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Article: Interactions between carbon nanotubes and external structures of SARS-CoV-2 using molecular docking and molecular dynamics.

Lobato, Júlio Cesar Mendes / Arouche, Tiago da Silva / Nero, Jordan Del / Filho, TarcisoAndrade / Borges, Rosivaldo Dos Santos / Neto, Antonio Maia de Jesus Chaves

Journal of molecular structure

2023 Volume 1286, Page(s) 135604

Abstract: Molecular modeling techniques are used to describe the process of interaction between nanotubes and the main structures of the Covid-19 virus: the envelope protein, the main protease, and the Spike glycoprotein. Molecular docking studies show that the ... ...

Abstract	Molecular modeling techniques are used to describe the process of interaction between nanotubes and the main structures of the Covid-19 virus: the envelope protein, the main protease, and the Spike glycoprotein. Molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics simulations provide information on the mean squared deviation of atomic positions between 0.5 and 3.0 Å. The Gibbs free energy model and solvent accessible surface area approaches are used. Through the results obtained through molecular dynamics simulations, it is noted that the zig-zag nanotube prefers to interact with E-pro, M-pro, and S-gly, respectively. Molecular couplings and free energy showed that the S-gly active site residues strongly interact with zigzag, chiral, and armchair nanotubes, in this order. The interactions demonstrated in this manuscript may predict some promising candidates for virus antagonists, which may be confirmed through experimental approaches.
Language	English
Publishing date	2023-04-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	194476-9
ISSN	0022-2860 ; 0377-046X
ISSN	0022-2860 ; 0377-046X
DOI	10.1016/j.molstruc.2023.135604
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Article ; Online: SARS-CoV-2 external structures interacting with nanospheres using docking and molecular dynamics.

Martins da Silva, Anderson Yuri / Arouche, Tiago da Silva / Siqueira, Marcelo Ricardo Souza / Ramalho, Teodorico Castro / de Faria, Lenio Jose Guerreiro / Gester, Rodrigo do Monte / Carvalho Junior, Raul Nunes de / Santana de Oliveira, Mozaniel / Neto, Antonio Maia de Jesus Chaves

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–16

Abstract: Coronavirus is caused by the SARS-CoV-2 virus has shown rapid proliferation and scarcity of treatments with proven effectiveness. In this way, we simulated the hospitalization of carbon nanospheres, with external active sites of the SARS-CoV-2 virus (M- ... ...

Abstract	Coronavirus is caused by the SARS-CoV-2 virus has shown rapid proliferation and scarcity of treatments with proven effectiveness. In this way, we simulated the hospitalization of carbon nanospheres, with external active sites of the SARS-CoV-2 virus (M-Pro, S-Gly and E-Pro), which can be adsorbed or inactivated when interacting with the nanospheres. The computational procedures performed in this work were developed with the SwissDock server for molecular docking and the GROMACS software for molecular dynamics, making it possible to extract relevant data on affinity energy, distance between molecules, free Gibbs energy and mean square deviation of atomic positions, surface area accessible to solvents. Molecular docking indicates that all ligands have an affinity for the receptor's active sites. The nanospheres interact favorably with all proteins, showing promising results, especially C60, which presented the best affinity energy and RMSD values for all protein macromolecules investigated. The C60 with E-Pro exhibited the highest affinity energy of -9.361 kcal/mol, demonstrating stability in both molecular docking and molecular dynamics simulations. Our RMSD calculations indicated that the nanospheres remained predominantly stable, fluctuating within a range of 2 to 3 Å. Additionally, the analysis of other structures yielded promising results that hold potential for application in other proteases.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-09-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2252930
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Article ; Online: Publisher Correction: Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics.

Alencar, Wilson Luna Machado / da Silva Arouche, Tiago / Neto, Abel Ferreira Gomes / de Castro Ramalho, Teodorico / de Carvalho Júnior, Raul Nunes / de Jesus Chaves Neto, Antonio Maia

Scientific reports

2022 Volume 12, Issue 1, Page(s) 4326

Language	English
Publishing date	2022-03-14
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-08312-y
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Article ; Online: Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics.

Alencar, Wilson Luna Machado / da Silva Arouche, Tiago / Neto, Abel Ferreira Gomes / de Castro Ramalho, Teodorico / de Carvalho Júnior, Raul Nunes / de Jesus Chaves Neto, Antonio Maia

Scientific reports

2022 Volume 12, Issue 1, Page(s) 3316

Abstract: The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present ... ...

Abstract	The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present several interactive properties of the phthalocyanines (Pc) of Cobalt (CoPc), Copper (CuPc) and without a metal group (NoPc) can interact with SARS-CoV-2, showing potential be used as filtering by adsorption on paints on walls, masks, clothes, and air conditioning filters. Molecular modeling techniques through Molecular Docking and Molecular Dynamics were used, where the target was the external structures of the virus, but specifically the envelope protein, main protease, and Spike glycoprotein proteases. Using the g_MM-GBSA module and with it, the molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics provided information on the root-mean-square deviation of the atomic positions provided values between 1 and 2.5. The generalized Born implicit solvation model, Gibbs free energy, and solvent accessible surface area approach were used. Among the results obtained through molecular dynamics, it was noticed that interactions occur since Pc could bind to residues of the active site of macromolecules, demonstrating good interactions; in particular with CoPc. Molecular couplings and free energy showed that S-gly active site residues interacted strongly with phthalocyanines with values of - 182.443 kJ/mol (CoPc), 158.954 kJ/mol (CuPc), and - 129.963 kJ/mol (NoPc). The interactions of Pc's with SARS-CoV-2 may predict some promising candidates for antagonists to the virus, which if confirmed through experimental approaches, may contribute to resolving the global crisis of the COVID-19 pandemic.
MeSH term(s)	COVID-19 ; Cobalt/chemistry ; Coordination Complexes/chemistry ; Copper/chemistry ; Humans ; Isoindoles/chemistry ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; SARS-CoV-2/chemistry ; Viral Proteins/chemistry
Chemical Substances	Coordination Complexes ; Isoindoles ; Viral Proteins ; Cobalt (3G0H8C9362) ; Copper (789U1901C5) ; phthalocyanine (V5PUF4VLGY)
Language	English
Publishing date	2022-02-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-07396-w
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Article ; Online: Publisher Correction

Wilson Luna Machado Alencar / Tiago da Silva Arouche / Abel Ferreira Gomes Neto / Teodorico de Castro Ramalho / Raul Nunes de Carvalho Júnior / Antonio Maia de Jesus Chaves Neto

Scientific Reports, Vol 12, Iss 1, Pp 1-

Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics

2022 Volume 1

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Density functional theory for the thermodynamic gas-phase investigation of butanol biofuel and its isomers mixed with gasoline and ethanol.

Martins, Marcelo Gonçalves / da Silva Arouche, Tiago / Neto, Abel Ferreira Gomes / da Cruz, Jorddy Neves / da Costa, Fabio Luiz Paranhos / Fernandes, Lindemberg Lima / de Carvalho Junior, Raul Nunes / da Silva Costa, José Francisco / de Jesus Chaves Neto, Antonio Maia

Journal of molecular modeling

2021 Volume 27, Issue 3, Page(s) 80

Abstract: Herein, we present the results of our study on the thermodynamic properties of the isomers of butanol (n-butanol, 2-butanol, i-butanol, and t-butanol) to evaluate their thermodynamic potential as a complementary biofuel and/or substitute for ethanol and ... ...

Abstract	Herein, we present the results of our study on the thermodynamic properties of the isomers of butanol (n-butanol, 2-butanol, i-butanol, and t-butanol) to evaluate their thermodynamic potential as a complementary biofuel and/or substitute for ethanol and gasoline. The Gaussian09W software was used to perform molecular geometry optimization calculations using density functional theory with the B3lyp hybrid function using the base set 6-311++g(d,p) and the compound methods G3, G4, and CBS-QB3. Calculations of the fundamental frequency of the molecules were performed to obtain the molecular vibration modes for the respective frequencies. These calculations provided thermodynamic parameters such as the entropy, enthalpy, and specific molar heat at constant pressure, all as a function of the temperature. The parameter values obtained by each method were compared to the experimental values available in the literature. The results showed good accuracy, especially those obtained at the B3lyp/6-311++g(d,p) level for n-butanol. The error between the theoretical and experimental values for the combustion enthalpy of n-butanol was less than 4% at 298.15 K; due to the good prediction of its thermodynamic properties, we used n-butanol as a model for the prediction of other thermodynamic properties. We started a molecular docking study of four ligands, namely, n-butanol, ethanol, propanol, heptane, isooctane, and methanol interacting with butanol isomers. The highest values of affinity energy found were for N-butanol. The possible formation of hydrogen bonds, associations by means of London forces, hydrogen, and alkyl interactions were analyzed. n-Butanol was added to ethanol-gasoline mixtures in the temperature range of 298.15 to 600 K and the results suggest that n-butanol has a higher calorific value than gasoline-ethanol mixtures in G30E, G40E, G50E, G60E, G70E, G80E, G90E, and E100 blends. As such, n-butanol releases greater amounts of heat during combustion and is thus a viable alternative to biofuels.
Language	English
Publishing date	2021-02-11
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-021-04681-9
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Article ; Online: Interactions Between Remdesivir, Ribavirin, Favipiravir, Galidesivir, Hydroxychloroquine and Chloroquine with Fragment Molecular of the COVID-19 Main Protease with Inhibitor N3 Complex (PDB ID:6LU7) Using Molecular Docking.

Silva Arouche, Tiago da / Reis, Arthur Ferreira / Martins, Anderson Yuri / S Costa, Jose Francisco / Carvalho Junior, Raul Nunes / J C Neto, Antonio Maia

Journal of nanoscience and nanotechnology

2020 Volume 20, Issue 12, Page(s) 7311–7323

Abstract: We started a study on the molecular docking of six potential pharmacologically active inhibitors compounds that can be used clinically against the COVID-19 virus, in this case, remdesivir, ribavirin, favipiravir, galidesivir, hydroxychloroquine and ... ...

Abstract	We started a study on the molecular docking of six potential pharmacologically active inhibitors compounds that can be used clinically against the COVID-19 virus, in this case, remdesivir, ribavirin, favipiravir, galidesivir, hydroxychloroquine and chloroquine interacting with the main COVID-19 protease in complex with a COVID-19 N3 protease inhibitor. The highest values of affinity energy found in order from highest to lowest were chloroquine (CHL), hydroxychloroquine (HYC), favipiravir (FAV), galidesivir (GAL), remdesivir (REM) and ribavirin (RIB). The possible formation of hydrogen bonds, associations through London forces and permanent electric dipole were analyzed. The values of affinity energy obtained for the hydroxychloroquine ligands was -9.9 kcal/mol and for the chloroquine of -10.8 kcal/mol which indicate that the coupling contributes to an effective improvement of the affinity energies with the protease. Indicating that, the position chosen to make the substitutions may be a pharmacophoric group, and cause changes in the protease.
MeSH term(s)	Adenine/administration & dosage ; Adenine/analogs & derivatives ; Adenine/chemistry ; Adenine/pharmacology ; Adenosine Monophosphate/administration & dosage ; Adenosine Monophosphate/analogs & derivatives ; Adenosine Monophosphate/chemistry ; Adenosine Monophosphate/pharmacology ; Alanine/administration & dosage ; Alanine/analogs & derivatives ; Alanine/chemistry ; Alanine/pharmacology ; Amides/administration & dosage ; Amides/chemistry ; Amides/pharmacology ; Antiviral Agents/administration & dosage ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/enzymology ; Binding Sites ; Chloroquine/administration & dosage ; Chloroquine/chemistry ; Chloroquine/pharmacology ; Coronavirus Infections/drug therapy ; Coronavirus Infections/virology ; Cysteine Endopeptidases/chemistry ; Drug Interactions ; Humans ; Hydrogen Bonding ; Hydroxychloroquine/administration & dosage ; Hydroxychloroquine/chemistry ; Hydroxychloroquine/pharmacology ; Ligands ; Molecular Docking Simulation ; Nanotechnology ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/virology ; Protease Inhibitors/administration & dosage ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Pyrazines/administration & dosage ; Pyrazines/chemistry ; Pyrazines/pharmacology ; Pyrrolidines/administration & dosage ; Pyrrolidines/chemistry ; Pyrrolidines/pharmacology ; Ribavirin/administration & dosage ; Ribavirin/chemistry ; Ribavirin/pharmacology ; Static Electricity ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/chemistry
Chemical Substances	Amides ; Antiviral Agents ; Ligands ; Protease Inhibitors ; Pyrazines ; Pyrrolidines ; Viral Nonstructural Proteins ; remdesivir (3QKI37EEHE) ; Adenosine Monophosphate (415SHH325A) ; Ribavirin (49717AWG6K) ; Hydroxychloroquine (4QWG6N8QKH) ; Chloroquine (886U3H6UFF) ; 3C-like proteinase, Coronavirus (EC 3.4.22.-) ; Cysteine Endopeptidases (EC 3.4.22.-) ; favipiravir (EW5GL2X7E0) ; Adenine (JAC85A2161) ; Alanine (OF5P57N2ZX) ; immucillin A (OLF97F86A7)
Keywords	covid19
Language	English
Publishing date	2020-07-23
Publishing country	United States
Document type	Journal Article
ISSN	1533-4899
ISSN (online)	1533-4899
DOI	10.1166/jnn.2020.18955
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Article ; Online: A Combined Molecular Docking and Density Functional Theory Nuclear Magnetic Resonance Study of Trans-Dehydrocrotonin Interacting with COVID-19 Main Protease and Severe Acute Respiratory Syndrome Coronavirus 2 3C-Like Protease.

Cardoso, Evani Ferreira / Giacomello, Thaís Forest / Rocha de Oliveira, Leandro Leal / da Silva, Tiago Arouche / de Jesus Chaves Neto, Antonio Maia / Da Silva Mota, Gunar Vingre / Souza Siqueira, Marcelo Ricardo / Paranhos Costa, Fabio Luiz

Journal of nanoscience and nanotechnology

2021 Volume 21, Issue 11, Page(s) 5399–5407

Abstract: For the development of drugs that treat SARS-CoV-2, the fastest way is to find potential molecules from drugs already on the market. Unfortunately, there is currently no specific drug or treatment for COVID-19. Among all structural proteins in SARS-CoV, ... ...

Abstract	For the development of drugs that treat SARS-CoV-2, the fastest way is to find potential molecules from drugs already on the market. Unfortunately, there is currently no specific drug or treatment for COVID-19. Among all structural proteins in SARS-CoV, the spike protein is the main antigenic component responsible for inducing host immune responses, neutralizing antibodies, and/or protecting immunity against virus infection. Molecular docking is a technique used to predict whether a molecule will bind to another. It is usually a protein to another or a protein to a binding compound. Natural products are potential binders in several studies involving coronavirus. The structure of the ligand plays a fundamental role in its biological properties. The nuclear magnetic resonance technique is one of the most powerful tools for the structural determination of ligands from the origin of natural products. Nowadays, molecular modeling is an important accessory tool to experimentally got nuclear magnetic resonance data. In the present work, molecular docking studies aimed is to investigate the limiting affinities of trans-dehydrocrotonin molecule and to identify the main amino acid residues that could play a fundamental role in their mechanism of action of the SARS-CoV spike protein. Another aim of this work is all about to evaluate 10 hybrid functionalities, along with three base pairs using computational programs to discover which ones are more reliable with the experimental result the best computational method to study organic compounds. We compared the results between the mean absolute deviation (MAD) and root-mean-square deviation (RMSD) of the molecules, and the smallest number between them was the best result. The positions assumed by the ligands in the active site of the spike glycoprotein allow assuming associations with different local amino acids.
MeSH term(s)	Antiviral Agents ; COVID-19 ; Density Functional Theory ; Diterpenes, Clerodane ; Humans ; Magnetic Resonance Spectroscopy ; Molecular Docking Simulation ; Peptide Hydrolases ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Diterpenes, Clerodane ; dehydrocrotonin ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2021-05-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1533-4899
ISSN (online)	1533-4899
DOI	10.1166/jnn.2021.19475
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Article ; Online: Molecular Docking of Azithromycin, Ritonavir, Lopinavir, Oseltamivir, Ivermectin and Heparin Interacting with Coronavirus Disease 2019 Main and Severe Acute Respiratory Syndrome Coronavirus-2 3C-Like Proteases.

Arouche, Tiago da Silva / Martins, Anderson Yuri / Ramalho, Teodorico de Castro / Júnior, Raul Nunes Carvalho / Costa, Fabio Luiz Paranhos / Filho, Tarciso Silva de Andrade / Neto, Antonio Maia Jesus Chaves

Journal of nanoscience and nanotechnology

2021 Volume 21, Issue 4, Page(s) 2075–2089

Abstract: In the current pandemic situation raised due to COVID-19, drug reuse is emerging as the first line of treatment. The viral agent that causes this highly contagious disease and the acute respiratory syndrome coronavirus (SARS-CoV) share high nucleotide ... ...

Abstract	In the current pandemic situation raised due to COVID-19, drug reuse is emerging as the first line of treatment. The viral agent that causes this highly contagious disease and the acute respiratory syndrome coronavirus (SARS-CoV) share high nucleotide similarity. Therefore, it is structurally expected that many existing viral targets are similar to the first SARS-CoV, probably being inhibited by the same compounds. Here, we selected two viral proteins based on their vital role in the viral life cycle: Structure of the main protease SARS-CoV-2 and the structural base of the SARS-CoV-2 protease 3CL, both supporting the entry of the virus into the human host. The approved drugs used were azithromycin, ritonavir, lopinavir, oseltamivir, ivermectin and heparin, which are emerging as promising agents in the fight against COVID-19. Our hypothesis behind molecular coupling studies is to determine the binding affinities of these drugs and to identify the main amino acid residues that play a fundamental role in their mechanism of action. Additional studies on a wide range of FDA-approved drugs, including a few more protein targets, molecular dynamics studies,
MeSH term(s)	Azithromycin/chemistry ; COVID-19/enzymology ; Coronavirus 3C Proteases/chemistry ; Heparin/chemistry ; Humans ; Ivermectin/chemistry ; Lopinavir/chemistry ; Molecular Docking Simulation ; Oseltamivir/chemistry ; Ritonavir/chemistry ; SARS-CoV-2/enzymology
Chemical Substances	Oseltamivir (20O93L6F9H) ; Lopinavir (2494G1JF75) ; Ivermectin (70288-86-7) ; Azithromycin (83905-01-5) ; Heparin (9005-49-6) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Ritonavir (O3J8G9O825)
Language	English
Publishing date	2021-01-26
Publishing country	United States
Document type	Journal Article
ISSN	1533-4899
ISSN (online)	1533-4899
DOI	10.1166/jnn.2021.19029
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Article ; Online: Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics

Wilson Luna Machado Alencar / Tiago da Silva Arouche / Abel Ferreira Gomes Neto / Teodorico de Castro Ramalho / Raul Nunes de Carvalho Júnior / Antonio Maia de Jesus Chaves Neto

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 20

Abstract: Abstract The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they ...

Abstract	Abstract The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present several interactive properties of the phthalocyanines (Pc) of Cobalt (CoPc), Copper (CuPc) and without a metal group (NoPc) can interact with SARS-CoV-2, showing potential be used as filtering by adsorption on paints on walls, masks, clothes, and air conditioning filters. Molecular modeling techniques through Molecular Docking and Molecular Dynamics were used, where the target was the external structures of the virus, but specifically the envelope protein, main protease, and Spike glycoprotein proteases. Using the g_MM-GBSA module and with it, the molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics provided information on the root-mean-square deviation of the atomic positions provided values between 1 and 2.5. The generalized Born implicit solvation model, Gibbs free energy, and solvent accessible surface area approach were used. Among the results obtained through molecular dynamics, it was noticed that interactions occur since Pc could bind to residues of the active site of macromolecules, demonstrating good interactions; in particular with CoPc. Molecular couplings and free energy showed that S-gly active site residues interacted strongly with phthalocyanines with values of − 182.443 kJ/mol (CoPc), 158.954 kJ/mol (CuPc), and − 129.963 kJ/mol (NoPc). The interactions of Pc's with SARS-CoV-2 may predict some promising candidates for antagonists to the virus, which if confirmed through experimental approaches, may contribute to resolving the global crisis of the COVID-19 pandemic.
Keywords	Medicine ; R ; Science ; Q
Subject code	541
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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