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Fibriani A, Taharuddin AAP, Yamahoki N, Stephanie R, Laurelia J, Agustiyanti DF, Wisnuwardhani PH, Angelina M, Rubiyana Y, Ningrum RA, Wardiana A, Desriani D, Iskandar F, Permatasari FA, Giri-Rachman EA. Porphyrin-derived carbon dots for an enhanced antiviral activity targeting the CTD of SARS-CoV-2 nucleocapsid. J Genet Eng Biotechnol 2023; 21:93. [PMID: 37801271 PMCID: PMC10558421 DOI: 10.1186/s43141-023-00548-z] [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: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Since effective antiviral drugs for COVID-19 are still limited in number, the exploration of compounds that have antiviral activity against SARS-CoV-2 is in high demand. Porphyrin is potentially developed as a COVID-19 antiviral drug. However, its low solubility in water restricts its clinical application. Reconstruction of porphyrin into carbon dots is expected to possess better solubility and bioavailability as well as lower biotoxicity. METHODS AND RESULTS In this study, we investigated the antiviral activity of porphyrin and porphyrin-derived carbon dots against SARS-CoV-2. Through the in silico analysis and assessment using a novel drug screening platform, namely dimer-based screening system, we demonstrated the capability of the antivirus candidates in inhibiting the dimerization of the C-terminal domain of SARS-CoV-2 Nucleocapsid. It was shown that porphyrin-derived carbon dots possessed lower cytotoxicity on Vero E6 cells than porphyrin. Furthermore, we also assessed their antiviral activity on the SARS-CoV-2-infected Vero E6 cells. The transformation of porphyrin into carbon dots substantially augmented its performance in disrupting SARS-CoV-2 propagation in vitro. CONCLUSIONS Therefore, this study comprehensively demonstrated the potential of porphyrin-derived carbon dots to be developed further as a promisingly safe and effective COVID-19 antiviral drug.
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Affiliation(s)
- Azzania Fibriani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia.
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Bandung, 40132, Indonesia.
| | | | - Nicholas Yamahoki
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Rebecca Stephanie
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Jessica Laurelia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Dian Fitria Agustiyanti
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Popi Hadi Wisnuwardhani
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Marissa Angelina
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, Indonesian National Research and Innovation Agency (BRIN), Serpong, 15314, Indonesia
| | - Yana Rubiyana
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Ratih Asmana Ningrum
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Andri Wardiana
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Desriani Desriani
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Ferry Iskandar
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Department of Physics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Collaboration Research Center for Advanced Energy Materials, National Research and Innovation Agency-Institut Teknologi, Bandung, Bandung, 40132, Indonesia
| | - Fitri Aulia Permatasari
- Department of Physics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Collaboration Research Center for Advanced Energy Materials, National Research and Innovation Agency-Institut Teknologi, Bandung, Bandung, 40132, Indonesia
- Research Center for Chemistry, National Research and Innovation Agency (BRIN), Serpong, 15314, Indonesia
| | - Ernawati Arifin Giri-Rachman
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
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Fluorine Atoms on C 6H 5-Corrole Affect the Interaction with M pro and PL pro Proteases of SARS-CoV-2: Molecular Docking and 2D-QSAR Approaches. Int J Mol Sci 2022; 23:ijms231810936. [PMID: 36142848 PMCID: PMC9505658 DOI: 10.3390/ijms231810936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/29/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
The chymotrypsin-like cysteine protease (3CLpro, also known as main protease—Mpro) and papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been used as the main targets for screening potential synthetic inhibitors for posterior in vitro evaluation of the most promising compounds. In this sense, the present work reports for the first time the evaluation of the interaction between Mpro/PLpro with a series of 17 porphyrin analogues-corrole (C1), meso-aryl-corrole (C2), and 15 fluorinated-meso-aryl-corrole derivatives (C3–C17) via molecular docking calculations. The impact of fluorine atoms on meso-aryl-corrole structure was also evaluated in terms of binding affinity and physical-chemical properties by two-dimensional quantitative structure–activity relationship (2D-QSAR). The presence of phenyl moieties increased the binding capacity of corrole for both proteases and depending on the position of fluorine atoms might impact positively or negatively the binding capacity. For Mpro the para-fluorine atoms might decrease drastically the binding capacity, while for PLpro there was a certain increase in the binding affinity of fluorinated-corroles with the increase of fluorine atoms into meso-aryl-corrole structure mainly from tri-fluorinated insertions. The 2D-QSAR models indicated two separated regions of higher and lower affinity for Mpro:C1–C17 based on dual electronic parameters (σI and σR), as well as one model was obtained with a correlation between the docking score value of Mpro:C2–C17 and the corresponding 13C nuclear magnetic resonance (NMR) chemical shifts of the sp2 carbon atoms (δC-1 and δC-2) of C2–C17. Overall, the fluorinated-meso-aryl-corrole derivatives showed favorable in silico parameters as potential synthetic compounds for future in vitro assays on the inhibition of SARS-CoV-2 replication.
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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: 31] [Impact Index Per Article: 15.5] [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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Syrbu SA, Kiselev AN, Lebedev MA, Gubarev YA, Yurina ES, Lebedeva NS. Interaction of 5-[4'-( N-Methyl-1,3-benzimidazol-2-yl)phenyl]-10,15,20-tri-( N-methyl-3'-pyridyl)porphyrin Triiodide with SARS-CoV-2 Spike Protein. RUSS J GEN CHEM+ 2022; 92:1005-1010. [PMID: 35756101 PMCID: PMC9207844 DOI: 10.1134/s1070363222060123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 03/17/2022] [Accepted: 04/10/2022] [Indexed: 11/22/2022]
Abstract
The results of experimental studies of the interaction of the S-protein with a monohetaryl-substituted porphyrin containing a benzimidazole residue are presented. It has been revealed that the S-protein forms high-affinity complexes with the specified porphyrin. The porphyrin binding by the SARS-CoV-2 S-protein has proceeded stepwise; at the first stage, the driving force of the complexation is electrostatic interaction between the surface negatively charged regions of the protein and cationic substituents of the porphyrin. At the second stage, the target complex of the S-protein with the porphyrin is formed. It has been established that the introduction of 5-[4'-(N-methyl-1,3-benzimidazol-2-yl)phenyl]-10,15,20-tri-(N-methyl-3'-pyridyl)porphyrin triiodide into a solution of the S-protein complex with the angiotensin-converting enzyme leads to the replacement of the latter with the porphyrin. Displacement of the angiotensin-converting enzyme from the complex with the S-protein under the action of 5-[4'-(N-methyl-1,3-benzimidazol-2-yl)phenyl]-10,15,20-tri-(N-methyl-3'-pyridyl)porphyrin triiodide is the experimental evidence for the porphyrin binding at the receptor-binding domain of the S-protein.
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Affiliation(s)
- S A Syrbu
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - A N Kiselev
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 153045 Ivanovo, Russia.,Ivanovo State University of Chemistry and Technology, 153000 Ivanovo, Russia
| | - M A Lebedev
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 153045 Ivanovo, Russia.,Ivanovo State University of Chemistry and Technology, 153000 Ivanovo, Russia
| | - Yu A Gubarev
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - E S Yurina
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - N Sh Lebedeva
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 153045 Ivanovo, Russia
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Functionalization of Porphyrins Using Metal-Catalyzed C–H Activation. INORGANICS 2022. [DOI: 10.3390/inorganics10050063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The review is devoted to the C–H functionalization of porphyrins. Porphyrins exhibit the properties of organic semiconductors, light energy converters, chemical and electrochemical catalysts, and photocatalysts. The review describes the iridium- and palladium-catalyzed direct functionalization of porphyrins, with more attention given to the results obtained in our laboratory. The development and improvement of synthetic methods that do not require preliminary modification of the substrate with various functional groups are extremely important for the preparation of new organic materials based on porphyrins. This makes it possible to simplify the synthetic procedure, to make the synthesis more economical, environmentally safe, and simple to perform.
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