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Mahmoudi S, Dehkordi MM, Asgarshamsi MH. The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects. Biophys Chem 2022; 288:106824. [PMID: 35728510 PMCID: PMC9095071 DOI: 10.1016/j.bpc.2022.106824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/13/2022] [Accepted: 05/07/2022] [Indexed: 02/07/2023]
Abstract
The novel coronavirus that caused COVID-19 pandemic is SARS-CoV-2. Although various vaccines are currently being used to prevent the disease's severe consequences, there is still a need for medications for those who become infected. The SARS-CoV-2 has a variety of proteins that have been studied extensively since the virus's advent. In this review article, we looked at chemical to molecular aspects of the various structures studied that have pharmaceutical activity and attempted to find a link between drug activity and compound structure. For example, designing of the compounds which bind to the allosteric site and modify hydrogen bonds or the salt bridges can disrupt SARS-CoV2 RBD–ACE2 complex. It seems that quaternary ammonium moiety and quinolin-1-ium structure could act as a negative allosteric modulator to reduce the tendency between spike-ACE2. Pharmaceutical structures with amino heads and hydrophobic tails can block envelope protein to prevent making mature SARS-CoV-2. Also, structures based on naphthalene pharmacophores or isosteres can form a strong bond with the PLpro and form a π-π and the Mpro's active site can be occupied by octapeptide compounds or linear compounds with a similar fitting ability to octapeptide compounds. And for protein RdRp, it is critical to consider pH and pKa so that pKa regulation of compounds to comply with patients is very effective, thus, the presence of tetrazole, phenylpyrazole groups, and analogs of pyrophosphate in the designed drugs increase the likelihood of the RdRp active site inhibition. Finally, it can be deduced that designing hybrid drug molecules along with considering the aforementioned characteristics would be a suitable approach for developing medicines in order to accurate targeting and complete inhibition this virus.
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Affiliation(s)
- Samira Mahmoudi
- Department of Microbial Biotechnology, School of Biological Sciences, Islamic Azad University Tehran North Branch, Tehran, Iran.
| | - Mehrdad Mohammadpour Dehkordi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mohammad Hossein Asgarshamsi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
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102
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Ruiz-Aravena M, McKee C, Gamble A, Lunn T, Morris A, Snedden CE, Yinda CK, Port JR, Buchholz DW, Yeo YY, Faust C, Jax E, Dee L, Jones DN, Kessler MK, Falvo C, Crowley D, Bharti N, Brook CE, Aguilar HC, Peel AJ, Restif O, Schountz T, Parrish CR, Gurley ES, Lloyd-Smith JO, Hudson PJ, Munster VJ, Plowright RK. Ecology, evolution and spillover of coronaviruses from bats. Nat Rev Microbiol 2022; 20:299-314. [PMID: 34799704 PMCID: PMC8603903 DOI: 10.1038/s41579-021-00652-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 12/24/2022]
Abstract
In the past two decades, three coronaviruses with ancestral origins in bats have emerged and caused widespread outbreaks in humans, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the first SARS epidemic in 2002-2003, the appreciation of bats as key hosts of zoonotic coronaviruses has advanced rapidly. More than 4,000 coronavirus sequences from 14 bat families have been identified, yet the true diversity of bat coronaviruses is probably much greater. Given that bats are the likely evolutionary source for several human coronaviruses, including strains that cause mild upper respiratory tract disease, their role in historic and future pandemics requires ongoing investigation. We review and integrate information on bat-coronavirus interactions at the molecular, tissue, host and population levels. We identify critical gaps in knowledge of bat coronaviruses, which relate to spillover and pandemic risk, including the pathways to zoonotic spillover, the infection dynamics within bat reservoir hosts, the role of prior adaptation in intermediate hosts for zoonotic transmission and the viral genotypes or traits that predict zoonotic capacity and pandemic potential. Filling these knowledge gaps may help prevent the next pandemic.
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Affiliation(s)
- Manuel Ruiz-Aravena
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Clifton McKee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Amandine Gamble
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tamika Lunn
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Aaron Morris
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Celine E Snedden
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Claude Kwe Yinda
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Julia R Port
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - David W Buchholz
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yao Yu Yeo
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Christina Faust
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Elinor Jax
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Lauren Dee
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Devin N Jones
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Maureen K Kessler
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
- Department of Ecology, Montana State University, Bozeman, MT, USA
| | - Caylee Falvo
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Daniel Crowley
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Nita Bharti
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Cara E Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Hector C Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Alison J Peel
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Colin R Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Emily S Gurley
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter J Hudson
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA
| | - Vincent J Munster
- National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Raina K Plowright
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA.
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103
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Figueiredo DLA, Ximenez JPB, Seiva FRF, Panis C, Bezerra RDS, Ferrasa A, Cecchini AL, de Medeiros AI, Almeida AMF, Ramão A, Boldt ABW, Moya CF, Chin CM, de Paula D, Rech D, Gradia DF, Malheiros D, Venturini D, Tavares ER, Carraro E, Ribeiro EMDSF, Pereira EM, Tuon FF, Follador FAC, Fernandes GSA, Volpato H, Cólus IMDS, de Oliveira JC, Rodrigues JHDS, dos Santos JL, Visentainer JEL, Brandi JC, Serpeloni JM, Bonini JS, de Oliveira KB, Fiorentin K, Lucio LC, Faccin-Galhardi LC, Ferreto LED, Lioni LMY, Consolaro MEL, Vicari MR, Arbex MA, Pileggi M, Watanabe MAE, Costa MAR, Giannini MJSM, Amarante MK, Khalil NM, de Lima QA, Herai RH, Guembarovski RL, Shinsato RN, Mainardes RM, Giuliatti S, Yamada-Ogatta SF, Gerber VKDQ, Pavanelli WR, da Silva WC, Petzl-Erler ML, Valente V, Soares CP, Cavalli LR, Silva WA. COVID-19: The question of genetic diversity and therapeutic intervention approaches. Genet Mol Biol 2022; 44:e20200452. [PMID: 35421211 PMCID: PMC9075701 DOI: 10.1590/1678-4685-gmb-2020-0452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/24/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), is the largest pandemic in modern history with very high infection rates and considerable mortality. The disease, which emerged in China's Wuhan province, had its first reported case on December 29, 2019, and spread rapidly worldwide. On March 11, 2020, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemic and global health emergency. Since the outbreak, efforts to develop COVID-19 vaccines, engineer new drugs, and evaluate existing ones for drug repurposing have been intensively undertaken to find ways to control this pandemic. COVID-19 therapeutic strategies aim to impair molecular pathways involved in the virus entrance and replication or interfere in the patients' overreaction and immunopathology. Moreover, nanotechnology could be an approach to boost the activity of new drugs. Several COVID-19 vaccine candidates have received emergency-use or full authorization in one or more countries, and others are being developed and tested. This review assesses the different strategies currently proposed to control COVID-19 and the issues or limitations imposed on some approaches by the human and viral genetic variability.
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Affiliation(s)
- David Livingstone Alves Figueiredo
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Medicina, Guarapuava, PR, Brazil
- Instituto para Pesquisa do Câncer (IPEC), Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - João Paulo Bianchi Ximenez
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicologia e Ciência de Alimentos, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Fábio Rodrigues Ferreira Seiva
- Universidade Estadual do Norte do Paraná (UENP), Centro de Ciências Biológicas, Bandeirantes, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Carolina Panis
- Universidade Estadual do Oeste do Paraná, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rafael dos Santos Bezerra
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro Regional de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Adriano Ferrasa
- Universidade Estadual de Ponta Grossa, Ponta Grossa, Programa de Pós Graduação em Computação Aplicada, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Alessandra Lourenço Cecchini
- Universidade Estadual de Londrina, Departamento de Patologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Alexandra Ivo de Medeiros
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ana Marisa Fusco Almeida
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Anelisa Ramão
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Ciências Biológicas, Guarapuava, PR, Brazil
| | - Angelica Beate Winter Boldt
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Carla Fredrichsen Moya
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Medicina Veterinária, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Chung Man Chin
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- União das Faculdades dos Grandes Lagos (UNILAGO), Centro de Pesquisa Avançada em Medicina, São José do Rio Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniel de Paula
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniel Rech
- Universidade Estadual do Oeste do Paraná (UNIOESTE), Hospital do Câncer Francisco Beltrão, Laboratório de Biologia de Tumores, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniela Fiori Gradia
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Danielle Malheiros
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Danielle Venturini
- Universidade Estadual de Londrina, Centro de Ciências da Saúde, Departamento de patologia, clínica e toxicologia, Laboratório de bioquímica clínica, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Eliandro Reis Tavares
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Emerson Carraro
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Virologia Clínica, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Enilze Maria de Souza Fonseca Ribeiro
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Evani Marques Pereira
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Enfermagem, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Felipe Francisco Tuon
- Universidade Católica do Paraná, Laboratório de Doenças Infecciosas Emergentes, Pontifícia Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Franciele Aní Caovilla Follador
- Universidade Estadual do Oeste do Paraná, Departamento de Ciências da Vida, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Glaura Scantamburlo Alves Fernandes
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Hélito Volpato
- Universidade Estadual do Paraná (UNESPAR), Faculdade de Ciências Biológicas, Centro de Ciências Humanas e Educação, Paranavaí, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ilce Mara de Syllos Cólus
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jaqueline Carvalho de Oliveira
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jean Henrique da Silva Rodrigues
- Universidade do Estado de São Paulo (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jean Leandro dos Santos
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jeane Eliete Laguila Visentainer
- Universidade Estadual de Maringá, Laboratório de Imunogenética, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Cristina Brandi
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Mara Serpeloni
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Sartori Bonini
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Neuropsicofarmacologia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Karen Brajão de Oliveira
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Genética Molecular e Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Karine Fiorentin
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Léia Carolina Lucio
- Universidade Estadual do Oeste do Paraná, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Centro de Ciências da Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ligia Carla Faccin-Galhardi
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Lirane Elize Defante Ferreto
- Universidade Estadual do Oeste do Paraná, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Centro de Ciências da Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Lucy Megumi Yamauchi Lioni
- Universidade Estadual do Norte do Paraná (UENP), Centro de Ciências Biológicas, Bandeirantes, PR, Brazil
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
| | - Marcia Edilaine Lopes Consolaro
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia e Genética Estrutural e Molecular, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcos Abdo Arbex
- Universidade de Araraquara, Faculdade de Medicina, Área temática de Pneumologia, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcos Pileggi
- Universidade Estadual de Ponta Grossa, Departamento de Biologia e Genética Estrutural e Molecular, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Angelica Ehara Watanabe
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Antônia Ramos Costa
- Universidade do Estado do Paraná, Colegiada de Enfermagem, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria José S. Mendes Giannini
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marla Karine Amarante
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Najeh Maissar Khalil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Quirino Alves de Lima
- Universidade Estadual de Maringá, Laboratório de Imunogenética, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Roberto H. Herai
- Universidade Católica do Paraná (PUCPR), Faculdade de Medicina, Programa de Pós-Graduação em Ciências da Saúde, Laboratório Experimental Multiusuário, Curitiba, PR, Brazil
- Universitário Católico Salesiano Auxilium (UNISALESIANO), Faculdade de Medicina, Centro Araçatuba, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Roberta Losi Guembarovski
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rogério N. Shinsato
- Universidade Católica do Paraná (PUCPR), Faculdade de Medicina, Programa de Pós-Graduação em Ciências da Saúde, Laboratório Experimental Multiusuário, Curitiba, PR, Brazil
- Universitário Católico Salesiano Auxilium (UNISALESIANO), Faculdade de Medicina, Centro Araçatuba, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rubiana Mara Mainardes
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Silvana Giuliatti
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro Regional de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Viviane Knuppel de Quadros Gerber
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Enfermagem, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Wander Rogério Pavanelli
- Universidade Estadual de Londrina, Laboratório de Imunoparasitologia de Doenças Negligenciadas e Câncer, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Weber Claudio da Silva
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Neuropsicofarmacologia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Luiza Petzl-Erler
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Valeria Valente
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Faculdade de Medicina de Ribeirão Preto, Centro de Terapia Celular (CEPID/FAPESP), Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Christiane Pienna Soares
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Luciane Regina Cavalli
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Wilson Araujo Silva
- Instituto para Pesquisa do Câncer (IPEC), Guarapuava, PR, Brazil
- Faculdade de Medicina de Ribeirão Preto, Centro de Terapia Celular (CEPID/FAPESP), Ribeirão Preto, SP, Brazil
- Instituto Nacional de Ciência e Tecnologia em Células-Tronco e Terapia Celular (INCT/CNPq), Ribeirão Preto, SP, Brazil
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
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One Health and Cattle Genetic Resources: Mining More than 500 Cattle Genomes to Identify Variants in Candidate Genes Potentially Affecting Coronavirus Infections. Animals (Basel) 2022; 12:ani12070838. [PMID: 35405828 PMCID: PMC8997118 DOI: 10.3390/ani12070838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary The conservation and exploitation of cattle genetic resources for selection and breeding purposes are important for the definition of sustainable livestock production sectors. One Health approaches should be integrated into these activities to reduce the risk posed by many zoonoses. Coronaviruses are emerging as important zoonotic agents, with the potential to easily cross species barriers, as also recently demonstrated by the COVID-19 pandemic derived by SARS-CoV-2. Genetic resistance to coronavirus infections can be determined by variants of the host (animal) genome segregating within species. In this study, we mined the genome of more than 500 cattle to identify variants that could be involved so as to define different levels of susceptibility and/or resistance to coronavirus diseases in this important livestock species. Using comparative analyses across species, we identified several single amino acid polymorphisms that might alter the function of key proteins involved in the basic biological mechanisms underlying the infection processes in cattle. This study provided new elements to consider genetic variability of the host (cattle) as a potential risk factor to be considered in One Health perspectives. Abstract Epidemiological and biological characteristics of coronaviruses and their ability to cross species barriers are a matter of increasing concerns for these zoonotic agents. To prevent their spread, One Health approaches should be designed to include the host (animal) genome variability as a potential risk factor that might confer genetic resistance or susceptibility to coronavirus infections. At present, there is no example that considers cattle genetic resources for this purpose. In this study, we investigated the variability of six genes (ACE2, ANPEP, CEACAM1 and DPP4 encoding for host receptors of coronaviruses; FURIN and TMPRSS2 encoding for host proteases involved in coronavirus infection) by mining whole genome sequencing datasets from more than 500 cattle of 34 Bos taurus breeds and three related species. We identified a total of 180 protein variants (44 already known from the ARS-UCD1.2 reference genome). Some of them determine altered protein functions or the virus–host interaction and the related virus entry processes. The results obtained in this study constitute a first step towards the definition of a One Health strategy that includes cattle genetic resources as reservoirs of host gene variability useful to design conservation and selection programs to increase resistance to coronavirus diseases.
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105
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Kouznetsova VL, Zhang A, Miller MA, Tatineni M, Greenberg JP, Tsigelny IF. Potential SARS-CoV-2 Spike Protein-ACE2 Interface Inhibitors: Repurposing FDA-approved Drugs. JOURNAL OF EXPLORATORY RESEARCH IN PHARMACOLOGY 2022; 7:17-29. [DOI: 10.14218/jerp.2021.00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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106
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Li J, Sun Y, Qin E, Yuan H, Liu M, Yi W, Chen Z, Huang C, Zhou F, Chen R, Zhang L, Yu N, Liu Q, Zhou X, He J, Li B, Wang F, Yang C, Yang S. Olfactory and gustatory dysfunctions of COVID-19 patients in China: A multicenter study. World J Otorhinolaryngol Head Neck Surg 2022; 8:WJO25. [PMID: 35599836 PMCID: PMC9111234 DOI: 10.1002/wjo2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/10/2021] [Indexed: 11/08/2022] Open
Abstract
Introduction With the spread of the epidemic worldwide, an increasing number of doctors abroad have observed the following atypical symptoms of coronavirus disease 2019 (COVID-19): olfactory or taste disorders. Therefore, clarifying the incidence and clinical characteristics of olfactory and taste disorders in Chinese COVID-19 patients is of great significance and urgency. Materials and Methods A retrospective study was conducted, which included 229 severe acute respiratory syndrome coronavirus 2 confirmed patients, through face-to-face interviews and telephone follow-up. Following the completion of questionnaires, the patients participating in the study, were categorized according to the degree of olfactory and taste disorders experienced, and the proportion of each clinical type of patient with olfactory and taste disorders and the time when symptoms appeared were recorded. Results Among the 229 patients, 31 (13.54%) had olfactory dysfunction, and 44 (19.21%) had gustatory dysfunction. For the patients with olfactory dysfunction, 6 (19.35%) developed severe disease and became critically ill. Olfactory dysfunction appeared before the other symptoms in 21.43% of cases. The proportion of females with olfactory and gustatory dysfunction was higher than that of males (P < 0.001). Conclusions The incidence of olfactory and gustatory dysfunction was much lower than that reported abroad; the prognosis of patients with olfactory dysfunction is relatively favorable; olfactory and gustatory dysfunction can be used as a sign for early screening; females are more prone to olfactory and gustatory dysfunction.
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Affiliation(s)
- Jianhui Li
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Department of Otolaryngology Head and Neck SurgeryChinese PLA General Hospital Hainan HospitalSanyaChina
- Hainan Clinical Research Center for Otolaryngologic DiseasesSanyaChina
| | - Yi Sun
- Department of Otolaryngology Head and Neck SurgeryGeneral Hospital of Central Theater CommandWuhanChina
| | - Enqiang Qin
- Treatment and Research Center for Infectious DiseasesThe Fifth Medical Center of Chinese PLA General HospitalBeijingChina
- National Clinical Research Center for Infectious DiseasesBeijingChina
| | - Hu Yuan
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
| | - Mingbo Liu
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Department of Otolaryngology Head and Neck SurgeryChinese PLA General Hospital Hainan HospitalSanyaChina
- Hainan Clinical Research Center for Otolaryngologic DiseasesSanyaChina
| | - Wenqi Yi
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
| | - Zhu Chen
- Treatment and Research Center for Infectious DiseasesThe Fifth Medical Center of Chinese PLA General HospitalBeijingChina
- National Clinical Research Center for Infectious DiseasesBeijingChina
| | - Chengcheng Huang
- Department of Otolaryngology Head and Neck SurgeryGeneral Hospital of Central Theater CommandWuhanChina
| | - Fengjie Zhou
- Department of Otolaryngology Head and Neck SurgeryGeneral Hospital of Central Theater CommandWuhanChina
| | - Ruiyao Chen
- Department of Otolaryngology Head and Neck SurgeryGeneral Hospital of Central Theater CommandWuhanChina
| | - Leibo Zhang
- Department of Otolaryngology Head and Neck SurgeryGeneral Hospital of Central Theater CommandWuhanChina
| | - Ning Yu
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
| | - Qiong Liu
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
| | - Xuejun Zhou
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
| | - Jingjing He
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
| | - Boyu Li
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
| | - Fusheng Wang
- Treatment and Research Center for Infectious DiseasesThe Fifth Medical Center of Chinese PLA General HospitalBeijingChina
- National Clinical Research Center for Infectious DiseasesBeijingChina
| | - Changliang Yang
- Department of Otolaryngology Head and Neck SurgeryGeneral Hospital of Central Theater CommandWuhanChina
| | - Shiming Yang
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- National Clinical Research Center for Otolaryngologic DiseasesBeijingChina
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107
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Structures of a deltacoronavirus spike protein bound to porcine and human receptors. Nat Commun 2022; 13:1467. [PMID: 35304871 PMCID: PMC8933513 DOI: 10.1038/s41467-022-29062-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Porcine deltacoronavirus (PDCoV) can experimentally infect a variety of animals. Human infection by PDCoV has also been reported. Consistently, PDCoV can use aminopeptidase N (APN) from different host species as receptors to enter cells. To understand this broad receptor usage and interspecies transmission of PDCoV, we determined the crystal structures of the receptor binding domain (RBD) of PDCoV spike protein bound to human APN (hAPN) and porcine APN (pAPN), respectively. The structures of the two complexes exhibit high similarity. PDCoV RBD binds to common regions on hAPN and pAPN, which are different from the sites engaged by two alphacoronaviruses: HCoV-229E and porcine respiratory coronavirus (PRCoV). Based on structure guided mutagenesis, we identified conserved residues on hAPN and pAPN that are essential for PDCoV binding and infection. We report the detailed mechanism for how a deltacoronavirus recognizes homologous receptors and provide insights into the cross-species transmission of PDCoV. As a potential zoonotic pathogen, porcine deltacoronavirus (PDCoV) has been shown to cause febrile illness in humans. Here, Ji et al. report the structures of PDCoV spike protein bound to porcine and human aminopeptidase receptors, pointing to the likely underlying mechanism of PDCoV zoonotic transmission.
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108
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Cheng MH, Krieger JM, Banerjee A, Xiang Y, Kaynak B, Shi Y, Arditi M, Bahar I. Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions. iScience 2022; 25:103939. [PMID: 35194576 PMCID: PMC8851820 DOI: 10.1016/j.isci.2022.103939] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 12/29/2022] Open
Abstract
The emergence of SARS-CoV-2 variants necessitates rational assessment of their impact on the recognition and neutralization of the virus by the host cell. We present a comparative analysis of the interactions of Alpha, Beta, Gamma, and Delta variants with cognate molecules (ACE2 and/or furin), neutralizing nanobodies (Nbs), and monoclonal antibodies (mAbs) using in silico methods, in addition to Nb-binding assays. Our study elucidates the molecular origin of the ability of Beta and Delta variants to evade selected antibodies, such as REGN10933, LY-CoV555, B38, C105, or H11-H4, while being insensitive to others including REGN10987. Experiments confirm that nanobody Nb20 retains neutralizing activity against the Delta variant. The substitutions T478K and L452R in the Delta variant enhance associations with ACE2, whereas P681R promotes recognition by proteases, thus facilitating viral entry. The Ab-specific responses of variants highlight how full-atomic structure and dynamics analyses are required for assessing the response to newly emerging variants.
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Affiliation(s)
- Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - James M. Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yufei Xiang
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Burak Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yi Shi
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Moshe Arditi
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, and Biomedical Sciences, Infectious and Immunologic Diseases Research Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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Sharma R, Rana A, Sharma V, Mehrotra A, Babu H, Gupta S, Singh R, Tyagi A, Sethi N, Bhatt P, Yadav V, Chopra P, Upadhyay D. Clinical correlation and assessment of olfactory dysfunction with n-butanol in COVID-19 patients: our experience. RHINOLOGY ONLINE 2022. [DOI: 10.4193/rhinol/21.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background: Studies showed olfactory disturbances in COVID patients. This has attracted focus of clinicians as an easy clinical screening tool in suspected population. Material and methods: 70 mild and moderate category COVID-19 RT-PCR positive patients, more than 10 years of age were tested on day of admission for olfaction with serial dilution of n-butanol and asked to grade severity of their olfactory dysfunction according to visual analogue score from 1-10. Results: Fatigue 42 (93.33%), sore throat 37 (82.22%), fever 36 (80%) and dyspnea 23 (51.11%) were the most common symptoms in moderate patients. Diabetes, hypertension and allergy were the three prominent risk factors. At time of admission, n-butanol diagnosed 20 patients having olfactory dysfunction compared to 11 by VAS. Patients tend to grade their dysfunction higher on VAS whereas the n-butanol test classified their olfactory dysfunction lower. Viral load and high CRP were not found to be significantly related with olfactory dysfunction. d-Dimer and LDH levels were found statistically associated with higher grading of olfactory dysfunction detected by n-butanol. Conclusion: The majority of cases developed hyposmia before they were admitted to hospital even before they realized that they were having hyposmia as revealed by n-butanol testing. We should go for objective tests of olfaction.
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110
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Govind Kumar V, Ogden DS, Isu UH, Polasa A, Losey J, Moradi M. Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1. J Biol Chem 2022; 298:101814. [PMID: 35278433 PMCID: PMC8907130 DOI: 10.1016/j.jbc.2022.101814] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 01/01/2023] Open
Abstract
Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV-2 has been significantly more widespread than the 2003 SARS epidemic caused by SARS-CoV-1, despite striking similarities between these two viruses. The SARS-CoV-1 and SARS-CoV-2 spike proteins, both of which bind to host cell angiotensin-converting enzyme 2, have been implied to be a potential source of their differential transmissibility. However, the mechanistic details of prefusion spike protein binding to angiotensin-converting enzyme 2 remain elusive at the molecular level. Here, we performed an extensive set of equilibrium and nonequilibrium microsecond-level all-atom molecular dynamics simulations of SARS-CoV-1 and SARS-CoV-2 prefusion spike proteins to determine their differential dynamic behavior. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. These results suggest that not only the receptor-binding domain but also other domains such as the N-terminal domain could play a crucial role in the differential binding behavior of SARS-CoV-1 and SARS-CoV-2 spike proteins.
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Affiliation(s)
- Vivek Govind Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Dylan S Ogden
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Ugochi H Isu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - James Losey
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA.
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111
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Shin YH, Jeong K, Lee J, Lee HJ, Yim J, Kim J, Kim S, Park SB. Inhibition of ACE2-Spike Interaction by an ACE2 Binder Suppresses SARS-CoV-2 Entry. Angew Chem Int Ed Engl 2022; 61:e202115695. [PMID: 35043545 PMCID: PMC9011661 DOI: 10.1002/anie.202115695] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Indexed: 12/20/2022]
Abstract
The emergence of SARS-CoV-2 variants is a significant concern in developing effective therapeutics and vaccines in the middle of the ongoing COVID-19 pandemic. Here, we have identified a novel small molecule that inhibited the interactions between SARS-CoV-2 spike RBDs and ACE2 by modulating ACE2 without impairing its enzymatic activity necessary for normal physiological functions. Furthermore, the identified compounds suppressed viral infection in cultured cells by inhibiting the entry of ancestral and variant SARS-CoV-2. Our study suggests that targeting ACE2 could be a novel therapeutic strategy to inhibit SARS-CoV-2 entry into host cells and prevent the development of COVID-19.
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Affiliation(s)
- Young-Hee Shin
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea.,Department of Chemical Engineering & Biotechnology, Korea Polytechnic University, Siheung, 15073, Korea
| | - Kiyoung Jeong
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Jihye Lee
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam, 13488, Korea
| | - Hyo Jung Lee
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam, 13488, Korea
| | - Junhyeong Yim
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul, 06978, Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam, 13488, Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826, Korea.,Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826, Korea
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112
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Different compounds against Angiotensin-Converting Enzyme 2 (ACE2) receptor potentially containing the infectivity of SARS-CoV-2: an in silico study. J Mol Model 2022; 28:82. [PMID: 35249180 PMCID: PMC8898033 DOI: 10.1007/s00894-022-05059-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022]
Abstract
Novel SARS coronavirus or SARS-CoV-2 is a novel coronavirus that was identified and spread from Wuhan in 2019. On January 30th, the World Health Organization declared the coronavirus outbreak as a Global Public Health Emergency. Although Remdesivir and Molnupiravir are FDA-approved drugs for COVID-19, finding new efficient and low-cost antiviral drugs against COVID-19 for applying in more countries can still be helpful. One of the potential sources for finding new and low-cost drugs is the herbal compounds in addition to repurposing FDA-approved drugs. So, in this study, we focused on finding effective drug candidates against COVID-19 based on the computational approaches. As ACE2 serves as a critical receptor for cell entry of this virus. Inhibiting the binding site of SARS-CoV-2 on human ACE2 provides a promising therapeutic approach for developing drugs against SARS-CoV-2. Herein, we applied a bioinformatics approach to identify possible potential inhibitors of SARS-CoV-2. A library of FDA-approved compounds and five natural compounds was screened using Smina docking. Top-docking compounds are then applied in Molecular Dynamics (MD) simulation to assess the stability of ACE2-inhibitor complexes. Results indicate that Luteolin and Chrysin represent high conformation stability with ACE2 during 120 ns of Molecular Dynamics simulation. The binding free energies of Luteolin and Chrysin were calculated by the Molecular Mechanics/Poisson–Boltzmann Surface Area method (MM/PBSA) which confirmed the relative binding free energy of these drugs to ACE2 in favor of the effective binding. So, Luteolin and Chrysin could sufficiently interact with ACE2 and block the Spike binding pocket of ACE2 and can be a potential inhibitor against the binding of SARS-CoV-2 to ACE2 receptor which is an early stage of infection. Luteolin and Chrysin could be suggestive as beneficial compounds for preventing or reducing SARS-CoV-2 transmission and infection which need experimental work to prove.
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113
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Srivastava A, Siddiqui S, Ahmad R, Mehrotra S, Ahmad B, Srivastava AN. Exploring nature's bounty: identification of Withania somnifera as a promising source of therapeutic agents against COVID-19 by virtual screening and in silico evaluation. J Biomol Struct Dyn 2022; 40:1858-1908. [PMID: 33246398 PMCID: PMC7755033 DOI: 10.1080/07391102.2020.1835725] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/02/2020] [Indexed: 10/25/2022]
Abstract
Coronaviruses are etiological agents of extreme human and animal infection resulting in abnormalities primarily in the respiratory tract. Presently, there is no defined COVID-19 intervention and clinical trials of prospective therapeutic agents are still in the nascent stage. Withania somnifera (L.) Dunal (WS), is an important medicinal plant in Ayurveda. The present study aimed to evaluate the antiviral potential of selected WS phytoconstituents against the novel SARS-CoV-2 target proteins and human ACE2 receptor using in silico methods. Most of the phytoconstituents displayed good absorption and transport kinetics and were also found to display no associated mutagenic or adverse effect(s). Molecular docking analyses revealed that most of the WS phytoconstituents exhibited potent binding to human ACE2 receptor, SAR-CoV and SARS-CoV-2 spike glycoproteins as well as the two main SARS-CoV-2 proteases. Most of the phytoconstituents were predicted to undergo Phase-I metabolism prior to excretion. All phytoconstituents had favorable bioactivity scores with respect to various receptor proteins and target enzymes. SAR analysis revealed that the number of oxygen atoms in the withanolide backbone and structural rearrangements were crucial for effective binding. Molecular simulation analyses of SARS-CoV-2 spike protein and papain-like protease with Withanolides A and B, respectively, displayed a stability profile at 300 K and constant RMSDs of protein side chains and Cα atoms throughout the simulation run time. In a nutshell, WS phytoconstituents warrant further investigations in vitro and in vivo to unravel their molecular mechanism(s) and modes of action for their future development as novel antiviral agents against COVID-19.
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Affiliation(s)
- Aditi Srivastava
- Department of Biochemistry, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Sahabjada Siddiqui
- Department of Biotechnology, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Rumana Ahmad
- Department of Biochemistry, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Sudhir Mehrotra
- Department of Biochemistry, University of Lucknow, Lucknow, UP, India
| | - Bilal Ahmad
- Research Cell, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - A. N. Srivastava
- Department of Pathology, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
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Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants. PLoS Comput Biol 2022; 18:e1009922. [PMID: 35235558 PMCID: PMC8920257 DOI: 10.1371/journal.pcbi.1009922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/14/2022] [Accepted: 02/13/2022] [Indexed: 12/19/2022] Open
Abstract
SARS-CoV-2 Spike (Spike) binds to human angiotensin-converting enzyme 2 (ACE2) and the strength of this interaction could influence parameters relating to virulence. To explore whether population variants in ACE2 influence Spike binding and hence infection, we selected 10 ACE2 variants based on affinity predictions and prevalence in gnomAD and measured their affinities and kinetics for Spike receptor binding domain through surface plasmon resonance (SPR) at 37°C. We discovered variants that reduce and enhance binding, including three ACE2 variants that strongly inhibited (p.Glu37Lys, ΔΔG = –1.33 ± 0.15 kcal mol-1 and p.Gly352Val, predicted ΔΔG = –1.17 kcal mol-1) or abolished (p.Asp355Asn) binding. We also identified two variants with distinct population distributions that enhanced affinity for Spike. ACE2 p.Ser19Pro (ΔΔG = 0.59 ± 0.08 kcal mol-1) is predominant in the gnomAD African cohort (AF = 0.003) whilst p.Lys26Arg (ΔΔG = 0.26 ± 0.09 kcal mol-1) is predominant in the Ashkenazi Jewish (AF = 0.01) and European non-Finnish (AF = 0.006) cohorts. We compared ACE2 variant affinities to published SARS-CoV-2 pseudotype infectivity data and confirmed that ACE2 variants with reduced affinity for Spike can protect cells from infection. The effect of variants with enhanced Spike affinity remains unclear, but we propose a mechanism whereby these alleles could cause greater viral spreading across tissues and cell types, as is consistent with emerging understanding regarding the interplay between receptor affinity and cell-surface abundance. Finally, we compared mCSM-PPI2 ΔΔG predictions against our SPR data to assess the utility of predictions in this system. We found that predictions of decreased binding were well-correlated with experiment and could be improved by calibration, but disappointingly, predictions of highly enhanced binding were unreliable. Recalibrated predictions for all possible ACE2 missense variants at the Spike interface were calculated and used to estimate the overall burden of ACE2 variants on Covid-19. One of the first things the SARS-CoV-2 virus does to invade human cells is bind to a cell surface receptor called angiotensin-converting enzyme 2 (ACE2). The virus attaches to this receptor through its Spike protein and knowledge from other viruses tells us that the strength of this interaction influences how infectious and or virulent it is. We hypothesised that the Spike-ACE2 affinity might vary in people who have different amino acids in the part of ACE2 where Spike binds and consequently might be protected–or more at risk–from the virus. To test this idea, we measured the affinity of several ACE2 mutants, representing different versions found in humans, for the Spike protein and we found that some strengthened the interactions alongside others that weakened it. Most of these variants are rare, but two are present in over 1 in 1,000 individuals in certain populations and so might be important for the epidemiology of COVID-19. We then used computational methods to predict the affinity of even more ACE2 mutants than we could test in the lab and again found many that might alter this interaction. These data may help identify people who are at higher or lower risk from COVID-19.
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Starr TN, Zepeda SK, Walls AC, Greaney AJ, Alkhovsky S, Veesler D, Bloom JD. ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Nature 2022; 603:913-918. [PMID: 35114688 PMCID: PMC8967715 DOI: 10.1038/s41586-022-04464-z] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/25/2022] [Indexed: 11/08/2022]
Abstract
Two different sarbecoviruses have caused major human outbreaks in the past two decades1,2. Both of these sarbecoviruses, SARS-CoV-1 and SARS-CoV-2, engage ACE2 through the spike receptor-binding domain2-6. However, binding to ACE2 orthologues of humans, bats and other species has been observed only sporadically among the broader diversity of bat sarbecoviruses7-11. Here we use high-throughput assays12 to trace the evolutionary history of ACE2 binding across a diverse range of sarbecoviruses and ACE2 orthologues. We find that ACE2 binding is an ancestral trait of sarbecovirus receptor-binding domains that has subsequently been lost in some clades. Furthermore, we reveal that bat sarbecoviruses from outside Asia can bind to ACE2. Moreover, ACE2 binding is highly evolvable-for many sarbecovirus receptor-binding domains, there are single amino-acid mutations that enable binding to new ACE2 orthologues. However, the effects of individual mutations can differ considerably between viruses, as shown by the N501Y mutation, which enhances the human ACE2-binding affinity of several SARS-CoV-2 variants of concern12 but substantially decreases it for SARS-CoV-1. Our results point to the deep ancestral origin and evolutionary plasticity of ACE2 binding, broadening the range of sarbecoviruses that should be considered to have spillover potential.
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Affiliation(s)
- Tyler N Starr
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Allison J Greaney
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sergey Alkhovsky
- N.F. Gamleya National Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - David Veesler
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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116
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Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review. Viruses 2022; 14:v14020351. [PMID: 35215937 PMCID: PMC8878323 DOI: 10.3390/v14020351] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/12/2022] Open
Abstract
This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
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117
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Abbasi F, Adatorwovor R, Davarpanah MA, Mansoori Y, Hajiani M, Azodi F, Sefidbakht S, Davoudi S, Rezaei F, Mohammadmoradi S, Asadipooya K. A Randomized Trial of Combination Therapy, Sitagliptin and Spironolactone, in Hospitalized Adult Patients with COVID-19. J Endocr Soc 2022; 6:bvac017. [PMID: 35261932 PMCID: PMC8898039 DOI: 10.1210/jendso/bvac017] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Indexed: 11/29/2022] Open
Abstract
Context COVID-19 may cause respiratory distress syndrome and death. Treatment of COVID-19 to prevent complications remains a priority. Objective Our investigation sought to determine whether combination of spironolactone and sitagliptin could reduce mortality for inpatients with SARS-CoV-2 infection. Methods This single-blind, 4-arm, prospective randomized clinical trial was conducted at Shiraz and Bushehr University of Medical Sciences hospitals between December 2020 and April 2021. We randomized hospitalized adult patients with COVID-19 pneumonia into 4 groups: control, combination therapy, sitagliptin add-on, or spironolactone add-on. The primary outcome was the clinical improvement of the patients in the hospital as measured on an 8-point numerical scale. The secondary outcomes included intubation, ICU admission, end organ damages, CT findings, and paraclinical information. Results A total of 263 admitted patients were randomly assigned to control group (87 patients), combination group (60 patients), sitagliptin group (66 patients), and spironolactone group (50 patients). There were no significant differences in baseline characteristics, except for higher age in control group. The intervention groups, especially combination therapy, had better clinical outcomes (clinical score on fifth day of admission: 3.11 ± 2.45 for controls, 1.33 ± 0.50 for combination, 1.68 ± 1.02 for sitagliptin, and 1.64 ± 0.81 for spironolactone; P = 0.004). However, the mortality rate was lower in patients who received spironolactone (21.84% control, 13.33% combination, 13.64% sitagliptin, 10.00% spironolactone; P = 0.275). Our intervention reduced lung infiltration but not the area of involvement in lungs. Conclusion Sitagliptin and spironolactone can potentially improve clinical outcomes of hospitalized COVID-19 patients.
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Affiliation(s)
- Farhad Abbasi
- Department of Infectious Diseases, Bushehr University of Medical Sciences, Bushehr, Iran
| | | | | | | | | | - Farzan Azodi
- Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Sepideh Sefidbakht
- Medical Imaging Research Center, Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | | | - Shayan Mohammadmoradi
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA. Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, USA
| | - Kamyar Asadipooya
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, Barnstable Brown Diabetes and Obesity Center, University of Kentucky, Lexington, USA
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Butnariu AB, Look A, Grillo M, Tabish TA, McGarvey MJ, Pranjol MZI. SARS-CoV-2-host cell surface interactions and potential antiviral therapies. Interface Focus 2022; 12:20200081. [PMID: 34956606 PMCID: PMC8662392 DOI: 10.1098/rsfs.2020.0081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
In this review, we reveal the latest developments at the interface between SARS-CoV-2 and the host cell surface. In particular, we evaluate the current and potential mechanisms of binding, fusion and the conformational changes of the spike (S) protein to host cell surface receptors, especially the human angiotensin-converting enzyme 2 (ACE2) receptor. For instance, upon the initial attachment, the receptor binding domain of the S protein forms primarily hydrogen bonds with the protease domain of ACE2 resulting in conformational changes within the secondary structure. These surface interactions are of paramount importance and have been therapeutically exploited for antiviral design, such as monoclonal antibodies. Additionally, we provide an insight into novel therapies that target viral non-structural proteins, such as viral RNA polymerase. An example of which is remdesivir which has now been approved for use in COVID-19 patients by the US Food and Drug Administration. Establishing further understanding of the molecular details at the cell surface will undoubtably aid the development of more efficacious and selectively targeted therapies to reduce the burden of COVID-19.
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Affiliation(s)
| | - Alex Look
- School of Life Sciences, University of Sussex, Falmer, UK
| | - Marta Grillo
- School of Life Sciences, University of Sussex, Falmer, UK
| | - Tanveer A. Tabish
- Faculty of Engineering, Department of Materials, Royal School of Mines, Imperial College London, London, UK
| | - Michael J. McGarvey
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
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119
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Glocker MO, Opuni KFM, Thiesen HJ. From Free Binding Energy Calculations of SARS-CoV-2-Receptor Interactions to Cellular Immune Responses. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:226. [PMID: 35208550 PMCID: PMC8876798 DOI: 10.3390/medicina58020226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022]
Abstract
Our study focuses on free energy calculations of SARS-CoV-2 spike protein receptor binding motives (RBMs) from wild type and variants of concern (VOCs), with emphasis on SARS-CoV-2 Omicron. Our computational analysis underlines the occurrence of positive selection processes that specify Omicron host adaption and bring changes on the molecular level into context with clinically relevant observations. Our free energy calculation studies regarding the interaction of Omicron's RBM with human angiotensin converting enzyme 2 (hACE2) indicate weaker binding to the receptor than Alpha's or Delta's RBMs. Upon weaker binding, fewer viruses are predicted to be generated in time per infected cell, resulting in a delayed induction of danger signals as a trade-off. Along with delayed immunogenicity and pathogenicity, more viruses may be produced in the upper respiratory tract, explaining enhanced transmissibility. Since in interdependence on the human leukocyte antigen type (HLA type), more SARS-CoV-2 Omicron viruses are assumed to be required to initiate inflammatory immune responses, and because of pre-existing partial immunity through previous infections and/or vaccinations, which mostly guard the lower respiratory tract, overall disease severity is expected to be reduced.
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Affiliation(s)
- Michael O. Glocker
- Proteome Center Rostock, University Medicine Rostock, University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Kwabena F. M. Opuni
- Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health Science, University of Ghana, Legon, Accra P.O. Box LG43, Ghana;
| | - Hans-Juergen Thiesen
- Institute of Immunology, University Medicine Rostock, Schillingallee 69, 18059 Rostock, Germany;
- Gesellschaft für Individualisierte Medizin mbH (IndyMed), Industriestrasse 15, 18069 Rostock, Germany
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120
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Shin Y, Jeong K, Lee J, Lee HJ, Yim J, Kim J, Kim S, Park SB. Inhibition of ACE2‐Spike Interaction by an ACE2 Binder Suppresses SARS‐CoV‐2 Entry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Young‐Hee Shin
- CRI Center for Chemical Proteomics Department of Chemistry Seoul National University Seoul 08826 Korea
- Department of Chemical Engineering & Biotechnology Korea Polytechnic University Siheung 15073 Korea
| | - Kiyoung Jeong
- CRI Center for Chemical Proteomics Department of Chemistry Seoul National University Seoul 08826 Korea
| | - Jihye Lee
- Zoonotic Virus Laboratory Institut Pasteur Korea Seongnam 13488 Korea
| | - Hyo Jung Lee
- Zoonotic Virus Laboratory Institut Pasteur Korea Seongnam 13488 Korea
| | - Junhyeong Yim
- Department of Biophysics and Chemical Biology Seoul National University Seoul 08826 Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science Soongsil University Seoul 06978 Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory Institut Pasteur Korea Seongnam 13488 Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics Department of Chemistry Seoul National University Seoul 08826 Korea
- Department of Biophysics and Chemical Biology Seoul National University Seoul 08826 Korea
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121
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Chutipongtanate S, Morrow AL, Newburg DS. Human Milk Oligosaccharides: Potential Applications in COVID-19. Biomedicines 2022; 10:biomedicines10020346. [PMID: 35203555 PMCID: PMC8961778 DOI: 10.3390/biomedicines10020346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/25/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has become a global health crisis with more than four million deaths worldwide. A substantial number of COVID-19 survivors continue suffering from long-COVID syndrome, a long-term complication exhibiting chronic inflammation and gut dysbiosis. Much effort is being expended to improve therapeutic outcomes. Human milk oligosaccharides (hMOS) are non-digestible carbohydrates known to exert health benefits in breastfed infants by preventing infection, maintaining immune homeostasis and nurturing healthy gut microbiota. These beneficial effects suggest the hypothesis that hMOS might have applications in COVID-19 as receptor decoys, immunomodulators, mucosal signaling agents, and prebiotics. This review summarizes hMOS biogenesis and classification, describes the possible mechanisms of action of hMOS upon different phases of SARS-CoV-2 infection, and discusses the challenges and opportunities of hMOS research for clinical applications in COVID-19.
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Affiliation(s)
- Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Faculty of Medicine Ramathibodi Hospital, Chakri Naruebodindra Medical Institute, Mahidol University, Samut Prakan 10540, Thailand
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Ardythe L. Morrow
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children′s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - David S. Newburg
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Correspondence: or
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122
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Bouare N, Minta DK, Dabo A, Gerard C. COVID-19: A pluralistic and integrated approach for efficient management of the pandemic. World J Virol 2022; 11:20-39. [PMID: 35117969 PMCID: PMC8788213 DOI: 10.5501/wjv.v11.i1.20] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/10/2021] [Accepted: 12/28/2021] [Indexed: 02/06/2023] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which triggered the ongoing pandemic, was first discovered in China in late 2019. SARS-CoV-2 is a respiratory virus responsible for coronavirus disease 2019 (COVID-19) that often manifests as a pneumonic syndrome. In the context of the pandemic, there are mixed views on the data provided by epidemiologists and the information collected by hospital clinicians about their patients. In addition, the literature reports a large proportion of patients free of pneumonia vs a small percentage of patients with severe pneumonia among confirmed COVID-19 cases. This raises the issue of the complexity of the work required to control or contain the pandemic. We believe that an integrative and pluralistic approach will help to put the analyses into perspective and reinforce collaboration and creativity in the fight against this major scourge. This paper proposes a comprehensive and integrative approach to COVID-19 research, prevention, control, and treatment to better address the pandemic. Thus, this literature review applies a pluralistic approach to fight the pandemic.
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Affiliation(s)
- Nouhoum Bouare
- Biomedical Sciences Researcher, National Institute of Public Health, Bamako 1771, Mali
| | | | - Abdoulaye Dabo
- Department Epidemiology & Infectiology Disease, Faculty Medicine & Dentistry, CNRST/Univ Bamako, Bamako 3052, Mali
| | - Christiane Gerard
- Formerly Responsible for the Blood Bank, CHU-Liège, University of Liège, Liège 4000, Belgium
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Fiorillo B, Marchianò S, Moraca F, Sepe V, Carino A, Rapacciuolo P, Biagioli M, Limongelli V, Zampella A, Catalanotti B, Fiorucci S. Discovery of Bile Acid Derivatives as Potent ACE2 Activators by Virtual Screening and Essential Dynamics. J Chem Inf Model 2022; 62:196-209. [PMID: 34914393 PMCID: PMC8691454 DOI: 10.1021/acs.jcim.1c01126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 12/15/2022]
Abstract
The angiotensin-converting enzyme II (ACE2) is a key molecular player in the regulation of vessel contraction, inflammation, and reduction of oxidative stress. In addition, ACE2 has assumed a prominent role in the fight against the COVID-19 pandemic-causing virus SARS-CoV-2, as it is the very first receptor in the host of the viral spike protein. The binding of the spike protein to ACE2 triggers a cascade of events that eventually leads the virus to enter the host cell and initiate its life cycle. At the same time, SARS-CoV-2 infection downregulates ACE2 expression especially in the lung, altering the biochemical signals regulated by the enzyme and contributing to the poor clinical prognosis characterizing the late stage of the COVID-19 disease. Despite its important biological role, a very limited number of ACE2 activators are known. Here, using a combined in silico and experimental approach, we show that ursodeoxycholic acid (UDCA) derivatives work as ACE2 activators. In detail, we have identified two potent ACE2 ligands, BAR107 and BAR708, through a docking virtual screening campaign and elucidated their mechanism of action from essential dynamics of the enzyme observed during microsecond molecular dynamics calculations. The in silico results were confirmed by in vitro pharmacological assays with the newly identified compounds showing ACE2 activity comparable to that of DIZE, the most potent ACE2 activator known so far. Our work provides structural insight into ACE2/ligand-binding interaction useful for the design of compounds with therapeutic potential against SARS-CoV-2 infection, inflammation, and other ACE2-related diseases.
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Affiliation(s)
- Bianca Fiorillo
- Department
of Pharmacy, Università di Napoli
“Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Silvia Marchianò
- Department
of Medicine and Surgery, Università
di Perugia School of Medicine, Piazza L. Severi, I-06132 Perugia, Italy
| | - Federica Moraca
- Department
of Pharmacy, Università di Napoli
“Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
- Net4Science
S.r.l., University “Magna Græcia” of Catanzaro, Campus Universitario “S.
Venuta”, I-88100 Catanzaro, Italy
| | - Valentina Sepe
- Department
of Pharmacy, Università di Napoli
“Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Adriana Carino
- Department
of Medicine and Surgery, Università
di Perugia School of Medicine, Piazza L. Severi, I-06132 Perugia, Italy
| | - Pasquale Rapacciuolo
- Department
of Pharmacy, Università di Napoli
“Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Michele Biagioli
- Department
of Medicine and Surgery, Università
di Perugia School of Medicine, Piazza L. Severi, I-06132 Perugia, Italy
| | - Vittorio Limongelli
- Department
of Pharmacy, Università di Napoli
“Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
- Faculty
of Biomedical Sciences, Euler Institute, Università della Svizzera italiana (USI), via G. Buffi 13, CH-6900 Lugano, Switzerland
| | - Angela Zampella
- Department
of Pharmacy, Università di Napoli
“Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Bruno Catalanotti
- Department
of Pharmacy, Università di Napoli
“Federico II”, Via D. Montesano, 49, I-80131 Napoli, Italy
| | - Stefano Fiorucci
- Department
of Medicine and Surgery, Università
di Perugia School of Medicine, Piazza L. Severi, I-06132 Perugia, Italy
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Zepeda-Cervantes J, Martínez-Flores D, Ramírez-Jarquín JO, Tecalco-Cruz ÁC, Alavez-Pérez NS, Vaca L, Sarmiento-Silva RE. Implications of the Immune Polymorphisms of the Host and the Genetic Variability of SARS-CoV-2 in the Development of COVID-19. Viruses 2022; 14:94. [PMID: 35062298 PMCID: PMC8778858 DOI: 10.3390/v14010094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current pandemic affecting almost all countries in the world. SARS-CoV-2 is the agent responsible for coronavirus disease 19 (COVID-19), which has claimed millions of lives around the world. In most patients, SARS-CoV-2 infection does not cause clinical signs. However, some infected people develop symptoms, which include loss of smell or taste, fever, dry cough, headache, severe pneumonia, as well as coagulation disorders. The aim of this work is to report genetic factors of SARS-CoV-2 and host-associated to severe COVID-19, placing special emphasis on the viral entry and molecules of the immune system involved with viral infection. Besides this, we analyze SARS-CoV-2 variants and their structural characteristics related to the binding to polymorphic angiotensin-converting enzyme type 2 (ACE2). Additionally, we also review other polymorphisms as well as some epigenetic factors involved in the immunopathogenesis of COVID-19. These factors and viral variability could explain the increment of infection rate and/or in the development of severe COVID-19.
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Affiliation(s)
- Jesús Zepeda-Cervantes
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Daniel Martínez-Flores
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Josué Orlando Ramírez-Jarquín
- Departamento de Neuropatología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Ángeles C. Tecalco-Cruz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico City 06720, Mexico;
| | - Noé Santiago Alavez-Pérez
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07340, Mexico;
| | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Rosa Elena Sarmiento-Silva
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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125
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SARS-CoV-2 spike engagement of ACE2 primes S2' site cleavage and fusion initiation. Proc Natl Acad Sci U S A 2022; 119:2111199119. [PMID: 34930824 PMCID: PMC8740742 DOI: 10.1073/pnas.2111199119] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 01/10/2023] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in tremendous loss worldwide. Although viral spike (S) protein binding of angiotensin-converting enzyme 2 (ACE2) has been established, the functional consequences of the initial receptor binding and the stepwise fusion process are not clear. By utilizing a cell-cell fusion system, in complement with a pseudoviral infection model, we found that the spike engagement of ACE2 primed the generation of S2' fragments in target cells, a key proteolytic event coupled with spike-mediated membrane fusion. Mutagenesis of an S2' cleavage site at the arginine (R) 815, but not an S2 cleavage site at arginine 685, was sufficient to prevent subsequent syncytia formation and infection in a variety of cell lines and primary cells isolated from human ACE2 knock-in mice. The requirement for S2' cleavage at the R815 site was also broadly shared by other SARS-CoV-2 spike variants, such as the Alpha, Beta, and Delta variants of concern. Thus, our study highlights an essential role for host receptor engagement and the key residue of spike for proteolytic activation, and uncovers a targetable mechanism for host cell infection by SARS-CoV-2.
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126
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Rynkiewicz P, Lynch ML, Cui F, Hudson AO, Babbitt GA. Functional binding dynamics relevant to the evolution of zoonotic spillovers in endemic and emergent Betacoronavirus strains. J Biomol Struct Dyn 2022; 40:10978-10996. [PMID: 34286673 PMCID: PMC8776918 DOI: 10.1080/07391102.2021.1953604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Comparative functional analysis of the dynamic interactions between various Betacoronavirus mutant strains and broadly utilized target proteins such as ACE2 and CD26, is crucial for a more complete understanding of zoonotic spillovers of viruses that cause diseases such as COVID-19. Here, we employ machine learning to replicated sets of nanosecond scale GPU accelerated molecular dynamics simulations to statistically compare and classify atom motions of these target proteins in both the presence and absence of different endemic and emergent strains of the viral receptor binding domain (RBD) of the S spike glycoprotein. A multi-agent classifier successfully identified functional binding dynamics that are evolutionarily conserved from bat CoV-HKU4 to human endemic/emergent strains. Conserved dynamics regions of ACE2 involve both the N-terminal helices, as well as a region of more transient dynamics encompassing residues K353, Q325 and a novel motif AAQPFLL 386-92 that appears to coordinate their dynamic interactions with the viral RBD at N501. We also demonstrate that the functional evolution of Betacoronavirus zoonotic spillovers involving ACE2 interaction dynamics are likely pre-adapted from two precise and stable binding sites involving the viral bat progenitor strain's interaction with CD26 at SAMLI 291-5 and SS 333-334. Our analyses further indicate that the human endemic strains hCoV-HKU1 and hCoV-OC43 have evolved more stable N-terminal helix interactions through enhancement of an interfacing loop region on the viral RBD, whereas the highly transmissible SARS-CoV-2 variants (B.1.1.7, B.1.351 and P.1) have evolved more stable viral binding via more focused interactions between the viral N501 and ACE2 K353 alone.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrick Rynkiewicz
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Miranda L. Lynch
- Hauptmann-Woodward Medical Research Institute, Buffalo NY, USA 14203
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Gregory A. Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623,corresponding
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127
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Treppiedi D, Marra G, Di Muro G, Catalano R, Mangili F, Esposito E, Barbieri AM, Arosio M, Mantovani G, Peverelli E. TMPRSS2 Expression and Activity Modulation by Sex-Related Hormones in Lung Calu-3 Cells: Impact on Gender-Specific SARS-CoV-2 Infection. Front Endocrinol (Lausanne) 2022; 13:862789. [PMID: 35712238 PMCID: PMC9193185 DOI: 10.3389/fendo.2022.862789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/22/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although males and females are at equivalent risk of infection, males are more prone to develop a higher severity disease, regardless of age. The factors that mediate susceptibility to SARS-CoV-2 and transmission are still under investigation. A potential role has been attributed to differences in the immune systems response to viral antigens between males and females as well as to different regulatory actions played by sex-related hormones on the two crucial molecular effectors for SARS-CoV-2 infection, TMPRSS2 and ACE2. While few and controversial data about TMPRSS2 transcript regulation in lung cells are emerging, no data on protein expression and activity of TMPRSS2 have been reported. Aim of the present study was to search for possible modulatory actions played by sex-related hormones on TMPRSS2 and ACE2 expression in Calu-3 cells, to test the effects of sex-steroids on the expression of the 32kDa C-term fragment derived from autocatalitic cleavage of TMPRSS2 and its impact on priming of transiently transfected spike protein. Cells were stimulated with different concentrations of methyltrienolone (R1881) or estradiol for 30 h. No difference in mRNA and protein expression levels of full length TMPRSS2 was observed. However, the 32 kDa cleaved serine protease domain was increased after 100 nM R1881 (+2.36 ± 1.13 fold-increase vs control untreated cells, p < 0.05) and 10 nM estradiol (+1.90 ± 0.64, fold-increase vs control untreated cells, p < 0.05) treatment. Both R1881 and estradiol significantly increased the activating proteolytic cleavage of SARS-CoV-2 Spike (S) transfected in Calu-3 cells (+1.76 ± 0.18 and +1.99±,0.76 increase in S cleavage products at R1881 100nM and 10 nM estradiol treatment, respectively, p < 0.001 and p < 0.05 vs control untreated cells, respectively). Finally, no significant differences in ACE2 expression were observed between hormones-stimulated cells and untreated control cells. Altogether, these data suggest that both male and female sex-related hormones are able to induce a proteolityc activation of TMPRSS2, thus promoting viral infection, in agreement with the observation that males and females are equally infected by SARS-CoV-2.
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Affiliation(s)
- Donatella Treppiedi
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Giusy Marra
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Genesio Di Muro
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- PhD Program in Endocrinological Sciences, University Sapienza of Rome, Rome, Italy
| | - Rosa Catalano
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Federica Mangili
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Emanuela Esposito
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- PhD Program in Experimental Medicine, University of Milan, Milan, Italy
| | - Anna Maria Barbieri
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Maura Arosio
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Endocrinology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanna Mantovani
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Endocrinology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Erika Peverelli
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Endocrinology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- *Correspondence: Erika Peverelli,
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128
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Abstract
The unprecedented public health and economic impact of the COVID-19 pandemic caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been met with an equally unprecedented scientific response. Much of this response has focused, appropriately, on the mechanisms of SARS-CoV-2 entry into host cells, and in particular the binding of the spike (S) protein to its receptor, angiotensin-converting enzyme 2 (ACE2), and subsequent membrane fusion. This Review provides the structural and cellular foundations for understanding the multistep SARS-CoV-2 entry process, including S protein synthesis, S protein structure, conformational transitions necessary for association of the S protein with ACE2, engagement of the receptor-binding domain of the S protein with ACE2, proteolytic activation of the S protein, endocytosis and membrane fusion. We define the roles of furin-like proteases, transmembrane protease, serine 2 (TMPRSS2) and cathepsin L in these processes, and delineate the features of ACE2 orthologues in reservoir animal species and S protein adaptations that facilitate efficient human transmission. We also examine the utility of vaccines, antibodies and other potential therapeutics targeting SARS-CoV-2 entry mechanisms. Finally, we present key outstanding questions associated with this critical process.
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Affiliation(s)
- Cody B Jackson
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Hyeryun Choe
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA.
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129
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Keep S, Carr BV, Lean FZX, Fones A, Newman J, Dowgier G, Freimanis G, Vatzia E, Polo N, Everest H, Webb I, Mcnee A, Paudyal B, Thakur N, Nunez A, MacLoughlin R, Maier H, Hammond J, Bailey D, Waters R, Charleston B, Tuthill T, Britton P, Bickerton E, Tchilian E. Porcine Respiratory Coronavirus as a Model for Acute Respiratory Coronavirus Disease. Front Immunol 2022; 13:867707. [PMID: 35418984 PMCID: PMC8995773 DOI: 10.3389/fimmu.2022.867707] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022] Open
Abstract
In the light of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, we have developed a porcine respiratory coronavirus (PRCV) model for in depth mechanistic evaluation of the pathogenesis, virology and immune responses of this important family of viruses. Pigs are a large animal with similar physiology and immunology to humans and are a natural host for PRCV. Four PRCV strains were investigated and shown to induce different degrees of lung pathology. Importantly, although all four strains replicated equally well in porcine cell lines in vitro and in the upper respiratory tract in vivo, PRCV strains causing more severe lung pathology were also able to replicate in ex vivo tracheal organ cultures as well as in vivo in the trachea and lung. The time course of infection of PRCV 135, which caused the most severe pulmonary pathology, was investigated. Virus was shed from the upper respiratory tract until day 10 post infection, with infection of the respiratory mucosa, as well as olfactory and sustentacular cells, providing an excellent model to study upper respiratory tract disease in addition to the commonly known lower respiratory tract disease from PRCV. Infected animals made antibody and T cell responses that cross reacted with the four PRCV strains and Transmissible Gastroenteritis Virus. The antibody response was reproduced in vitro in organ cultures. Comparison of mechanisms of infection and immune control in pigs infected with PRCVs of differing pathogenicity with human data from SARS-CoV-2 infection and from our in vitro organ cultures, will enable key events in coronavirus infection and disease pathogenesis to be identified.
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Affiliation(s)
- Sarah Keep
- The Pirbright Institute, Pirbright, United Kingdom
| | | | - Fabian Z X Lean
- Department of Pathology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Albert Fones
- The Pirbright Institute, Pirbright, United Kingdom
| | | | | | | | - Eleni Vatzia
- The Pirbright Institute, Pirbright, United Kingdom
| | - Noemi Polo
- The Pirbright Institute, Pirbright, United Kingdom
| | | | - Isobel Webb
- The Pirbright Institute, Pirbright, United Kingdom
| | - Adam Mcnee
- The Pirbright Institute, Pirbright, United Kingdom
| | - Basu Paudyal
- The Pirbright Institute, Pirbright, United Kingdom
| | - Nazia Thakur
- The Pirbright Institute, Pirbright, United Kingdom
| | - Alejandro Nunez
- Department of Pathology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Ronan MacLoughlin
- Research and Development, Science and Emerging Technologies, Aerogen, Galway, Ireland
| | - Helena Maier
- The Pirbright Institute, Pirbright, United Kingdom
| | - John Hammond
- The Pirbright Institute, Pirbright, United Kingdom
| | - Dalan Bailey
- The Pirbright Institute, Pirbright, United Kingdom
| | - Ryan Waters
- The Pirbright Institute, Pirbright, United Kingdom
| | | | - Toby Tuthill
- The Pirbright Institute, Pirbright, United Kingdom
| | - Paul Britton
- The Pirbright Institute, Pirbright, United Kingdom
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130
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Ruiz A, Flores-Gonzalez J, Buendia-Roldan I, Chavez-Galan L. Telomere Shortening and Its Association with Cell Dysfunction in Lung Diseases. Int J Mol Sci 2021; 23:425. [PMID: 35008850 PMCID: PMC8745057 DOI: 10.3390/ijms23010425] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 01/10/2023] Open
Abstract
Telomeres are localized at the end of chromosomes to provide genome stability; however, the telomere length tends to be shortened with each cell division inducing a progressive telomere shortening (TS). In addition to age, other factors, such as exposure to pollutants, diet, stress, and disruptions in the shelterin protein complex or genes associated with telomerase induce TS. This phenomenon favors cellular senescence and genotoxic stress, which increases the risk of the development and progression of lung diseases such as idiopathic pulmonary fibrosis, chronic obstructive pulmonary disease, SARS-CoV-2 infection, and lung cancer. In an infectious environment, immune cells that exhibit TS are associated with severe lymphopenia and death, whereas in a noninfectious context, naïve T cells that exhibit TS are related to cancer progression and enhanced inflammatory processes. In this review, we discuss how TS modifies the function of the immune system cells, making them inefficient in maintaining homeostasis in the lung. Finally, we discuss the advances in drug and gene therapy for lung diseases where TS could be used as a target for future treatments.
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Affiliation(s)
| | | | | | - Leslie Chavez-Galan
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (A.R.); (J.F.-G.); (I.B.-R.)
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131
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ÇILDIR B. An age-related investigation of audio-vestibular symptoms in individuals with Covid-19 positive. CUKUROVA MEDICAL JOURNAL 2021. [DOI: 10.17826/cumj.987374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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132
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Sobitan A, Mahase V, Rhoades R, Williams D, Liu D, Xie Y, Li L, Tang Q, Teng S. Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Front Mol Biosci 2021; 8:784303. [PMID: 34957216 PMCID: PMC8696472 DOI: 10.3389/fmolb.2021.784303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/18/2021] [Indexed: 12/24/2022] Open
Abstract
Severe Acute respiratory syndrome coronavirus (SARS-CoV-1) attaches to the host cell surface to initiate the interaction between the receptor-binding domain (RBD) of its spike glycoprotein (S) and the human Angiotensin-converting enzyme (hACE2) receptor. SARS-CoV-1 mutates frequently because of its RNA genome, which challenges the antiviral development. Here, we per-formed computational saturation mutagenesis of the S protein of SARS-CoV-1 to identify the residues crucial for its functions. We used the structure-based energy calculations to analyze the effects of the missense mutations on the SARS-CoV-1 S stability and the binding affinity with hACE2. The sequence and structure alignment showed similarities between the S proteins of SARS-CoV-1 and SARS-CoV-2. Interestingly, we found that target mutations of S protein amino acids generate similar effects on their stabilities between SARS-CoV-1 and SARS-CoV-2. For example, G839W of SARS-CoV-1 corresponds to G857W of SARS-CoV-2, which decrease the stability of their S glycoproteins. The viral mutation analysis of the two different SARS-CoV-1 isolates showed that mutations, T487S and L472P, weakened the S-hACE2 binding of the 2003–2004 SARS-CoV-1 isolate. In addition, the mutations of L472P and F360S destabilized the 2003–2004 viral isolate. We further predicted that many mutations on N-linked glycosylation sites would increase the stability of the S glycoprotein. Our results can be of therapeutic importance in the design of antivirals or vaccines against SARS-CoV-1 and SARS-CoV-2.
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Affiliation(s)
- Adebiyi Sobitan
- Department of Biology, Howard University, Washington, DC, United States
| | - Vidhyanand Mahase
- Department of Biology, Howard University, Washington, DC, United States
| | - Raina Rhoades
- Department of Biology, Howard University, Washington, DC, United States
| | - Dejaun Williams
- Department of Biology, Howard University, Washington, DC, United States
| | - Dongxiao Liu
- Howard University College of Medicine, Washington, DC, United States
| | - Yixin Xie
- Computational Science Program, University of Texas at El Paso, El Paso, TX, United States
| | - Lin Li
- Computational Science Program, University of Texas at El Paso, El Paso, TX, United States.,Physics Department, University of Texas at El Paso, El Paso, TX, United States
| | - Qiyi Tang
- Howard University College of Medicine, Washington, DC, United States
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC, United States
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133
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Dormoy V, Perotin JM, Gosset P, Maskos U, Polette M, Deslée G. Nicotinic receptors as SARS-CoV-2 spike co-receptors? Med Hypotheses 2021; 158:110741. [PMID: 34924680 PMCID: PMC8669939 DOI: 10.1016/j.mehy.2021.110741] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 11/16/2021] [Accepted: 12/10/2021] [Indexed: 12/18/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) play an important role in homeostasis and respiratory diseases. Controversies regarding the association between COVID-19 hospitalizations and smoking suggest that nAChRs may contribute to SARS-CoV-2 respiratory syndrome. We recently detailed the expression and localization of all nAChR subunits in the human lung. Since virus association with nAChRs has been shown in the past, we hypothesize that nAChR subunits act as SARS-CoV-2 Spike co-receptors. Based on sequence alignment analysis, we report domains of high molecular similarities in nAChRs with the binding domain of hACE2 for SARS-CoV-2 Spike protein. This hypothesis supported by in silico pilot data provides a rational for the modelling and the in vitro experimental validation of the interaction between SARS-CoV-2 and the nAChRs.
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Affiliation(s)
- Valérian Dormoy
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, 51092 Reims, France
| | - Jeanne-Marie Perotin
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, 51092 Reims, France.,CHU of Reims, Hôpital Maison Blanche, Department of Respiratory Diseases, 51092 Reims, France
| | - Philippe Gosset
- University of Lille, CNRS UMR8204, Inserm U1019, CHRU Lille, Institut Pasteur Lille, CIIL - Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Uwe Maskos
- Institut Pasteur Paris, Université de Paris, Integrative Neurobiology of Cholinergic Systems, CNRS, UMR 3571, Paris, France
| | - Myriam Polette
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, 51092 Reims, France.,CHU Reims, Hôpital Maison Blanche, Department of Biopathology, 51092 Reims, France
| | - Gaëtan Deslée
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, 51092 Reims, France.,CHU of Reims, Hôpital Maison Blanche, Department of Respiratory Diseases, 51092 Reims, France
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134
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Singh B, Singh D, Verma V, Yadav R, Kumar R. Angiotensin-converting enzyme 2 as a potential therapeutic target for COVID-19: A review. J Pharm Anal 2021; 12:215-220. [PMID: 34934510 PMCID: PMC8677424 DOI: 10.1016/j.jpha.2021.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 12/04/2021] [Accepted: 12/14/2021] [Indexed: 02/06/2023] Open
Abstract
As of August 16, 2021, there have been 207,173,086 confirmed cases and 4,361,996 deaths due to the coronavirus disease (COVID-19), and the pandemic remains a global challenge. To date, no effective and approved drugs are available for the treatment of COVID-19. Angiotensin-converting enzyme 2 (ACE2) plays a crucial role in the invasion into host cells by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19. Notably, ACE2 density is influenced by medical conditions, such as hypertension, or by drugs, including angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs), which can change the fate of SARS-CoV-2 infectivity. ACE2 is a target for these drugs and can be manipulated to limit the viral entry and replication within the cells. Different strategies aimed at blocking ACE2 with small molecules, peptides, and antibodies, or by neutralizing the virus through its competitive binding with human recombinant soluble ACE2 (hrsACE2) are currently under investigation. In this article, we review the current state of knowledge that emphasizes the need to find effective therapeutic agents against COVID-19 by exploiting ACE2 as a potential target. The increased soluble ACE2 levels and the application of hrsACE2 in patients with COVID-19 can be implemented to control the disease. It has not yet been established whether hypertension and other comorbidities, independent of age, have a direct role in COVID-19. Therefore, the use of renin-angiotensin system inhibitors, ACEIs and ARBs, should not be discontinued during COVID-19 treatment. Blockage of the interaction between the SARS-CoV-2 S protein and ACE2 as a strategy to treat COVID-19 is underway. ACE2 upregulation leads to the increased release of soluble ACE2. Increasing the levels of soluble ACE2 and hrsACE2 has the potential to prevent SARS-CoV-2 infection and reverse lung injury.
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Affiliation(s)
- Bhagat Singh
- Department of Medical Laboratory Technology, Faculty of Paramedical Sciences, Uttar Pradesh University of Medical Sciences, Etawah, 206130, India
| | - Dheer Singh
- Department of Anaesthesiology and Critical Care, Uttar Pradesh University of Medical Sciences, Etawah, 206130, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India
| | - Ramakant Yadav
- Department of Neurology, Uttar Pradesh University of Medical Sciences, Etawah, 206130, India
| | - Raj Kumar
- Department of Neurosurgery, Uttar Pradesh University of Medical Sciences, Etawah, 206130, India
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135
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Grover A, Sinha R, Jyoti D, Faggio C. Imperative role of electron microscopy in toxicity assessment: A review. Microsc Res Tech 2021; 85:1976-1989. [PMID: 34904321 DOI: 10.1002/jemt.24029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
Electron microscope (EM) was developed in 1931 and since then microscopical examination of both the biological and non-biological samples has been revolutionized. Modifications in electron microscopy techniques, such as scanning EM and transmission EM, have widened their applicability in the various sectors such as understanding of drug toxicity, development of mechanism, criminal site investigation, and characterization of the nano-molecule. The present review summarizes its role in important aspects such as toxicity assessment and disease diagnosis in special reference to SARS-COV2. In the biological system, EM studies have elucidated the impact of toxicants at the ultra-structural level in various tissue in conformity to physiological alterations. Thus, EM can be concluded as an important tool in toxicity assessment and disease prognosis.
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Affiliation(s)
- Aseem Grover
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, India
| | - Reshma Sinha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, India
| | - Divya Jyoti
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, India
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Italy
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136
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Rahbar MR, Jahangiri A, Khalili S, Zarei M, Mehrabani-Zeinabad K, Khalesi B, Pourzardosht N, Hessami A, Nezafat N, Sadraei S, Negahdaripour M. Hotspots for mutations in the SARS-CoV-2 spike glycoprotein: a correspondence analysis. Sci Rep 2021; 11:23622. [PMID: 34880279 PMCID: PMC8654821 DOI: 10.1038/s41598-021-01655-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
Spike glycoprotein (Sgp) is liable for binding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the host receptors. Since Sgp is the main target for vaccine and drug designing, elucidating its mutation pattern could help in this regard. This study is aimed at investigating the correspondence of specific residues to the SgpSARS-CoV-2 functionality by explorative interpretation of sequence alignments. Centrality analysis of the Sgp dissects the importance of these residues in the interaction network of the RBD-ACE2 (receptor-binding domain) complex and furin cleavage site. Correspondence of RBD to threonine500 and asparagine501 and furin cleavage site to glutamine675, glutamine677, threonine678, and alanine684 was observed; all residues are exactly located at the interaction interfaces. The harmonious location of residues dictates the RBD binding property and the flexibility, hydrophobicity, and accessibility of the furin cleavage site. These species-specific residues can be assumed as real targets of evolution, while other substitutions tend to support them. Moreover, all these residues are parts of experimentally identified epitopes. Therefore, their substitution may affect vaccine efficacy. Higher rate of RBD maintenance than furin cleavage site was predicted. The accumulation of substitutions reinforces the probability of the multi-host circulation of the virus and emphasizes the enduring evolutionary events.
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Affiliation(s)
- Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamran Mehrabani-Zeinabad
- Department of Biostatistics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine, and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Navid Pourzardosht
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran
| | - Anahita Hessami
- School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saman Sadraei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran.
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Butowt R, von Bartheld CS. Anosmia in COVID-19: Underlying Mechanisms and Assessment of an Olfactory Route to Brain Infection. Neuroscientist 2021; 27:582-603. [PMID: 32914699 PMCID: PMC7488171 DOI: 10.1177/1073858420956905] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In recent months it has emerged that the novel coronavirus-responsible for the COVID-19 pandemic-causes reduction of smell and taste in a large fraction of patients. The chemosensory deficits are often the earliest, and sometimes the only signs in otherwise asymptomatic carriers of the SARS-CoV-2 virus. The reasons for the surprisingly early and specific chemosensory dysfunction in COVID-19 are now beginning to be elucidated. In this hypothesis review, we discuss implications of the recent finding that the prevalence of smell and taste dysfunction in COVID-19 patients differs between populations, possibly because of differences in the spike protein of different virus strains or because of differences in the host proteins that enable virus entry, thus modifying infectivity. We review recent progress in defining underlying cellular and molecular mechanisms of the virus-induced anosmia, with a focus on the emerging crucial role of sustentacular cells in the olfactory epithelium. We critically examine the current evidence whether and how the SARS-CoV-2 virus can follow a route from the olfactory epithelium in the nose to the brain to achieve brain infection, and we discuss the prospects for using the smell and taste dysfunctions seen in COVID-19 as an early and rapid diagnostic screening tool.
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Affiliation(s)
- Rafal Butowt
- Department of Molecular Cell Genetics, L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- Department of Anatomy, L. Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Christopher S. von Bartheld
- Center of Biomedical Research Excellence in Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, USA
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, USA
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138
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Bakhtazad A, Garmabi B, Joghataei MT. Neurological manifestations of coronavirus infections, before and after COVID-19: a review of animal studies. J Neurovirol 2021; 27:864-884. [PMID: 34727365 PMCID: PMC8561685 DOI: 10.1007/s13365-021-01014-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 07/15/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This virus, which was first identified in December 2019 in China, has resulted in a yet ongoing viral pandemic. Coronaviridae could potentially cause several disorders in a wide range of hosts such as birds and mammals. Although infections caused by this family of viruses are predominantly limited to the respiratory tract, Betacoronaviruses are potentially able to invade the central nervous system (CNS) as well as many other organs, thereby inducing neurological damage ranging from mild to lethal in both animals and humans. Over the past two decades, three novel CoVs, SARS-CoV-1, MERS-CoV, and SARS-CoV-2, emerging from animal reservoirs have exhibited neurotropic properties causing severe and even fatal neurological diseases. The pathobiology of these neuroinvasive viruses has yet to be fully known. Both clinical features of the previous CoV epidemics (SARS-CoV-1 and MERS-CoV) and lessons from animal models used in studying neurotropic CoVs, especially SARS and MERS, constitute beneficial tools in comprehending the exact mechanisms of virus implantation and in illustrating pathogenesis and virus dissemination pathways in the CNS. Here, we review the animal research which assessed CNS infections with previous more studied neurotropic CoVs to demonstrate how experimental studies with appliable animal models can provide scientists with a roadmap in the CNS impacts of SARS-CoV-2. Indeed, animal studies can finally help us discover the underlying mechanisms of damage to the nervous system in COVID-19 patients and find novel therapeutic agents in order to reduce mortality and morbidity associated with neurological complications of SARS-CoV-2 infection.
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Affiliation(s)
- Atefeh Bakhtazad
- Cellular and Molecular Research Center (CMRC), Iran University of Medical Sciences, 1449614535 Tehran, Iran
| | - Behzad Garmabi
- School of Medicine, Shahroud University of Medical Sciences, Haft-Tir Sq, University Blv, 3614773947 Shahroud, Iran
| | - Mohammad Taghi Joghataei
- Cellular and Molecular Research Center (CMRC), Iran University of Medical Sciences, 1449614535 Tehran, Iran
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139
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Ramírez-de-Arellano A, Gutiérrez-Franco J, Sierra-Diaz E, Pereira-Suárez AL. The role of estradiol in the immune response against COVID-19. Hormones (Athens) 2021; 20:657-667. [PMID: 34142358 PMCID: PMC8210971 DOI: 10.1007/s42000-021-00300-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the pathogen agent causing coronavirus disease (COVID)-19, which was declared a global pandemic in 2020. The spike protein of this virus and the angiotensin-converter enzyme (ACE)-2 in host cells in humans play a vital role in infection and in COVID-19 pathogenesis. Estradiol is known to modulate the actions of immune cells, and, therefore, the antiviral mechanisms of these cells could also be modified by this hormone stimulus. Even though estradiol is not considered a protective factor, evidence shows that women with high levels of this hormone have a lower risk of developing severe symptoms and an even a lower incidence of death. Understanding the mechanism of action of estradiol with regard to viral infections and COVID-19 is essential for the improvement of therapeutic strategies. This review aims to describe the effects that estradiol exerts on immune cells during viral infections and COVID-19.
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Affiliation(s)
- Adrián Ramírez-de-Arellano
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de La Salud, Universidad de Guadalajara, Guadalajara, Jalisco, 44 340, México
| | - Jorge Gutiérrez-Franco
- Unidad Académica de Ciencias Químico Biológicas Y Farmacéuticas, Universidad Autónoma de Nayarit, Tepic, Nayarit, 63 000, México
| | - Erick Sierra-Diaz
- Departamento de Salud Pública, Centro Universitario de Ciencias de La Salud, Universidad de Guadalajara, División de Epidemiología, Unidad Medica de Alta Especialidad, Hospital de Especialidades, Centro Médico Nacional de Occidente, Guadalajara, Jalisco, 44340, México
| | - Ana Laura Pereira-Suárez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de La Salud, Universidad de Guadalajara, Guadalajara, Jalisco, 44 340, México.
- Departamento de Microbiología Y Patología, Centro Universitario de Ciencias de La Salud, Universidad de Guadalajara, Sierra Mojada # 950, Colonia Independencia, CP, 44340, Guadalajara, Jalisco, México.
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140
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Choi Y, Jeon H, Brännström M, Akin JW, Curry TE, Jo M. Ovulatory upregulation of angiotensin-converting enzyme 2, a receptor for SARS-CoV-2, in dominant follicles of the human ovary. Fertil Steril 2021; 116:1631-1640. [PMID: 34538460 PMCID: PMC8354803 DOI: 10.1016/j.fertnstert.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/25/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To determine the temporal expression of angiotensin-converting enzyme 2 (ACE2), a receptor for SARS-CoV-2, in dominant follicles throughout the periovulatory period in women and the regulatory mechanisms underlying ACE2 expression in human granulosa/lutein cells (hGLC). DESIGN Experimental prospective clinical study and laboratory-based investigation. SETTING University Medical Center and private in vitro fertilization center. PATIENT(S) Thirty premenopausal women undergoing surgery for tubal ligation and 16 premenopausal women undergoing in vitro fertilization. INTERVENTION(S) Administration of human chorionic gonadotropin (hCG) and harvesting of preovulatory/ovulatory follicles by timed laparoscopy, and collection of granulosa/lutein cells and cumulus cells at the time of oocyte retrieval. MAIN OUTCOME MEASURE(S) Expression and localization of ACE2 in granulosa cells and dominant follicles collected throughout the periovulatory period of the menstrual cycle and in hGLC using quantitative polymerase chain reaction, immunoblotting, and immunohistochemistry. RESULT(S) ACE2 expression (mRNA and protein) is up-regulated in human ovulatory follicles after administration of hCG. ACE2 expression was higher in cumulus cells than in granulosa cells. hCG increased the expression of ACE2 in primary hGLC cultures; the increase was inhibited by RU486 (an antagonist for progesterone receptor and glucocorticoid receptor) and CORT125281 (a selective glucocorticoid receptor antagonist), but not by AG1478 (an EGF receptor tyrosine kinase inhibitor) or by dexamethasone. CONCLUSION(S) The hormone-regulated expression of ACE2 in granulosa cells suggests a potential role of ACE2 in the ovulatory process. These data also imply the possible impact of COVID-19 on a vital cyclic event of ovarian function and thus on women's overall reproductive health. However, SAR-CoV-2 infection in ovarian cells in vivo or in vitro has yet to be determined.
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Affiliation(s)
- Yohan Choi
- Department of Obstetrics and Gynecology, University of Kentucky College of Medicine, Lexington, Kentucky
| | - Hayce Jeon
- Department of Obstetrics and Gynecology, University of Kentucky College of Medicine, Lexington, Kentucky
| | - Mats Brännström
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, University of Gothenburg, Gothenburg, Sweden, and Stockholm IVF-EUGIN, Stockholm, Sweden
| | | | - Thomas E Curry
- Department of Obstetrics and Gynecology, University of Kentucky College of Medicine, Lexington, Kentucky
| | - Misung Jo
- Department of Obstetrics and Gynecology, University of Kentucky College of Medicine, Lexington, Kentucky.
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141
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Chen P, Wang J, Xu X, Li Y, Zhu Y, Li X, Li M, Hao P. Molecular dynamic simulation analysis of SARS-CoV-2 spike mutations and evaluation of ACE2 from pets and wild animals for infection risk. Comput Biol Chem 2021; 96:107613. [PMID: 34896769 PMCID: PMC8634692 DOI: 10.1016/j.compbiolchem.2021.107613] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/29/2021] [Indexed: 12/28/2022]
Abstract
Coronavirus Disease 2019 (COVID-19) is an ongoing global health emergency that has caused tremendous stress and loss of life worldwide. The viral spike glycoprotein is a critical molecule mediating transmission of SARS-CoV-2 by interacting with human ACE2. However, through the course of the pandemics, there has not been a thorough analysis of the spike protein mutations, and on how these mutants influence the transmission of SARS-CoV-2. Besides, cases of SARS-CoV-2 infection among pets and wild animals have been reported, so the susceptibility of these animals requires great attention to investigate, as they may also link to the renewed question of a possible intermediate host for SARS-CoV-2 before it was transmitted to humans. With over 226,000 SARS-CoV-2 sequences obtained, we found 1573 missense mutations in the spike gene, and 226 of them were within the receptor-binding domain (RBD) region that directly interacts with human ACE2. Modeling the interactions between SARS-CoV-2 spike mutants and ACE2 molecules showed that most of the 74 missense mutations in the RBD region of the interaction interface had little impact on spike binding to ACE2, whereas several within the spike RBD increased the binding affinity toward human ACE2 thus making the virus likely more contagious. On the other hand, modeling the interactions between animal ACE2 molecules and SARS-CoV-2 spike revealed that many pets and wild animals' ACE2 had a variable binding ability. Particularly, ACE2 of bamboo rat had stronger binding to SARS-CoV-2 spike protein, whereas that of mole, vole, Mus pahari, palm civet, and pangolin had a weaker binding compared to human ACE2. Our results provide structural insights into the impact on interactions of the SARS-CoV-2 spike mutants to human ACE2, and shed light on SARS-CoV-2 transmission in pets and wild animals, and possible clues to the intermediate host(s) for SARS-CoV-2.
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Affiliation(s)
- Ping Chen
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jingfang Wang
- Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xintian Xu
- Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yuping Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Yan Zhu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Science, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Ming Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China.
| | - Pei Hao
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China.
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Role of multiple factors likely contributing to severity-mortality of COVID-19. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 96:105101. [PMID: 34624542 PMCID: PMC8491954 DOI: 10.1016/j.meegid.2021.105101] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 02/08/2023]
Abstract
COVID-19 stalled the world in 2020 and continues to be the greatest health crisis of this generation. While the apparent case fatality rates across fluctuates around ~2% globally, associated mortality/death rate (deaths per million population) varies distinctly across regions from the global average of ~600 per million population. Heterogeneous factors have been linked with COVID-19 associated mortalities and these include age, share of geriatric population, comorbidities, trained immunity and climatic conditions. Apart from direct or indirect role of endemic diseases, dietary factors and host immunity in regulating COVID-19 severity, human behaviour will inevitably control outcome of this pandemic. Comprehensive understanding of these factors will have a bearing on management of future health crises.
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143
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Alshammary AF, Al-Sulaiman AM. The journey of SARS-CoV-2 in human hosts: a review of immune responses, immunosuppression, and their consequences. Virulence 2021; 12:1771-1794. [PMID: 34251989 PMCID: PMC8276660 DOI: 10.1080/21505594.2021.1929800] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly infectious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Laboratory findings from a significant number of patients with COVID-19 indicate the occurrence of leukocytopenia, specifically lymphocytopenia. Moreover, infected patients can experience contrasting outcomes depending on lymphocytopenia status. Patients with resolved lymphocytopenia are more likely to recover, whereas critically ill patients with signs of unresolved lymphocytopenia develop severe complications, sometimes culminating in death. Why immunodepression manifests in patients with COVID-19 remains unclear. Therefore, the evaluation of clinical symptoms and laboratory findings from infected patients is critical for understanding the disease course and its consequences. In this review, we take a logical approach to unravel the reasons for immunodepression in patients with COVID-19. Following the footprints of the virus within host tissues, from entry to exit, we extrapolate the mechanisms underlying the phenomenon of immunodepression.
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Affiliation(s)
- Amal F. Alshammary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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144
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Dastar S, Gharesouran J, Mortazavi D, Hosseinzadeh H, Kian SJ, Taheri M, Ghafouri-Fard S, Jamali E, Rezazadeh M. COVID-19 pandemic: Insights into genetic susceptibility to SARS-CoV-2 and host genes implications on virus spread, disease severity and outcomes. Hum Antibodies 2021; 30:1-14. [PMID: 34864654 DOI: 10.3233/hab-211506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The outbreak of the newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) all over the world has caused global public health emergencies, international concern and economic crises. The systemic SARS-CoV-2 disease (COVID-19) can lead to death through causing unrestrained cytokines-storm and subsequent pulmonary shutdown among the elderly and patients with pre-existing comorbidities. Additionally, in comparison with poor nations without primary health care services, in developed countries with advanced healthcare system we can witness higher number of infections per one million people. In this review, we summarize the latest studies on genes associated with SARS-CoV-2 pathogenesis and propose possible mechanisms of the virus replication cycle and its triggered signaling pathways to encourage researchers to investigate genetic and immune profiles of the disease and try strategies for its treatment. Our review shows that immune response in people with different genetic background might vary as African and then Asian populations have lowest number of affected cases compared with European and American nations. Considering SARS-CoV-2 pathogenesis, we put forward some potentially important genetic gateways to COVID-19 infection including genes involved in the entry and replication of SARS-CoV-2 and the regulation of host immune response which might represent explanation for its spread, severity, and morality. Finally, we suggest that genetic alterations within these gateways could be critical factors in influencing geographical discrepancies of the virus, so it is essential to fully study them and design appropriated and reliable therapeutic agents against COVID-19.
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Affiliation(s)
- Saba Dastar
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Fatih, Istanbul, Turkey
| | - Jalal Gharesouran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Deniz Mortazavi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hassan Hosseinzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Jalal Kian
- Department of Virology, Iran University of Medical Sciences, School of Medicine, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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145
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Gusmão PAO, Roveda JRC, Leite ASM, Leite AS, Marinho CC. Changes in olfaction and taste in patients hospitalized for COVID-19 and their relationship to patient evolution during hospitalization. Braz J Otorhinolaryngol 2021; 88 Suppl 5:S75-S82. [PMID: 34876382 PMCID: PMC8610827 DOI: 10.1016/j.bjorl.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/08/2021] [Accepted: 11/02/2021] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES During the COVID-19 pandemic, several cases of changes in olfaction and taste associated with the infection have been reported. Therefore, otolaryngologists are frequently the first medical professionals sought by patients. The aim of this study was to evaluate the frequency of olfaction and taste disorders in patients hospitalized with COVID-19, and their association with other clinical manifestations and patient evolution during hospitalization. METHODS 248 patients, admitted to three public hospitals in Belo Horizonte, Minas Gerais, Brazil, were prospectively included: Hospital das Clínicas da Universidade Federal de Minas Gerais (HC-UFMG), Hospital Júlia Kubitschek (HJK) and Hospital Eduardo de Menezes (HEM), who, upon admission to hospital, presented with Severe Acute Respiratory Syndrome due to COVID-19. Clinical and laboratory variables and outcomes during hospitalization were prospectively collected from the electronic medical records. The collection of sociodemographic and symptomatology data during the acute phase was carried out prospectively in electronic medical records and confirmed with the patients at a subsequent outpatient visit. RESULTS The most frequently reported symptoms were dyspnea (77.4%), cough (69.8%) and fever (55.2%). During the acute phase of the disease, 95 (38.3%) and 87 (35.1%) patients reported taste and olfaction disorders, respectively. There was a lower prevalence of dysosmia among patients with previous comorbidities (p < 0.05). Both symptoms were associated with less need for intensive care admission (p = 0.001 for dysgeusia and p = 0.021 for dysosmia) and a negative correlation with length of hospital stay (dysosmia: r = -0.175, p < 0.05; dysgeusia: r = -0.29, p < 0.001) and length of stay in the ICU (dysosmia: r = -0.136, p < 0.05; dysgeusia: r = -0.215, p < 0.05). The absence of taste disorders was also associated with a greater need for mechanical ventilation (p < 0.001). CONCLUSION Changes in taste and olfaction were reported by a large number of patients in the acute phase of COVID-19. In this study, both were markers of better clinical patient evolution. LEVEL OF EVIDENCE 1B.
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Affiliation(s)
- Pedro Antônio O.A. Gusmão
- Universidade Federal de Minas Gerais, Faculdade de Medicina, Belo Horizonte, MG, Brazil,Corresponding author.
| | | | | | - Arnaldo S. Leite
- Universidade Federal de Minas Gerais, Faculdade de Medicina, Departamento de Clínica Médica, Belo Horizonte, MG, Brazil
| | - Carolina C. Marinho
- Universidade Federal de Minas Gerais, Faculdade de Medicina, Departamento de Clínica Médica, Belo Horizonte, MG, Brazil
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Celewicz A, Celewicz M, Michalczyk M, Woźniakowska-Gondek P, Krejczy K, Misiek M, Rzepka R. Pregnancy as a Risk Factor of Severe COVID-19. J Clin Med 2021; 10:jcm10225458. [PMID: 34830740 PMCID: PMC8625663 DOI: 10.3390/jcm10225458] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Since first being identified in December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as an etiological agent behind Coronavirus disease 19 (COVID-19), has caused three waves of a global pandemic, with a fourth in progress. Despite its high percentage of asymptomatic and low-symptomatic courses of illness, the SARS-CoV-2 pandemic has claimed a higher death toll than the SARS-CoV and MERS-CoV epidemics because of its high infectivity when compared to the other coronaviruses. High COVID-19 mortality is associated with age and other coexisting morbidities, as well as healthcare quality. According to several studies, pregnant women are at a higher risk of severe COVID-19 infection and adverse pregnancy outcomes (caesarean delivery, pre-term birth, low birth weight, preeclampsia, ICU admission, and need for mechanical ventilation). In our review of recent literature, we focused on the effects of COVID-19 in pregnant women, emphasizing the subcellular pathophysiology of SARS-CoV-2. In this paper, we concentrate on the pathophysiology of sub-cellular changes in COVID-19 and endeavor to highlight the aspects that manifest in physiological pregnancy and potentially create a higher risk of SARS-CoV-2 infection and acute COVID-19 symptoms. Understanding how pregnancy-associated changes can cause a synergistic effect with COVID-19 may point us in the right direction for future prophylaxis and treatment for women undergoing COVID-19 during pregnancy.
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Affiliation(s)
- Aleksander Celewicz
- Department of Gynecology and Obstetrics, Collegium Medicum, University of Zielona Góra, 65-001 Zielona Góra, Poland; (M.C.); (M.M.); (P.W.-G.); (K.K.); (R.R.)
- Correspondence:
| | - Marta Celewicz
- Department of Gynecology and Obstetrics, Collegium Medicum, University of Zielona Góra, 65-001 Zielona Góra, Poland; (M.C.); (M.M.); (P.W.-G.); (K.K.); (R.R.)
| | - Michał Michalczyk
- Department of Gynecology and Obstetrics, Collegium Medicum, University of Zielona Góra, 65-001 Zielona Góra, Poland; (M.C.); (M.M.); (P.W.-G.); (K.K.); (R.R.)
| | - Paula Woźniakowska-Gondek
- Department of Gynecology and Obstetrics, Collegium Medicum, University of Zielona Góra, 65-001 Zielona Góra, Poland; (M.C.); (M.M.); (P.W.-G.); (K.K.); (R.R.)
| | - Kamila Krejczy
- Department of Gynecology and Obstetrics, Collegium Medicum, University of Zielona Góra, 65-001 Zielona Góra, Poland; (M.C.); (M.M.); (P.W.-G.); (K.K.); (R.R.)
| | - Marcin Misiek
- Holy Cross Cancer Center, Clinical Gynecology, 25-743 Kielce, Poland;
| | - Rafał Rzepka
- Department of Gynecology and Obstetrics, Collegium Medicum, University of Zielona Góra, 65-001 Zielona Góra, Poland; (M.C.); (M.M.); (P.W.-G.); (K.K.); (R.R.)
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Abstract
Since the start of the pandemic, SARS-CoV-2 has infected almost 200 million human hosts and is set to encounter and gain entry in many more in the coming months. As the coronavirus flourish, the evolutionary pressure selects those variants that can complete the infection cycle faster and reproduce in large numbers compared to others. This increase in infectivity and transmissibility coupled with the immune response from high viral load may cause moderate to severe disease. Whether this leads to enhanced virulence in the prevalent Alpha and Delta variants is still not clear. This review describes the different types of SARS-CoV-2 variants that are now prevalent, their emergence, the mutations responsible for their growth advantages, and how they affect vaccine efficacy and increase chances of reinfection. Finally, we have also summarized the efforts made to recognize and predict the mutations, which can cause immune escape and track their emergence through impactful genomic surveillance.
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MESH Headings
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Binding Sites
- COVID-19/epidemiology
- COVID-19/pathology
- COVID-19/transmission
- COVID-19/virology
- COVID-19 Vaccines
- Genome, Viral
- Humans
- Immune Evasion/genetics
- Models, Molecular
- Mutation
- Phylogeny
- Protein Binding
- Protein Interaction Domains and Motifs
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Receptors, Virus/immunology
- SARS-CoV-2/classification
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/genetics
- Serine Endopeptidases/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Virulence
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Affiliation(s)
- Raju Mukherjee
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Rohit Satardekar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
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148
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Lopes LR, de Mattos Cardillo G, de Lucca Pina NC, da Silva Junior AC, Kasinski SK, Bandiera-Paiva P. Prediction of SARS-CoV-2 hosts among Brazilian mammals and new coronavirus transmission chain using evolutionary bioinformatics. ANIMAL DISEASES 2021; 1:20. [PMID: 34778882 PMCID: PMC8475823 DOI: 10.1186/s44149-021-00020-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 are thought to transmit to humans via wild mammals, especially bats. However, evidence for direct bat-to-human transmission is lacking. Involvement of intermediate hosts is considered a reason for SARS-CoV-2 transmission to humans and emergence of outbreak. Large biodiversity is found in tropical territories, such as Brazil. On the similar line, this study aimed to predict potential coronavirus hosts among Brazilian wild mammals based on angiotensin-converting enzyme 2 (ACE2) sequences using evolutionary bioinformatics. Cougar, maned wolf, and bush dogs were predicted as potential hosts for coronavirus. These indigenous carnivores are philogenetically closer to the known SARS-CoV/SARS-CoV-2 hosts and presented low ACE2 divergence. A new coronavirus transmission chain was developed in which white-tailed deer, a susceptible SARS-CoV-2 host, have the central position. Cougar play an important role because of its low divergent ACE2 level in deer and humans. The discovery of these potential coronavirus hosts will be useful for epidemiological surveillance and discovery of interventions that can contribute to break the transmission chain. Supplementary Information The online version contains supplementary material available at 10.1186/s44149-021-00020-w.
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Affiliation(s)
- Luciano Rodrigo Lopes
- Bioinformatics and Bio-Data Science Division - Health Informatics Department, Universidade Federal de São Paulo - UNIFESP, Rua Botucatu 862 - Prédio Leal Prado (térreo), CEP: 04023-062, Sao Paulo [SP], SP Brasil
| | - Giancarlo de Mattos Cardillo
- Department of Neurology and Neurosurgery, Universidade Federal de São Paulo - UNIFESP, Sao Paulo [SP], SP Brasil
| | - Natália Carvalho de Lucca Pina
- Bioinformatics and Bio-Data Science Division - Health Informatics Department, Universidade Federal de São Paulo - UNIFESP, Rua Botucatu 862 - Prédio Leal Prado (térreo), CEP: 04023-062, Sao Paulo [SP], SP Brasil
| | - Antonio Carlos da Silva Junior
- Bioinformatics and Bio-Data Science Division - Health Informatics Department, Universidade Federal de São Paulo - UNIFESP, Rua Botucatu 862 - Prédio Leal Prado (térreo), CEP: 04023-062, Sao Paulo [SP], SP Brasil
| | - Silvana Kertzer Kasinski
- Bioinformatics and Bio-Data Science Division - Health Informatics Department, Universidade Federal de São Paulo - UNIFESP, Rua Botucatu 862 - Prédio Leal Prado (térreo), CEP: 04023-062, Sao Paulo [SP], SP Brasil
| | - Paulo Bandiera-Paiva
- Bioinformatics and Bio-Data Science Division - Health Informatics Department, Universidade Federal de São Paulo - UNIFESP, Rua Botucatu 862 - Prédio Leal Prado (térreo), CEP: 04023-062, Sao Paulo [SP], SP Brasil
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149
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Ghafari M, Simmonds P, Pybus OG, Katzourakis A. A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses. Curr Biol 2021; 31:4689-4696.e5. [PMID: 34478645 PMCID: PMC8585505 DOI: 10.1016/j.cub.2021.08.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/02/2021] [Accepted: 08/05/2021] [Indexed: 01/16/2023]
Abstract
Estimating viral timescales is fundamental in understanding the evolutionary biology of viruses. Molecular clocks are widely used to reveal the recent evolutionary histories of viruses but may severely underestimate their longer-term origins because of the inverse correlation between inferred rates of evolution and the timescale of their measurement. Here, we provide a predictive mechanistic model that readily explains the rate decay phenomenon over a wide range of timescales and recapitulates the ubiquitous power-law rate decay with a slope of -0.65. We show that standard substitution models fail to correctly estimate divergence times once the most rapidly evolving sites saturate, typically after hundreds of years in RNA viruses and thousands of years in DNA viruses. Our model successfully recreates the observed pattern of decay and explains the evolutionary processes behind the time-dependent rate phenomenon. We then apply our model to re-estimate the date of diversification of genotypes of hepatitis C virus to 423,000 (95% highest posterior density [HPD]: 394,000-454,000) years before present, a time preceding the dispersal of modern humans out of Africa, and show that the most recent common ancestor of sarbecoviruses dates back to 21,000 (95% HPD: 19,000-22,000) years ago, nearly thirty times older than previous estimates. This creates a new perspective for our understanding of the origins of these viruses and also suggests that a substantial revision of evolutionary timescales of other viruses can be similarly achieved.
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Affiliation(s)
- Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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150
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Lupala CS, Kumar V, Su XD, Wu C, Liu H. Computational insights into differential interaction of mammalian angiotensin-converting enzyme 2 with the SARS-CoV-2 spike receptor binding domain. Comput Biol Med 2021; 141:105017. [PMID: 34758907 PMCID: PMC8565036 DOI: 10.1016/j.compbiomed.2021.105017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 01/29/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Angiotensin-converting enzyme 2 (ACE2) has been identified as the host cell receptor that binds to the receptor-binding domain (RBD) of the SARS-COV-2 spike protein and mediates cell entry. Because the ACE2 proteins are widely available in mammals, it is important to investigate the interactions between the RBD and the ACE2 of other mammals. Here we analyzed the sequences of ACE2 proteins from 16 mammals, predicted the structures of ACE2-RBD complexes by homology modeling, and refined the complexes using molecular dynamics simulation. Analyses on sequence, structure, and dynamics synergistically provide valuable insights into the interactions between ACE2 and RBD. The analysis outcomes suggest that the ACE2 of bovine, cat, and panda form strong binding interactions with RBD, while in the cases of rat, least horseshoe bat, horse, pig, mouse, and civet, the ACE2 proteins interact weakly with RBD.
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Affiliation(s)
- Cecylia Severin Lupala
- Complex Systems Division, Beijing Computational Science Research Center, Haidian, Beijing, 100193, People's Republic of China.
| | - Vikash Kumar
- Complex Systems Division, Beijing Computational Science Research Center, Haidian, Beijing, 100193, People's Republic of China.
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, People's Republic of China
| | - Chun Wu
- Department of Chemistry & Biochemistry and Molecular & Cellular Biosciences, Rowan University, Glassboro, NJ, 08028, USA
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, Haidian, Beijing, 100193, People's Republic of China; Physics Department, Beijing Normal University, Haidian, Beijing, 100875, People's Republic of China
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