator. Our simulations reveal distinct binding geometries and free energies for the flavonoids in the active site of the protein, which are driven by a range of noncovalent forces encompassing van der Waals, electrostatic, and hydrogen bonding interactions. The interplay of molecular structures, substituent patterns, and intermolecular interactions effectively stabilizes the bound flavonoids, confining their movements within the TtgR binding pocket. These findings yield valuable insights into the molecular determinants that govern ligand recognition in TtgR and shed light on the mechanism of antimicrobial resistance in P. putida DOT-T1E.
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Affiliation(s)
- Yuxuan Wu
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Laboratory for Biomolecular Simulation Research, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Shi Zhang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Laboratory for Biomolecular Simulation Research, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Darrin M York
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Laboratory for Biomolecular Simulation Research, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Laboratory for Biomolecular Simulation Research, Rutgers University, Piscataway, New Jersey 08854, United States
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7
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Yan Y, Chen Y, Hu H, Jiang Y, Kang Z, Wu J. Discovery of a New Class of Lipophilic Pyrimidine-Biphenyl Herbicides Using an Integrated Experimental-Computational Approach. Molecules 2024; 29:2409. [PMID: 38893290 PMCID: PMC11173721 DOI: 10.3390/molecules29112409] [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: 04/22/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Herbicides are useful tools for managing weeds and promoting food production and sustainable agriculture. In this study, we report on the development of a novel class of lipophilic pyrimidine-biphenyl (PMB) herbicides. Firstly, three PMBs, Ia, IIa, and IIIa, were rationally designed via a scaffold hopping strategy and were determined to inhibit acetohydroxyacid synthase (AHAS). Computational simulation was carried out to investigate the molecular basis for the efficiency of PMBs against AHAS. With a rational binding mode, and the highest in vitro as well as in vivo potency, Ia was identified as a preferable hit. Furthermore, these integrated analyses guided the design of eighteen new PMBs, which were synthesized via a one-step Suzuki-Miyaura cross-coupling reaction. These new PMBs, Iba-ic, were more effective in post-emergence control of grass weeds compared with Ia. Interestingly, six of the PMBs displayed 98-100% inhibition in the control of grass weeds at 750 g ai/ha. Remarkably, Ica exhibited ≥ 80% control against grass weeds at 187.5 g ai/ha. Overall, our comprehensive and systematic investigation revealed that a structurally distinct class of lipophilic PMB herbicides, which pair excellent herbicidal activities with new interactions with AHAS, represent a noteworthy development in the pursuit of sustainable weed control solutions.
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Affiliation(s)
- Yitao Yan
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yinglu Chen
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Hanxian Hu
- School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Youwei Jiang
- Hangzhou Jingyinkang Biological Technology Co., Ltd., Hangzhou 311110, China
| | | | - Jun Wu
- Department of Chemistry, Zhejiang University, Hangzhou 310058, China
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8
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Salaikumaran M, Gopal PP. Rational Design of TDP-43 Derived α-Helical Peptide Inhibitors: An In Silico Strategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders. ACS Chem Neurosci 2024; 15:1096-1109. [PMID: 38466778 PMCID: PMC10959110 DOI: 10.1021/acschemneuro.3c00659] [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: 10/12/2023] [Revised: 01/21/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
TDP-43, an essential RNA/DNA-binding protein, is central to the pathology of neurodegenerative diseases, such as amyotrophic lateral sclerosis and frontotemporal dementia. Pathological mislocalization and aggregation of TDP-43 disrupt RNA splicing, mRNA stability, and mRNA transport, thereby impairing neuronal function and survival. The formation of amyloid-like TDP-43 filaments is largely facilitated by the destabilization of an α-helical segment within the disordered C-terminal region. In this study, we hypothesized that preventing the destabilization of the α-helical domain could potentially halt the growth of these pathological filaments. To explore this, we utilized a range of in silico techniques to design and evaluate peptide-based therapeutics that bind to pathological TDP-43 amyloid-like filament crystal structures and resist β sheet conversion. Our computational approaches, including biophysical and secondary structure property prediction, molecular docking, 3D structure prediction, and molecular dynamics simulations, were used to assess the structure, stability, and binding affinity of these peptides in relation to pathological TDP-43 filaments. The results of our in silico analyses identified a selection of promising peptides which displayed a stable α-helical structure, exhibited an increased number of intramolecular hydrogen bonds within the helical domain, and demonstrated high binding affinities for pathological TDP-43 amyloid-like filaments. Molecular dynamics simulations provided further support for the structural and thermodynamic stability of these peptides, as they exhibited lower root-mean-square deviation and more favorable free energy landscapes over 300 ns. These findings establish α-helical propensity peptides as potential lead molecules for the development of novel therapeutics against TDP-43 aggregation. This structure-based computational approach for the rational design of peptide inhibitors opens a new direction in the search for effective interventions for ALS, FTD, and other related neurodegenerative diseases. The peptides identified as the most promising candidates in this study are currently subject to further testing and validation through both in vitro and in vivo experiments.
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Affiliation(s)
- Muthu
Raj Salaikumaran
- Department
of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Pallavi P. Gopal
- Department
of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Program
in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, New Haven, Connecticut 06520-8055, United States
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9
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Karami O, de Jong H, Somovilla VJ, Villanueva Acosta B, Sugiarta AB, Ham M, Khadem A, Wennekes T, Offringa R. Structure-activity relationship of 2,4-D correlates auxinic activity with the induction of somatic embryogenesis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1355-1369. [PMID: 37647363 DOI: 10.1111/tpj.16430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic analogue of the plant hormone auxin that is commonly used in many in vitro plant regeneration systems, such as somatic embryogenesis (SE). Its effectiveness in inducing SE, compared to the natural auxin indole-3-acetic acid (IAA), has been attributed to the stress triggered by this compound rather than its auxinic activity. However, this hypothesis has never been thoroughly tested. Here we used a library of forty 2,4-D analogues to test the structure-activity relationship with respect to the capacity to induce SE and auxinic activity in Arabidopsis thaliana. Four analogues induced SE as effectively as 2,4-D and 13 analogues induced SE but were less effective. Based on root growth inhibition and auxin response reporter expression, the 2,4-D analogues were classified into different groups, ranging from very active to not active auxin analogues. A halogen at the 4-position of the aromatic ring was important for auxinic activity, whereas a halogen at the 3-position resulted in reduced activity. Moreover, a small substitution at the carboxylate chain was tolerated, as was extending the carboxylate chain with an even number of carbons. The auxinic activity of most 2,4-D analogues was consistent with their simulated TIR1-Aux/IAA coreceptor binding characteristics. A strong correlation was observed between SE induction efficiency and auxinic activity, which is in line with our observation that 2,4-D-induced SE and stress both require TIR1/AFB auxin co-receptor function. Our data indicate that the stress-related effects triggered by 2,4-D and considered important for SE induction are downstream of auxin signalling.
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Affiliation(s)
- Omid Karami
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Hanna de Jong
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomedical Research, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Victor J Somovilla
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastián, Spain
| | - Beatriz Villanueva Acosta
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Aldo Bryan Sugiarta
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Marvin Ham
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Azadeh Khadem
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Tom Wennekes
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomedical Research, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
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10
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Nath J, Baruah JB. E- or Z-Isomers Arising from the Geometries of Ligands in the Mercury Complex of 2-(Anthracen-9-ylmethylene)- N-phenylhydrazine Carbothioamide. ACS OMEGA 2023; 8:42827-42839. [PMID: 38024736 PMCID: PMC10653070 DOI: 10.1021/acsomega.3c05806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/30/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
An anionic mercury(II) complex of 2-(anthracen-9-ylmethylene)-N-phenylhydrazine carbothioamide (HATU) and two isomers of a neutral mercury(II) complex of the anion of the same ligand (ATU) were reported. The anionic complex [Hg(HATU)2Cl2]·CH2Cl2 had a monodentate HATU ligand (a neutral form of the ligand) and chloride ligands. The two conformational isomers were of the neutral mercury(II) complex Hg(ATU)2·2DMF. The two isomers were from the E or Z geometry of the ligands across the conjugated C=N-N=C-N scaffold of the coordinated ligand. The two isomers of the complex were independently prepared and characterized. The spectroscopic properties of the isomers in solution were studied by 1H NMR as well as fluorescence spectroscopy. Facile conversion of the E-isomer to the Z-isomer in solution was observed. Density functional theory (DFT) calculations revealed that the Z-isomer of the complex was stable compared to the E-isomer by an energy of 14.35 kJ/mol; whereas, E isomer of the ligand was more stable than Z isomer by 8.37 KJ/mol. The activation barrier for the conversion of the E-isomer to the Z-isomer of the ligand was 167.37 kJ/mol. The role of the mercury ion in the conversion of the E-form to the Z-form was discussed. The mercury complex [Hg(HATU)2Cl2]·CH2Cl2 had the E-form of the ligand. Distinct photophysical features of these mercury complexes were presented.
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Affiliation(s)
- Jitendra Nath
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam India
| | - Jubaraj B. Baruah
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam India
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11
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Li L, Peng X, Batliwala M, Bouvier M. Crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing. Nat Commun 2023; 14:5020. [PMID: 37596268 PMCID: PMC10439229 DOI: 10.1038/s41467-023-40736-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Studies have suggested that MHC class I (MHC I) molecules fluctuate rapidly between numerous conformational states and these motions support peptide sampling. To date, MHC I intermediates are largely uncharacterized experimentally and remain elusive. Here, we present x-ray crystal structures of HLA-B8 loaded with 20mer peptides that show pronounced distortions at the N-terminus of the groove. Long stretches of N-terminal amino acid residues are missing in the electron density maps creating an open-ended groove. Our structures also reveal highly unusual features in MHC I-peptide interaction at the N-terminus of the groove. Molecular dynamics simulations indicate that the complexes have varying degrees of conformational flexibility in a manner consistent with the structures. We suggest that our structures have captured the remarkable molecular dynamics of MHC I-peptide interaction. The visualization of peptide-dependent conformational motions in MHC I is a major step forward in our conceptual understanding of dynamics in high-affinity peptide selection.
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Affiliation(s)
- Lenong Li
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Xubiao Peng
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements, School of Physics, Beijing Institute of Technology, Beijing, 100081, China
| | - Mansoor Batliwala
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA.
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12
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Herman KM, Aprà E, Xantheas SS. A critical comparison of CH⋯π versus π⋯π interactions in the benzene dimer: obtaining benchmarks at the CCSD(T) level and assessing the accuracy of lower scaling methods. Phys Chem Chem Phys 2023; 25:4824-4838. [PMID: 36692338 DOI: 10.1039/d2cp04335a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We have established CCSD(T)/CBS (Complete Basis Set) limits for 3 stationary points on the benzene dimer potential energy surface, corresponding to the π⋯π (parallel displaced or PD(C2h), minimum) and CH⋯π (T-shaped or T(C2v), transition state) and tilted T-shaped (or TT(Cs), minimum) bonding scenarios considering both the structure and binding energy. The CCSD(T)/CBS binding energies are -2.65 ± 0.02 (PD), -2.74 ± 0.03 (T), and -2.83 ± 0.01 kcal mol-1 (TT). To this end, the CH⋯π is ∼0.2 kcal mol-1 stronger than the π⋯π interaction, whereas the tilting of the CH donating benzene molecule with respect to the other benzene is worth 0.1 kcal mol-1. As previously discussed in the literature, the MP2 level of theory does not provide a close match for either the energy or structure, yet the SCS-MP2 yields structures in excellent agreement with respect to the CCSD(T) result. It is found that the SCS-MI-MP2 also gives optimized structures very close to SCS-MP2 (within ∼0.01 Å of the benchmark). Despite the closer match in structure, the spin-biased MP2 methods (SCS-, SCS-MI-, and SOS-MP2) incorrectly predict the relative stabilities of the isomers. That said, none of the spin biased MP2 methods offers a good compromise between energy and structure for the systems examined. Finally, the CCSD(T)/CBS benchmarks were used to assess the performance of 13 DFT functionals selected from different rungs of Jacob's ladder. Several functionals such as TPSS-D3, B3LYP-D3, B97-D, B97-D3, and B2PLYP-D3 provided a good description of the binding energies for both CH⋯π and π⋯π interactions, yielding values within 6% of the CCSD(T)/CBS benchmark values. Unlike the MP2 methods, these functionals correctly predict the relative stability of the PD(C2h) and T(C2v) dimers. Further, we find that there is no systematic improvement as Jacob's ladder is ascended (increased complexity of functional). The best functionals that result in a good compromise between structure and energy accuracy are B97-D3 and B2PLYP-D3 for both the CH⋯π and π⋯π interaction. Despite the impressive performance of these functionals, a challenge that remains is ensuring the transferability of these density functionals in accurately describing the interaction between dimers of larger aromatic molecules, the latter requiring high-level benchmarks for these systems.
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Affiliation(s)
- Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Edoardo Aprà
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA. .,Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, WA, 99352, USA
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13
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Mitra A, Chattaraj KG, Paul S. Elucidating the Hydrotropic Mechanism of the Antagonistic Salt PPh 4Cl. J Phys Chem B 2023; 127:996-1012. [PMID: 36653942 DOI: 10.1021/acs.jpcb.2c07892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
PPh4Cl is an antagonistic salt that recently showed promise as a hydrotropic agent. Here, we give mechanistic insights into the PPh4Cl-assisted solubility of a dye molecule using molecular dynamics simulations. Our findings reveal that dye molecules aggregate into a cluster which leads to an accumulation of PPh4+ ions in its vicinity and subsequent exclusion of water molecules from the region. The structural organization is attributed to the preferential interaction of dye molecules and PPh4Cl. The origin of such preference arises from the difference in π-π and CH-π interaction among the pairs. The hydrodynamic radius of PPh4Cl indicates a low propensity for cluster formation, which enhances its hydrotropic behavior. The process of dye dissolution is thermodynamically favored and occurs through a cooperative mechanism. Our studies provide molecular insight into experimental observations crucial for the design of novel hydrotropes with enhanced solubilizing properties.
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Affiliation(s)
- Aritra Mitra
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam781039, India
| | | | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam781039, India
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14
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Li L, Peng X, Batliwala M, Bouvier M. Unusual crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing in antigen presentation. RESEARCH SQUARE 2023:rs.3.rs-2500847. [PMID: 36747752 PMCID: PMC9901037 DOI: 10.21203/rs.3.rs-2500847/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Studies have suggested that MHC class I (MHC I) molecules fluctuate rapidly between conformational states as they sample peptides for potential ligands. To date, MHC I intermediates are largely uncharacterized experimentally and remain elusive. We present x-ray crystal structures of HLA-B8 loaded with 20mer peptides that show significant conformational heterogeneity at the N-terminus of the groove. Long stretches of N-terminal residues were missing in the electron density maps creating an unstructured and widely open-ended groove. Our structures also revealed highly unusual features in MHC I and peptide conformations, and in MHC I-peptide interaction at the N-terminus of the groove. Molecular dynamics simulations showed that the complexes have varying degrees of flexibility in a manner consistent with the structures. We suggest that our structures represent transient substates explored by MHC I molecules during peptide editing. The visualization of peptide-dependent conformational flexibility in MHC I groove is a major step forward in our conceptual understanding of peptide repertoire development in antigen presentation. Our study also raises questions about the role of the N-terminus of the groove in peptide editing.
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Affiliation(s)
- Lenong Li
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Xubiao Peng
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Mansoor Batliwala
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
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15
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Innocent MT, Zhang Z, Cao R, Dai H, Zhang Y, Geng Y, Zhang Z, Jia G, Zhai M, Hu Z, Boland CS, Xiang H, Zhu M. Piezoresistive Fibers with Large Working Factors for Strain Sensing Applications. ACS APPLIED MATERIALS & INTERFACES 2023; 15:2277-2288. [PMID: 36576915 DOI: 10.1021/acsami.2c19830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Piezoresistive fibers with large working factors remain of great interest for strain sensing applications involving large strains, yet difficult to achieve. Here, we produced strain-sensitive fibers with large working factors by dip-coating nanocomposite piezoresistive inks on surface-modified polyether block amide (PEBA) fibers. Surface modification of neat PEBA fibers was carried out with polydopamine (PDA) while nanocomposite conductive inks consisted of styrene-ethylene-butylene-styrene (SEBS) elastomer and carbon black (CB). As such, the deposition of piezoresistive coatings was enabled through nonconventional hydrogen-bonding interactions. The resultant fibers demonstrated well-defined piezoresistive linear relationships, which increased with CB filler loading in SEBS. In addition, gauge factors decreased with increasing CB mass fractions from ∼15 to ∼7. Furthermore, we used the fatigue theory to predict the endurance limit (Ce) of our fibers toward resistance signal stability. Such a piezoresistive performance allowed us to explore the application of our fibers as strain sensors for monitoring the movement of finger joints.
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Affiliation(s)
- Mugaanire Tendo Innocent
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Ziling Zhang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Ran Cao
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Hongmei Dai
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Yuxuan Zhang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Yaqi Geng
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Zhihao Zhang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Guosheng Jia
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Mian Zhai
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Zexu Hu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Conor S Boland
- School of Mathematical and Physical Sciences, University of Sussex, BrightonBN19QH, U.K
| | - Hengxue Xiang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
| | - Meifang Zhu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai201620, China
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16
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Kumpost V, Hilbert L, Mikut R. Noise facilitates entrainment of a population of uncoupled limit cycle oscillators. J R Soc Interface 2023; 20:20220781. [PMID: 36628527 PMCID: PMC9832296 DOI: 10.1098/rsif.2022.0781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Many biological oscillators share two properties: they are subject to stochastic fluctuations (noise) and they must reliably adjust their period to changing environmental conditions (entrainment). While noise seems to distort the ability of single oscillators to entrain, in populations of uncoupled oscillators noise allows population-level entrainment for a wider range of input amplitudes and periods. Here, we investigate how this effect depends on the noise intensity and the number of oscillators in the population. We have found that, if a population consists of a sufficient number of oscillators, increasing noise intensity leads to faster entrainment after a phase change of the input signal (jet lag) and increases sensitivity to low-amplitude input signals.
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Affiliation(s)
- Vojtech Kumpost
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Institute of Biological and Chemical Systems—Biological Information Processing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Lennart Hilbert
- Institute of Biological and Chemical Systems—Biological Information Processing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Systems Biology and Bioinformatics, Zoological Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ralf Mikut
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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17
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Asghar S, Hameed S, Tahir MN, Naseer MM. Molecular duplexes featuring NH···N, CH···O and CH···π interactions in solid-state self-assembly of triazine-based compounds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220603. [PMID: 36397969 PMCID: PMC9626258 DOI: 10.1098/rsos.220603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Synthetic supramolecular structures constructed through the cooperative action of numerous non-covalent forces are highly desirable as models to unravel and understand the complexity of systems created in nature via self-assembly. Taking advantage of the low cost of 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and the sequential nucleophilic substitution reactions with almost all types of nucleophiles, a series of six structurally related novel s-triazine derivatives 1-6 were synthesized and structurally characterized based on their physical, spectral and crystallographic data. The solid-state structures of all the six compounds showed intriguing and unique molecular duplexes featuring NH···N, CH···O and CH···π interactions. Careful analysis of different geometric parameters of the involved H-bonds indicates that they are linear, significant and are therefore responsible for guiding the three-dimensional structure of these compounds in the solid state. The prevalence of sextuple hydrogen bond array-driven molecular duplexes and the possibility of structural modifications on the s-triazine ring render these novel triazine derivatives 1-6 attractive as a platform to create heteroduplex constructs and their subsequent utility in the field of supramolecular chemistry and crystal engineering.
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Affiliation(s)
- Shazia Asghar
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Shahid Hameed
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
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18
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Nandi S, Sarkar R, Jaiswar A, Roy S, Haldar D. Miniature β-Hairpin Mimetic by Intramolecular Hydrogen Bond and C-H···π Interactions. ACS OMEGA 2022; 7:17245-17252. [PMID: 35647431 PMCID: PMC9134230 DOI: 10.1021/acsomega.2c01168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Canonically, protein β-hairpin motifs are stabilized by intramolecular hydrogen bonds. Here, we attempt to develop a rational design recipe for a miniature hairpin structure stabilized by hydrogen bonding as well as C-H···π interaction and try to understand how such a stabilization effect varies with different functional groups at each terminus. Database analysis shows that the α-amino acids with an aromatic side chain will not favor that kind of C-H···π stabilized hairpin structure. However, hybrid tripeptides with an N-terminal Boc-Trp-Aib corner residue and C-terminal aromatic ω-amino acids fold into the hairpin conformation with a central β-turn/open-turn that is reinforced by a C-H···π interaction. The CCDC database analysis further confirms that this C-H···π stabilized hairpin motif is general for Boc-protected tripeptides containing Aib in the middle and aromatic functionality at the C-terminus. The different α-amino acids like Leu/Ala/Phe/Pro/Ser at the N-terminus have a minor influence on the C-H···π interaction and stabilities of the folded structures in solid-state. However, the hybrid peptides exhibit different degrees of conformational heterogeneity both in the solid and solution phase, which is common for this kind of flexible small molecule. Conformational heterogeneity in the solution phase including the C-H···π stabilized β-hairpin structures are characterized by the molecular dynamics (MD) simulations explaining their plausible origin at an atomistic level.
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Affiliation(s)
- Sujay
Kumar Nandi
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Raju Sarkar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Akhilesh Jaiswar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Susmita Roy
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Debasish Haldar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
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19
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Hanazono Y, Hirano Y, Takeda K, Kusaka K, Tamada T, Miki K. Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis. SCIENCE ADVANCES 2022; 8:eabn2276. [PMID: 35594350 PMCID: PMC9122329 DOI: 10.1126/sciadv.abn2276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
The planarity of the peptide bond is important for the stability and structure formation of proteins. However, substantial distortion of peptide bonds has been reported in several high-resolution structures and computational analyses. To investigate the peptide bond planarity, including hydrogen atoms, we report a 1.2-Å resolution neutron structure of the oxidized form of high-potential iron-sulfur protein. This high-resolution neutron structure shows that the nucleus positions of the amide protons deviate from the peptide plane and shift toward the acceptors. The planarity of the H─N─C═O plane depends strongly on the pyramidalization of the nitrogen atom. Moreover, the orientation of the amide proton of Cys75 is different in the reduced and oxidized states, possibly because of the electron storage capacity of the iron-sulfur cluster.
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Affiliation(s)
- Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Yu Hirano
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki 319-1106, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106 Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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20
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Gibbs CA, Fedoretz-Maxwell BP, Warren JJ. On the roles of methionine and the importance of its microenvironments in redox metalloproteins. Dalton Trans 2022; 51:4976-4985. [PMID: 35253809 DOI: 10.1039/d1dt04387k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The amino acid residue methionine (Met) is commonly thought of as a ligand in redox metalloproteins, for example in cytochromes c and in blue copper proteins. However, the roles of Met can go beyond a simple ligand. The thioether functional group of Met allows it to be considered as a hydrophobic residue as well as one that is capable of weak dipolar interactions. In addition, the lone pairs on sulphur allow Met to interact with other groups, inluding the aforementioned metal ions. Because of its properties, Met can play diverse roles in metal coordination, fine tuning of redox reactions, or supporting protein structures. These roles are strongly influenced by the nature of the surrounding medium. Herein, we describe several common interactions between Met and surrounding aromatic amino acids and how they affect the physical properties of both copper and iron metalloproteins. While the importance of interactions between Met and other groups is established in biological systems, less is known about their roles in redox metalloproteins and our view is that this is an area that is ready for greater attention.
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Affiliation(s)
- Curtis A Gibbs
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada.
| | | | - Jeffrey J Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada.
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21
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Dutta J, Sahu AK, Bhadauria AS, Biswal HS. Carbon-Centered Hydrogen Bonds in Proteins. J Chem Inf Model 2022; 62:1998-2008. [PMID: 35293733 DOI: 10.1021/acs.jcim.2c00015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hydrogen bonding (H-bonding) without lone pair(s) of electrons and π-electrons is a concept developed 2-3 years ago. H-bonds involving less electronegative tetrahedral carbon are beyond the classical concept of H-bonds. Herein, we present the first report on H-bonds with tetravalent carbons in proteins. A special bonding arrangement is needed to increase the negative charge density around the sp3-hybridized carbon atom. Therefore, less electronegative elements such as As and Mg, when bonded to sp3-C, enable the C-atoms as H-bond acceptors. Careful protein structure analysis aided by several quantum chemical calculations suggests that these H-bonds are weak to moderate in strength. We developed an empirical equation to estimate the C-H···C H-bond energy in proteins from the distances between the C- and H-atoms. In proteins, the binding energies range from -5.4 to -14.0 kJ/mol. The C-H···C H-bonds assist the substrate binding in proteins. We also explored the potential role of these carbon-centered H-bonds in C-H bond activation through σ-bond metathesis. To our surprise, contribution from these H-bonds is almost of similar magnitude as that from C-H···π H-bonds for C-H bond activation.
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Affiliation(s)
- Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Abhijeet S Bhadauria
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, Bhubaneswar 752050, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
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22
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Fan Y, Li J. The synthesis and crystal structures of two μ-oxo iron(III) porphyrin complexes. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two [Formula: see text]-oxo iron(III) porphyrin complexes, [Formula: see text]-oxo-bis[meso-tetra-[Formula: see text],[Formula: see text],[Formula: see text],[Formula: see text]-([Formula: see text]-nicotina-midophenyl)porphinatoiron(III)] ([Fe(TPyPP)]2O) and its copper adduct ([Fe(TPyPP)(CuCl)]2O[CF3SO3][Formula: see text], which are derived from Gunter’s porphyrin model for cytochrome [Formula: see text]oxidase are reported. The two complexes were isolated and characterized by single crystal X-ray diffraction, UV-vis and IR spectroscopies. Crystal structural analysis including comparisons to [Formula: see text]-oxo analogues and Hirshfeld surface calculations revealed several noteworthy structural features [Formula: see text] the various picket orientations which are partially attributed to intra- and/or inter-molecular nonbonded interactions.
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Affiliation(s)
- Yingying Fan
- College of Materials Science and Optoelectronic Technology, CAS Center for Excellence in Topological Quantum Computation, & Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology, CAS Center for Excellence in Topological Quantum Computation, & Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing 101408, China
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23
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Ahirwar MB, Gurav ND, Gadre SR, Deshmukh MM. Molecular Tailoring Approach for Estimating Individual Intermolecular Interaction Energies in Benzene Clusters. J Phys Chem A 2021; 125:6131-6140. [PMID: 34251827 DOI: 10.1021/acs.jpca.1c03907] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is no general method available for the estimation of individual intermolecular interaction energies in weakly bound molecular clusters, and such studies are limited only to the dimer. Recently, we proposed a molecular tailoring approach-based method for the estimation of individual O-H···O hydrogen bond energies in water clusters. In the present work, we extend the applicability of this method for estimating the individual intermolecular interaction energies in benzene clusters, which are expected to be small. The basis set superposition error (BSSE)-corrected individual intermolecular interaction energies in linear (LN) benzene clusters, LN-(Bz)n n = 3-7, were calculated to be in the range from -1.75 to -2.33 kcal/mol with the cooperativity contribution falling between 0.05 and 0.20 kcal/mol, calculated at the MP2.5/aug-cc-pVDZ level of theory. In the case of non-linear (NLN) benzene clusters, NLN-(Bz)n n = 3-5, the BSSE-corrected individual intermolecular interaction energies exhibit a wider range from -1.16 to -2.55 kcal/mol with cooperativity contribution in the range from 0.02 to -0.61 kcal/mol. The accuracy of these estimated values was validated by adding the sum of interaction energies to the sum of monomer energies. These estimated molecular energies of clusters were compared with their actual calculated values. The small difference (<0.3 kcal/mol) in these two values suggests that our estimated individual intermolecular interaction energies in benzene clusters are quite reliable.
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Affiliation(s)
- Mini Bharati Ahirwar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
| | - Nalini D Gurav
- Department of Scientific Computing, Modelling and Simulation, Savitribai Phule Pune University, Pune 411 007, India
| | - Shridhar R Gadre
- Department of Scientific Computing, Modelling and Simulation, Savitribai Phule Pune University, Pune 411 007, India
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, India
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24
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Draper SRE, Jones ZB, Earl SO, Dalley NA, Ashton DS, Carter AJ, Conover BM, Price JL. PEGylation Increases the Strength of a Nearby NH-π Hydrogen Bond in the WW Domain. Biochemistry 2021; 60:2064-2070. [PMID: 34137579 DOI: 10.1021/acs.biochem.1c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we show that an NH-π interaction between a highly conserved Asn and a nearby Trp stabilizes the WW domain of the human protein Pin1. The strength of this NH-π interaction depends on the structure of the arene, with NH-π interactions involving Trp or naphthylalanine being substantially more stabilizing than those involving Tyr or Phe. Calculations suggest arene size and polarizability are key structural determinants of NH-π interaction strength. Methylation or PEGylation of the Asn side-chain amide nitrogen each strengthens the associated NH-π interaction, though likely for different reasons. We hypothesize that methylation introduces steric clashes that destabilize conformations in which the NH-π interaction is not possible, whereas PEGylation strengthens the NH-π interaction via localized desolvation of the protein surface.
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Affiliation(s)
| | | | - Seth O Earl
- Brigham Young University, Provo, Utah 84602, United States
| | | | | | | | | | - Joshua L Price
- Brigham Young University, Provo, Utah 84602, United States
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25
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Takishima R, Nishii Y, Miura M. Synthesis and Optical Properties of Axially Chiral Bibenzo[ b]carbazole Derivatives. Org Lett 2021; 23:1349-1354. [PMID: 33533627 DOI: 10.1021/acs.orglett.1c00011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pure organic materials with the circularly polarized luminescence (CPL) property have attracted significant research interest over the past few decades. In this study, a series of axially chiral bibenzo[b]carbazole derivatives were synthesized by adopting palladium- and iridium-catalyzed direct C-H functionalization reactions as the key steps. These compounds exhibited CPL characteristics with considerably large dissymmetry factors up to 2.81 × 10-2 in the solid state, indicating the formation of well-ordered aggregates.
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Affiliation(s)
- Ryo Takishima
- Department of Applied Chemistry, Graduate School of Engineering, Suita, Osaka 565-0871, Japan
| | - Yuji Nishii
- Department of Applied Chemistry, Graduate School of Engineering, Suita, Osaka 565-0871, Japan
| | - Masahiro Miura
- Department of Applied Chemistry, Graduate School of Engineering, Suita, Osaka 565-0871, Japan
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26
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Stasyuk OA, Stasyuk AJ, Solà M, Voityuk AA. Photoinduced electron transfer in nano-Saturn complexes of fullerene. Phys Chem Chem Phys 2021; 23:2126-2133. [PMID: 33437974 DOI: 10.1039/d0cp05919f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The photoinduced electron transfer is studied computationally in several Saturn-shaped inclusion complexes of carbo-aromatic rings and C60 fullerene - C72⊃C60, C96⊃C60, C120⊃C60, and C168⊃C60. Analysis of their structural and electronic properties shows that the charge separation process is efficient in C120⊃C60 and C168⊃C60 where the host molecule resembles the conjugated [24]circulene unit. In contrast, the electron transfer is not feasible in the complexes of the oligophenylene-based rings C72⊃C60 and C96⊃C60.
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Affiliation(s)
- O A Stasyuk
- Institut de Química Computacional and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany 69, 17003 Girona, Spain.
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27
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Cholasseri R, De S. Dual-Site Binding of Quaternary Ammonium Ions as Internal K +-Ion Channel Blockers: Nonclassical (C-H···O) H Bonding vs Dispersive (C-H···H-C) Interaction. J Phys Chem B 2021; 125:86-100. [PMID: 33371683 DOI: 10.1021/acs.jpcb.0c09604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA K+-ion channel is carried out by molecular dynamics (MD) simulations as well as quantum mechanics/molecular mechanics (QM/MM) methods. The present work unveils distinct modes of binding for different QAs, due to differences in size and hydrophobicity. The QAs bind near the channel gate as well as at the central cavity, leading to a possible dual-site blocking action. Small-sized tetraethylammonium (TEA) and tetrabutylammonium (TBA) ions enter inside the channel cavity in the open state of KcsA but bind strongly in the closed state. TEA binds to the polar hydroxyl group of threonine residues situated at the channel gate via nonclassical H-bonding interaction (C-H···O), while TBA binds to a second binding site, the central cavity, with hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues via alkyl-π and hydrophobic interactions (C-H···H-C). On the contrary, large tetrahexylammonium (THA) and tetraoctylammonium (TOA) ions bind the hydrophobic side-chain methyl and isopropyl of alanine and valine at the channel gate both in the open and closed states, thereby restricting the free movement of large QAs toward the center of the cavity. However, the binding to the hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues in the closed state is thermodynamically preferable. Also, the binding energy is found to increase with an increase in the alkyl chain length from ethyl (-16.4 kcal/mol) to octyl (-65.5 kcal/mol), due to an almost linear increase in dispersive interaction.
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Affiliation(s)
- Rinsha Cholasseri
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673 601, India
| | - Susmita De
- Department of Applied Chemistry, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India.,Inter University Centre for Nanomaterials and Devices, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India
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28
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Rosa GP, Palmeira A, Resende DISP, Almeida IF, Kane-Pagès A, Barreto MC, Sousa E, Pinto MMM. Xanthones for melanogenesis inhibition: Molecular docking and QSAR studies to understand their anti-tyrosinase activity. Bioorg Med Chem 2020; 29:115873. [PMID: 33242700 DOI: 10.1016/j.bmc.2020.115873] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
The human skin is constantly exposed to external factors that affect its integrity, UV radiation being one of the main stress factors. The repeated exposure to this radiation leads to increased production of Reactive Oxygen Species (ROS) which activate a series of processes involved in photoaging. Excessive UV exposure also exacerbates melanin production leading to a variety of pigmentation disorders. Xanthones are reported to exhibit properties that prevent deleterious effects of UV exposure and high levels of ROS in the organism, so in this work a wide library of xanthones with different patterns of substitution was synthesized and tested for their inhibitory activity against the skin enzymes tyrosinase, elastase, collagenase and hyaluronidase, many of which were evaluated for the first time. Most of the compounds were tyrosinase inhibitors, with the best one (xanthone 27) presenting an IC50 of 1.9 µM, which is approximately 6 times lower than the IC50 of the positive control kojic acid. Concerning the other enzymes, only one compound presented IC50 lower than 150 µM in elastase inhibition (xanthone 14 = 91.8 µM) and none in collagenase and hyaluronidase inhibition. A QSAR model for tyrosinase inhibitory activity was built using six molecular descriptors, with a partial negative surface area descriptor and the relative number of oxygen atoms being positively contributing to the tyrosinase inhibitory activity. Docking using AutoDock Vina shows that all the tested compounds have more affinity to mushroom tyrosinase than kojic acid. Docking results implied that the tyrosinase inhibitory mechanisms of xanthonic derivatives are attributed to an allosteric interaction. Taken together, these data suggest that xanthones might be useful scaffolds for the development of new and promising candidates for the treatment of pigmentation-related disorders and for skin whitening cosmetic products.
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Affiliation(s)
- G P Rosa
- cE3c-Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group, 9501-801 Ponta Delgada, Portugal; Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9501-801 Ponta Delgada, Portugal
| | - A Palmeira
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Portugal; CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - D I S P Resende
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Portugal; CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - I F Almeida
- UCIBIO/REQUIMTE, MedTec-Laboratório de Tecnologia Farmacêutica, Departamento de Ciências do Medicamento, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - A Kane-Pagès
- Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9501-801 Ponta Delgada, Portugal
| | - M C Barreto
- cE3c-Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group, 9501-801 Ponta Delgada, Portugal; Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9501-801 Ponta Delgada, Portugal.
| | - E Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Portugal; CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.
| | - M M M Pinto
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Portugal; CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
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