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Petit B, Marguerite E, Van Elslande E, Nedev H, Iorga BI, Pham VC, Doan TMH, Séron K, Litaudon M, El Kalamouni C, Apel C. Antiviral miliusanes and isolation of an unprecedented miliusane dimer from Miliusa balansae. Fitoterapia 2024; 177:106083. [PMID: 38897253 DOI: 10.1016/j.fitote.2024.106083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/03/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
In an extensive screening endeavor for anti-coronaviral compounds, we examined 824 tropical plant extracts from the Annonaceae and Rutaceae families. The screening identified an ethyl acetate extract from the aerial parts of Miliusa balansae for its potent inhibitory activity against Human coronavirus HCoV-229E. Subsequent bioassay-guided fractionation of this extract revealed two unreported miliusanes including a complex dimeric structure and seven known compounds, comprising miliusane XXXVI, (+)-miliusol, bistyryls, styryl-pyranones, and the flavonoid rhamnetin. The absolute configuration of the new dimeric miliusane was determined by X-ray crystallography and a putative biogenetic origin was proposed. Investigation of the antiviral effect of these nine phytochemicals within HCoV-229E-infected Huh-7 cells showed that (+)-miliusol and miliusane XXXVI exert antiviral activity at non-cytotoxic concentrations, with IC50 values of 1.15 μM and 19.20 μM, respectively. Furthermore, these compounds significantly inhibited SARS-CoV-2 infection in Vero cells, presenting IC50 values of 11.31 μM for (+)-miliusol and 17.92 μM for miliusane XXXVI. Additionally, both compounds exhibited a potent antiviral effect against the emergent mosquito-borne Zika virus, with IC50 values of 1.34 μM and 23.45 μM, respectively. Time-of-addition assays suggest that their mechanism of action might target later stages of the viral cycle, indicating potential modulation of specific cellular pathways. These findings reinforce the invaluable contribution of medicinal flora as reservoirs of natural antiviral agents and emphasize their prospective role in combatting viruses of medical interest.
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Affiliation(s)
- Bastien Petit
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Elodie Marguerite
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France
| | - Elsa Van Elslande
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Hristo Nedev
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Bogdan I Iorga
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Van Cuong Pham
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, CauGiay, Hanoi, Viet Nam
| | - Thi Mai Huong Doan
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, CauGiay, Hanoi, Viet Nam
| | - Karin Séron
- Université de Lille, INSERM U1019, CNRS UMR 8204, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), F-59000 Lille, France
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
| | - Chaker El Kalamouni
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Plateforme Technologique CYROI, 94791 Sainte Clotilde, La Réunion, France.
| | - Cécile Apel
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.
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Badawi MAAH, Khairbek AA, Thomas R. Computational studies of the CuAAC reaction mechanism with diimine and phosphorus ligands for the synthesis of 1,4-disubstituted 1,2,3-triazoles. NEW J CHEM 2023; 47:3683-3691. [DOI: 10.1039/d2nj06173b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC) reactions with diimine and phosphorus ligands have been studied using DFT calculations in order to understand the effect of the nature of the ligands on the catalytic cycle for the formation of the 1,4-regioisomer.
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Affiliation(s)
| | - Ali A. Khairbek
- Department of Chemistry, Faculty of Science, Tishreen University, Lattakia, Syrian Arab Republic
| | - Renjith Thomas
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala-686101, India
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Geethapriya J, Shanthidevi A, Arivazhagan M, Elangovan N, Sowrirajan S, Manivel S, Thomas R. Synthesis, characterization, computational, excited state properties, wave function and molecular docking studies of (E)-1-(perfluorophenyl)-N-(p-tolyl) methanimine. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Al-Otaibi JS, Mary YS, Mary S, Trivedi R, Chakraborty B, Yadav R, Celik I, Soman S. DFT and MD investigations of the biomolecules of phenothiazine derivatives: interactions with gold and water molecules and investigations in search of effective drug for SARS-CoV-2. J Biomol Struct Dyn 2022:1-12. [PMID: 35470781 DOI: 10.1080/07391102.2022.2068649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Theoretical analyses of two phenothiazine derivatives, 10-[3-(dimethylamino)-2-methylpropyl]phenothiazine-2-carbonitrile (CYM) and 2-[4-[3-(2-chlorophenothiazin-10-yl)propyl]piperazin-1-yl]ethanol (PAZ) are reported using density functional theory (DFT) and molecular dynamics (MD) simulations. Spectroscopic studies, different electronic and chemical parameters are predicted. Red and yellow in electrostatic potential plot is in rings and oxygen atom in PAZ and C≡N and rings in CYM are sensitive to nucleophilic attacks. The blue in hydrogen atoms refer to electrophilic attack in both PAZ and CYM. Stability of the protein-ligand complex formed with these derivatives and angiotensin-converting enzyme 2 (ACE2) was investigated using MD simulation. Radius of gyration of C-alpha atom of 6VW1 displayed the conformational convergence toward a compact structure leading to stable 6VW1-ligand complex which are also in agreement with root mean square fluctuation (RMSF) values. Localized area predicts reactive sites for Au and H2O molecules interaction with these compounds for further practical applications. Charge density is localized on both molecules and also tries to move toward Au-Au dimer and water molecule and such they are expected to contribute to the sensing performance. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Ravi Trivedi
- Department of Physics, Indian Institute of Technology, Mumbai, India
| | - Brahmananda Chakraborty
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Sreejit Soman
- Stemskills Research and Education Lab Private Limited, Faridabad, Hariyana, India
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Al-Otaibi JS, Mary YS, Mary YS, Yadav R. Structural and reactivity studies of pravadoline –An ionic liquid, with reference to its wavefunction-relative properties using DFT and MD simulation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Diana EJ, Kanchana US, Mathew TV. Current developments in the synthesis of 4-chromanone-derived compounds. Org Biomol Chem 2021; 19:7995-8008. [PMID: 34494068 DOI: 10.1039/d1ob01352a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The chroman-4-one framework is a significant structural entity that belongs to the class of oxygen-containing heterocycles. It acts as a major building block in a large class of medicinal compounds, and synthetic compounds exhibit a broad variety of remarkable biological and pharmaceutical activities. Several studies have been performed to improve the methodologies of 4-chromanone-derived compounds. This review focuses on the major synthetic methods of preparation reported on chroman-4-one derivatives from 2016 to 2021.
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Affiliation(s)
- Elizabeth J Diana
- Department of Chemistry, St. Thomas College Pala, Arunapuram P.O., Kottayam, Kerala, 686574, India. .,Department of Chemistry, Alphonsa College Pala, Arunapuram P.O., Kottayam, Kerala, 686574, India.
| | - U S Kanchana
- Department of Chemistry, St. Thomas College Pala, Arunapuram P.O., Kottayam, Kerala, 686574, India.
| | - Thomas V Mathew
- Department of Chemistry, St. Thomas College Pala, Arunapuram P.O., Kottayam, Kerala, 686574, India.
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Sheena Mary Y, Shyma Mary Y, Temiz-Arpaci O, Yadav R, Celik I. DFT, docking, MD simulation, and vibrational spectra with SERS analysis of a benzoxazole derivative: an anti-cancerous drug. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01659-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Mary YS, Mary YS, Rad AS, Yadav R, Celik I, Sarala S. Theoretical investigation on the reactive and interaction properties of sorafenib – DFT, AIM, spectroscopic and Hirshfeld analysis, docking and dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115652] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Al-Otaibi JS, Mary YS, Mary YS, Kaya S, Serdaroglu G. DFT computational study of trihalogenated aniline derivative's adsorption onto graphene/fullerene/fullerene-like nanocages, X 12Y 12 (X = Al, B, and Y = N, P). J Biomol Struct Dyn 2021; 40:8630-8643. [PMID: 33876711 DOI: 10.1080/07391102.2021.1914172] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Adsorption of 2,4,6-tribromoaniline (BA), 2,4,6-trifluoroaniline (FA) and 2,4,6-trichloroaniline (CA) onto the surface of coronene/fullerene/fullerene-like nanocages was investigated by theoretical calculations. Due to the adsorption of BA/FA/CA, there are significant changes in chemical descriptors and nonlinear optical properties. Energy gap values of all nanoclusters are lowered, giving an increase in conductivity of complexes except for fullerene. All complex's ultraviolet visible wavenumber is blue-shifted and especially for fullerene complex, the values are very high. The enhancement of Raman intensities shows that it is possible to design a nanocage sensor for detecting these compounds by surface-enhanced Raman scattering (SERS).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | | | | | - Savaş Kaya
- Health Services Vocational School, Department of Pharmacy, Sivas Cumhuriyet University, Sivas, Turkey
| | - Goncagül Serdaroglu
- Faculty of Education, Math. and Sci. Edu, Sivas Cumhuriyet University, Sivas, Turkey
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Investigation of reactive properties of an antiviral azatricyclo derivative–KDFT, MD and docking simulations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129937] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Spectroscopic and DFT investigations of 8-hydroxy quinoline-5-sulfonic acid-5-chloro-8-hydroxyquinoline cocrystal. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01579-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, SERS-concentration and solvent dependent and docking studies of a bioactive benzenesulfonamide derivative. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129680] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Pooventhiran T, Al-Zaqri N, Alsalme A, Bhattacharyya U, Thomas R. Structural aspects, conformational preference and other physico-chemical properties of Artesunate and the formation of self-assembly with graphene quantum dots: A first principle analysis and surface enhancement of Raman activity investigation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114810] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Kumar VS, Mary YS, Mary YS, Krátký M, Vinsova J, Baraldi C, Roxy MS, Gamberini MC. Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a hydroxybenzylidene derivative. J Biomol Struct Dyn 2021; 40:6952-6964. [PMID: 33645445 DOI: 10.1080/07391102.2021.1891971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering (SERS) of (E)-N'-(5-chloro-2-hydroxybenzylidene)-4-trifluoromethyl) benzohydrazide (CHTB) have been studied on different silver colloids in order to know the particular chemical species responsible for the spectra. Very significant shifts are observed for Raman and SERS wavenumbers. Observed changes in the υ-ring modes may be due to surface interaction of the π-electrons and the presence of this suggested that RingII is more tilted in both cases than RingI and the molecule assumes a tilted orientation for the concentration 10-3 M. Orientation changes are seen in concentration dependent SERS spectra. The molecular electrostatic potential has also been constructed to determine the electron rich and poor site of CHTB. The molecular docking studies indicate that the binding affinity and hydrogen bond interactions with the receptors may be supporting evidence for further studies in designing other pharmaceutical applications of CHTB.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Veena S Kumar
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | | | | | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Jarmila Vinsova
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - M S Roxy
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
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Alharthi FA, Al-Zaqri N, Alsalme A, Al-Taleb A, Pooventhiran T, Thomas R, Rao DJ. Excited-state electronic properties, structural studies, noncovalent interactions, and inhibition of the novel severe acute respiratory syndrome coronavirus 2 proteins in Ripretinib by first-principle simulations. J Mol Liq 2021; 324:115134. [PMID: 33390634 PMCID: PMC7765765 DOI: 10.1016/j.molliq.2020.115134] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/02/2022]
Abstract
Ripretinib is a recently developed drug for the treatment of adults with advanced gastrointestinal stromal tumors. This paper reports an attempt to study this molecule by electronic modeling and molecular mechanics to determine its composition and other specific chemical features via the density-functional theory (DFT), thereby affording sufficient information on the electronic properties and descriptors that can enable the estimation of its molecular bioactivity. We explored most of the physico-chemical properties of the molecule, as well as its stabilization, via the studies of the natural bond orbitals and noncovalent interactions. The electronic excitation, which is a time-dependent process, was examined by the time-dependent DFT with a CAM-B3LYP functional. The molecular docking study indicated that Ripretinib strongly docks with three known novel severe acute respiratory syndrome coronavirus 2 (SARS-n-CoV-2) proteins with a reasonably good docking score.
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Affiliation(s)
- Fahad A Alharthi
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Nabil Al-Zaqri
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ali Alsalme
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Afnan Al-Taleb
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - T Pooventhiran
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - D Jagadeeswara Rao
- Department of Physics, Dr. Lankapalli Bullayya College, Visakhapatnam, Andhra Pradesh, India
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Mary YS, Mary YS. DFT Analysis and Molecular Docking Studies of the Cocrystals of Sulfathiazole-Theophylline and Sulfathiazole-Sulfanilamide. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1873809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Structural, physico-chemical landscapes, ground state and excited state properties in different solvent atmosphere of Avapritinib and its ultrasensitive detection using SERS/GERS on self-assembly formation with graphene quantum dots. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114555] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Al-Zaqri N, Pooventhiran T, Alharthi FA, Bhattacharyya U, Thomas R. Structural investigations, quantum mechanical studies on proton and metal affinity and biological activity predictions of selpercatinib. J Mol Liq 2020; 325:114765. [PMID: 33746318 PMCID: PMC7957184 DOI: 10.1016/j.molliq.2020.114765] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/23/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
Cancer of the lungs and thyroid is particularly difficult to manage and treat. Notably, selpercatinib has recently been suggested as an effective drug to combat these diseases. The entire world is currently tackling the pandemic caused by the SARS-CoV-19 virus. Numerous pharmaceuticals have been evaluated for the management of the disease caused by SARS-CoV-19 (i.e., COVID-19). In this study, selpercatinib was proposed as a potential inhibitor of different SARS-CoV-19 proteins. Several intriguing effects of the molecule were found during the conducted computational investigations. Selpercatinib could effectively act as a proton sponge and exhibited high proton affinity in solution. Moreover, it was able to form complexes with metal ions in aqueous solutions. Specifically, the compound displayed high affinity towards zinc ions, which are important for the prevention of virus multiplication inside human cells. However, due to their charge, zinc ions are not able to pass the lipid bilayer and enter the cell. Thus, it was determined that selpercatinib could act as an ionophore, effectively transporting active zinc ions into cells. Furthermore, various quantum mechanical analyses, including energy studies, evaluation of the reactivity parameters, examination of the electron localisation and delocalisation properties, as well as assessment of the nonlinear optical (NLO) properties and information entropy, were conducted herein. The performed docking studies (docking scores -9.3169, -9.1002, -8.1853 and -8.1222 kcal mol-1) demonstrated that selpercatinib strongly bound with four isolated SARS-CoV-2 proteins.
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Affiliation(s)
- Nabil Al-Zaqri
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.,Department of Chemistry, College of Science, Ibb University, P. O. Box 70270, Ibb, Yemen
| | - T Pooventhiran
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Fahad A Alharthi
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Utsab Bhattacharyya
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
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