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Archana VP, Armaković SJ, Armaković S, Celik I, Bhagyasree J, Dinesh Babu K, Rudrapal M, Divya IS, Pillai RR. Exploring the structural, photophysical and optoelectronic properties of a diaryl heptanoid curcumin derivative and identification as a SARS-CoV-2 inhibitor. J Mol Struct 2023; 1281:135110. [PMID: 36785704 PMCID: PMC9910092 DOI: 10.1016/j.molstruc.2023.135110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Developing modifiable natural products those having antiviral activities against SARS-CoV-2 is a key research area which is popular in current scenario of COVID pandemic. A diaryl heptanoid curcumin and its derivatives are already presenting promising candidates for anti-viral drug development. We have synthesized single crystals of a dimethylamino derivative of natural curcumin and structural characterization was done by single crystal XRD analysis. Using steady-state absorption and emission spectra and guided by complimentary ab initio calculations, we unraveled the solvent effects on the photophysical properties of the dimethyl amino curcumin derivative. Chemical reactivity of the compound has investigated using frontier molecular orbitals and molecular electrostatic potential surface. High stability of the curcumin derivative in water environment has evaluated by Radial Distributions Functions (RDF) calculated via Molecular Dynamics (MD) simulations. The inhibitory activity of the title compound was evaluated by in silico methods and the stability of the protein-ligand complexes were studied using Molecular Dynamics simulations and MM-PBSA analysis. With this detailed study, we hope to motivate scientific community to develop new curcumin derivatives against SARS-CoV-2 virus.
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Affiliation(s)
- Vikaraman P. Archana
- Department of Polymer Chemistry, Government College, Attingal, University of Kerala, Thiruvananthapuram, Kerala, India,Department of Chemistry, Government College for Women, University of Kerala, Vazhuthacaud, Thiruvananthapuram, Kerala, India
| | - Sanja J. Armaković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000 Novi Sad, Serbia,Association for the International Development of Academic and Scientific Collaboration (AIDASCO), Novi Sad, Serbia
| | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000 Novi Sad, Serbia,Association for the International Development of Academic and Scientific Collaboration (AIDASCO), Novi Sad, Serbia
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38280, Turkey
| | - J.B. Bhagyasree
- Department of Polymer Chemistry, Government College, Attingal, University of Kerala, Thiruvananthapuram, Kerala, India
| | - K.V. Dinesh Babu
- Department of Chemistry, Government College for Women, University of Kerala, Vazhuthacaud, Thiruvananthapuram, Kerala, India
| | - Mithun Rudrapal
- Department of Pharmaceutical Sciences, School of Biotechnology & Pharmaceutical Sciences, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Guntur-522213, India
| | - Indira S. Divya
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India
| | - Renjith Raveendran Pillai
- Department of Physics, University College, University of Kerala, Thiruvananthapuram, Kerala, India,Association for the International Development of Academic and Scientific Collaboration (AIDASCO), Novi Sad, Serbia,Corresponding author
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Hu J, Wang Y, shao T, Lian G, Hu K, Liu Y, Zhou M, Wang X, Huang L, Meng X, Jin G. Simple and practical, highly sensitive and responsive recognition of cysteine: Design, synthesis and mechanism study of a novel curcumin fluorescent probe. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates. Molecules 2022; 27:molecules27113456. [PMID: 35684394 PMCID: PMC9182218 DOI: 10.3390/molecules27113456] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M−1cm−1) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.
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Biaggne A, Knowlton WB, Yurke B, Lee J, Li L. Substituent Effects on the Solubility and Electronic Properties of the Cyanine Dye Cy5: Density Functional and Time-Dependent Density Functional Theory Calculations. Molecules 2021; 26:molecules26030524. [PMID: 33498306 PMCID: PMC7863957 DOI: 10.3390/molecules26030524] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
The aggregation ability and exciton dynamics of dyes are largely affected by properties of the dye monomers. To facilitate aggregation and improve excitonic function, dyes can be engineered with substituents to exhibit optimal key properties, such as hydrophobicity, static dipole moment differences, and transition dipole moments. To determine how electron donating (D) and electron withdrawing (W) substituents impact the solvation, static dipole moments, and transition dipole moments of the pentamethine indocyanine dye Cy5, density functional theory (DFT) and time-dependent (TD-) DFT calculations were performed. The inclusion of substituents had large effects on the solvation energy of Cy5, with pairs of withdrawing substituents (W-W pairs) exhibiting the most negative solvation energies, suggesting dyes with W-W pairs are more soluble than others. With respect to pristine Cy5, the transition dipole moment was relatively unaffected upon substitution while numerous W-W pairs and pairs of donating and withdrawing substituents (D-W pairs) enhanced the static dipole difference. The increase in static dipole difference was correlated with an increase in the magnitude of the sum of the Hammett constants of the substituents on the dye. The results of this study provide insight into how specific substituents affect Cy5 monomers and which pairs can be used to engineer dyes with desired properties.
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Affiliation(s)
- Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
- Correspondence:
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Yang M, Lee SC, Kim M, Lim MH, Kim C. A multi-functional picolinohydrazide-based chemosensor for colorimetric detection of iron and dual responsive detection of hypochlorite. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 245:118899. [PMID: 32932033 DOI: 10.1016/j.saa.2020.118899] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
A novel effective chemosensor HPHN, (E)-6-hydroxy-N'-((2-hydroxynaphthalen-1-yl)methylene) picolinohydrazide, was synthesized. HPHN sensed Fe3+/2+ with the changes of color from yellow to orange without obvious inhibition from other cations. In addition, HPHN could detect ClO- by both the color change from yellow to colorless and the fluorescence quenching. The binding modes of HPHN with Fe3+/2+ and ClO- were determined to be 1:1 with Job plot and ESI-mass analysis. HPHN displayed low detection limits of 0.29 μM for Fe3+ and 0.77 μM for Fe2+. For ClO-, the detection limit was 6.20 μM by colorimetric method and 3.99 μM by fluorescent one, respectively. Moreover, HPHN can be employed to quantify Fe3+ and ClO- in environmental samples and apply to cell imaging for ClO-.
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Affiliation(s)
- Minuk Yang
- Department of Fine Chem., Seoul Nat. Univ. of Sci. and Tech., Seoul 01821, Republic of Korea
| | - Su Chan Lee
- Department of Fine Chem., Seoul Nat. Univ. of Sci. and Tech., Seoul 01821, Republic of Korea
| | - Mingeun Kim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, KAIST, Daejeon 34141, Republic of Korea.
| | - Cheal Kim
- Department of Fine Chem., Seoul Nat. Univ. of Sci. and Tech., Seoul 01821, Republic of Korea.
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