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Article ; Online: Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1).

de Souza, Anacleto Silva / de Souza, Robson Francisco / Guzzo, Cristiane Rodrigues

Journal of computer-aided molecular design

2023 Volume 37, Issue 12, Page(s) 585–606

Abstract: Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. ...

Abstract	Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the Spike
MeSH term(s)	Humans ; Antibodies, Neutralizing ; COVID-19 ; Hydrogen Bonding ; Linear Models ; Mutation
Chemical Substances	Antibodies, Neutralizing
Language	English
Publishing date	2023-10-04
Publishing country	Netherlands
Document type	Editorial ; Research Support, Non-U.S. Gov't
ZDB-ID	808166-9
ISSN	1573-4951 ; 0920-654X
ISSN (online)	1573-4951
ISSN	0920-654X
DOI	10.1007/s10822-023-00534-0
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Article ; Online: Molecular dynamics simulations of the spike trimeric ectodomain of the SARS-CoV-2 Omicron variant: structural relationships with infectivity, evasion to immune system and transmissibility.

de Souza, Anacleto Silva / Amorim, Vitor Martins de Freitas / de Souza, Robson Francisco / Guzzo, Cristiane Rodrigues

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 19, Page(s) 9326–9343

Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron is currently the most prevalent SARS-CoV-2 variant worldwide. Herein, we calculated molecular dynamics simulations of the trimeric ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron is currently the most prevalent SARS-CoV-2 variant worldwide. Herein, we calculated molecular dynamics simulations of the trimeric spike
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Molecular Dynamics Simulation ; COVID-19 ; Immune System ; Mutation
Language	English
Publishing date	2022-11-08
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	10.1080/07391102.2022.2142296
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Article ; Online: Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1)

Souza, Anacleto Silva de / Souza, Robson Francisco de / Guzzo, Cristiane Rodrigues

bioRxiv

Abstract: Herein, we simulated the trimeric Spike of the variants B.1.617.2, BA.2, BA.5 and BQ.1 for 300 ns. We derived mechanisms by which the substitutions K417N, L452R, N444T and N460K may favor resistance to neutralizing antibodies. The K417N and L452R ... ...

Abstract	Herein, we simulated the trimeric Spike of the variants B.1.617.2, BA.2, BA.5 and BQ.1 for 300 ns. We derived mechanisms by which the substitutions K417N, L452R, N444T and N460K may favor resistance to neutralizing antibodies. The K417N and L452R contribute to the expansion of the networks of hydrogen bonding interactions with neighboring residues, decreasing their capacity to interact with neutralizing antibodies. The SpikeBQ.1 possesses two unique K444T and N460K mutations that expand the network of hydrogen bonding interactions. This lysine also contributes one novel strong saline interaction and both substitutions may favor resistance to neutralizing antibodies. We also investigated how the substitutions D614G, P681R, and P681H impact Spike structural conformations and discuss the impact of these changes to infectivity and lethality. The prevalent D614G substitution plays a key role in the communication between the glycine and the residues of a β-strand located between the NTD and the RBD, impacting the transition between up- and down-RBD states. The P681R mutation, found in the Delta variant, favors intra- and inter-protomer correlations between the subunits S1 and S2. Conversely, in Omicron sub-variants, P681H decreases the intra- and inter-protomer long-range interactions within the trimeric Spike, providing an explanation for the reduced fusogenicity of this variant. Taken together, our results enhance the knowledge on how novel mutations lead to changes in infectivity and reveal mechanisms by which SARS-CoV-2 may evade the immune system.
Keywords	covid19
Language	English
Publishing date	2023-03-07
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.03.06.531335
Database	COVID19

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Article ; Online: Quantitative structure-activity relationships, molecular docking and molecular dynamics simulations reveal drug repurposing candidates as potent SARS-CoV-2 main protease inhibitors.

de Souza, Anacleto Silva / de Souza, Robson Francisco / Guzzo, Cristiane Rodrigues

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 21, Page(s) 11339–11356

Abstract: The current outbreak of COVID-19 is leading an unprecedented scientific effort focusing on targeting SARS-CoV-2 proteins critical for its viral replication. Herein, we performed high-throughput virtual screening of more than eleven thousand FDA-approved ... ...

Abstract	The current outbreak of COVID-19 is leading an unprecedented scientific effort focusing on targeting SARS-CoV-2 proteins critical for its viral replication. Herein, we performed high-throughput virtual screening of more than eleven thousand FDA-approved drugs using backpropagation-based artificial neural networks (
MeSH term(s)	Acarbose ; Angiotensin Amide ; Dihydrostreptomycin Sulfate ; Drug Repositioning ; Enviomycin ; Fenoterol ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors/pharmacology ; Quantitative Structure-Activity Relationship ; SARS-CoV-2/drug effects ; Antiviral Agents/pharmacology
Chemical Substances	3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Acarbose (T58MSI464G) ; Angiotensin Amide (53-73-6) ; Dihydrostreptomycin Sulfate (T7D4876IUE) ; Enviomycin (XU299C23A2) ; Fenoterol (22M9P70OQ9) ; laninamivir (B408IW3GL5) ; naratriptan (QX3KXL1ZA2) ; Protease Inhibitors ; Antiviral Agents
Language	English
Publishing date	2021-08-09
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	10.1080/07391102.2021.1958700
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Article ; Online: Monomeric Esterase: Insights into Cooperative Behavior, Hysteresis/Allokairy.

Vinces, Tania Churasacari / de Souza, Anacleto Silva / Carvalho, Cecília F / Visnardi, Aline Biazola / Teixeira, Raphael D / Llontop, Edgar E / Bismara, Beatriz Aparecida Passos / Vicente, Elisabete J / Pereira, José O / de Souza, Robson Francisco / Yonamine, Mauricio / Marana, Sandro Roberto / Farah, Chuck Shaker / Guzzo, Cristiane R

Biochemistry

2024 Volume 63, Issue 9, Page(s) 1178–1193

Abstract: Herein, we present a novel esterase enzyme, Ade1, isolated from a metagenomic library of Amazonian dark earths soils, demonstrating its broad substrate promiscuity by hydrolyzing ester bonds linked to aliphatic groups. The three-dimensional structure of ... ...

Abstract	Herein, we present a novel esterase enzyme, Ade1, isolated from a metagenomic library of Amazonian dark earths soils, demonstrating its broad substrate promiscuity by hydrolyzing ester bonds linked to aliphatic groups. The three-dimensional structure of the enzyme was solved in the presence and absence of substrate (tributyrin), revealing its classification within the α/β-hydrolase superfamily. Despite being a monomeric enzyme, enzymatic assays reveal a cooperative behavior with a sigmoidal profile (initial velocities vs substrate concentrations). Our investigation brings to light the allokairy/hysteresis behavior of Ade1, as evidenced by a transient burst profile during the hydrolysis of substrates such as
MeSH term(s)	Esterases/chemistry ; Esterases/metabolism ; Esterases/genetics ; Substrate Specificity ; Molecular Dynamics Simulation ; Catalytic Domain ; Crystallography, X-Ray ; Protein Conformation ; Hydrolysis ; Kinetics ; Models, Molecular
Chemical Substances	Esterases (EC 3.1.-)
Language	English
Publishing date	2024-04-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.3c00668
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Article ; Online: Molecular dynamics simulations of the Spike trimeric ectodomain of the SARS-CoV-2 Omicron variant: structural relationships with infectivity, evasion to immune system and transmissibility

Amorim, Vitor Martins de Freitas / de Souza, Robson F / Souza, Anacleto Silva de / Guzzo, Cristiane Rodrigues

bioRxiv

Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is replacing Delta, the most prevalent variant worldwide from the beginning of 2021 until early 2022. The Omicron variant is highly transmissible and responsible for a new ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is replacing Delta, the most prevalent variant worldwide from the beginning of 2021 until early 2022. The Omicron variant is highly transmissible and responsible for a new worldwide COVID-19 wave. Herein, we calculated molecular dynamics simulations of the SARS-CoV-2 trimeric spike protein of Wuhan-Hu-1 strain (wild type, WT) and the Omicron variant of concern. Structural analyses reveal that the SpikeOmicron presents more conformational flexibility than SpikeWT, mainly in the N-terminal domain (NTD) and receptor-binding domain (RBD). Such flexibility results in a broader spectrum of different conformations for SpikeOmicron, whereby the RBD can more easily visit an up-conformational state. We reported how the mutations in this variant may influence the intra- and inter-protomer contacts caused by conformational flexibility. Based on our analysis, we suggest that the differences in conformational flexibility between SpikeOmicron and SpikeWT may explain the observed gains in infectivity, immune system evasion and transmissibility in this novel variant.
Keywords	covid19
Language	English
Publishing date	2022-02-14
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.02.14.480347
Database	COVID19

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Article ; Online: Digital pharmacists: the new wave in pharmacy practice and education.

Silva, Rafaella de Oliveira Santos / de Araújo, Dyego Carlos Souza Anacleto / Dos Santos Menezes, Pedro Wlisses / Neves, Eugênio Rodrigo Zimmer / de Lyra, Divaldo Pereira

International journal of clinical pharmacy

2022 Volume 44, Issue 3, Page(s) 775–780

Abstract: Pharmacists now face the biggest challenges in the history of the profession: the use of digital technologies in pharmacy practice and education and the outbreak of coronavirus disease 2019. Worldwide, pharmaceutical care and pharmacy education via ... ...

Abstract	Pharmacists now face the biggest challenges in the history of the profession: the use of digital technologies in pharmacy practice and education and the outbreak of coronavirus disease 2019. Worldwide, pharmaceutical care and pharmacy education via digital technologies have significantly increased and will be incorporated into patient care and the teaching-learning process, respectively. Thus, in this new era of pharmacy practice and education, curricula should promote the development of specific competencies for the cognitive, conscious, and effective use of digital tools. This requires the training of "disruptive" educators, who are capable of using teaching-learning methods adapted to the digital environment and educational processes suitable for stimulating the use of effective disruptive technologies. This commentary argues that the pharmacy profession can no longer wait for the slow integration of digital technologies into pharmacy practice and education.
MeSH term(s)	COVID-19/epidemiology ; Education, Pharmacy ; Humans ; Pharmaceutical Services ; Pharmacists/psychology ; Pharmacy
Language	English
Publishing date	2022-04-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2601204-2
ISSN	2210-7711 ; 2210-7703 ; 0928-1231
ISSN (online)	2210-7711
ISSN	2210-7703 ; 0928-1231
DOI	10.1007/s11096-021-01365-5
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Article ; Online: Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains.

de Souza, Anacleto Silva / de Freitas Amorim, Vitor Martins / Guardia, Gabriela D A / Dos Santos, Filipe F / Ulrich, Henning / Galante, Pedro A F / de Souza, Robson Francisco / Guzzo, Cristiane Rodrigues

Viruses

2022 Volume 14, Issue 4

Abstract: Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of ... ...

Abstract	Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host's immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) the increase in Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with the increase in RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment in Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
MeSH term(s)	COVID-19/prevention & control ; COVID-19/virology ; COVID-19 Vaccines ; Humans ; Mutation ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus
Chemical Substances	COVID-19 Vaccines ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-04-16
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14040827
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Article ; Online: Factors contributing to the incident occurrence of security related to drug use in intensive care / Fatores que contribuem para a ocorrência de incidentes relacionados à terapia medicamentosa em terapia intensiva

Éder Luís Arboit / Silviamar Camponogara / Tânia Bosi de Souza Magnago / Janete de Souza Urbanetto / Carmem Lúcia Colomé Beck / Luiz Anido Anacleto da Silva

Revista de Pesquisa : Cuidado é Fundamental Online, Vol

2021 Volume 12

Abstract: Objetivo: identificar os fatores que contribuem para a ocorrência de incidentes relacionados à terapia medicamentosa em terapia intensiva, sob a ótica dos trabalhadores de enfermagem. Métodos: pesquisa descritivo-exploratória, com abordagem qualitativa ... ...

Abstract	Objetivo: identificar os fatores que contribuem para a ocorrência de incidentes relacionados à terapia medicamentosa em terapia intensiva, sob a ótica dos trabalhadores de enfermagem. Métodos: pesquisa descritivo-exploratória, com abordagem qualitativa realizada em um hospital do Sul do Brasil. Os participantes foram quinze trabalhadores de enfermagem. A coleta de dados ocorreu entre fevereiro e março de 2014, por meio de entrevista semiestruturada, sendo os dados analisados por meio de Análise de Conteúdo. Resultados: os dados foram agrupados em duas categorias: Incidentes de segurança relacionados aos fatores institucionais/organizacionais, que evidencia aspectos ligados à organização e processo de trabalho e, Incidentes de segurança relacionados aos fatores humanos, apontando aspectos relativos a assistência de enfermagem. Conclusão: vários fatores institucionais/organizacionais e humanos contribuem para a ocorrência de incidentes de segurança relacionados à terapia medicamentosa, devendo, tanto os trabalhador quanto as instituições, implementar estratégias para minimizar tais eventos.
Keywords	Enfermagem ; Erros de Medicação ; Segurança do Paciente ; Unidades de Terapia Intensiva ; Medicine ; R ; Nursing ; RT1-120
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Universidade Federal do Estado do Rio de Janeiro
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Factors contributing to the incident occurrence of security related to drug use in intensive care / Fatores que contribuem para a ocorrência de incidentes relacionados à terapia medicamentosa em terapia intensiva

Éder Luís Arboit / Silviamar Camponogara / Tânia Bosi de Souza Magnago / Janete de Souza Urbanetto / Carmem Lúcia Colomé Beck / Luiz Anido Anacleto da Silva

Revista de Pesquisa : Cuidado é Fundamental Online, Vol

2021 Volume 12

Abstract	Objetivo: identificar os fatores que contribuem para a ocorrência de incidentes relacionados à terapia medicamentosa em terapia intensiva, sob a ótica dos trabalhadores de enfermagem. Métodos: pesquisa descritivo-exploratória, com abordagem qualitativa realizada em um hospital do Sul do Brasil. Os participantes foram quinze trabalhadores de enfermagem. A coleta de dados ocorreu entre fevereiro e março de 2014, por meio de entrevista semiestruturada, sendo os dados analisados por meio de Análise de Conteúdo. Resultados: os dados foram agrupados em duas categorias: Incidentes de segurança relacionados aos fatores institucionais/organizacionais, que evidencia aspectos ligados à organização e processo de trabalho e, Incidentes de segurança relacionados aos fatores humanos, apontando aspectos relativos a assistência de enfermagem. Conclusão: vários fatores institucionais/organizacionais e humanos contribuem para a ocorrência de incidentes de segurança relacionados à terapia medicamentosa, devendo, tanto os trabalhador quanto as instituições, implementar estratégias para minimizar tais eventos.
Keywords	Enfermagem ; Erros de Medicação ; Segurança do Paciente ; Unidades de Terapia Intensiva ; Medicine ; R ; Nursing ; RT1-120
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Universidade Federal do Estado do Rio de Janeiro
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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