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Ullah Z, Sonawane PM, Mary YS, Mary YS, Yohannan Panicker C, Churchill DG. A foundational theoreticalAl 12E 12(E = N, P) adsorption and quinolone docking study: cage–quinolone pairs, optics and possible therapeutic and diagnostic applications. J Biomol Struct Dyn 2022; 41:3630-3646. [PMID: 35380095 DOI: 10.1080/07391102.2022.2053742] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This combined Al12E12 (E = N, P) surface adsorption and docking study describes the new possibility of prospective potential probing(photophysical/optical) and therapy(medicinal/biochemical) with these adsorbent conjugates. DFT investigations were undertaken herein to help generate geometrical models and better understand the possible favorable adsorption energetics. We attempt to explain their adsorption behaviors and docking involving SARS-CoV-2 viruses (PDB)to assess their possible pharmaceutical potential against the pandemic virus (COVID-19). The adsorption behavior of 8-hydroxy-2-methylquinoline (MQ) and its halogenated derivatives, 5,7-diiodo-8-hydroxy-2-methylquinoline (MQI), 5,7-dichloro-8-hydroxy-2-methylquinoline (MQCl), and 5,7-dibromo-8-hydroxy-2-methylquinoline (MQBr), with aluminum-nitrogen (AlN), and aluminum-phosphorous (AlP) fullerene-like nanocages is reported. A decrease in the hardness of the nanoclusters when adsorbed with drug molecules resulted in an incrementally improved chemical softness (see e.g., Hard-Soft Acid Base theory) indicating that reactivity of the drug molecule in the resulting complex increases upon cluster chemical adsorption. The energy gap is found to be maximized for AlN-MQ and minimized for AlP-MQI; the reduced density gradient (RDG) iso-surfaces and AIM studies also corroborated this. Therefore, these two were found, respectively, to be the least and most electrically conductive of the species under study. We selected a simple medicinal building block (chelator)in addition to selecting the cluster based on previous literature reports. Important parameters such as gap energies and global indices were determined. We assessed NLO properties. The SARS-CoV-2 virus PDB docking data for 6VW1, 6VYO, 6WKQ, 7AD1, 7AOL, 7B3C, were enlisted as ligand targets for studies of docking (PatchDock Server) using the requisite PDB geometries (For the structure of 6VW1, kindly see reference, 2020; For the structure of 6VYO kindly see reference, 2020; For the structure of 6WKQ kindly see reference, 2020; For the structure of 7AD1 kindly see reference, 2021; For the structure of 7AOL kindly see reference, 2021; For the structure of 7B3C kindly see reference, 2021). Such findings indicate that the AlN-drug conjugation have inhibitory effect against these selected receptors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zakir Ullah
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Graduate School of Energy, Environment, Water and Sustainability (EEWS) Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
- Convergence Research Center for Insect Vectors, Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, South Korea
| | - Prasad M. Sonawane
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Department of Chemistry & Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | | | | | | | - David G. Churchill
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Therapeutic Bioengineering Section, KAIST Institute for Health Science and Technology (KIHST), Daejeon, Republic of Korea
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2
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Moriuchi-Kawakami T, Mizuno Y, Inoue T, Matsubara S, Moriuchi T. A C3-substituted cyclotriveratrylene derivative with 8-quinolinyl groups as a fluorescence-enhanced probe for the sensing of Cu2+ ions. Analyst 2019; 144:1140-1146. [DOI: 10.1039/c8an01615a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
C3-Substituted CTV derivatives with 8-quinolinyl groups exhibited a selective response of fluorescence enhancement toward Cu2+ ions even in the presence of other co-existing cations.
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Affiliation(s)
- Takayo Moriuchi-Kawakami
- Department of Applied Chemistry
- Faculty of Engineering
- Osaka Institute of Technology
- Osaka 535-8585
- Japan
| | - Yohei Mizuno
- Department of Applied Chemistry
- Faculty of Engineering
- Osaka Institute of Technology
- Osaka 535-8585
- Japan
| | - Tsubasa Inoue
- Department of Applied Chemistry
- Faculty of Engineering
- Osaka Institute of Technology
- Osaka 535-8585
- Japan
| | - Shota Matsubara
- Department of Applied Chemistry
- Faculty of Engineering
- Osaka Institute of Technology
- Osaka 535-8585
- Japan
| | - Toshiyuki Moriuchi
- Division of Molecular Materials Science
- Graduate School of Science
- Osaka City University
- Osaka 558-8585
- Japan
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3
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Xiao F, Tan H, Wu Y, Liao S, Wu Z, Shen G, Yu R. A novel logic gate based on liquid-crystals responding to the DNA conformational transition. Analyst 2018; 141:2870-3. [PMID: 27102781 DOI: 10.1039/c6an00504g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Described herein is a novel liquid crystal (LC)-based DNA logic gate constructed via employing the reorientation of LCs triggered by metal-ion-mediated DNA probe conformational changes.
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Affiliation(s)
- Fubing Xiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Hui Tan
- Technology Center of Juhua Group, Quzhou, 324004, P. R. China.
| | - Yan Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Shuzhen Liao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Zhaoyang Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Guoli Shen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Ruqin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
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6
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Huerta-Aguilar CA, Raj P, Thangarasu P, Singh N. Fluorescent organic nanoparticles (FONs) for selective recognition of Al3+: application to bio-imaging for bacterial sample. RSC Adv 2016. [DOI: 10.1039/c6ra01231k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
(a) Changes in fluorescence upon successive addition of Al3+ ions to salpn-ONPs; (b) titration profile of fluorescence; (c) recognition of Al3+ through bio-fluorescence Staphylococcus aureus bacterial cells.
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Affiliation(s)
| | - Pushap Raj
- Department of Chemistry
- Indian Institute of Technology (IIT)
- Ropar
- India
| | - Pandiyan Thangarasu
- Facultad de Química
- Universidad Nacional Autónoma de México (UNAM)
- Ciudad Universitaria
- México D. F
- Mexico
| | - Narinder Singh
- Department of Chemistry
- Indian Institute of Technology (IIT)
- Ropar
- India
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7
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Adhikari S, Sahana A, Kumari B, Ganguly D, Das S, Banerjee PP, Banerjee G, Chattopadhyay A, Fondo M, Matalobos JS, Brandão P, Félix V, Das D. Molecular diversity in several pyridyl based Cu( ii) complexes: biophysical interaction and redox triggered fluorescence switch. NEW J CHEM 2016. [DOI: 10.1039/c6nj02381a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A novel approach for detection of intra-cellular Cu+inE. coliand human blood cells is reported. Studies on several pyridyl based Cu(ii) complexes and interaction of ct DNA with one of them are carried out for plausible application in biology concerning disruption of normal DNA activity.
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Affiliation(s)
| | - Animesh Sahana
- Department of Chemistry
- The University of Burdwan
- Burdwan
- India
| | - Babli Kumari
- Department of Chemistry
- The University of Burdwan
- Burdwan
- India
| | - Durba Ganguly
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | - Saurabh Das
- Department of Chemistry
- Jadavpur University
- Kolkata-700032
- India
| | | | - Gautam Banerjee
- Department of Zoology
- VisvaBharati University
- Santiniketan
- India
| | | | - Matilde Fondo
- Departamento de Quimica Inorganica
- Facultade de Quimica
- 15782 Santiago de Compostela
- Spain
| | | | - Paula Brandão
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- 3810-193 Aveiro
- Portugal
| | - Vítor Félix
- Department of Chemistry
- CICECO – Aveiro Institute of Materials
- 3810-193 Aveiro
- Portugal
- Department of Medical Sciences
| | - Debasis Das
- Department of Chemistry
- The University of Burdwan
- Burdwan
- India
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8
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Johnson AD, Paterson KA, Spiteri JC, Denisov SA, Jonusauskas G, Tron A, McClenaghan ND, Magri DC. Water-soluble naphthalimide-based ‘Pourbaix sensors’: pH and redox-activated fluorescent AND logic gates based on photoinduced electron transfer. NEW J CHEM 2016. [DOI: 10.1039/c6nj02023b] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Naphthalimide-based ‘Pourbaix sensors’ for redox potential and pH fluoresce with a lifetime of 8.5 ns while photoinduced electron transfer occurs on a time scale of 20 ps.
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Affiliation(s)
- Alex D. Johnson
- Department of Chemistry
- Faculty of Science
- University of Malta
- Msida
- Malta
| | - Kyle A. Paterson
- Department of Chemistry
- Faculty of Science
- University of Malta
- Msida
- Malta
| | - Jake C. Spiteri
- Department of Chemistry
- Faculty of Science
- University of Malta
- Msida
- Malta
| | - Sergey A. Denisov
- Institut des Sciences Moléculaires
- CNRS UMR 5255
- University of Bordeaux
- 33405 Talence
- France
| | - Gediminas Jonusauskas
- Laboratoire Ondes et Matières d'Aquitaine
- CNRS UMR 5798
- University of Bordeaux
- 33405 Talence
- France
| | - Arnaud Tron
- Institut des Sciences Moléculaires
- CNRS UMR 5255
- University of Bordeaux
- 33405 Talence
- France
| | - Nathan D. McClenaghan
- Institut des Sciences Moléculaires
- CNRS UMR 5255
- University of Bordeaux
- 33405 Talence
- France
| | - David C. Magri
- Department of Chemistry
- Faculty of Science
- University of Malta
- Msida
- Malta
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9
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Grimm JB, Gruber TD, Ortiz G, Brown TA, Lavis LD. Virginia Orange: A Versatile, Red-Shifted Fluorescein Scaffold for Single- and Dual-Input Fluorogenic Probes. Bioconjug Chem 2015; 27:474-80. [DOI: 10.1021/acs.bioconjchem.5b00566] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Todd D. Gruber
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Gloria Ortiz
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
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Zhao J, Xu K, Yang W, Wang Z, Zhong F. The triplet excited state of Bodipy: formation, modulation and application. Chem Soc Rev 2015; 44:8904-39. [DOI: 10.1039/c5cs00364d] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The accessing of the triplet excited state of one of the most popular fluorophores, boron-dipyrromethene (Bodipy), was summarized.
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Affiliation(s)
- Jianzhang Zhao
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- Dalian University of Technology
- Dalian 116012
- P. R. China
| | - Kejing Xu
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- Dalian University of Technology
- Dalian 116012
- P. R. China
| | - Wenbo Yang
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- Dalian University of Technology
- Dalian 116012
- P. R. China
| | - Zhijia Wang
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- Dalian University of Technology
- Dalian 116012
- P. R. China
| | - Fangfang Zhong
- State Key Laboratory of Fine Chemicals
- School of Chemical Engineering
- Dalian University of Technology
- Dalian 116012
- P. R. China
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