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Article: Omicron SARS-CoV-2 Variant Spike Protein Shows an Increased Affinity to the Human ACE2 Receptor: An In Silico Analysis.

Ortega, Joseph Thomas / Jastrzebska, Beata / Rangel, Hector Rafael

2021 Volume 11, Issue 1

Abstract: The rise of SARS-CoV-2 variants, with changes that could be related to an increased virus pathogenicity, have received the interest of the scientific and medical community. In this study, we evaluated the changes that occurred in the viral spike of the ... ...

Abstract	The rise of SARS-CoV-2 variants, with changes that could be related to an increased virus pathogenicity, have received the interest of the scientific and medical community. In this study, we evaluated the changes that occurred in the viral spike of the SARS-CoV-2 Omicron variant and whether these changes modulate the interactions with the angiotensin-converting enzyme 2 (ACE2) host receptor. The mutations associated with the Omicron variant were retrieved from the GISAID and covariants.org databases, and a structural model was built using the SWISS-Model server. The interaction between the spike and the human ACE2 was evaluated using two different docking software, Zdock and Haddock. We found that the binding free energy was lower for the Omicron variant as compared to the WT spike. In addition, the Omicron spike protein showed an increased number of electrostatic interactions with ACE2 than the WT spike, especially the interactions related to charged residues. This study contributes to a better understanding of the changes in the interaction between the Omicron spike and the human host ACE2 receptor.
Language	English
Publishing date	2021-12-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11010045
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Omicron SARS-CoV-2 Variant Spike Protein Shows an Increased Affinity to the Human ACE2 Receptor: An In Silico Analysis

Ortega, Joseph Thomas / Jastrzebska, Beata / Rangel, Hector Rafael

Pathogens. 2021 Dec. 31, v. 11, no. 1

2021

Abstract	The rise of SARS-CoV-2 variants, with changes that could be related to an increased virus pathogenicity, have received the interest of the scientific and medical community. In this study, we evaluated the changes that occurred in the viral spike of the SARS-CoV-2 Omicron variant and whether these changes modulate the interactions with the angiotensin-converting enzyme 2 (ACE2) host receptor. The mutations associated with the Omicron variant were retrieved from the GISAID and covariants.org databases, and a structural model was built using the SWISS-Model server. The interaction between the spike and the human ACE2 was evaluated using two different docking software, Zdock and Haddock. We found that the binding free energy was lower for the Omicron variant as compared to the WT spike. In addition, the Omicron spike protein showed an increased number of electrostatic interactions with ACE2 than the WT spike, especially the interactions related to charged residues. This study contributes to a better understanding of the changes in the interaction between the Omicron spike and the human host ACE2 receptor.
Keywords	Gibbs free energy ; Severe acute respiratory syndrome coronavirus 2 ; computer simulation ; computer software ; haddock ; humans ; models ; pathogenicity ; peptidyl-dipeptidase A ; viruses
Language	English
Dates of publication	2021-1231
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11010045
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Lasting SARS-CoV-2 specific IgG Antibody response in health care workers from Venezuela, 6 months after vaccination with Sputnik V.

Claro, Franklin / Silva, Douglas / Pérez Bogado, Jesús A / Rangel, Hector Rafael / de Waard, Jacobus H

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2022 Volume 122, Page(s) 850–854

Abstract: Background: Scarce information is available regarding the long-term immunogenicity of the Sputnik V vaccine. Here Sputnik V vaccinated subjects were evaluated 6 months after receiving the 2-dose prime-boost schedule.: Methods: Eighty-six hospital ... ...

Abstract	Background: Scarce information is available regarding the long-term immunogenicity of the Sputnik V vaccine. Here Sputnik V vaccinated subjects were evaluated 6 months after receiving the 2-dose prime-boost schedule. Methods: Eighty-six hospital workers from Venezuela, 32 with a previous COVID-19 infection and 54 SARS-CoV-2 naïve subjects, were enrolled. IgG antibodies levels against the wild-type Receptor Binding Domain (RBD) were measured in an ELISA and with an in vitro ACE2-surrogate RBD binding inhibition assay at day 42 and day 180 after receiving the second dose. IgG levels were expressed in BAU/ml. Binding inhibition antibodies were expressed in IU/ml. Results: On average, RBD-IgG levels decreased by approximately 50% between the two time-points in the COVID-19 naïve cohort (geometric mean concentration (GMC) 675 BAU/mL vs. 327 BAU/ml) and decreased by approximately 25% in the previously infected cohort (GMC 1209 BAU/mL vs 910 BAU/ml). Within our cohort, 94% showed a "good to excellent" neutralizing activity measured with the in vitro test 6 months after vaccination. Conclusions: The Sputnik V vaccine provided long-term and durable humoral immunity in our cohort specially if a person has been both vaccinated and had a previous infection with SARS-CoV-2.
MeSH term(s)	Animals ; Antibodies, Viral ; Antibody Formation ; COVID-19/prevention & control ; Health Personnel ; Humans ; Immunoglobulin G ; Mice ; Mice, Inbred BALB C ; SARS-CoV-2 ; Vaccination ; Venezuela ; Viral Vaccines
Chemical Substances	Antibodies, Viral ; Immunoglobulin G ; Viral Vaccines
Language	English
Publishing date	2022-06-08
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2022.06.008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Unrevealing sequence and structural features of novel coronavirus using

Ortega, Joseph Thomas / Serrano, Maria Luisa / Pujol, Flor Helene / Rangel, Hector Rafael

EXCLI journal

2020 Volume 19, Page(s) 400–409

Abstract: Direct-acting antivirals are effective tools to control viral infections. SARS-CoV-2 is a coronavirus associated with the epidemiological outbreak in late 2019. Previous reports showed that HIV-1 protease inhibitors could block SARS-CoV main protease. ... ...

Abstract	Direct-acting antivirals are effective tools to control viral infections. SARS-CoV-2 is a coronavirus associated with the epidemiological outbreak in late 2019. Previous reports showed that HIV-1 protease inhibitors could block SARS-CoV main protease. Based on that and using an
Keywords	covid19
Language	English
Publishing date	2020-03-17
Publishing country	Germany
Document type	Journal Article
ISSN	1611-2156
ISSN	1611-2156
DOI	10.17179/excli2020-1189
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An

Ortega, Joseph Thomas / Serrano, Maria Luisa / Pujol, Flor Helene / Rangel, Hector Rafael

EXCLI journal

2020 Volume 19, Page(s) 410–417

Abstract: Many human viral diseases are a consequence of a zoonotic event. Some of the diseases caused by these zoonotic events have affected millions of people around the world, some of which have resulted in high rates of morbidity/mortality in humans. Changes ... ...

Abstract	Many human viral diseases are a consequence of a zoonotic event. Some of the diseases caused by these zoonotic events have affected millions of people around the world, some of which have resulted in high rates of morbidity/mortality in humans. Changes in the viral proteins that function as ligands of the host receptor may promote the spillover between species. The most recent of these zoonotic events that have caused an ongoing epidemic of high magnitude is the Covid-19 epidemics caused by SARS-CoV-2. The aim of this study was to determine the mutation(s) in the sequence of the spike protein of the SARS-CoV-2 that might be favoring human to human transmission. An
Keywords	covid19
Language	English
Publishing date	2020-03-18
Publishing country	Germany
Document type	Journal Article
ISSN	1611-2156
ISSN	1611-2156
DOI	10.17179/excli2020-1167
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Immunoglobulin G antibody response to the Sputnik V vaccine: previous SARS-CoV-2 seropositive individuals may need just one vaccine dose.

Claro, Franklin / Silva, Douglas / Rodriguez, Melissa / Rangel, Hector Rafael / de Waard, Jacobus H

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2021 Volume 111, Page(s) 261–266

Abstract: Introduction: We evaluated the immunoglobulin (Ig) G antibody response against the nucleocapsid protein (NP) and the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 in a cohort of 86 individuals in Venezuela, before and after receiving ... ...

Abstract	Introduction: We evaluated the immunoglobulin (Ig) G antibody response against the nucleocapsid protein (NP) and the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 in a cohort of 86 individuals in Venezuela, before and after receiving the Sputnik V vaccine. Methods: Antibody responses against NP and RBD were determined with an enzyme-linked immunosorbent assay just before, 3 weeks after the first, and 6 weeks after the second dose of the vaccine. Results: Before vaccination, 59 individuals were seronegative, and 27 seropositive for NP and/or RBD. Of the seronegative cohort, 42% did not develop an IgG immune response against RBD after the first vaccine dose, but 100% had a strong IgG response after 2 doses. All seropositive individuals developed a strong IgG antibody response against RBD after the first vaccine dose, with antibody levels ∼40% higher than seronegative individuals who had received 2 doses. Previously seropositive subjects showed no significant increase in IgG antibody response against RBD after the second vaccine dose. Conclusions: We demonstrate that 2 doses of the Sputnik V vaccine triggered antibody response in all study individuals. The second Sputnik V dose had no impact on IgG response for those seropositive for SARS-CoV-2 antigens before vaccination.
MeSH term(s)	Antibodies, Viral ; Antibody Formation ; COVID-19 ; Humans ; Immunoglobulin G ; SARS-CoV-2 ; Vaccines
Chemical Substances	Antibodies, Viral ; Immunoglobulin G ; Vaccines
Language	English
Publishing date	2021-07-31
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2021.07.070
Database	MEDical Literature Analysis and Retrieval System OnLINE

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bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Neutralization of Different Variants of SARS-CoV-2 by a F(ab')2 Preparation from Sera of Horses Immunized with the Viral Receptor Binding Domain.

Rodriguez-Nuñez, Mariajosé / Cepeda, Mariana Del Valle / Bello, Carlos / Lopez, Miguel Angel / Sulbaran, Yoneira / Loureiro, Carmen Luisa / Liprandi, Ferdinando / Jaspe, Rossana Celeste / Pujol, Flor Helene / Rangel, Héctor Rafael

Antibodies (Basel, Switzerland)

2023 Volume 12, Issue 4

Abstract: The Receptor Binding Domain (RBD) of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is the functional region of the viral Spike protein (S), which is involved in cell attachment to target cells. The virus has accumulated progressively ... ...

Abstract	The Receptor Binding Domain (RBD) of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is the functional region of the viral Spike protein (S), which is involved in cell attachment to target cells. The virus has accumulated progressively mutations in its genome, particularly in the RBD region, many of them associated with immune evasion of the host neutralizing antibodies. Some of the viral lineages derived from this evolution have been classified as Variant of Interest (VOI) or Concern (VOC). The neutralizing capacity of a F(ab')2 preparation from sera of horses immunized with viral RBD was evaluated by lytic plaque reduction assay against different SARS-CoV-2 variants. A F(ab')2 preparation of a hyperimmune serum after nine immunizations with RBD exhibited a high titer of neutralizing antibodies against the ancestral-like strain (1/18,528). A reduction in the titer of the F(ab')2 preparation was observed against the different variants tested compared to the neutralizing activity against the ancestral-like strain. The highest reduction in the neutralization titer was observed for the Omicron VOC (4.7-fold), followed by the Mu VOI (2.6), Delta VOC (1.8-fold), and Gamma VOC (1.5). Even if a progressive reduction in the neutralizing antibodies titer against the different variants evaluated was observed, the serum still exhibited a neutralizing titer against the Mu VOI and the Omicron VOC (1/7113 and 1/3918, respectively), the evaluated strains most resistant to neutralization. Therefore, the preparation retained neutralizing activity against all the strains tested.
Language	English
Publishing date	2023-12-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661514-9
ISSN	2073-4468 ; 2073-4468
ISSN (online)	2073-4468
ISSN	2073-4468
DOI	10.3390/antib12040080
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: An in silico analysis

Ortega, Joseph Thomas / Serrano, Maria Luisa / Pujol, Flor Helene / Rangel, Hector Rafael

EXCLI J.

Abstract	Many human viral diseases are a consequence of a zoonotic event. Some of the diseases caused by these zoonotic events have affected millions of people around the world, some of which have resulted in high rates of mor-bidity/mortality in humans. Changes in the viral proteins that function as ligands of the host receptor may promote the spillover between species. The most recent of these zoonotic events that have caused an ongoing epidemic of high magnitude is the Covid-19 epidemics caused by SARS-CoV-2. The aim of this study was to determine the mutation(s) in the sequence of the spike protein of the SARS-CoV-2 that might be favoring human to human transmission. An in silico approach was performed, and changes were detected in the S1 subunit of the receptor-binding domain of spike. The observed changes have significant effect on SARS-CoV-2 spike/ACE2 interaction and produce a reduction in the binding energy, compared to the one of the Bat-CoV to this receptor. The data presented in this study suggest a higher affinity of the SARS-Cov-2 spike protein to the human ACE2 receptor, compared to the one of Bat-CoV spike and ACE2. This could be the cause of the rapid viral spread of SARS-CoV-2 in humans.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #18568
Database	COVID19

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Article: Unrevealing sequence and structural features of novel coronavirus using in silico approaches: The main protease as molecular target

Ortega, Joseph Thomas / Serrano, Maria Luisa / Pujol, Flor Helene / Rangel, Hector Rafael

EXCLI J.

Abstract	Direct-acting antivirals are effective tools to control viral infections. SARS-CoV-2 is a coronavirus associated with the epidemiological outbreak in late 2019. Previous reports showed that HIV-1 protease inhibitors could block SARS-CoV main protease. Based on that and using an in silico approach, we evaluated SARS-CoV-2 main protease as a target for HIV-1 protease inhibitors to reveal the structural features related to their antiviral effect. Our results showed that several HIV inhibitors such as lopinavir, ritonavir, and saquinavir produce strong interaction with the active site of SARS-CoV-2 main protease. Furthermore, broad library protease inhibitors obtained from PubChem and ZINC (www.zinc.docking.org) were evaluated. Our analysis revealed 20 compounds that could be clustered into three groups based on their chemical features. Then, these structures could serve as leading compounds to develop a series of derivatives optimizing their activity against SARS-CoV-2 and other coronaviruses. Altogether, the results presented in this work contribute to gain a deep understanding of the molecular pharmacology of SARS-CoV-2 treatment and validate the use of protease inhibitors against SARS-CoV-2.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #18567
Database	COVID19

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Article: Molecular characteristics and replication mechanism of dengue, zika and chikungunya arboviruses, and their treatments with natural extracts from plants: An updated review.

Rodriguez, Anny Karely / Muñoz, Ana Luisa / Segura, Nidya Alexandra / Rangel, Héctor Rafael / Bello, Felio

EXCLI journal

2019 Volume 18, Page(s) 988–1006

Abstract: Viruses transmitted by arthropods (arboviruses) are the etiological agents of several human diseases with worldwide distribution; including dengue (DENV), zika (ZIKV), yellow fever (YFV), and chikungunya (CHIKV) viruses. These viruses are especially ... ...

Abstract	Viruses transmitted by arthropods (arboviruses) are the etiological agents of several human diseases with worldwide distribution; including dengue (DENV), zika (ZIKV), yellow fever (YFV), and chikungunya (CHIKV) viruses. These viruses are especially important in tropical and subtropical regions; where, ZIKV and CHIKV are involved in epidemics worldwide, while the DENV remains as the biggest problem in public health. Factors, such as, environmental conditions promote the distribution of vectors, deficiencies in health services, and lack of effective vaccines, guarantee the presence of these vector-borne diseases. Treatment against these viral diseases is only palliative since available therapies formulated lack to demonstrate specific antiviral activity and vaccine candidates fail to demonstrate enough effectiveness. The use of natural products, as therapeutic tools, is an ancestral practice in different cultures. According to WHO 80 % of the population of some countries from Africa and Asia depend on the use of traditional medicines to deal with some diseases. Molecular characteristics of these viruses are important in determining its cellular pathogenesis, emergence, and dispersion mechanisms, as well as for the development of new antivirals and vaccines to control strategies. In this review, we summarize the current knowledge of the molecular structure and replication mechanisms of selected arboviruses, as well as their mechanism of entry into host cells, and a brief overview about the potential targets accessed to inhibit these viruses
Language	English
Publishing date	2019-10-31
Publishing country	Germany
Document type	Journal Article ; Review
ISSN	1611-2156
ISSN	1611-2156
DOI	10.17179/excli2019-1825
Database	MEDical Literature Analysis and Retrieval System OnLINE

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