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Article: The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus.

García-Machorro, Jazmín / Ramírez-Salinas, Gema Lizbeth / Martinez-Archundia, Marlet / Correa-Basurto, José

2022 Volume 10, Issue 11

Abstract: After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. ... ...

Abstract	After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines.
Language	English
Publishing date	2022-10-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines10111844
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Two MP2CL5 Antigen Vaccines from Naegleria fowleri Stimulate the Immune Response against Meningitis in the BALB/c Model.

Gutiérrez-Sánchez, Mara / Carrasco-Yépez, María Maricela / Correa-Basurto, José / Ramírez-Salinas, Gema Lizbeth / Rojas-Hernández, Saúl

Infection and immunity

2023 Volume 91, Issue 7, Page(s) e0018123

Abstract: Naegleria fowleri is an etiological agent that generates primary amoebic meningoencephalitis; unfortunately, no effective treatment or vaccine is available. The objective of this work was to determine the immunoprotective response of two vaccine antigens, ...

Abstract	Naegleria fowleri is an etiological agent that generates primary amoebic meningoencephalitis; unfortunately, no effective treatment or vaccine is available. The objective of this work was to determine the immunoprotective response of two vaccine antigens, as follows: (i) the polypeptide band of 19 kDa or (ii) a predicted immunogenic peptide from the membrane protein MP2CL5 (Smp145). Both antigens were administered intranasally in mice using cholera toxin (CT) as an adjuvant. The survival rate and immune response of immunized mice with both antigens and challenged with N. fowleri trophozoites were measured in the nose-associated lymphoid tissue (NALT) and nasal passages (NPs) by flow cytometry and enzyme-linked immunosorbent assay (ELISA). We also determined the immunolocalization of both antigens in N. fowleri trophozoites by confocal microscopy. Immunization with the polypeptide band of 19 kDa alone or coadministered with CT was able to confer 80% and 100% of protection, respectively. The immunization with both antigens (alone or coadministered with CT) showed an increase in T and B lymphocytes. In addition, there was an increase in the expression of integrin α4β1 and IgA in the nasal cavity of protected mice, and the IgA, IgG, and IgM levels were increased in serum and nasal washes. The immunolocalization of both antigens in N. fowleri trophozoites was observed in the plasma membrane, specifically in pseudopod-like structures. The MP2CL5 antigens evaluated in this work were capable of conferring protection which would lead us to consider them as potential candidates for vaccines against meningitis caused by N. fowleri.
MeSH term(s)	Animals ; Mice ; Naegleria fowleri ; Cholera Toxin ; Vaccines ; Meningitis ; Immunity ; Immunoglobulin A
Chemical Substances	Cholera Toxin (9012-63-9) ; Vaccines ; Immunoglobulin A
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218698-6
ISSN	1098-5522 ; 0019-9567
ISSN (online)	1098-5522
ISSN	0019-9567
DOI	10.1128/iai.00181-23
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Article ; Online: The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus

Jazmín García-Machorro / Gema Lizbeth Ramírez-Salinas / Marlet Martinez-Archundia / José Correa-Basurto

Vaccines, Vol 10, Iss 1844, p

2022 Volume 1844

Abstract	After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines.
Keywords	SARS-CoV-2 ; COVID-19 ; bioinformatics ; immunoinformatics ; epitope ; vaccine ; Medicine ; R
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Repositioning of Ligands That Target the Spike Glycoprotein as Potential Drugs for SARS-CoV-2 in an In Silico Study.

Ramírez-Salinas, Gema Lizbeth / Martínez-Archundia, Marlet / Correa-Basurto, José / García-Machorro, Jazmín

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 23

Abstract: The worldwide health emergency of the SARS-CoV-2 pandemic and the absence of a specific treatment for this new coronavirus have led to the use of computational strategies (drug repositioning) to search for treatments. The aim of this work is to identify ... ...

Abstract	The worldwide health emergency of the SARS-CoV-2 pandemic and the absence of a specific treatment for this new coronavirus have led to the use of computational strategies (drug repositioning) to search for treatments. The aim of this work is to identify FDA (Food and Drug Administration)-approved drugs with the potential for binding to the spike structural glycoprotein at the hinge site, receptor binding motif (RBM), and fusion peptide (FP) using molecular docking simulations. Drugs that bind to amino acids are crucial for conformational changes, receptor recognition, and fusion of the viral membrane with the cell membrane. The results revealed some drugs that bind to hinge site amino acids (varenicline, or steroids such as betamethasone while other drugs bind to crucial amino acids in the RBM (naldemedine, atovaquone, cefotetan) or FP (azilsartan, maraviroc, and difluprednate); saquinavir binds both the RBM and the FP. Therefore, these drugs could inhibit spike glycoprotein and prevent viral entry as possible anti-COVID-19 drugs. Several drugs are in clinical studies; by focusing on other pharmacological agents (candesartan, atovaquone, losartan, maviroc and ritonavir) in this work we propose an additional target: the spike glycoprotein. These results can impact the proposed use of treatments that inhibit the first steps of the virus replication cycle.
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Computer Simulation ; Drug Repositioning/methods ; Ligands ; Membrane Fusion/drug effects ; Models, Molecular ; Molecular Docking Simulation ; Protein Conformation ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Varenicline/chemistry ; Varenicline/metabolism ; Varenicline/pharmacology
Chemical Substances	Antiviral Agents ; Ligands ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Varenicline (W6HS99O8ZO)
Language	English
Publishing date	2020-11-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules25235615
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Article ; Online: Immunoinformatics study to search epitopes of spike glycoprotein from SARS-CoV-2 as potential vaccine.

Lizbeth, Ramírez-Salinas Gema / Jazmín, García-Machorro / José, Correa-Basurto / Marlet, Martínez-Archundia

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 13, Page(s) 4878–4892

Abstract: The Coronavirus disease named COVID-19 is caused by the virus reported in 2019 first identified in China. The cases of this disease have increased and as of June ... ...

Abstract	The Coronavirus disease named COVID-19 is caused by the virus reported in 2019 first identified in China. The cases of this disease have increased and as of June 1
MeSH term(s)	COVID-19 ; COVID-19 Vaccines/immunology ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Glycoproteins ; Humans ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/immunology
Chemical Substances	COVID-19 Vaccines ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Glycoproteins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-06-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1780944
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Zs.A 2093: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: The β

Roldán, María Luisa / Ramírez-Salinas, Gema Lizbeth / Martinez-Archundia, Marlet / Cuellar-Perez, Francisco / Vilchis-Nestor, Claudia Andrea / Cancino-Diaz, Juan Carlos / Shoshani, Liora

International journal of molecular sciences

2022 Volume 23, Issue 14

Abstract: ... The ... ...

Abstract	The β
MeSH term(s)	Adenosine Triphosphatases/metabolism ; Animals ; CHO Cells ; Cation Transport Proteins/metabolism ; Cell Adhesion ; Cell Adhesion Molecules/metabolism ; Cell Adhesion Molecules, Neuronal/metabolism ; Cricetinae ; Cricetulus ; Dogs ; Humans ; Sodium/metabolism ; Sodium-Potassium-Exchanging ATPase/metabolism
Chemical Substances	ATP1B2 protein, human ; Cation Transport Proteins ; Cell Adhesion Molecules ; Cell Adhesion Molecules, Neuronal ; Sodium (9NEZ333N27) ; Adenosine Triphosphatases (EC 3.6.1.-) ; Sodium-Potassium-Exchanging ATPase (EC 7.2.2.13)
Language	English
Publishing date	2022-07-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23147753
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Article ; Online: Repositioning of Ligands That Target the Spike Glycoprotein as Potential Drugs for SARS-CoV-2 in an In Silico Study

Gema Lizbeth Ramírez-Salinas / Marlet Martínez-Archundia / José Correa-Basurto / Jazmín García-Machorro

Molecules, Vol 25, Iss 5615, p

2020 Volume 5615

Abstract	The worldwide health emergency of the SARS-CoV-2 pandemic and the absence of a specific treatment for this new coronavirus have led to the use of computational strategies (drug repositioning) to search for treatments. The aim of this work is to identify FDA (Food and Drug Administration)-approved drugs with the potential for binding to the spike structural glycoprotein at the hinge site, receptor binding motif (RBM), and fusion peptide (FP) using molecular docking simulations. Drugs that bind to amino acids are crucial for conformational changes, receptor recognition, and fusion of the viral membrane with the cell membrane. The results revealed some drugs that bind to hinge site amino acids (varenicline, or steroids such as betamethasone while other drugs bind to crucial amino acids in the RBM (naldemedine, atovaquone, cefotetan) or FP (azilsartan, maraviroc, and difluprednate); saquinavir binds both the RBM and the FP. Therefore, these drugs could inhibit spike glycoprotein and prevent viral entry as possible anti-COVID-19 drugs. Several drugs are in clinical studies; by focusing on other pharmacological agents (candesartan, atovaquone, losartan, maviroc and ritonavir) in this work we propose an additional target: the spike glycoprotein. These results can impact the proposed use of treatments that inhibit the first steps of the virus replication cycle.
Keywords	SARS-CoV-2 ; COVID-19 ; docking studies ; FDA-approved drugs ; spike glycoprotein ; Organic chemistry ; QD241-441
Subject code	500
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Immunoinformatics study to search epitopes of spike glycoprotein from SARS-CoV-2 as potential vaccine

Lizbeth, Ramírez-Salinas Gema / Jazmín, García-Machorro / José, Correa-Basurto / Marlet, Martínez-Archundia

Journal of Biomolecular Structure and Dynamics

2020 , Page(s) 1–15

Keywords	Molecular Biology ; Structural Biology ; General Medicine ; covid19
Language	English
Publisher	Informa UK Limited
Publishing country	uk
Document type	Article ; Online
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1780944
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Zs.A 2093: Show issues

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Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article: In Silico Screening of Drugs That Target Different Forms of E Protein for Potential Treatment of COVID-19.

Ramírez Salinas, Gema Lizbeth / López Rincón, Alejandro / García Machorro, Jazmín / Correa Basurto, José / Martínez Archundia, Marlet

Pharmaceuticals (Basel, Switzerland)

2023 Volume 16, Issue 2

Abstract: Recently the E protein of SARS-CoV-2 has become a very important target in the potential treatment of COVID-19 since it is known to regulate different stages of the viral cycle. There is biochemical evidence that E protein exists in two forms, as monomer ...

Abstract	Recently the E protein of SARS-CoV-2 has become a very important target in the potential treatment of COVID-19 since it is known to regulate different stages of the viral cycle. There is biochemical evidence that E protein exists in two forms, as monomer and homopentamer. An in silico screening analysis was carried out employing 5852 ligands (from Zinc databases), and performing an ADMET analysis, remaining a set of 2155 compounds. Furthermore, docking analysis was performed on specific sites and different forms of the E protein. From this study we could identify that the following ligands showed the highest binding affinity: nilotinib, dutasteride, irinotecan, saquinavir and alectinib. We carried out some molecular dynamics simulations and free energy MM-PBSA calculations of the protein-ligand complexes (with the mentioned ligands). Of worthy interest is that saquinavir, nilotinib and alectinib are also considered as a promising multitarget ligand because it seems to inhibit three targets, which play an important role in the viral cycle. On the other side, saquinavir was shown to be able to bind to E protein both in its monomeric as well as pentameric forms. Finally, further experimental assays are needed to probe our hypothesis derived from in silico studies.
Language	English
Publishing date	2023-02-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph16020296
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Article ; Online: Theophylline: Old Drug in a New Light, Application in COVID-19 through Computational Studies.

Montaño, Luis M / Sommer, Bettina / Gomez-Verjan, Juan C / Morales-Paoli, Genaro S / Ramírez-Salinas, Gema Lizbeth / Solís-Chagoyán, Héctor / Sanchez-Florentino, Zuly A / Calixto, Eduardo / Pérez-Figueroa, Gloria E / Carter, Rohan / Jaimez-Melgoza, Ruth / Romero-Martínez, Bianca S / Flores-Soto, Edgar

International journal of molecular sciences

2022 Volume 23, Issue 8

Abstract: Theophylline (3-methyxanthine) is a historically prominent drug used to treat respiratory diseases, alone or in combination with other drugs. The rapid onset of the COVID-19 pandemic urged the development of effective pharmacological treatments to ... ...

Abstract	Theophylline (3-methyxanthine) is a historically prominent drug used to treat respiratory diseases, alone or in combination with other drugs. The rapid onset of the COVID-19 pandemic urged the development of effective pharmacological treatments to directly attack the development of new variants of the SARS-CoV-2 virus and possess a therapeutical battery of compounds that could improve the current management of the disease worldwide. In this context, theophylline, through bronchodilatory, immunomodulatory, and potentially antiviral mechanisms, is an interesting proposal as an adjuvant in the treatment of COVID-19 patients. Nevertheless, it is essential to understand how this compound could behave against such a disease, not only at a pharmacodynamic but also at a pharmacokinetic level. In this sense, the quickest approach in drug discovery is through different computational methods, either from network pharmacology or from quantitative systems pharmacology approaches. In the present review, we explore the possibility of using theophylline in the treatment of COVID-19 patients since it seems to be a relevant candidate by aiming at several immunological targets involved in the pathophysiology of the disease. Theophylline down-regulates the inflammatory processes activated by SARS-CoV-2 through various mechanisms, and herein, they are discussed by reviewing computational simulation studies and their different applications and effects.
MeSH term(s)	Antiviral Agents/pharmacokinetics ; Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; Humans ; Molecular Docking Simulation ; Pandemics ; SARS-CoV-2 ; Theophylline/pharmacology ; Theophylline/therapeutic use
Chemical Substances	Antiviral Agents ; Theophylline (C137DTR5RG)
Language	English
Publishing date	2022-04-09
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23084167
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