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Evtushenko EG, Gavrilina ES, Vasilyeva AD, Yurina LV, Kurochkin IN. Highly Sensitive Measurement of Horseradish Peroxidase Using Surface-Enhanced Raman Scattering of 2,3-Diaminophenazine. Molecules 2024; 29:793. [PMID: 38398545 PMCID: PMC10891785 DOI: 10.3390/molecules29040793] [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: 10/31/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
The development of various enzyme-linked immunosorbent assays (ELISAs) coupled with surface-enhanced Raman scattering (SERS) detection is a growing area in analytical chemistry due to their potentially high sensitivity. A SERS-based ELISA with horseradish peroxidase (HRP) as an enzymatic label, an o-phenylenediamine (oPD) substrate, and a 2,3-diaminophenazine (DAP) enzymatic product was one of the first examples of such a system. However, the full capabilities of this long-known approach have yet to be revealed. The current study addresses a previously unrecognized problem of SERS detection stage performance. Using silver nanoparticles and model mixtures of oPD and DAP, the effects of the pH, the concentration of the aggregating agent, and the particle surface chloride stabilizer were extensively evaluated. At the optimal mildly acidic pH of 3, a 0.93 to 1 M citrate buffer, and AgNPs stabilized with 20 mM chloride, a two orders of magnitude advantage in the limits of detection (LODs) for SERS compared to colorimetry was demonstrated for both DAP and HRP. The resulting LOD for HRP of 0.067 pmol/L (1.3 amol per assay) underscores that the developed approach is a highly sensitive technique. We suppose that this improved detection system could become a useful tool for the development of SERS-based ELISA protocols.
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Affiliation(s)
- Evgeniy G. Evtushenko
- N.M. Emanuel Institute of Biochemical Physics RAS, Kosygina Str. 4, 119334 Moscow, Russia (A.D.V.); (I.N.K.)
- Faculty of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
| | - Elizaveta S. Gavrilina
- N.M. Emanuel Institute of Biochemical Physics RAS, Kosygina Str. 4, 119334 Moscow, Russia (A.D.V.); (I.N.K.)
| | - Alexandra D. Vasilyeva
- N.M. Emanuel Institute of Biochemical Physics RAS, Kosygina Str. 4, 119334 Moscow, Russia (A.D.V.); (I.N.K.)
| | - Lyubov V. Yurina
- N.M. Emanuel Institute of Biochemical Physics RAS, Kosygina Str. 4, 119334 Moscow, Russia (A.D.V.); (I.N.K.)
| | - Ilya N. Kurochkin
- N.M. Emanuel Institute of Biochemical Physics RAS, Kosygina Str. 4, 119334 Moscow, Russia (A.D.V.); (I.N.K.)
- Faculty of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russia
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Bashir M, Mantoo IA, Yousuf I. Peroxidase-like oxidative activity of cobalt-based 1D coordination polymer; experimental and theoretical investigations. J Mol Model 2023; 29:221. [PMID: 37400745 DOI: 10.1007/s00894-023-05639-9] [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: 05/17/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
CONTEXT The present work describes the synthesis, structural characterization, and catalytic activity of a Co(II)-based one-dimensional coordination polymer (CP1). To validate the chemotherapeutic potential of CP1, in vitro DNA binding assessment was carried out by employing multispectroscopic techniques. Moreover, the catalytic activity of CP1 was also ascertained during the oxidative conversion of o-phenylenediamine (OPD) to diaminophenazine (DAP) under aerobic conditions. METHODS The molecular structure of CP1 was solved with the olex2.solve structure solution program using charge flipping and refined with the olex2.refine refinement package by using Gauss-Newton minimization. The DFT studies were performed by utilizing ORCA Program Version 4.1.1 to calculate the electronic and chemical properties of CP1 by calculating the HOMO-LUMO energy gap. All calculations were carried out at B3LYP hybrid functional using def2-TZVP as the basis set. Contour plots of various FMOs were visualized by using Avogadro software. Hirshfeld surface analysis was carried out by Crystal explorer Program 17.5.27 to examine the various non-covalent interactions which are crucial for the stability of crystal lattice. In addition, molecular docking studies of CP1 with DNA were performed by using AutoDock Vina software and AutoDock tools (version 1.5.6). Discovery studio 3.5 Client 2020 was used for visualization of the docked pose and binding interactions of CP1 with ct-DNA.
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Affiliation(s)
- Masrat Bashir
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Imtiyaz Ahmad Mantoo
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Imtiyaz Yousuf
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India.
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Mudi PK, Mahato RK, Verma H, Panda SJ, Purohit CS, Silakari O, Biswas B. In silico anti-SARS-CoV-2 activities of five-membered heterocycle-substituted benzimidazoles. J Mol Struct 2022; 1261:132869. [PMID: 35340531 PMCID: PMC8934690 DOI: 10.1016/j.molstruc.2022.132869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 12/16/2022]
Abstract
The manuscript deals with cost-effective synthesis, structural characterization and in silico SARS-CoV-2 screening activity of 5-membered heterocycle-substituted benzimidazole derivatives, 1-((1H-pyrrol-2-yl)methyl)-2-(1H-pyrrol-2-yl)-1H-benzo[d]imidazole (L1), 2-(furan-2-yl)-1-(furan-2-ylmethyl)-1H-benzo[d]imidazole (L2), 2-(thiophen-2-yl)-1-(thiophen-2-ylmethyl)-1H-benzo[d]imidazole (L3). The benzimidazole compounds were synthesized through a green-synthetic approach by coupling of 5-membered heterocyclic-carboxaldehyde and o-phenylenediamine in water under an aerobic condition. The compounds were characterized by various spectroscopic methods and X-ray structural analysis. The suitable single-crystals of the methyl derivative of L3 were grown as L3' which crystallized in a monoclinic system and the thiophene groups co-existed in a nearly a perpendicular orientation. Further, in silico anti-SARS-CoV-2 proficiency of the synthetic derivatives is evaluated against main protease (Mpro) and non-structural proteins (nsp2 and nsp7) of SARS-CoV-2. Molecular docking and molecular dynamics analysis of the ligands (L1-L3) against Mpro and nsp2 and nsp7 for 50 ns reveal that L3 turns out to be the superlative antiviral candidate against Mpro, nsp2 and nsp7 of SARS-CoV-2 as evident from the binding score and stability of the ligand-docked complexes with considerable binding energy changes.
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Affiliation(s)
| | - Rajani Kanta Mahato
- Department of Chemistry, University of North Bengal, Darjeeling 734013, India
| | - Himanshu Verma
- Molecular Modeling Lab, Department Pharmaceutical Sciences and Drug Research, Punjabi University, India
| | - Subhra Jyoti Panda
- Department of Chemical Sciences, National School of Science Education and Research, Bhubaneswar 752050, India
| | - Chandra Sekhar Purohit
- Department of Chemical Sciences, National School of Science Education and Research, Bhubaneswar 752050, India
| | - Om Silakari
- Molecular Modeling Lab, Department Pharmaceutical Sciences and Drug Research, Punjabi University, India
| | - Bhaskar Biswas
- Department of Chemistry, University of North Bengal, Darjeeling 734013, India,Corresponding author
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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