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Galván-Ojeda HJ, Acosta-Elias J, Saavedra-Alanis VM, Espinosa-Tanguma R, Del Carmen Rodríguez-Aranda M, Hernández-Arteaga AC, Navarro-Contreras HR. Raman spectroscopy study of 7,8-dihydrofolate inhibition on the Wuhan strain SARS-CoV-2 binding to human ACE2 receptor. Spectrochim Acta A Mol Biomol Spectrosc 2024; 312:124050. [PMID: 38402702 DOI: 10.1016/j.saa.2024.124050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/27/2024]
Abstract
Emerging evidence suggests that elevated levels of folic acid in the bloodstream may confer protection against Wuhan-SARS-CoV-2 infection and mitigate its associated symptoms. Notably, two comprehensive studies of COVID-19 patients in Israel and UK uncovered a remarkable trend, wherein individuals with heightened folic acid levels exhibited only mild symptoms and necessitated no ventilatory support. In parallel, research has underscored the potential connection between decreased folic acid levels and the severity of Covid-19 among hospitalized patients. Yet, the underlying mechanisms governing this intriguing inhibition remain elusive. In a quest to elucidate these mechanisms, we conducted a molecular dynamics simulation approach followed by a Raman spectroscopy study to delve into the intricate interplay between the folic acid metabolite, 7,8-dihydrofolate (DHF), and the angiotensin-converting enzyme ACE2 receptor, coupled with its interaction with the receptor-binding domain (RBD) of the Wuhan strain of SARS-CoV-2. Through a meticulous exploration, we scrutinized the transformation of the ACE2 + RBD complex, allowing these reactants to form bonds. This was juxtaposed with a similar investigation where ACE2 was initially permitted to react with DHF, followed by the exposure of the ACE2 + DHF complex to RBD. We find that DHF, when bonded to ACE2, functions as a physical barrier, effectively inhibiting the binding of the Wuhan strain RBD. This physicochemical process offers a cogent explanation for the observed inhibition of host cell infection in subjects receiving supplementary folic acid doses, as epidemiologically substantiated in multiple studies. This study not only sheds light on a potential avenue for mitigating SARS-CoV-2 infection but also underscores the crucial role of folic acid metabolites in host-virus interactions. This research paves the way for novel therapeutic strategies in the battle against COVID-19 and reinforces the significance of investigating the molecular mechanisms underlying the protective effects of folic acid in the context of viral infections.
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Affiliation(s)
- Hiram Joazet Galván-Ojeda
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - Jesus Acosta-Elias
- Facultad de Ciencias, Universidad Autónoma de San Luís Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, Mexico
| | - Victor M Saavedra-Alanis
- Facultad de Medicina, Universidad Autónoma de San Luís Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, Mexico
| | - Ricardo Espinosa-Tanguma
- Facultad de Medicina, Universidad Autónoma de San Luís Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, Mexico
| | - Ma Del Carmen Rodríguez-Aranda
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - Aida Catalina Hernández-Arteaga
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - Hugo Ricardo Navarro-Contreras
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico.
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Ramos-Duarte VA, Orlowski A, Jaquenod de Giusti C, Corigliano MG, Legarralde A, Mendoza-Morales LF, Atela A, Sánchez MA, Sander VA, Angel SO, Clemente M. Safe plant Hsp90 adjuvants elicit an effective immune response against SARS-CoV2-derived RBD antigen. Vaccine 2024:S0264-410X(24)00450-X. [PMID: 38631949 DOI: 10.1016/j.vaccine.2024.04.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
To better understand the role of pHsp90 adjuvant in immune response modulation, we proposed the use of the Receptor Binding Domain (RBD) of the Spike protein of SARS-CoV2, the principal candidate in the design of subunit vaccines. We evaluated the humoral and cellular immune responses against RBD through the strategy "protein mixture" (Adjuvant + Antigen). The rRBD adjuvanted with rAtHsp81.2 group showed a higher increase of the anti-rRBD IgG1, while the rRBD adjuvanted with rNbHsp90.3 group showed a significant increase in anti-rRBD IgG2b/2a. These results were consistent with the cellular immune response analysis. Spleen cell cultures from rRBD + rNbHsp90.3-immunized mice showed significantly increased IFN-γ production. In contrast, spleen cell cultures from rRBD + rAtHsp81.2-immunized mice showed significantly increased IL-4 levels. Finally, vaccines adjuvanted with rNbHsp90.3 induced higher neutralizing antibody responses compared to those adjuvanted with rAtHsp81.2. To know whether both chaperones must form complexes to generate an effective immune response, we performed co-immunoprecipitation (co-IP) assays. The results indicated that the greater neutralizing capacity observed in the rRBD adjuvanted with rNbHsp90.3 group would be given by the rRBD-rNbHsp90.3 interaction rather than by the quality of the immune response triggered by the adjuvants. These results, together with our previous results, provide a comparative benchmark of these two novel and safe vaccine adjuvants for their capacity to stimulate immunity to a subunit vaccine, demonstrating the capacity of adjuvanted SARS-CoV2 subunit vaccines. Furthermore, these results revealed differences in the ability to modulate the immune response between these two pHsp90s, highlighting the importance of adjuvant selection for future rational vaccine and adjuvant design.
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Affiliation(s)
- Victor A Ramos-Duarte
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Alejandro Orlowski
- Centro de Investigaciones Cardiovasculares "Dr. Horacio E. Cingolani" (CONICET), Universidad Nacional de La Plata, Facultad de Ciencias Médicas, La Plata, Argentina
| | - Carolina Jaquenod de Giusti
- Centro de Investigaciones Cardiovasculares "Dr. Horacio E. Cingolani" (CONICET), Universidad Nacional de La Plata, Facultad de Ciencias Médicas, La Plata, Argentina
| | - Mariana G Corigliano
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Ariel Legarralde
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Luisa F Mendoza-Morales
- Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina; Laboratorio de Biotecnologías en Bovinos y Ovinos, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Provincia de Buenos Aires, Argentina
| | - Agustín Atela
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Manuel A Sánchez
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina
| | - Valeria A Sander
- Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina; Laboratorio de Biotecnologías en Bovinos y Ovinos, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Provincia de Buenos Aires, Argentina
| | - Sergio O Angel
- Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina; Laboratorio de Parasitología Molecular-UB2, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires, Argentina
| | - Marina Clemente
- Laboratorio de Molecular Farming y Vacunas-UB6, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, Chascomús, Provincia de Buenos Aires 7030, Argentina; Escuela de Bio y Nanotecnologías, Campus Miguelete, 25 de Mayo y Francia, San Martín, Provincia de Buenos Aires 1650, Argentina.
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Tiwary BK. A positive selection at binding site 501 in the B.1 lineage might have triggered the highly infectious sub-lineages of SARS-CoV-2. Gene 2024; 915:148427. [PMID: 38575097 DOI: 10.1016/j.gene.2024.148427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
The descendants of the B lineage are the most predominant variants among the SARS-CoV-2 virus due to the incorporation of new mutations augmenting the infectivity of the virus. There is a substantial increase in the transition transversion bias, nucleotide diversity and purifying selection on the spike protein in the descendants of the B lineage of the SARS-CoV-2 virus on a temporal scale. A strong bias for C-to-U substitutions is found in the genes encoding spike protein in this lineage. The positive selection has operated on the spike gene of B lineages and its sub-lineages. The B.1 lineage has undergone positive selection on site 501 of the receptor binding domain ultimately reflected in a key substitution N501Y in its three descendant lineages namely B.1.1.7, B.1.351 and P.1. The intensity of purifying selection on the multiple sites of the spike gene has increased substantially in the sub-lineages of B.1 in a timescale. The binding site 501 on the spike protein in B lineage is found to coevolve with other amino acid sites. This study sheds light on the evolutionary trajectory of the B lineage into highly infectious descendants in the recent past under the influence of positive and purifying selection exerted by natural immunity and vaccination of the host.
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Affiliation(s)
- Basant K Tiwary
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605 014, India.
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Ozden B, Şamiloğlu E, Özsan A, Erguven M, Yükrük C, Koşaca M, Oktayoğlu M, Menteş M, Arslan N, Karakülah G, Barlas AB, Savaş B, Karaca E. Benchmarking the accuracy of structure-based binding affinity predictors on Spike-ACE2 deep mutational interaction set. Proteins 2024; 92:529-539. [PMID: 37991066 DOI: 10.1002/prot.26645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 11/23/2023]
Abstract
Since the start of COVID-19 pandemic, a huge effort has been devoted to understanding the Spike (SARS-CoV-2)-ACE2 recognition mechanism. To this end, two deep mutational scanning studies traced the impact of all possible mutations across receptor binding domain (RBD) of Spike and catalytic domain of human ACE2. By concentrating on the interface mutations of these experimental data, we benchmarked six commonly used structure-based binding affinity predictors (FoldX, EvoEF1, MutaBind2, SSIPe, HADDOCK, and UEP). These predictors were selected based on their user-friendliness, accessibility, and speed. As a result of our benchmarking efforts, we observed that none of the methods could generate a meaningful correlation with the experimental binding data. The best correlation is achieved by FoldX (R = -0.51). When we simplified the prediction problem to a binary classification, that is, whether a mutation is enriching or depleting the binding, we showed that the highest accuracy is achieved by FoldX with a 64% success rate. Surprisingly, on this set, simple energetic scoring functions performed significantly better than the ones using extra evolutionary-based terms, as in Mutabind and SSIPe. Furthermore, we demonstrated that recent AI approaches, mmCSM-PPI and TopNetTree, yielded comparable performances to the force field-based techniques. These observations suggest plenty of room to improve the binding affinity predictors in guessing the variant-induced binding profile changes of a host-pathogen system, such as Spike-ACE2. To aid such improvements we provide our benchmarking data at https://github.com/CSB-KaracaLab/RBD-ACE2-MutBench with the option to visualize our mutant models at https://rbd-ace2-mutbench.github.io/.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Eda Şamiloğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Atakan Özsan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehmet Erguven
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Can Yükrük
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehdi Koşaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Melis Oktayoğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Muratcan Menteş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Nazmiye Arslan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ayşe Berçin Barlas
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Büşra Savaş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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Castelnovo A, Schraemli M, Schenck CH, Manconi M. The parasomnia defense in sleep-related homicide: A systematic review and a critical analysis of the medical literature. Sleep Med Rev 2024; 74:101898. [PMID: 38364685 DOI: 10.1016/j.smrv.2024.101898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/27/2023] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
This review critically analyzes the forensic application of the Parasomnia Defense in homicidal incidents, drawing from medical literature on disorders of arousal (DOA) and rapid-eye-movement sleep behavior disorder (RBD). A systematic search of PubMed, Scopus, Embase, and Cochrane databases was conducted until October 16, 2022. We screened English-language articles in peer-reviewed journals discussing murders committed during sleep with a Parasomnia Defense. We followed PRISMA guidelines, extracting event details, diagnosis methods, factors influencing the acts, perpetrator behavior, timing, motives, concealment, mental experiences, victim demographics, and court verdicts. Three sleep experts evaluated each case. We selected ten homicides, four attempted homicides, and one homicide/attempted homicide that met inclusion/exclusion criteria. Most cases were suspected DOA as unanimously confirmed by experts. RBD cases were absent. Among aggressors, a minority reported dream-like experiences. Victims were primarily female family members killed in or near the bed by hands and/or with sharp objects. Objective sleep data and important crime scene details were often missing. Verdicts were ununiform. Homicides during DOA episodes, though rare, are documented, validating the Parasomnia Defense's use in forensics. RBD-related fatal aggression seems very uncommon. However, cases often lack diagnostic clarity. We propose updated guidelines to enhance future reporting and understanding of such incidents.
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Affiliation(s)
- Anna Castelnovo
- Neurocenter of Italian Switzerland, Ente Ospedaliero Cantonale, Ospedale Civico, Lugano, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland; University Hospital of Psychiatry and Psychotherapy, University of Bern, Bern, Switzerland.
| | - Matthias Schraemli
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Carlos H Schenck
- Minnesota Regional Sleep Disorders Center, Departments of Psychiatry, Hennepin County Medical Center, And University of Minnesota Medical School, Minneapolis, MN, United States.
| | - Mauro Manconi
- Neurocenter of Italian Switzerland, Ente Ospedaliero Cantonale, Ospedale Civico, Lugano, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland; Department of Neurology, University Hospital, Inselspital, Bern, Switzerland
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Niu S, Zhao Z, Liu Z, Rong X, Chai Y, Bai B, Han P, Shang G, Ren J, Wang Y, Zhao X, Liu K, Tian WX, Wang Q, Gao GF. Structural basis and analysis of hamster ACE2 binding to different SARS-CoV-2 spike RBDs. J Virol 2024; 98:e0115723. [PMID: 38305152 PMCID: PMC10949455 DOI: 10.1128/jvi.01157-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
Pet golden hamsters were first identified being infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant of concern (VOC) and transmitted the virus back to humans in Hong Kong in January 2022. Here, we studied the binding of two hamster (golden hamster and Chinese hamster) angiotensin-converting enzyme 2 (ACE2) proteins to the spike protein receptor-binding domains (RBDs) of SARS-CoV-2 prototype and eight variants, including alpha, beta, gamma, delta, and four omicron sub-variants (BA.1, BA.2, BA.3, and BA.4/BA.5). We found that the two hamster ACE2s present slightly lower affinity for the RBDs of all nine SARS-CoV-2 viruses tested than human ACE2 (hACE2). Furthermore, the similar infectivity to host cells expressing hamster ACE2s and hACE2 was confirmed with the nine pseudotyped SARS-CoV-2 viruses. Additionally, we determined two cryo-electron microscopy (EM) complex structures of golden hamster ACE2 (ghACE2)/delta RBD and ghACE2/omicron BA.3 RBD. The residues Q34 and N82, which exist in many rodent ACE2s, are responsible for the lower binding affinity of ghACE2 compared to hACE2. These findings suggest that all SARS-CoV-2 VOCs may infect hamsters, highlighting the necessity of further surveillance of SARS-CoV-2 in these animals.IMPORTANCESARS-CoV-2 can infect many domestic animals, including hamsters. There is an urgent need to understand the binding mechanism of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants to hamster receptors. Herein, we showed that two hamster angiotensin-converting enzyme 2s (ACE2s) (golden hamster ACE2 and Chinese hamster ACE2) can bind to the spike protein receptor-binding domains (RBDs) of SARS-CoV-2 prototype and eight variants and that pseudotyped SARS-CoV-2 viruses can infect hamster ACE2-expressing cells. The binding pattern of golden hamster ACE2 to SARS-CoV-2 RBDs is similar to that of Chinese hamster ACE2. The two hamster ACE2s present slightly lower affinity for the RBDs of all nine SARS-CoV-2 viruses tested than human ACE2. We solved the cryo-electron microscopy (EM) structures of golden hamster ACE2 in complex with delta RBD and omicron BA.3 RBD and found that residues Q34 and N82 are responsible for the lower binding affinity of ghACE2 compared to hACE2. Our work provides valuable information for understanding the cross-species transmission mechanism of SARS-CoV-2.
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Affiliation(s)
- Sheng Niu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Zhennan Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhimin Liu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Xiaoyu Rong
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bin Bai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Pengcheng Han
- School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Guijun Shang
- Cryo-EM Center, Shanxi Academy of Advanced Research and Innovation, Taiyuan, China
| | - Jianle Ren
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Ying Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Xin Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wen-xia Tian
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Qihui Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George Fu Gao
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Wang Y, Song J, Deng X, Wang J, Zhang M, Liu Y, Tang P, Liu H, Zhou Y, Tong G, Li G, Yu L. Nanoparticle vaccines based on the receptor binding domain of porcine deltacoronavirus elicit robust protective immune responses in mice. Front Immunol 2024; 15:1328266. [PMID: 38550592 PMCID: PMC10972852 DOI: 10.3389/fimmu.2024.1328266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
Background Porcine deltacoronavirus (PDCoV), a novel swine enteropathogenic coronavirus, challenges the global swine industry. Currently, there are no approaches preventing swine from PDCoV infection. Methods A new PDCoV strain named JS2211 was isolated. Next, the dimer receptor binding domain of PDCoV spike protein (RBD-dimer) was expressed using the prokaryotic expression system, and a novel nanoparticle containing RBD-dimer and ferritin (SC-Fe) was constructed using the SpyTag/SpyCatcher system. Finally, the immunoprotection of RBD-Fe nanoparticles was evaluated in mice. Results The novel PDCoV strain was located in the clade of the late Chinese isolate strains and close to the United States strains. The RBD-Fe nanoparticles were successfully established. Immune responses of the homologous prime-boost regime showed that RBD-Fe nanoparticles efficiently elicited specific humoral and cellular immune responses in mice. Notably, high level PDCoV RBD-specific IgG and neutralizing antibody (NA) could be detected, and the histopathological results showed that PDCoV infection was dramatically reduced in mice immunized with RBD-Fe nanoparticles. Conclusion This study effectively developed a candidate nanoparticle with receptor binding domain of PDCoV spike protein that offers protection against PDCoV infection in mice.
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Affiliation(s)
- Yuanhong Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Junhan Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xiaoying Deng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Junna Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Miao Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yun Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Pan Tang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Huili Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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8
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Feinstein P. Rapid Degradation of the Human ACE2 Receptor Upon Binding and Internalization of SARS-Cov-2-Spike- RBD Protein. bioRxiv 2024:2024.03.07.583884. [PMID: 38496410 PMCID: PMC10942428 DOI: 10.1101/2024.03.07.583884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
It is widely accepted that the SARS-CoV-2 betacoronavirus infects humans through binding the human Angiotensin Receptor 2 (ACE2) that lines the nasal cavity and lungs, followed by import into a cell utilizing the Transmembrane Protease, Serine 2 (TMPRSS2) cofactor. ACE2 binding is mediated by an approximately 200-residue portion of the SARS-CoV-2 extracellular spike protein, the receptor binding domain (RBD). Robust interactions are shown using a novel cell-based assay between an RBD membrane tethered-GFP fusion protein and the membrane bound ACE2-Cherry fusion protein. Several observations were not predicted including, quick and sustained interactions leading to internalization of RBD fusion protein into the ACE2 cells and rapid downregulation of the ACE2-Cherry fluorescence. Targeted mutation in the RBD disulfide Loop 4 led to a loss of internalization for several variants tested. However, a secreted RBD did not cause ACE2 downregulation of ACE2-Cherry fluorescence. Thus, the membrane associated form of RBD found on the viral coat may have long-term system wide consequences on ACE2 expressing cells.
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Affiliation(s)
- Paul Feinstein
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065
- The Graduate Center Programs in Biochemistry, Biology and CUNY Neuroscience Collaborative, 365 5th Ave, New York, NY 10016
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Feinstein P. Coronavirus Spike- RBD Variants Differentially Bind to the Human ACE2 Receptor. bioRxiv 2024:2024.03.07.583944. [PMID: 38496407 PMCID: PMC10942415 DOI: 10.1101/2024.03.07.583944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The SARS-CoV-2 betacoronavirus infects people through binding the human Angiotensin Receptor 2 (ACE2), followed by import into a cell utilizing the Transmembrane Protease, Serine 2 (TMPRSS2) and Furin cofactors. Analysis of the SARS-CoV-2 extracellular spike protein has suggested critical amino acids necessary for binding within a 197-residue portion, the receptor binding domain (RBD). A cell-based assay between a membrane tethered RBD-GFP fusion protein and the membrane bound ACE2-Cherry fusion protein allowed for mutational intersection of both RBD and ACE2 proteins. Data shows Omicron BA.1 and BA.2 variants have altered dependency on the amino terminus of ACE2 protein and suggests multiple epitopes on both proteins stabilize their interactions at the Nt and internal region of ACE2. In contrast, the H-CoV-NL63 RBD is only dependent on the ACE2 internal region for binding. A peptide inhibitor approach to this internal region thus far have failed to block binding of RBDs to ACE2, suggesting that several binding regions on ACE2 are sufficient to allow functional interactions. In sum, the RBD binding surface of ACE2 appears relatively fluid and amenable to bind a range of novel variants.
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Affiliation(s)
- Paul Feinstein
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065
- The Graduate Center Programs in Biochemistry, Biology and CUNY Neuroscience Collaborative, 365 5th Ave, New York, NY 10016
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Zhang RG, Liu XJ, Guo YL, Chen CL. SARS-CoV-2 spike protein receptor binding domain promotes IL-6 and IL-8 release via ATP/P2Y 2 and ERK1/2 signaling pathways in human bronchial epithelia. Mol Immunol 2024; 167:53-61. [PMID: 38359646 DOI: 10.1016/j.molimm.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
The spike protein of SARS-CoV-2 as well as its receptor binding domain (RBD) has been demonstrated to be capable of activating the release of pro-inflammatory mediators in endothelial cells and immune cells such as monocytes. However, the effects of spike protein or its RBD on airway epithelial cells and mechanisms underlying these effects have not been adequately characterized. Here, we show that the RBD of spike protein alone can induce bronchial epithelial inflammation in a manner of ATP/P2Y2 dependence. Incubation of human bronchial epithelia with RBD induced IL-6 and IL-8 release, which could be inhibited by antibody. The incubation of RBD also up-regulated the expression of inflammatory indicators such as ho-1 and mkp-1. Furthermore, ATP secretion was observed after RBD treatment, P2Y2 receptor knock down by siRNA significantly suppressed the IL-6 and IL-8 release evoked by RBD. Additionally, S-RBD elevated the phosphorylation level of ERK1/2, and the effect that PD98059 can inhibit the pro-inflammatory cytokine release suggested the participation of ERK1/2. These novel findings provide new evidence of SARS-CoV-2 on airway inflammation and introduce purinergic signaling as promising treatment target.
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Affiliation(s)
- Rui-Gang Zhang
- Department of Physiology, Basic Medical School, Guangdong Medical University, Zhanjiang, China.
| | - Xing-Jian Liu
- Department of Physiology, Basic Medical School, Guangdong Medical University, Zhanjiang, China
| | - Yu-Ling Guo
- First Clinical School, Guangdong Medical University, Zhanjiang, China
| | - Chun-Ling Chen
- Department of Physiology, Basic Medical School, Guangdong Medical University, Zhanjiang, China
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11
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Winiger RR, Perez L. Therapeutic antibodies and alternative formats against SARS-CoV-2. Antiviral Res 2024; 223:105820. [PMID: 38307147 DOI: 10.1016/j.antiviral.2024.105820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) heavily burdened the entire world. Despite a prompt generation of vaccines and therapeutics to confront infection, the virus remains a threat. The ancestor viral strain has evolved into several variants of concern, with the Omicron variant now having many distinct sublineages. Consequently, most available antibodies targeting the spike went obsolete and thus new therapies or therapeutic formats are needed. In this review we focus on antibody targets, provide an overview of the therapeutic progress made so far, describe novel formats being explored, and lessons learned from therapeutic antibodies that can enhance pandemic preparedness.
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Affiliation(s)
- Rahel R Winiger
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
| | - Laurent Perez
- University of Lausanne (UNIL), Lausanne University Hospital (CHUV), Service of Immunology and Allergy, and Center for Human Immunology Lausanne (CHIL), Switzerland.
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Chen J, Chen B, Zhao D, Feng X, Wang Q, Li Y, Chen J, Bai C, Guo X, He X, Zhang L, Yuan J. Predictors for early-onset psychotic symptoms in patients newly diagnosed with Parkinson's disease without psychosis at baseline: A 5-year cohort study. CNS Neurosci Ther 2024; 30:e14651. [PMID: 38432692 PMCID: PMC10909617 DOI: 10.1111/cns.14651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/20/2024] [Accepted: 02/08/2024] [Indexed: 03/05/2024] Open
Abstract
AIMS To investigate the risk factors for early-onset psychosis in Parkinson's disease (PD) in a cohort of patients from the Parkinson's Progression Markers Initiative. METHODS Longitudinal data on motor and non-motor features, dopamine transporter (DAT) imaging, and cerebrospinal fluid (CSF) measurements were collected. The survival probability of psychotic symptoms, potential risk factors for psychosis development over a 5-year follow-up period, and the performance of the prediction model were evaluated. RESULTS Among the 338 newly diagnosed patients with PD, 83 developed psychotic symptoms. Gastrointestinal autonomic dysfunction, presence of probable rapid-eye-movement sleep behavior disorder, and the ratio Aβ42: total-tau could independently predict onset of psychosis in PD (hazard ratio (HR) = 1.157, 95% confidence interval (CI) 1.022-1.309, p = 0.021, HR = 2.596, 95% CI 1.287-5.237, p = 0.008, and HR = 0.842, 95% CI 0.723-0.980, p = 0.027, respectively). The combined model integrating baseline clinical predictors, DAT imaging, and CSF measurements achieved better sensitivity than the clinical predictors alone (area under the curve = 0.770 [95% CI 0.672-0.868] vs. 0.714 [95% CI 0.625-0.802], p = 0.098). CONCLUSION We identified clinical and CSF predictors of early-onset psychosis in patients with PD. Our study provides evidence and implications for prognostic stratification and therapeutic approaches for PD psychosis.
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Affiliation(s)
- Jing Chen
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Baoyu Chen
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Danhua Zhao
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Xiaotong Feng
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Qi Wang
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Yuan Li
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Junyi Chen
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Chaobo Bai
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Xintong Guo
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Xiaoyu He
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
| | - Lin Zhang
- Department of Neurology, PF Center of Excellence, UC Davis Medical Center, UC Davis School of MedicineSacramentoCaliforniaUSA
| | - Junliang Yuan
- Department of NeurologyPeking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Peking UniversityBeijingChina
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Li J, Zhang BS, Wu HW, Liu CL, Guo HS, Zhao JH. The RNA-binding domain of DCL3 is required for long-distance RNAi signaling. aBIOTECH 2024; 5:17-28. [PMID: 38576436 PMCID: PMC10987413 DOI: 10.1007/s42994-023-00124-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 04/06/2024]
Abstract
Small RNA (sRNA)-mediated RNA silencing (also known as RNA interference, or RNAi) is a conserved mechanism in eukaryotes that includes RNA degradation, DNA methylation, heterochromatin formation and protein translation repression. In plants, sRNAs can move either cell-to-cell or systemically, thereby acting as mobile silencing signals to trigger noncell autonomous silencing. However, whether and what proteins are also involved in noncell autonomous silencing have not been elucidated. In this study, we utilized a previously reported inducible RNAi plant, PDSi, which can induce systemic silencing of the endogenous PDS gene, and we demonstrated that DCL3 is involved in systemic PDS silencing through its RNA binding activity. We confirmed that the C-terminus of DCL3, including the predicted RNA-binding domain, is capable of binding short RNAs. Mutations affecting RNA binding, but not processing activity, reduced systemic PDS silencing, indicating that DCL3 binding to RNAs is required for the induction of systemic silencing. Cucumber mosaic virus infection assays showed that the RNA-binding activity of DCL3 is required for antiviral RNAi in systemically noninoculated leaves. Our findings demonstrate that DCL3 acts as a signaling agent involved in noncell autonomous silencing and an antiviral effect in addition to its previously known function in the generation of 24-nucleotide sRNAs. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00124-6.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Bo-Sen Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Hua-Wei Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Cheng-Lan Liu
- Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250022 China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, 100049 China
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Wang E, Cohen AA, Caldera LF, Keeffe JR, Rorick AV, Aida YM, Gnanapragasam PN, Bjorkman PJ, Chakraborty AK. Designed mosaic nanoparticles enhance cross-reactive immune responses in mice. bioRxiv 2024:2024.02.28.582544. [PMID: 38464322 PMCID: PMC10925254 DOI: 10.1101/2024.02.28.582544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
1Using computational methods, we designed 60-mer nanoparticles displaying SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs) by (i) creating RBD sequences with 6 mutations in the SARS-COV-2 WA1 RBD that were predicted to retain proper folding and abrogate antibody responses to variable epitopes (mosaic-2COMs; mosaic-5COM), and (ii) selecting 7 natural sarbecovirus RBDs (mosaic-7COM). These antigens were compared with mosaic-8b, which elicits cross-reactive antibodies and protects from sarbecovirus challenges in animals. Immunizations in naïve and COVID-19 pre-vaccinated mice revealed that mosaic-7COM elicited higher binding and neutralization titers than mosaic-8b and related antigens. Deep mutational scanning showed that mosaic-7COM targeted conserved RBD epitopes. Mosaic-2COMs and mosaic-5COM elicited higher titers than homotypic SARS-CoV-2 Beta RBD-nanoparticles and increased potencies against some SARS-CoV-2 variants than mosaic-7COM. However, mosaic-7COM elicited more potent responses against zoonotic sarbecoviruses and highly mutated Omicrons. These results support using mosaic-7COM to protect against highly mutated SARS-CoV-2 variants and zoonotic sarbecoviruses with spillover potential.
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Affiliation(s)
- Eric Wang
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- These authors contributed equally
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- These authors contributed equally
| | - Luis F. Caldera
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- These authors contributed equally
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Annie V. Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Yusuf M. Aida
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Present address: School of Clinical Medicine, University of Cambridge, Hills Rd, Cambridge, CB2 0SP, UK
| | | | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Arup K. Chakraborty
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
- Lead contact
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Shi K, Li L, Luo C, Xu Z, Huang B, Ma S, Liu K, Yu G, Gao GF. Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency. mBio 2024; 15:e0298823. [PMID: 38112468 PMCID: PMC10870819 DOI: 10.1128/mbio.02988-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
The potential host range of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been expanding alongside its evolution during the pandemic, with rabbits and hares being considered important potential hosts, supported by a report of rabbit sero-prevalence in nature. We measured the binding affinities of rabbit and hare angiotensin-converting enzyme 2 (ACE2) with receptor-binding domains (RBDs) from SARS-CoV, SARS-CoV-2, and its variants and found that rabbit and hare ACE2s had broad variant tropism, with significantly enhanced affinities to Omicron BA.4/5 and its subsequent-emerged sub-variants (>10 fold). The structures of rabbit ACE2 complexed with either SARS-CoV-2 prototype (PT) or Omicron BA.4/5 spike (S) proteins were determined, thereby unveiling the importance of rabbit ACE2 Q34 in RBD-interaction and elucidating the molecular basis of the enhanced binding with Omicron BA.4/5 RBD. These results address the highly enhanced risk of rabbits infecting SARS-CoV-2 Omicron sub-variants and the importance of constant surveillance.IMPORTANCEThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has swept the globe and caused immense health and economic damage. SARS-CoV-2 has demonstrated a broad host range, indicating a high risk of interspecies transmission and adaptive mutation. Therefore, constant monitoring for potential hosts is of immense importance. In this study, we found that Omicron BA.4/5 and subsequent-emerged sub-variants exhibited enhanced binding to both rabbit and hare angiotensin-converting enzyme 2 (ACE2), and we elucidated the structural mechanism of their recognition. From the structure, we found that Q34, a unique residue of rabbit ACE2 compared to other ACE2 orthologs, plays an important role in ACE2 recognition. These results address the probability of rabbits/hares being potential hosts of SARS-CoV-2 and broaden our knowledge regarding the molecular mechanism of SARS-CoV-2 interspecies transmission.
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Affiliation(s)
- Kaiyuan Shi
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linjie Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chunliang Luo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Baihan Huang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Sufang Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guanghui Yu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Chen F, Liu Z, Kang W, Jiang F, Yang X, Yin F, Zhou Z, Li Z. Single-domain antibodies against SARS-CoV-2 RBD from a two-stage phage screening of universal and focused synthetic libraries. BMC Infect Dis 2024; 24:199. [PMID: 38350843 PMCID: PMC10865538 DOI: 10.1186/s12879-024-09022-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is an evolving global pandemic, and nanobodies, as well as other single-domain antibodies (sdAbs), have been recognized as a potential diagnostic and therapeutic tool for infectious diseases. High-throughput screening techniques such as phage display have been developed as an alternative to in vivo immunization for the discovery of antibody-like target-specific binders. METHODS We designed and constructed a highly diverse synthetic phage library sdAb-U (single-domain Antibody - Universal library ) based on a human framework. The SARS-CoV-2 receptor-binding domain (RBD) was expressed and purified. The universal library sdAb-U was panned against the RBD protein target for two rounds, followed by monoclonal phage ELISA (enzyme-linked immunosorbent assay) to identify RBD-specific binders (the first stage). High-affinity binders were sequenced and the obtained CDR1 and CDR2 sequences were combined with fully randomized CDR3 to construct a targeted (focused) phage library sdAb-RBD, for subsequent second-stage phage panning (also two rounds) and screening. Then, sequences with high single-to-background ratios in phage ELISA were selected for expression. The binding affinities of sdAbs to RBD were measured by an ELISA-based method. In addition, we conducted competition ELISA (using ACE2 ectodomain S19-D615) and SARS-CoV-2 pseudovirus neutralization assays for the high-affinity RBD-binding sdAb39. RESULTS Significant enrichments were observed in both the first-stage (universal library) and the second-stage (focused library) phage panning. Five RBD-specific binders were identified in the first stage with high ELISA signal-to-background ratios. In the second stage, we observed a much higher possibility of finding RBD-specific clones in phage ELISA. Among 45 selected RBD-positive sequences, we found eight sdAbs can be well expressed, and five of them show high-affinity to RBD (EC50 < 100nM). We finally found that sdAb39 (EC50 ~ 4nM) can compete with ACE2 for binding to RBD. CONCLUSION Overall, this two-stage strategy of synthetic phage display libraries enables rapid selection of SARS-CoV-2 RBD sdAb with potential therapeutic activity, and this two-stage strategy can potentially be used for rapid discovery of sdAbs against other targets.
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Affiliation(s)
- Fangfang Chen
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Zhihong Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei Kang
- NanoAI Biotech Co., Ltd, Pingshan District, Shenzhen, China
| | - Fan Jiang
- NanoAI Biotech Co., Ltd, Pingshan District, Shenzhen, China.
| | - Xixiao Yang
- Department of Pharmacy, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Ziyuan Zhou
- National Cancer Center, National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China.
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
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Ingravallo F, D'Alterio A, Rossetti A, Antelmi E, Plazzi G. Disclosing the Risk Associated with Isolated REM Behavior Disorder: The Sleep Experts' Perspective. Mov Disord Clin Pract 2024. [PMID: 38341655 DOI: 10.1002/mdc3.13998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/21/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Isolated rapid-eye-movement sleep behavior disorder (iRBD) is associated with a high risk for phenoconversion to a neurodegenerative disorder, but the optimal approach for disclosure of this risk to patients is still debated. OBJECTIVES The aim of this study was to explore views and experiences of iRBD experts regarding risk disclosure. METHODS In this qualitative study, semi-structured interviews with sleep experts caring for patients with iRBD were analyzed through a conventional content analysis approach. RESULTS We interviewed 22 iRBD experts (eight female, average age of 51.8 years) from 18 Italian sleep centers; 21/22 regularly disclosed the risks associated with iRBD, usually after the video-polysomnography, and 8/22 regularly mentioned phenoconversion rates. Content analysis allowed us to identify three main themes. First, sleep experts reported several points in favor of risk disclosure, especially related to the principle of beneficence, but some highlighted the need for specific learning on the topic. Second, experts favored a patient-tailored disclosure that should not upset the patient unnecessarily, since phenoconversion is uncertain. Third, risk disclosure was seen by participants as a relational task that should be carried out in person in the context of a trusting patient-physician relationship, while they had contrasting views regarding patients' previous knowledge. CONCLUSIONS Sleep experts generally preferred a tailored and reassuring approach to risk disclosure within a framework of relational autonomy. The results of this study indicate the need for specific education, training, and recommendations concerning risk disclosure that should also include patients' and families' preferences.
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Affiliation(s)
- Francesca Ingravallo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Alessandra D'Alterio
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Andrea Rossetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Elena Antelmi
- Department of Engineering and Medicine of Innovation (DIMI), University of Verona, Verona, Italy
| | - Giuseppe Plazzi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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18
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Cohen AA, Keeffe JR, Schiepers A, Dross SE, Greaney AJ, Rorick AV, Gao H, Gnanapragasam PN, Fan C, West AP, Ramsingh AI, Erasmus JH, Pata JD, Muramatsu H, Pardi N, Lin PJ, Baxter S, Cruz R, Quintanar-Audelo M, Robb E, Serrano-Amatriain C, Magneschi L, Fotheringham IG, Fuller DH, Victora GD, Bjorkman PJ. Mosaic sarbecovirus vaccination elicits cross-reactive responses in pre-immunized animals. bioRxiv 2024:2024.02.08.576722. [PMID: 38370696 PMCID: PMC10871317 DOI: 10.1101/2024.02.08.576722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Immunization with mosaic-8b [60-mer nanoparticles presenting 8 SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs)] elicits more broadly cross-reactive antibodies than homotypic SARS-CoV-2 RBD-only nanoparticles and protects against sarbecoviruses. To investigate original antigenic sin (OAS) effects on mosaic-8b efficacy, we evaluated effects of prior COVID-19 vaccinations in non-human primates and mice on sarbecovirus response breadths elicited by mosaic-8b, admix-8b (8 homotypics), and homotypic SARS-CoV-2, finding greatest cross-reactivity for mosaic-8b. As demonstrated by molecular fate-mapping in which antibodies derived from specific cohorts of B cells are differentially detected, B cells primed by WA1 spike mRNA-LNP dominated antibody responses after RBD-nanoparticle boosting. While mosaic-8b- and homotypic-nanoparticles boosted cross-reactive antibodies, de novo antibodies were predominantly induced with mosaic-8b boosting, and these were specific for variant RBDs with increased identity to RBDs on mosaic-8b. These results inform OAS mechanisms and support using mosaic-8b to protect COVID-19 vaccinated/infected humans against as-yet-unknown SARS-CoV-2 variants and animal sarbecoviruses with human spillover potential.
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Affiliation(s)
- Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- These authors contributed equally
| | - Ariën Schiepers
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Sandra E. Dross
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Allison J. Greaney
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Annie V. Rorick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | - Janice D. Pata
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany, Albany, NY, 12201, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Scott Baxter
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Rita Cruz
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Martina Quintanar-Audelo
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
- Present address: Centre for Inflammation Research and Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Ellis Robb
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | | | - Leonardo Magneschi
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Ian G. Fotheringham
- Ingenza Ltd, Roslin Innovation Centre, Charnock Bradley Building, Roslin, EH25 9RG, UK
| | - Deborah H. Fuller
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- National Primate Research Center, Seattle, WA 98121, USA
| | - Gabriel D. Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, 10065, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Lead contact
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19
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Zadeh SMM, Bayat AA, Shahsavarani H, Karimi-Busheri F, Kiani J, Ghods R, Madjd Z. Novel neutralizing SARS-CoV-2-specific mAbs offer detection of RBD linear epitopes. Virol J 2024; 21:37. [PMID: 38317249 PMCID: PMC10845636 DOI: 10.1186/s12985-024-02304-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/26/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND To stop the spread of the COVID-19 disease, it is crucial to create molecular tools to investigate and diagnose COVID-19. Current efforts focus on developing specific neutralizing monoclonal antibodies (NmAbs) elicited against the receptor-binding domain (RBD). METHODS In the present study, recombinant RBD (rRBD) protein was produced in E. coli, followed by immunizing mice with purified rRBD. ELISA was applied to screen the hybridomas for positive reactivity with rRBD protein. The linear and conformational epitopes of the mAbs were subsequently identified using western blot. Finally, the reactivity, affinity, and neutralization activity of the purified mAbs were evaluated using ELISA. RESULTS All mAbs exhibited similar reactivity trends towards both eukaryotic RBD and prokaryotic rRBD in ELISA. Among them, 2E7-D2 and 2B4-G8 mAbs demonstrated higher reactivity than other mAbs. Additionally, in western blot assays, these two mAbs could detect reducing and non-reducing rRBD, indicating recognition of linear epitopes. Notably, five mAbs effectively blocked rRBD- angiotensin-converting enzyme 2 (ACE2) interaction, while two high-affinity mAbs exhibited potent neutralizing activity against eukaryotic RBD. CONCLUSION In the current study, we generated and characterized new RBD-specific mAbs using the hybridoma technique that recognized linear and conformational epitopes in RBD with neutralization potency. Our mAbs are novel candidates for diagnosing and treating SARS-CoV-2.
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Affiliation(s)
- Seyed Mostafa Mostafavi Zadeh
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Ahmad Bayat
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Hosein Shahsavarani
- Laboratory of Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, National Cell Bank, Tehran, Iran
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Feridoun Karimi-Busheri
- Department of Oncology, Faculty of Medicine, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Roya Ghods
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
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20
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Zhang DQ, Ma QH, Yang MC, Belyakova YY, Yang ZF, Radulov PS, Chen RH, Yang LJ, Wei JY, Peng YT, Zheng WY, Yaremenko IA, Terent'ev AO, Coghi P, Wong VKW. Peroxide derivatives as SARS-CoV-2 entry inhibitors. Virus Res 2024; 340:199295. [PMID: 38081457 PMCID: PMC10733699 DOI: 10.1016/j.virusres.2023.199295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 11/14/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Host cell invasion is mediated by the interaction of the viral spike protein (S) with human angiotensin-converting enzyme 2 (ACE2) through the receptor-binding domain (RBD). In this work, bio-layer interferometry (BLI) was used to screen a series of fifty-two peroxides, including aminoperoxides and bridged 1,2,4 - trioxolanes (ozonides), with the aim of identifying small molecules that interfere with the RBD-ACE2 interaction. We found that two compounds, compound 21 and 29, exhibit the activity to inhibit RBD-ACE2. They are further demonstrated to inhibit SARS-CoV-2 cell entry, as shown in pseudovirus assay and experiment with authentic SARS-CoV-2. A comprehensive in silico analysis was carried out to study the physicochemical and pharmacokinetic properties, revealing that both compounds have good physicochemical properties as well as good bioavailability. Our results highlight the potential of small molecules targeting RBD inhibitors as potential therapeutic drugs for COVID-19.
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Affiliation(s)
- Ding-Qi Zhang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Qin-Hai Ma
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Meng-Chu Yang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Yulia Yu Belyakova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Zi-Feng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Peter S Radulov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Rui-Hong Chen
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Li-Jun Yang
- Institute of Translational Medicine, Zhejiang Shuren University, Hangzhou, China
| | - Jing-Yuan Wei
- School of Pharmacy, Macau University of Science and Technology, Macau, China
| | - Yu-Tong Peng
- School of Pharmacy, Macau University of Science and Technology, Macau, China
| | - Wu-Yan Zheng
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Ivan A Yaremenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation; Faculty of Chemical and Pharmaceutical Technology and Biomedical Products, D .I . Mendeleev University of Chemical Technology of Russia, Moscow, Russian Federation
| | - Alexander O Terent'ev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.
| | - Paolo Coghi
- School of Pharmacy, Macau University of Science and Technology, Macau, China.
| | - Vincent Kam Wai Wong
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
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21
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Milane T, Hansen C, Correno MB, Chardon M, Barbieri FA, Bianchini E, Vuillerme N. Comparison of sleep characteristics between Parkinson's disease with and without freezing of gait: A systematic review. Sleep Med 2024; 114:24-41. [PMID: 38150950 DOI: 10.1016/j.sleep.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/03/2023] [Accepted: 11/15/2023] [Indexed: 12/29/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized by a range of motor and non-motor symptoms. Among the motor complaints, freezing of gait (FOG) is a common and disabling phenomenon that episodically hinders patients' ability to produce efficient steps. Concurrently, sleep disorders are prevalent in PD and significantly impact the quality of life of affected individuals. Numerous studies have suggested a bidirectional relationship between FOG and sleep disorders. Therefore, our objective was to systematically review the literature and compare sleep outcomes in PD patients with FOG (PD + FOG) and those without FOG (PD-FOG). By conducting a comprehensive search of the PubMed and Web of Science databases, we identified 20 eligible studies for inclusion in our analysis. Our review revealed that compared to PD-FOG, PD + FOG patients exhibited more severe symptoms of rapid eye movement sleep behavior disorder in nine studies, increased daytime sleepiness in eight studies, decreased sleep quality in four studies, and more frequent and severe sleep disturbances in four studies. These findings indicate that PD + FOG patients generally experience worse sleep quality, higher levels of daytime sleepiness, and more disruptive sleep disturbances compared to those without FOG (PD-FOG). The association between sleep disturbances and FOG highlights the importance of evaluating and monitoring these symptoms in PD patients and open the possibility for future studies to assess the impact of managing sleep disturbances on the severity and occurrence of FOG, and vice versa.
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Affiliation(s)
- Tracy Milane
- AGEIS, Université Grenoble Alpes, 38000, Grenoble, France; Department of Neurology, UKSH Campus Kiel, Kiel University, Arnold-Heller-Str. 3, Haus D, 24105, Kiel, Germany
| | - Clint Hansen
- AGEIS, Université Grenoble Alpes, 38000, Grenoble, France; Department of Neurology, UKSH Campus Kiel, Kiel University, Arnold-Heller-Str. 3, Haus D, 24105, Kiel, Germany.
| | - Mathias Baptiste Correno
- AGEIS, Université Grenoble Alpes, 38000, Grenoble, France; Department of Neurology, UKSH Campus Kiel, Kiel University, Arnold-Heller-Str. 3, Haus D, 24105, Kiel, Germany
| | - Matthias Chardon
- AGEIS, Université Grenoble Alpes, 38000, Grenoble, France; São Paulo State University (Unesp), School of Sciences, Department of Physical Education, Human Movement Research Laboratory (MOVI-LAB), Bauru, Brazil
| | - Fabio A Barbieri
- São Paulo State University (Unesp), School of Sciences, Department of Physical Education, Human Movement Research Laboratory (MOVI-LAB), Bauru, Brazil
| | - Edoardo Bianchini
- AGEIS, Université Grenoble Alpes, 38000, Grenoble, France; Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Sapienza University of Rome, 00189, Rome, Italy
| | - Nicolas Vuillerme
- AGEIS, Université Grenoble Alpes, 38000, Grenoble, France; LabCom Telecom4Health, Orange Labs & Université Grenoble Alpes, CNRS, Inria, Grenoble INP-UGA, 38000, Grenoble, France; Institut Universitaire de France, 75005, Paris, France.
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22
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Sharma D, Rawat P, Greiff V, Janakiraman V, Gromiha MM. Predicting the immune escape of SARS-CoV-2 neutralizing antibodies upon mutation. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166959. [PMID: 37967796 DOI: 10.1016/j.bbadis.2023.166959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
COVID-19 has resulted in millions of deaths and severe impact on economies worldwide. Moreover, the emergence of SARS-CoV-2 variants presented significant challenges in controlling the pandemic, particularly their potential to avoid the immune system and evade vaccine immunity. This has led to a growing need for research to predict how mutations in SARS-CoV-2 reduces the ability of antibodies to neutralize the virus. In this study, we assembled a set of 1813 mutations from the interface of SARS-CoV-2 spike protein's receptor binding domain (RBD) and neutralizing antibody complexes and developed a machine learning model to classify high or low escape mutations using interaction energy, inter-residue contacts and predicted binding free energy change. Our approach achieved an Area under the Receiver Operating Characteristics (ROC) Curve (AUC) of 0.91 using the Random Forest classifier on the test dataset with 217 mutations. The model was further utilized to predict the escape mutations on a dataset of 29,165 mutations located at the interface of 83 RBD-neutralizing antibody complexes. A small subset of this dataset was also validated based on available experimental data. We found that top 10 % high escape mutations were dominated by charged to nonpolar mutations whereas low escape mutations were dominated by polar to nonpolar mutations. We believe that the present method will allow prioritization of high/low escape mutations in the context of neutralizing antibodies targeting SARS-CoV-2 RBD region and assist antibody design for current and emerging variants.
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Affiliation(s)
- Divya Sharma
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Puneet Rawat
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Vani Janakiraman
- Infection Biology Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India; International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama 226-8501, Japan; Department of Computer Science, National University of Singapore, Singapore.
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23
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Zhan XY, Chen Y, Zhang X, Shi Q, Chen K, Zeng C, Zhang Y, Liang Y, Li W, Li M, Peng Q, Qin C, Liu T, Xu H, Yuan D, Ye Z, Yan L, Cheng S, Zhang Y, Xu Y, Chen Y, Chen M, Li K, Ke C, Zhu Y, Huang B. Characterization of SARS-CoV-2-specific humoral immunity and associated factors in the healthy population post-vaccination. Vaccine 2024; 42:175-185. [PMID: 38103966 DOI: 10.1016/j.vaccine.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
OBJECTIVES To investigate factors that may influence humoral immunity post-vaccination with a COVID-19-inactivated vaccine (SC2IV). METHODS A total of 1596 healthy individuals from the Seventh Affiliated Hospital, Sun Yat-sen University (1217) and Shenzhen Baotian Hospital (379) were enrolled in this study among which 694 and 218 participants were vaccinated with two-dose SC2IV, respectively. Physical examination indices were recorded. The levels of neutralizing antibody (NA), Spike IgG, receptor-binding domain (RBD) IgG, RBD IgG + IgM + IgA, and nucleocapsid IgG of SARS-CoV-2 were measured by a non-virus ELISA kit. Multiple statistical analyses were carried out to identify factors that influence humoral immunity post-vaccination. RESULTS The two-dosage vaccination could induce NA in more than 90 % of recipients. The NA has the strongest correlation with anti-RBD IgG. Age is the most important independent index that affects the NA level, while basophil count, creatine kinase-MB, mean corpuscular hemoglobin, the ratio of albumin to urine creatinine, and thyroglobulin antibody have relatively minor contributions. Indices that affect the NA level were different between males and females. Antibodies targeting other epitopes of SARS-CoV-2 were detected in recipients without anti-RBD. CONCLUSIONS The factors identified in association with the NA level post-vaccination may help to evaluate the protective effect, risk of re-infection, the severity of symptoms, and prognosis for vaccine recipients in clinical.
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Affiliation(s)
- Xiao-Yong Zhan
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Yun Chen
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Xiaoying Zhang
- Health Management Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Qipeng Shi
- Shenzhen Mindray Bio-medical Co., Ltd, Shenzhen 518057, PR China
| | - Kaiyin Chen
- Health Management Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Changchun Zeng
- Shenzhen Longhua District Central Hospital, Shenzhen 518110, PR China
| | - Yi Zhang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Yuhong Liang
- School of Pharmacy, Macau University of Science and Technology, 999078, Macau
| | - Wenxia Li
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Manli Li
- Shenzhen Genrui Biotechnology Co., Ltd, Shenzhen 518106, PR China
| | - Qin Peng
- Shenzhen Longhua District Central Hospital, Shenzhen 518110, PR China
| | - Changfei Qin
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Taoli Liu
- Department of Chinese Medicine, The Seventh Affiliated Hospital, Shenzhen 518107, PR China
| | - Haifeng Xu
- Department of Infectious Diseases, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Dasen Yuan
- Department of Neurology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, PR China
| | - Ziheng Ye
- Department of Chinese Medicine, The Seventh Affiliated Hospital, Shenzhen 518107, PR China
| | - Ling Yan
- Department of Chinese Medicine, The Seventh Affiliated Hospital, Shenzhen 518107, PR China
| | - Shuming Cheng
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Ying Zhang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Yunsheng Xu
- Department of Dermatology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Youpeng Chen
- Department of Infectious Diseases, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China
| | - Ming Chen
- Shenzhen Genrui Biotechnology Co., Ltd, Shenzhen 518106, PR China.
| | - Ke Li
- Health Management Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China.
| | - Changneng Ke
- Shenzhen Longhua District Central Hospital, Shenzhen 518110, PR China.
| | - Yunxiao Zhu
- Health Management Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China.
| | - Bihui Huang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, PR China.
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24
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Bergmann M, Högl B, Stefani A. Clinical neurophysiology of REM parasomnias: Diagnostic aspects and insights into pathophysiology. Clin Neurophysiol Pract 2024; 9:53-62. [PMID: 38328386 PMCID: PMC10847011 DOI: 10.1016/j.cnp.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/17/2023] [Accepted: 10/22/2023] [Indexed: 02/09/2024] Open
Abstract
Parasomnias are due to a transient unstable state dissociation during entry into sleep, within sleep, or during arousal from sleep, and manifest with abnormal sleep related behaviors, perceptions, emotions, dreams, and autonomic nervous system activity. Rapid eye movement (REM) parasomnias include REM sleep behavior disorder (RBD), isolated recurrent sleep paralysis and nightmare disorder. Neurophysiology is key for diagnosing these disorders and provides insights into their pathophysiology. RBD is very well characterized from a neurophysiological point of view, also thank to the fact that polysomnography is needed for the diagnosis. Diagnostic criteria are provided by the American Academy of Sleep Medicine and video-polysomnography guidelines for the diagnosis by the International REM Sleep Behavior Disorder Study Group. Differences between the two sets of criteria are presented and discussed. Availability of polysomnography in RBD provides data on sleep electroencephalography (EEG), electrooculography (EOG) and electromyography (EMG). Sleep EEG in RBD shows e.g. changes in delta and theta power, in sleep spindles and K complexes. EMG during REM sleep is essential for RBD diagnosis and is an important neurodegeneration biomarker. RBD patients present alterations also in wake EEG, autonomic function, evoked potentials, and transcranial magnetic stimulation. Clinical neurophysiological data on recurrent isolated sleep paralysis and nightmare disorder are scant. The few available data provide insights into the pathophysiology of these disorders, demonstrating a state dissociation in recurrent isolated sleep paralysis and suggesting alterations in sleep macro- and microstructure as well as autonomic changes in nightmare disorder.
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Affiliation(s)
- Melanie Bergmann
- Department of Neurology, Sleep Laboratory, Medical University Innsbruck, Austria
| | - Birgit Högl
- Department of Neurology, Sleep Laboratory, Medical University Innsbruck, Austria
| | - Ambra Stefani
- Department of Neurology, Sleep Laboratory, Medical University Innsbruck, Austria
- Neurological Clinical Research Institute, Massachusetts General Hospital, Boston, USA
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25
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Elliott JE, Ligman BR, Bryant-Ekstrand MD, Keil AT, Powers K, Olivo C, Neilson L, Postuma RB, Pelletier A, Gagnon JF, Gan-Or Z, Yu E, Liu L, St Louis EK, Forsberg LK, Fields JA, Ross OA, Huddleston DE, Bliwise DL, Avidan AY, Howell MJ, Schenck CH, McLeland J, Criswell SR, Videnovic A, During EH, Miglis MG, Shprecher DR, Lee-Iannotti JK, Boeve BF, Ju YES, Lim MM. Comorbid neurotrauma increases neurodegenerative-relevant cognitive, motor, and autonomic dysfunction in patients with REM sleep behavior disorder: A substudy of the North American Prodromal Synucleinopathy Consortium. Sleep 2024:zsae007. [PMID: 38181205 DOI: 10.1093/sleep/zsae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Indexed: 01/07/2024] Open
Abstract
STUDY OBJECTIVES Rapid eye movement (REM) sleep behavior disorder (RBD) is strongly associated with phenoconversion to an overt synucleinopathy, e.g., Parkinson's disease (PD), Lewy Body Dementia (LBD), and related disorders. Comorbid traumatic brain injury (TBI) and posttraumatic stress disorder (PTSD) - henceforth "neurotrauma" (NT) - increase the odds of RBD by ~2.5-fold and is associated with an increased rate of service-connected PD in Veterans. Thus, RBD and NT are both independently associated with PD; however, it is unclear how NT influences neurological function in patients with RBD. METHODS Participants ≥18 years with overnight-polysomnogram-confirmed RBD were enrolled between 8/2018 to 4/2021 through the North American Prodromal Synucleinopathy (NAPS) Consortium. Standardized assessments for RBD, TBI, and PTSD history, as well as cognitive, motor, sensory and autonomic function were completed. This cross-sectional analysis compared cases (n=24; RBD+NT) to controls (n=96; RBD), matched for age (~60 years), sex (15% female), and years of education (~15 years). RESULTS RBD+NT reported earlier RBD symptom onset (37.5±11.9 vs. 52.2±15.1 years of age) and a more severe RBD phenotype. Similarly, RBD+NT reported more severe anxiety and depression, greater frequency of hypertension, and significantly worse cognitive, motor, and autonomic function compared to RBD. No differences in olfaction or color vision were observed. CONCLUSION This cross-sectional, matched case:control study shows individuals with RBD+NT have significantly worse neurological measures related to common features of an overt synucleinopathy. Confirmatory longitudinal studies are ongoing; however, these results suggest RBD+NT may be associated with more advanced neurological symptoms related to an evolving neurodegenerative process.
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Affiliation(s)
- Jonathan E Elliott
- VA Portland Health Care System, Research Service, Portland, OR, USA
- Oregon Health & Science University, Department of Neurology, Portland, OR, USA
| | | | | | - Allison T Keil
- VA Portland Health Care System, Research Service, Portland, OR, USA
- McGill University, Montreal Neurological Institute and Department of Neurology and Neurosurgery, Montréal, Québec, Canada
| | - Katherine Powers
- VA Portland Health Care System, Research Service, Portland, OR, USA
| | - Cosette Olivo
- VA Portland Health Care System, Research Service, Portland, OR, USA
| | - Lee Neilson
- VA Portland Health Care System, Research Service, Portland, OR, USA
- Oregon Health & Science University, Department of Neurology, Portland, OR, USA
| | - Ronald B Postuma
- McGill University, Montreal Neurological Institute and Department of Neurology and Neurosurgery, Montréal, Québec, Canada
- Université du Québec à Montréal, Département of Psychology, Montréal, Québec, Canada
- Hôpital du Sacré-Coeur de Montréal, Center for Advanced Research in Sleep Medicine, Montréal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Amélie Pelletier
- Hôpital du Sacré-Coeur de Montréal, Center for Advanced Research in Sleep Medicine, Montréal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Jean-François Gagnon
- Université du Québec à Montréal, Département of Psychology, Montréal, Québec, Canada
- Hôpital du Sacré-Coeur de Montréal, Center for Advanced Research in Sleep Medicine, Montréal, Quebec, Canada
| | - Ziv Gan-Or
- McGill University, Montreal Neurological Institute and Department of Neurology and Neurosurgery, Montréal, Québec, Canada
- McGill University, Department of Human Genetics, Montréal, Québec, Canada
| | - Eric Yu
- McGill University, Montreal Neurological Institute and Department of Neurology and Neurosurgery, Montréal, Québec, Canada
- McGill University, Department of Human Genetics, Montréal, Québec, Canada
| | - Lang Liu
- McGill University, Montreal Neurological Institute and Department of Neurology and Neurosurgery, Montréal, Québec, Canada
- McGill University, Department of Human Genetics, Montréal, Québec, Canada
| | | | | | | | - Owen A Ross
- Mayo Clinic, Neurology and Medicine, Rochester, MN, USA
| | | | | | - Alon Y Avidan
- University of California Los Angeles, Neurology, Sleep Disorders Center, Los Angeles, CA, USA
| | - Michael J Howell
- University of Minnesota Medical Center, Neurology, Minneapolis, MN, USA
- Hennepin County Medical Center, Minnesota Regional Sleep Disorders Center, Minneapolis, MN, USA
| | - Carlos H Schenck
- University of Minnesota Medical Center, Neurology, Minneapolis, MN, USA
| | | | | | - Aleksandar Videnovic
- Massachusetts General Hospital, Movement Disorders Unit, Division of Sleep Medicine, Boston, MA, USA
- Harvard Medical School, Neurological Clinical Research Institute, Boston, MA, USA
| | - Emmanuel H During
- Stanford University, Psychiatry and Behavioral Sciences, Redwood City, CA, USA
- Stanford University, Neurology & Neurological Sciences, Palo Alto, CA, USA
- Mt Sinai School of Medicine, Neurology, New York, NY, USA
| | - Mitchell G Miglis
- Stanford University, Psychiatry and Behavioral Sciences, Redwood City, CA, USA
- Stanford University, Neurology & Neurological Sciences, Palo Alto, CA, USA
| | | | | | | | - Yo-El S Ju
- Washington University School of Medicine, Saint Louis, MO, USA
| | - Miranda M Lim
- Oregon Health & Science University, Department of Neurology, Portland, OR, USA
- Oregon Health & Science University, Department of Behavioral Neuroscience; Department of Pulmonary and Critical Care Medicine; Oregon Institute of Occupational Health Sciences, Portland, OR, USA
- VA Portland Health Care System, Mental Illness Research Education and Clinical Center; Neurology; National Center for Rehabilitative Auditory Research, Portland, OR, USA
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Jia J, Garbarino E, Wang Y, Li J, Song M, Zhang X, Wang X, Li L, Chi J, Cui L, Tang H. Generation of SARS-CoV-2 spike receptor binding domain mutants and functional screening for immune evaders using a novel lentivirus-based system. J Med Virol 2024; 96:e29425. [PMID: 38258313 DOI: 10.1002/jmv.29425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/19/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
The emergence of rapid and continuous mutations of severe acute respiratory syndrome 2 (SARS-CoV-2) spike glycoprotein that increased with the Omicron variant points out the necessity to anticipate such mutations for conceiving specific and adaptable therapies to avoid another pandemic. The crucial target for the antibody treatment and vaccine design is the receptor binding domain (RBD) of the SARS-CoV-2 spike. It is also the site where the virus has shown its high ability to mutate and consequently escape immune response. We developed a robust and simple method for generating a large number of functional SARS-CoV-2 spike RBD mutants by error-prone PCR and a novel nonreplicative lentivirus-based system. We prepared anti-RBD wild type (WT) polyclonal antibodies and used them to screen and select for mutant libraries that escape inhibition of virion entry into recipient cells expressing human angiotensin-converting enzyme 2 and transmembrane serine protease 2. We isolated, cloned, and sequenced six mutants totally bearing nine mutation sites. Eight mutations were found in successive WT variants, including Omicron and other recombinants, whereas one is novel. These results, together with the detailed functional analyses of two mutants provided the proof of concept for our approach.
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Affiliation(s)
- Junli Jia
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Emanuela Garbarino
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuhang Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- Department of Blood Transfusion, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiaming Li
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Minmin Song
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xin Zhang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xinjie Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Lingyun Li
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Jing Chi
- Department of Microbiological Laboratory, Baoan District Center for Disease Control and Prevention, Shenzhen, China
| | - Lunbiao Cui
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Huamin Tang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- The Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing, China
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Zhang Y, Wang D, Xiang Q, Hu X, Zhang Y, Wu L, Zhang Z, Wang Y, Zhao J, McCormick PJ, Fu J, Fu Y, Zhang J, Jiang H, Li J. A potent neutralizing nanobody targeting a unique epitope on the receptor-binding domain of SARS-CoV-2 spike protein. Virology 2024; 589:109925. [PMID: 37984151 DOI: 10.1016/j.virol.2023.109925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
SARS-CoV-2 and its variants continue to threaten public health. Nanobodies that block the attachment of the RBD to host cell angiotensin-converting enzyme 2 (ACE2) represent promising drug candidates. In this study, we reported the identification and structural biological characterization of a nanobody from a RBD-immunized alpaca. The nanobody, termed as 2S-1-19, shows outstanding neutralizing activity against both pseudotyped and authentic SARS-CoV-2 viruses. The crystal structure of 2S-1-19 bound to SARS-CoV-2 RBD reveals an epitope that overlaps with the binding site for ACE2. We also showed that 2S-1-19 reserves promising, though compromised, neutralizing activity against the Delta variant and that the trivalent form of 2S-1-19 remarkably increases its neutralizing capacity. Despite this, neither the monomeric or trimeric 2S-1-19 could neutralize the Omicron BA.1.1 variant, possibility due to the E484A and Q493K mutations found within this virus variant. These data provide insights into immune evasion caused by SARS-CoV-2 variants.
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Affiliation(s)
- Yuting Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Dan Wang
- Key Lab for Agro-product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qi Xiang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiaohui Hu
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Yuting Zhang
- Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen, 518118, China
| | - Lijie Wu
- IHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 511436, China; Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510060, China; Guangzhou Laboratory, Bio-island, Guangzhou, Guangdong, 510320, China; Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Peter J McCormick
- William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jinheng Fu
- Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, 330047, China.
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.
| | - Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
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Safitri IA, Sugijo Y, Puspasari F, Masduki FF, Ihsanawati, Giri-Rachman EA, Artarini AA, Tan MI, Natalia D. Immunogenicity studies of recombinant RBD SARS-CoV-2 as a COVID-19 vaccine candidate produced in Escherichia coli. Vaccine X 2024; 16:100443. [PMID: 38304876 PMCID: PMC10832452 DOI: 10.1016/j.jvacx.2024.100443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 -related global COVID-19 pandemic has been impacting millions of people since its outbreak in 2020. COVID-19 vaccination has proven highly efficient in reducing illness severity and preventing infection-related fatalities. The World Health Organization has granted emergency use approval to multiple, including protein subunit technology-based, COVID-19 vaccines. Foreseeably, additional COVID-19 subunit vaccine development would be essential to meet the accessible and growing demand for effective vaccines, especially for Low-Middle-Income Countries (LMIC). The SARS-CoV-2 spike protein receptor binding domain (RBD), as the primary target for neutralizing antibodies, holds significant potential for future COVID-19 subunit vaccine development. In this study, we developed a recombinant Escherichia coli-expressed RBD (rRBD) as a vaccine candidate and evaluated its immunogenicity and preliminary toxicity in BALB/c mice. The rRBD induced humoral immune response from day 7 post-vaccination and, following the booster doses, the IgG levels increased dramatically in mice. Interestingly, our vaccine candidate also significantly induced cellular immune response, indicated by the incrased IFN-ɣ-producing cell numbers. We observed no adverse effect or local reactogenicity either in control or treated mice. Taken together, our discoveries could potentially support efficient and cost-effective vaccine antigen production, from which LMICs could particularly benefit.
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Affiliation(s)
- Intan Aghniya Safitri
- Biology Department, School of Life Science and Technology, Bandung Institute of Technology, Bandung, Indonesia
| | - Yovin Sugijo
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
| | - Fernita Puspasari
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
| | - Fifi Fitriyah Masduki
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Ihsanawati
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
| | - Ernawati Arifin Giri-Rachman
- Biology Department, School of Life Science and Technology, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Aluicia Anita Artarini
- Pharmaceutical Biotechnology Laboratory, Pharmaceutics Department, School of Pharmacy, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Marselina Irasonia Tan
- Biology Department, School of Life Science and Technology, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Dessy Natalia
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
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Sun Y, Li Q, Luo Y, Zhu H, Xu F, Lu H, Yao P, Wang Z, Zhao W, Zhou Z. Development of an RBD-Fc fusion vaccine for COVID-19. Vaccine X 2024; 16:100444. [PMID: 38327768 PMCID: PMC10847155 DOI: 10.1016/j.jvacx.2024.100444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
Although the global pandemic of SARS-CoV-2 has passed, there are still regional outbreaks that continue to jeopardize human health. Hence, there is still a great deal of interest in developing an efficient vaccine that can quickly and effectively prevent reemerging outbreaks of SARS-CoV-2. Delta variant was once a dominant strain in the world in 2021, and we first constructed a recombinant RBDdelta-Fc fusion vaccine by coupling the RBD of Delta variant with the human Fc fragment. This Fc fusion strategy increases the immunogenicity of the recombinant RBD vaccine, with a long-lasting high level of IgG antibodies and neutralizing antibodies induced by RBDdelta-Fc vaccine. This RBDdelta-Fc vaccine, as well as the RBD-Fc vaccine prepared in our previously study, could trigger a durable immune effect by the heterologous boosting immunity, and the RBD-Fc induced a quicker humoral immune response than the homologous immunization with inactivated vaccines. In conclusion, the Fc fusion strategy has a significant role in enhancing the immunogenicity of recombinant protein vaccines, thus promising the development of a safe and efficient vaccine for the heterologous boosting against SARS-CoV-2.
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Affiliation(s)
- Yisheng Sun
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Qiaomin Li
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Luo
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hanping Zhu
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Fang Xu
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Hangjing Lu
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Pingping Yao
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Zhen Wang
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Wenbin Zhao
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China
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Lovell JF, Miura K, Baik YO, Lee C, Lee JY, Park YS, Hong I, Lee JH, Kim T, Seo SH, Kim JO, Song M, Kim CJ, Choi JK, Kim J, Choo EJ, Choi JH. One-year antibody durability induced by EuCorVac-19, a liposome-displayed COVID-19 receptor binding domain subunit vaccine, in healthy Korean subjects. Int J Infect Dis 2024; 138:73-80. [PMID: 37944586 DOI: 10.1016/j.ijid.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE EuCorVac-19 (ECV-19), an adjuvanted liposome-displayed receptor binding domain (RBD) COVID-19 vaccine, previously reported interim Phase 2 trial results showing induction of neutralizing antibodies 3 weeks after prime-boost immunization. The objective of this study was to determine the longer-term antibody response of the vaccine. METHODS To assess immunogenicity 6 and 12 months after vaccination, participants in the Phase 2 trial (NCT04783311) were excluded if they: 1) withdrew, 2) reported COVID-19 infection or additional vaccination, or 3) exhibited increasing Spike (S) antibodies (representing possible non-reported infection). Following exclusions, of the 197 initial subjects, anti-S IgG antibodies and neutralizing antibodies were further assessed in 124 subjects at the 6-month timepoint, and 36 subjects at the 12-month timepoint. RESULTS Median anti-S antibody half-life was 52 days (interquartile range [IQR]:42-70), in the "early" period from 3 weeks to 6 months, and 130 days (IQR:97-169) in the "late" period from 6 to 12 months. There was a negative correlation between initial antibody titer and half-life. Anti-S and neutralizing antibody responses were correlated. Neutralizing antibody responses showed longer half-lives; the early period had a median half-life of 120 days (IQR:81-207), and the late period had a median half-life of 214 days (IQR:140-550). CONCLUSION These data establish antibody durability of ECV-19, using a framework to analyze COVID-19 vaccine-induced antibodies during periods of high infection.
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Affiliation(s)
- Jonathan F Lovell
- Department of Biomedical Engineering, University at Buffalo, Buffalo, New York, USA.
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Yeong Ok Baik
- Eubiologics, R&D Center, EuBiologics Co., Ltd., Chuncheon, Korea
| | - Chankyu Lee
- Eubiologics, R&D Center, EuBiologics Co., Ltd., Chuncheon, Korea
| | - Jeong-Yoon Lee
- Eubiologics, R&D Center, EuBiologics Co., Ltd., Chuncheon, Korea
| | | | - Ingi Hong
- International Vaccine Institute, Gwanak-gu, Seoul, Korea
| | - Jung Hyuk Lee
- International Vaccine Institute, Gwanak-gu, Seoul, Korea
| | - Taewoo Kim
- International Vaccine Institute, Gwanak-gu, Seoul, Korea
| | - Sang Hwan Seo
- International Vaccine Institute, Gwanak-gu, Seoul, Korea
| | - Jae-Ouk Kim
- International Vaccine Institute, Gwanak-gu, Seoul, Korea
| | - Manki Song
- International Vaccine Institute, Gwanak-gu, Seoul, Korea
| | - Chung-Jong Kim
- Department of Internal Medicine, Ewha Womans University, Seoul, Korea
| | - Jae-Ki Choi
- Department of Infectious Diseases, Bucheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jieun Kim
- Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Eun Ju Choo
- Department of Infectious Diseases, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Jung-Hyun Choi
- Department of Infectious Diseases, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Zhao J, Kang M, Wu H, Sun B, Baele G, He WT, Lu M, Suchard MA, Ji X, He N, Su S, Veit M. Risk assessment of SARS-CoV-2 replicating and evolving in animals. Trends Microbiol 2024; 32:79-92. [PMID: 37541811 DOI: 10.1016/j.tim.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 08/06/2023]
Abstract
The retransmissions of SARS-CoV-2 from several mammals - primarily mink and white-tailed deer - to humans have raised concerns for the emergence of a new animal-derived SARS-CoV-2 variant to worsen the pandemic. Here, we discuss animal species that are susceptible to natural or experimental infection with SARS-CoV-2 and can transmit the virus to mates or humans. We describe cutting-edge techniques to assess the impact of a mutation in the viral spike (S) protein on its receptor and on antibody binding. Our review of spike sequences of animal-derived viruses identified nine unique amino acid exchanges in the receptor-binding domain (RBD) that are not present in any variant of concern (VOC). These mutations are present in SARS-CoV-2 found in companion animals such as dogs and cats, and they exhibit a higher frequency in SARS-CoV-2 found in mink and white-tailed deer, suggesting that sustained transmissions may contribute to maintaining novel mutations. Four of these exchanges, such as Leu452Met, could undermine acquired immune protection in humans while maintaining high affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor. Finally, we discuss important avenues of future research into animal-derived viruses with public health risks.
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Affiliation(s)
- Jin Zhao
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Mei Kang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyan Wu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Bowen Sun
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Guy Baele
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Wan-Ting He
- School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Meng Lu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA; Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Na He
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Shuo Su
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China.
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany.
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Amin FG, Elfiky AA, Nassar AM. In silico targeting of SARS-CoV-2 spike receptor-binding domain from different variants with chaga mushroom terpenoids. J Biomol Struct Dyn 2024; 42:1079-1087. [PMID: 37042960 DOI: 10.1080/07391102.2023.2199084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/30/2023] [Indexed: 04/13/2023]
Abstract
Terpenoids from the chaga mushroom have been identified as potential antiviral agents against SARS-CoV-2. This is because it can firmly bind to the viral spike receptor binding domain (RBD) and the auxiliary host cell receptor glucose-regulated protein 78 (GRP78). The current work examines the association of the chaga mushroom terpenoids with the RBD of various SARS-CoV-2 variants, including alpha, beta, gamma, delta, and omicron. This association was compared to the SARS-CoV-2 wild-type (WT) RBD using molecular docking analysis and molecular dynamics modeling. The outcomes demonstrated that the mutant RBDs, which had marginally greater average binding affinities (better binding) than the WT, were successfully inhibited by the chaga mushroom terpenoids. The results suggest that the chaga mushroom can be effective against various SARS-CoV-2 variants by targeting both the host-cell surface receptor GRP78 and the viral spike RBD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatma G Amin
- Physics Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Aaya M Nassar
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- Department of Clinical Research and Leadership, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
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Barrow J, Vendrame M. Treatment of REM sleep behavior disorder with trazodone: report of three cases. J Clin Sleep Med 2023. [PMID: 38156419 DOI: 10.5664/jcsm.10970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Rapid eye movement sleep behavior disorder (RBD) is a sleep disturbance characterized by the absence of regular paralysis during REM sleep, accompanied by dream enactment behavior. The available pharmacotherapy options for treating RBD are limited, and the utilization of antidepressants has yielded mixed results. We report three cases of isolated RBD improved with trazodone. Doses of trazodone 50-100 mg at bedtime over 4-6 months resulted in significant clinical improvement. These cases highlight that trazodone could serve as a treatment for isolated RBD that does not respond to traditional treatments at submaximal dosages.
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Affiliation(s)
- Jorden Barrow
- Lehigh Valley Fleming Neuroscience Institute, Lehigh Valley Health Network, Allentown PA
- Morsani College of Medicine, University of South Florida, Tampa FL
| | - Martina Vendrame
- Lehigh Valley Fleming Neuroscience Institute, Lehigh Valley Health Network, Allentown PA
- Morsani College of Medicine, University of South Florida, Tampa FL
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Wang S, Guirakhoo F, Periasamy S, Ryan V, Wiggins J, Subramani C, Thibodeaux B, Sahni J, Hellerstein M, Kuzmina NA, Bukreyev A, Dodart JC, Rumyantsev A. RBD-Protein/Peptide Vaccine UB-612 Elicits Mucosal and Fc-Mediated Antibody Responses against SARS-CoV-2 in Cynomolgus Macaques. Vaccines (Basel) 2023; 12:40. [PMID: 38250853 PMCID: PMC10818657 DOI: 10.3390/vaccines12010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Antibodies provide critical protective immunity against COVID-19, and the Fc-mediated effector functions and mucosal antibodies also contribute to the protection. To expand the characterization of humoral immunity stimulated by subunit protein-peptide COVID-19 vaccine UB-612, preclinical studies in non-human primates were undertaken to investigate mucosal secretion and the effector functionality of vaccine-induced antibodies in antibody-dependent monocyte phagocytosis (ADMP) and antibody-dependent NK cell activation (ADNKA) assays. In cynomolgus macaques, UB-612 induced potent serum-neutralizing, RBD-specific IgG binding, ACE2 binding-inhibition antibodies, and antibodies with Fc-mediated effector functions in ADMP and ADNKA assays. Additionally, immunized animals developed mucosal antibodies in bronchoalveolar lavage fluids (BAL). The level of mucosal or serum ADMP and ADNKA antibodies was found to be UB-612 dose-dependent. Our results highlight that the novel subunit UB-612 vaccine is a potent B-cell immunogen inducing polyfunctional antibody responses contributing to anti-viral immunity and vaccine efficacy.
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Affiliation(s)
- Shixia Wang
- Vaxxinity, Inc., Merritt Island, FL 32953, USA; (F.G.); (V.R.); (J.W.); (B.T.); (J.S.); (M.H.); (J.-C.D.)
| | - Farshad Guirakhoo
- Vaxxinity, Inc., Merritt Island, FL 32953, USA; (F.G.); (V.R.); (J.W.); (B.T.); (J.S.); (M.H.); (J.-C.D.)
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA; (S.P.); (C.S.); (N.A.K.); (A.B.)
- Galveston National Laboratory, Galveston, TX 77550, USA
| | - Valorie Ryan
- Vaxxinity, Inc., Merritt Island, FL 32953, USA; (F.G.); (V.R.); (J.W.); (B.T.); (J.S.); (M.H.); (J.-C.D.)
| | - Jonathan Wiggins
- Vaxxinity, Inc., Merritt Island, FL 32953, USA; (F.G.); (V.R.); (J.W.); (B.T.); (J.S.); (M.H.); (J.-C.D.)
| | - Chandru Subramani
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA; (S.P.); (C.S.); (N.A.K.); (A.B.)
- Galveston National Laboratory, Galveston, TX 77550, USA
| | - Brett Thibodeaux
- Vaxxinity, Inc., Merritt Island, FL 32953, USA; (F.G.); (V.R.); (J.W.); (B.T.); (J.S.); (M.H.); (J.-C.D.)
| | - Jaya Sahni
- Vaxxinity, Inc., Merritt Island, FL 32953, USA; (F.G.); (V.R.); (J.W.); (B.T.); (J.S.); (M.H.); (J.-C.D.)
| | - Michael Hellerstein
- Vaxxinity, Inc., Merritt Island, FL 32953, USA; (F.G.); (V.R.); (J.W.); (B.T.); (J.S.); (M.H.); (J.-C.D.)
| | - Natalia A. Kuzmina
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA; (S.P.); (C.S.); (N.A.K.); (A.B.)
- Galveston National Laboratory, Galveston, TX 77550, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA; (S.P.); (C.S.); (N.A.K.); (A.B.)
- Galveston National Laboratory, Galveston, TX 77550, USA
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Jean-Cosme Dodart
- Vaxxinity, Inc., Merritt Island, FL 32953, USA; (F.G.); (V.R.); (J.W.); (B.T.); (J.S.); (M.H.); (J.-C.D.)
| | - Alexander Rumyantsev
- Vaxxinity, Inc., Merritt Island, FL 32953, USA; (F.G.); (V.R.); (J.W.); (B.T.); (J.S.); (M.H.); (J.-C.D.)
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Kim TH, Bae S, Goo S, Myoung J. Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant. J Microbiol Biotechnol 2023; 33:1587-1295. [PMID: 37915256 PMCID: PMC10772562 DOI: 10.4014/jmb.2308.08020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023]
Abstract
Since its first report in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a grave threat to public health. Virus-specific countermeasures, such as vaccines and therapeutics, have been developed and have contributed to the control of the viral pandemic, which has become endemic. Nonetheless, new variants continue to emerge and could cause a new pandemic. Consequently, it is important to comprehensively understand viral evolution and the roles of mutations in viral infectivity and transmission. SARS-CoV-2 beta variant encode mutations (D614G, N501Y, E484K, and K417N) in the spike which are frequently found in other variants as well. While their individual role in viral infectivity has been elucidated against various therapeutic antibodies, it still remains unclear whether those mutations may act additively or synergistically when combined. Here, we report that N501Y mutation shows differential effect on two therapeutic antibodies tested. Interestingly, the relative importance of E484K and K417N mutations in antibody evasion varies depending on the antibody type. Collectively, these findings suggest that continuous efforts to develop effective antibody therapeutics and combinatorial treatment with multiple antibodies are more rational and effective forms of treatment.
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Affiliation(s)
- Tae-Hun Kim
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea
| | - Sojung Bae
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea
| | - Sunggeun Goo
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea
| | - Jinjong Myoung
- Korea Zoonosis Research Institute, Department of Bioactive Material Science and Genetic Engineering Research Institute, Jeonbuk National University, Jeonju 54531, Republic of Korea
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Wang Z, Zhang B, Ou L, Qiu Q, Wang L, Bylund T, Kong WP, Shi W, Tsybovsky Y, Wu L, Zhou Q, Chaudhary R, Choe M, Dickey TH, El Anbari M, Olia AS, Rawi R, Teng IT, Wang D, Wang S, Tolia NH, Zhou T, Kwong PD. Extraordinary Titer and Broad Anti-SARS-CoV-2 Neutralization Induced by Stabilized RBD Nanoparticles from Strain BA.5. Vaccines (Basel) 2023; 12:37. [PMID: 38250850 PMCID: PMC10821209 DOI: 10.3390/vaccines12010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike is a primary target of neutralizing antibodies and a key component of licensed vaccines. Substantial mutations in RBD, however, enable current variants to escape immunogenicity generated by vaccination with the ancestral (WA1) strain. Here, we produce and assess self-assembling nanoparticles displaying RBDs from WA1 and BA.5 strains by using the SpyTag:SpyCatcher system for coupling. We observed both WA1- and BA.5-RBD nanoparticles to degrade substantially after a few days at 37 °C. Incorporation of nine RBD-stabilizing mutations, however, increased yield ~five-fold and stability such that more than 50% of either the WA1- or BA.5-RBD nanoparticle was retained after one week at 37 °C. Murine immunizations revealed that the stabilized RBD-nanoparticles induced ~100-fold higher autologous neutralization titers than the prefusion-stabilized (S2P) spike at a 2 μg dose. Even at a 25-fold lower dose where S2P-induced neutralization titers were below the detection limit, the stabilized BA.5-RBD nanoparticle induced homologous titers of 12,795 ID50 and heterologous titers against WA1 of 1767 ID50. Assessment against a panel of β-coronavirus variants revealed both the stabilized BA.5-RBD nanoparticle and the stabilized WA1-BA.5-(mosaic)-RBD nanoparticle to elicit much higher neutralization breadth than the stabilized WA1-RBD nanoparticle. The extraordinary titer and high neutralization breadth elicited by stabilized RBD nanoparticles from strain BA.5 make them strong candidates for next-generation COVID-19 vaccines.
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Affiliation(s)
- Zhantong Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Qi Qiu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Wing-Pui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 20701, USA
| | - Lingyuan Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Qiong Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Ridhi Chaudhary
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Thayne H. Dickey
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (T.H.D.)
| | - Mohammed El Anbari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Adam S. Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Danyi Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Niraj H. Tolia
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (T.H.D.)
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (Z.W.); (Q.Q.); (T.B.); (L.W.); (M.C.); (D.W.); (S.W.)
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Li K, Huntwork RHC, Horn GQ, Abraha M, Hastie KM, Li H, Rayaprolu V, Olmedillas E, Feeney E, Cronin K, Schendel SL, Heise M, Bedinger D, Mattocks MD, Baric RS, Alam SM, Ollmann Saphire E, Tomaras GD, Dennison SM. Cryptic-site-specific antibodies to the SARS-CoV-2 receptor binding domain can retain functional binding affinity to spike variants. J Virol 2023; 97:e0107023. [PMID: 38019013 PMCID: PMC10746274 DOI: 10.1128/jvi.01070-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/05/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Multiple SARS-CoV-2 variants of concern have emerged and caused a significant number of infections and deaths worldwide. These variants of concern contain mutations that might significantly affect antigen-targeting by antibodies. It is therefore important to further understand how antibody binding and neutralization are affected by the mutations in SARS-CoV-2 variants. We highlighted how antibody epitope specificity can influence antibody binding to SARS-CoV-2 spike protein variants and neutralization of SARS-CoV-2 variants. We showed that weakened spike binding and neutralization of Beta (B.1.351) and Omicron (BA.1) variants compared to wildtype are not universal among the panel of antibodies and identified antibodies of a specific binding footprint exhibiting consistent enhancement of spike binding and retained neutralization to Beta variant. These data and analysis can inform how antigen-targeting by antibodies might evolve during a pandemic and prepare for potential future sarbecovirus outbreaks.
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Affiliation(s)
- Kan Li
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Richard H. C. Huntwork
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Gillian Q. Horn
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Milite Abraha
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Kathryn M. Hastie
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Haoyang Li
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Vamseedhar Rayaprolu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Elizabeth Feeney
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Kenneth Cronin
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Sharon L. Schendel
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Mark Heise
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Melissa D. Mattocks
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ralph S. Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Pathology, Duke University, Durham, North Carolina, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Georgia D. Tomaras
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
- Department of Integrative Immunobiology, Duke University, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - S. Moses Dennison
- Center for Human Systems Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
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Zhang Q, Yang Y, Lan J, Wang Z, Gao Y, Li X, Mao W, Xie J, Mi LZ, Zhang X, Wang X, Mu X, Mei K. Inducing enhanced neutralizing antibodies against broad SARS-CoV-2 variants through glycan-shielding multiple non-neutralizing epitopes of RBD. Front Immunol 2023; 14:1259386. [PMID: 38149245 PMCID: PMC10750354 DOI: 10.3389/fimmu.2023.1259386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction Since the outbreak of SARS-CoV-2, vaccines have demonstrated their effectiveness in resisting virus infection, reducing severity, and lowering the mortality rate in infected individuals. However, due to the rapid and ongoing mutations of SARS-CoV-2, the protective ability of many available vaccines has been challenged. Therefore, there is an urgent need for vaccines capable of eliciting potent broadly neutralizing antibodies against various SARS-CoV-2 variants. Methods In this study, we developed a novel subunit vaccine candidate for SARS-CoV-2 by introducing a series of shielding glycans to the Fc-fused receptor-binding domain (RBD) of the prototypic spike protein. This approach aims to mask non-neutralizing epitopes and focus the immune response on crucial neutralizing epitopes. Results All modified sites were confirmed to be highly glycosylated through mass spectrometry analysis. The binding affinity of the glycan-shielded RBD (gsRBD) to the human ACE2 receptor was comparable to that of the wildtype RBD (wtRBD). Immunizing mice with gsRBD when combined with either Freund's adjuvant or aluminum adjuvant demonstrated that the introduction of the glycan shield did not compromise the antibody-inducing ability of RBD. Importantly, the gsRBD significantly enhanced the generation of neutralizing antibodies against SARS-CoV-2 pseudoviruses compared to the wtRBD. Notably, it exhibited remarkable protective activity against Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529), approximately 3-fold, 7- fold, and 17-fold higher than wtRBD, respectively. Discussion Our data proved this multiple-epitope masking strategy as an effective approach for highly active vaccine production.
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Affiliation(s)
- Qingyun Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yi Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Jun Lan
- School of Life Sciences, Tsinghua University, Beijing, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Ziyi Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xiao Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Weidong Mao
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Jing Xie
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Li-Zhi Mi
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Xiangyang Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xinquan Wang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
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Ng JPL, Xiao Yun Y, Adnan Nasim A, Gianoncelli A, Yuan Kwan Law B, Ribaudo G, Kam Wai Wong V, Coghi P. Synthesis, docking studies and biological evaluation of 1H-1,2,3-triazole-7-chloroquinoline derivatives against SARS-CoV-2. Bioorg Chem 2023; 141:106882. [PMID: 37839144 DOI: 10.1016/j.bioorg.2023.106882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded enveloped positive RNA virus and the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Chloroquine (CQ), an antimalarial drug, was reported to be active against several viruses including coronaviruses. The mechanism of host cell invasion by SARS-CoV-2 involves the interaction of angiotensin-converting enzyme (ACE2) with receptor-binding domain (RBD) of spike protein (S). The main protease (Mpro/3CLpro) is an attractive drug target due to its vital function in regulation of polyprotein translated from viral RNA. In this study, a series of novel quinoline-triazole hybrid compounds was synthesized and subjected to evaluations on their cytotoxicity, interactions with different variants of RBD in SARS-CoV-2 and with 3CLpro enzyme by experimental and computational techniques to identify their ability of counteracting viral infection. The results of bio-layer interferometry showed that quinoline derivative 11 has good interaction with delta plus and omicron RBD variants (KD = 3.46 × 10-5 and 6.38 × 10-5 M) while derivative 1 is the best binder for recent variant omicron (KD = 26.9 µM) among the series. Potent compounds 1-4 and 11 also demonstrated a suppressive effect on 3CLpro activity in a non-dose-dependent manner. Further docking study revealed that these compounds interacted within the same area of RBD, while no correlation was found for 3CLpro. Furthermore, the molecular dynamics simulations were carried out to assess the conformational stability of docked complexes for preliminary verification.
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Affiliation(s)
- Jerome P L Ng
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Yun Xiao Yun
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Ali Adnan Nasim
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Betty Yuan Kwan Law
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
| | - Vincent Kam Wai Wong
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Paolo Coghi
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; School of Pharmacy, Macau University of Science and Technology, Macau, China.
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40
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Hsieh HC, Chen CC, Chou PH, Liu WC, Wu SC. Induction of neutralizing antibodies and mucosal IgA through intranasal immunization with the receptor binding domain of SARS-CoV-2 spike protein fused with the type IIb E. coli heat-labile enterotoxin A subunit. Antiviral Res 2023; 220:105752. [PMID: 37949318 DOI: 10.1016/j.antiviral.2023.105752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
The outbreak of SARS-CoV-2 infections had led to the COVID-19 pandemic which has a significant impact on global public health and the economy. The spike (S) protein of SARS-CoV-2 contains the receptor binding domain (RBD) which binds to human angiotensin-converting enzyme 2 receptor. Numerous RBD-based vaccines have been developed and recently focused on the induction of neutralizing antibodies against the immune evasive Omicron BQ.1.1 and XBB.1.5 subvariants. In this preclinical study, we reported the use of a direct fusion of the type IIb Escherichia coli heat-labile enterotoxin A subunit with SARS CoV-2 RBD protein (RBD-LTA) as an intranasal vaccine candidate. The results showed that intranasal immunization with the RBD-LTA fusion protein in BALB/c mice elicited potent neutralizing antibodies against the Wuhan-Hu-1 and several SARS-CoV-2 variants as well as the production of IgA antibodies in bronchoalveolar lavage fluids (BALFs). Furthermore, the heterologous RBD representing the same strains used in the bivalent mRNA vaccine were used as a second-dose RBD-LTA/RBD protein booster after bivalent mRNA vaccination. The results showed that the neutralizing antibody titers elicited by the intranasal bivalent RBD-LTA/RBD protein booster were similar to the intramuscular bivalent mRNA booster, but the RBD-specific IgA titers in sera and BALFs significantly increased. Overall, this preclinical study suggests that the RBD-LTA fusion protein could be a promising candidate as a mucosal booster COVID-19 vaccine.
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Affiliation(s)
- He-Chin Hsieh
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Chung-Chu Chen
- Department of Internal Medicine, MacKay Memorial Hospital, Hsinchu, 30071, Taiwan; Teaching Center of Natural Science, Minghsin University of Science and Technology, Hsinchu, 30401, Taiwan.
| | - Pin-Han Chou
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan.
| | - Wen-Chun Liu
- Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Suh-Chin Wu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Medical Science, National Tsing Hua University, Hsinchu, 30013, Taiwan; Adimmune Corporation, Taichung, 42723, Taiwan.
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41
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Mayer-Suess L, Ibrahim A, Moelgg K, Cesari M, Knoflach M, Högl B, Stefani A, Kiechl S, Heidbreder A. Sleep disorders as both risk factors for, and a consequence of, stroke: A narrative review. Int J Stroke 2023:17474930231212349. [PMID: 37885093 DOI: 10.1177/17474930231212349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
BACKGROUND AND PURPOSE Sleep disorders are increasingly implicated as risk factors for stroke, as well as a determinant of stroke outcome. They can also occur secondary to the stroke itself. In this review, we describe the variety of different sleep disorders associated with stroke and analyze their effect on stroke risk and outcome. METHODS A search term-based literature review ("sleep," "insomnia," "narcolepsy," "restless legs syndrome," "periodic limb movements during sleep," "excessive daytime sleepiness" AND "stroke" OR "cerebrovascular" in PubMed; "stroke" and "sleep" in ClinicalTrials.gov) was performed. English articles from 1990 to March 2023 were considered. RESULTS Increasing evidence suggests that sleep disorders are risk factors for stroke. In addition, sleep disturbance has been reported in half of all stroke sufferers; specifically, an increase is not only sleep-related breathing disorders but also periodic limb movements during sleep, narcolepsy, rapid eye movement (REM) sleep behavior disorder, insomnia, sleep duration, and circadian rhythm sleep-wake disorders. Poststroke sleep disturbance has been associated with worse outcome. CONCLUSION Sleep disorders are risk factors for stroke and associated with worse stroke outcome. They are also a common consequence of stroke. Recent guidelines suggest screening for sleep disorders after stroke. It is possible that treatment of sleep disorders could both reduce stroke risk and improve stroke outcome, although further data from clinical trials are required.
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Affiliation(s)
- Lukas Mayer-Suess
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Abubaker Ibrahim
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Kurt Moelgg
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Matteo Cesari
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Knoflach
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
- VASCage-Research Centre on Clinical Stroke Research, Innsbruck, Austria
| | - Birgit Högl
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ambra Stefani
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
- Neurological Clinical Research Institute, Massachusetts General Hospital, Boston, MA, USA
| | - Stefan Kiechl
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
- VASCage-Research Centre on Clinical Stroke Research, Innsbruck, Austria
| | - Anna Heidbreder
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Neurology, Johannes Kepler University Linz, Linz, Austria
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Boggiano-Ayo T, Palacios-Oliva J, Lozada-Chang S, Relova-Hernandez E, Gomez-Perez J, Oliva G, Hernandez L, Bueno-Soler A, Montes de Oca D, Mora O, Machado-Santisteban R, Perez-Martinez D, Perez-Masson B, Cabrera Infante Y, Calzadilla-Rosado L, Ramirez Y, Aymed-Garcia J, Ruiz-Ramirez I, Romero Y, Gomez T, Espinosa LA, Gonzalez LJ, Cabrales A, Guirola O, de la Luz KR, Pi-Estopiñan F, Sanchez-Ramirez B, Garcia-Rivera D, Valdes-Balbin Y, Rojas G, Leon-Monzon K, Ojito-Magaz E, Hardy E. Development of a scalable single process for producing SARS-CoV-2 RBD monomer and dimer vaccine antigens. Front Bioeng Biotechnol 2023; 11:1287551. [PMID: 38050488 PMCID: PMC10693982 DOI: 10.3389/fbioe.2023.1287551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023] Open
Abstract
We have developed a single process for producing two key COVID-19 vaccine antigens: SARS-CoV-2 receptor binding domain (RBD) monomer and dimer. These antigens are featured in various COVID-19 vaccine formats, including SOBERANA 01 and the licensed SOBERANA 02, and SOBERANA Plus. Our approach involves expressing RBD (319-541)-His6 in Chinese hamster ovary (CHO)-K1 cells, generating and characterizing oligoclones, and selecting the best RBD-producing clones. Critical parameters such as copper supplementation in the culture medium and cell viability influenced the yield of RBD dimer. The purification of RBD involved standard immobilized metal ion affinity chromatography (IMAC), ion exchange chromatography, and size exclusion chromatography. Our findings suggest that copper can improve IMAC performance. Efficient RBD production was achieved using small-scale bioreactor cell culture (2 L). The two RBD forms - monomeric and dimeric RBD - were also produced on a large scale (500 L). This study represents the first large-scale application of perfusion culture for the production of RBD antigens. We conducted a thorough analysis of the purified RBD antigens, which encompassed primary structure, protein integrity, N-glycosylation, size, purity, secondary and tertiary structures, isoform composition, hydrophobicity, and long-term stability. Additionally, we investigated RBD-ACE2 interactions, in vitro ACE2 recognition of RBD, and the immunogenicity of RBD antigens in mice. We have determined that both the monomeric and dimeric RBD antigens possess the necessary quality attributes for vaccine production. By enabling the customizable production of both RBD forms, this unified manufacturing process provides the required flexibility to adapt rapidly to the ever-changing demands of emerging SARS-CoV-2 variants and different COVID-19 vaccine platforms.
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Affiliation(s)
- Tammy Boggiano-Ayo
- Process Development Direction, Center of Molecular Immunology, Havana, Cuba
| | | | | | | | | | - Gonzalo Oliva
- Process Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Alexi Bueno-Soler
- Process Development Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Osvaldo Mora
- Process Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Dayana Perez-Martinez
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Beatriz Perez-Masson
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | | | | | - Yaima Ramirez
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Judey Aymed-Garcia
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Yamile Romero
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Tania Gomez
- Quality Direction, Center of Molecular Immunology, Havana, Cuba
| | | | | | - Annia Cabrales
- Center for Genetic Engineering and Biotechnology, Playa, Cuba
| | - Osmany Guirola
- Center for Genetic Engineering and Biotechnology, Playa, Cuba
| | | | | | | | | | | | - Gertrudis Rojas
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | - Kalet Leon-Monzon
- Immunology and Immunobiology Direction, Center of Molecular Immunology, Havana, Cuba
| | | | - Eugenio Hardy
- Process Development Direction, Center of Molecular Immunology, Havana, Cuba
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43
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Li B, Zhang T, Cao H, Ferro V, Li J, Yu M. Identification of a Pentasaccharide Lead Compound with High Affinity to the SARS-CoV-2 Spike Protein via In Silico Screening. Int J Mol Sci 2023; 24:16115. [PMID: 38003304 PMCID: PMC10671481 DOI: 10.3390/ijms242216115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The spike (S) protein on the surface of the SARS-CoV-2 virus is critical to mediate fusion with the host cell membrane through interaction with angiotensin-converting enzyme 2 (ACE2). Additionally, heparan sulfate (HS) on the host cell surface acts as an attachment factor to facilitate the binding of the S receptor binding domain (RBD) to the ACE2 receptor. Aiming at interfering with the HS-RBD interaction to protect against SARS-CoV-2 infection, we have established a pentasaccharide library composed of 14,112 compounds covering the possible sulfate substitutions on the three sugar units (GlcA, IdoA, and GlcN) of HS. The library was used for virtual screening against RBD domains of SARS-CoV-2. Molecular modeling was carried out to evaluate the potential antiviral properties of the top-hit pentasaccharide focusing on the interactive regions around the interface of RBD-HS-ACE2. The lead pentasaccharide with the highest affinity for RBD was analyzed via drug-likeness calculations, showing better predicted druggable profiles than those currently reported for RBD-binding HS mimetics. The results provide significant information for the development of HS-mimetics as anti-SARS-CoV-2 agents.
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Affiliation(s)
- Binjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China;
| | - Tianji Zhang
- Division of Chemistry and Analytical Science, National Institute of Metrology, Beijing 100029, China;
| | - Hui Cao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China;
| | - Vito Ferro
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia;
| | - Jinping Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China;
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Mingjia Yu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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44
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Ojo OO, Bandres-Ciga S, Makarious MB, Crea PW, Hernandez DG, Houlden H, Rizig M, Singleton AB, Noyce AJ, Nalls MA, Blauwendraat C, Okubadejo NU. The non-coding GBA1 rs3115534 variant is associated with REM sleep behavior disorder in Nigerians. medRxiv 2023:2023.11.07.23298092. [PMID: 38076854 PMCID: PMC10705662 DOI: 10.1101/2023.11.07.23298092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Background Damaging coding variants in GBA1 are a genetic risk factor for rapid eye movement sleep behavior disorder (RBD), which is a known early feature of synucleinopathies. Recently, a population-specific non-coding variant (rs3115534) was found to be associated with PD risk and earlier disease onset in individuals of African ancestry. Objectives To investigate whether the GBA1 rs3115534 PD risk variant is associated with RBD. Methods We studied 709 persons with PD and 776 neurologically healthy controls from Nigeria. The GBA1 rs3115534 risk variant status was imputed from previous genotyping for all. Symptoms of RBD were assessed with the RBD screening questionnaire (RBDSQ). Results The non-coding GBA1 rs3115534 risk variant is associated with possible RBD in individuals of Nigerian origin (Beta = 0.3640, SE = 0.103, P =4.093e-04), as well as after adjusting for PD status (Beta = 0.2542, SE = 0.108, P = 0.019) suggesting that this variant may have the same downstream consequences as GBA1 coding variants. Conclusions We show that the non-coding GBA1 rs3115534 risk variant is associated with increased RBD symptomatology in Nigerians with PD. Further research is required to assess association with polysomnography-defined RBD.
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Affiliation(s)
- Oluwadamilola O. Ojo
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
- Lagos University Teaching Hospital, Idi Araba, Lagos State, Nigeria
| | - Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mary B. Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- UCL Movement Disorders Centre, University College London, London, United Kingdom
| | - Peter Wild Crea
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- UCL Movement Disorders Centre, University College London, London, United Kingdom
| | - Dena G. Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, United Kingdom
| | - Mie Rizig
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, United Kingdom
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Alastair J. Noyce
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, United Kingdom
| | - Mike A. Nalls
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- DataTecnica LLC, Washington, DC, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Njideka U. Okubadejo
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
- Lagos University Teaching Hospital, Idi Araba, Lagos State, Nigeria
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45
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Belenkaya SV, Merkuleva IA, Yarovaya OI, Chirkova VY, Sharlaeva EA, Shanshin DV, Volosnikova EA, Vatsadze SZ, Khvostov MV, Salakhutdinov NF, Shcherbakov D. Corrigendum: The main protease 3CLpro of the SARS-CoV-2 virus: how to turn an enemy into a helper. Front Bioeng Biotechnol 2023; 11:1294266. [PMID: 38026885 PMCID: PMC10658891 DOI: 10.3389/fbioe.2023.1294266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fbioe.2023.1187761.].
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Affiliation(s)
- Svetlana V. Belenkaya
- Laboratory of Bionanotechnology, Microbiology and Virology, Novosibirsk State University, Novosibirsk, Russia
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Russia
- Department of Medicinal Chemistry, N.N Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - Iuliia A. Merkuleva
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Russia
| | - Olga I. Yarovaya
- Laboratory of Bionanotechnology, Microbiology and Virology, Novosibirsk State University, Novosibirsk, Russia
- Department of Medicinal Chemistry, N.N Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - Varvara Yu Chirkova
- Department of Physical-Chemistry Biology and Biotechnology, Altay State University, Barnaul, Russia
| | - Elena A. Sharlaeva
- Department of Physical-Chemistry Biology and Biotechnology, Altay State University, Barnaul, Russia
| | - Daniil V. Shanshin
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Russia
| | | | - Sergey Z. Vatsadze
- N.D Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail V. Khvostov
- Department of Medicinal Chemistry, N.N Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
| | - Dmitriy Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo, Russia
- Department of Medicinal Chemistry, N.N Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia
- Department of Physical-Chemistry Biology and Biotechnology, Altay State University, Barnaul, Russia
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46
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Feuerstein JS, Amara A. REM Behavior Disorder: Implications for PD Therapeutics. Curr Neurol Neurosci Rep 2023; 23:727-734. [PMID: 37831394 DOI: 10.1007/s11910-023-01310-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 10/14/2023]
Abstract
PURPOSE Rapid eye movement (REM) sleep behavior disorder (RBD) is a parasomnia that occurs during REM sleep, characterized by REM sleep without atonia (RSWA) and dream enactment behavior (DEB). RBD is associated with several diseases and medications but most notably is a prodromal feature of synucleinopathies, including Parkinson's disease (PD). This article reviews RBD, its treatments, and implications for PD therapeutics. RECENT FINDINGS Recent research recognizes RBD as a prodromal marker of PD, resulting in expansion of basic science and clinical investigations of RBD. Current basic science research investigates the pathophysiology of RBD and explores animal models to allow therapeutic development. Clinical research has focused on natural history observation, as well as potential RBD treatments and their impact on sleep and phenoconversion to neurodegenerative disease. RBD serves as a fresh access point to develop both neuroprotective and symptomatic therapies in PD. These types of investigations are novel and will benefit from the more established basic science infrastructure to develop new interventions.
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Affiliation(s)
- Jeanne S Feuerstein
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO, USA.
- Department of Neurology, Rocky Mountain Regional VA Medical Center, 12631 E. 17th Ave Room 5508, Mail Stop B185, Aurora, CO, 80045, USA.
| | - Amy Amara
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO, USA
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47
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Wang WB, Ma YB, Lei ZH, Zhang XF, Li J, Li SS, Dong ZY, Liang Y, Li QM, Su JG. Identification of key mutations responsible for the enhancement of receptor-binding affinity and immune escape of SARS-CoV-2 Omicron variant. J Mol Graph Model 2023; 124:108540. [PMID: 37352723 PMCID: PMC10254043 DOI: 10.1016/j.jmgm.2023.108540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/25/2023]
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised concerns worldwide due to its enhanced transmissibility and immune escapability. The first dominant Omicron BA.1 subvariant harbors more than 30 mutations in the spike protein from the prototype virus, of which 15 mutations are located at the receptor binding domain (RBD). These mutations in the RBD region attracted significant attention, which potentially enhance the binding of the receptor human angiotensin-converting enzyme 2 (hACE2) and decrease the potency of neutralizing antibodies/nanobodies. This study applied the molecular dynamics simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method, to investigate the molecular mechanism behind the impact of the mutations acquired by Omicron on the binding affinity between RBD and hACE2. Our results indicate that five key mutations, i.e., N440K, T478K, E484A, Q493R, and G496S, contributed significantly to the enhancement of the binding affinity by increasing the electrostatic interactions of the RBD-hACE2 complex. Moreover, fourteen neutralizing antibodies/nanobodies complexed with RBD were used to explore the effects of the mutations in Omicron RBD on their binding affinities. The calculation results indicate that the key mutations E484A and Y505H reduce the binding affinities to RBD for most of the studied neutralizing antibodies/nanobodies, mainly attributed to the elimination of the original favorable gas-phase electrostatic and hydrophobic interactions between them, respectively. Our results provide valuable information for developing effective vaccines and antibody/nanobody drugs.
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Affiliation(s)
- Wei Bu Wang
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Yi Bo Ma
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Ze Hua Lei
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Xue Feng Zhang
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Jiao Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Shan Shan Li
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Ze Yuan Dong
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China
| | - Yu Liang
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China
| | - Qi Ming Li
- National Engineering Center for New Vaccine Research, Beijing, China; The Sixth Laboratory, National Vaccine and Serum Institute (NVSI), Beijing, China.
| | - Ji Guo Su
- High Performance Computing Center, National Vaccine and Serum Institute (NVSI), Beijing, China; National Engineering Center for New Vaccine Research, Beijing, China.
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48
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Barbey C, Su J, Billmeier M, Stefan N, Bester R, Carnell G, Temperton N, Heeney J, Protzer U, Breunig M, Wagner R, Peterhoff D. Immunogenicity of a silica nanoparticle-based SARS-CoV-2 vaccine in mice. Eur J Pharm Biopharm 2023; 192:41-55. [PMID: 37774890 DOI: 10.1016/j.ejpb.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/12/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Safe and effective vaccines have been regarded early on as critical in combating the COVID-19 pandemic. Among the deployed vaccine platforms, subunit vaccines have a particularly good safety profile but may suffer from a lower immunogenicity compared to mRNA based or viral vector vaccines. In fact, this phenomenon has also been observed for SARS-CoV-2 subunit vaccines comprising the receptor-binding domain (RBD) of the spike (S) protein. Therefore, RBD-based vaccines have to rely on additional measures to enhance the immune response. It is well accepted that displaying antigens on nanoparticles can improve the quantity and quality of vaccine-mediated both humoral and cell-mediated immune responses. Based on this, we hypothesized that SARS-CoV-2 RBD as immunogen would benefit from being presented to the immune system via silica nanoparticles (SiNPs). Herein we describe the preparation, in vitro characterization, antigenicity and in vivo immunogenicity of SiNPs decorated with properly oriented RBD in mice. We found our RBD-SiNP conjugates show narrow, homogeneous particle distribution with optimal size of about 100 nm for efficient transport to and into the lymph node. The colloidal stability and binding of the antigen was stable for at least 4 months at storage- and in vivo-temperatures. The antigenicity of the RBD was maintained upon binding to the SiNP surface, and the receptor-binding motif was readily accessible due to the spatial orientation of the RBD. The particles were efficiently taken up in vitro by antigen-presenting cells. In a mouse immunization study using an mRNA vaccine and spike protein as benchmarks, we found that the SiNP formulation was able to elicit a stronger RBD-specific humoral response compared to the soluble protein. For the adjuvanted RBD-SiNP we found strong S-specific multifunctional CD4+ T cell responses, a balanced T helper response, improved auto- and heterologous virus neutralization capacity, and increased serum avidity, suggesting increased affinity maturation. In summary, our results provide further evidence for the possibility of optimizing the cellular and humoral immune response through antigen presentation on SiNP.
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Affiliation(s)
- Clara Barbey
- Department of Pharmaceutical Technology, University of Regensburg, Regensburg, Germany
| | - Jinpeng Su
- Institute of Virology, Technical University of Munich / Helmholtz Munich, Munich, Germany
| | - Martina Billmeier
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Nadine Stefan
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Romina Bester
- Institute of Virology, Technical University of Munich / Helmholtz Munich, Munich, Germany
| | - George Carnell
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Chatham ME4 4BF, United Kingdom
| | - Jonathan Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich / Helmholtz Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich Partner Site, Germany
| | - Miriam Breunig
- Department of Pharmaceutical Technology, University of Regensburg, Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany; Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany; Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany.
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49
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Prasad R, Ajith H, Kumar Chandrakumaran N, Dnyaneshwar Khangar P, Mohan A, Nelson-Sathi S. In silico study identifies peptide inhibitors that negate the effect of non-synonymous mutations in major drug targets of SARS-CoV-2 variants. J Biomol Struct Dyn 2023; 41:9551-9561. [PMID: 36377464 DOI: 10.1080/07391102.2022.2143426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/29/2022] [Indexed: 11/16/2022]
Abstract
Since its advent in December 2019, SARS-CoV-2 has diverged into multiple variants with differing levels of virulence owing to the accumulation of mutations in its genome. The structural changes induced by non-synonymous mutations in major drug targets of the virus are known to alter the binding of potential antagonistic inhibitors. Here, we analyzed the effects of non-synonymous mutations in major targets of SARS-CoV-2 in response to potential peptide inhibitors. We screened 12 peptides reported to have anti-viral properties against RBD and 5 peptides against Mpro of SARS-CoV-2 variants using molecular docking and simulation approaches. The mutational landscape of RBD among SARS-CoV-2 variants had 21 non-synonymous mutations across 18 distinct sites. Among these, 14 mutations were present in the RBM region directly interacting with the hACE2 receptor. However, Only 3 non-synonymous mutations were observed in Mpro. We found that LCB1 - a de novo-synthesized peptide has the highest binding affinity to RBD despite non-synonymous mutations in variants and engages key residues of RBD-hACE2 interaction such as K417, E484, N487, and N501. Similarly, an antimicrobial peptide; 2JOS, was identified against Mpro with high binding affinity as it interacts with key residues in dimerization sites such as E166 and F140 crucial for viral replication. MD simulations affirm the stability of RBD-LCB1 and Mpro-2JOS complexes with an average RMSD of 1.902 and 2.476 respectively. We ascertain that LCB1 and 2JOS peptides are promising inhibitors to combat emerging variants of SARS-CoV-2 and thus warrant further investigations using in-vitro and in-vivo analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Roshny Prasad
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Harikrishnan Ajith
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | | | | | - Anand Mohan
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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50
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Ramasubburayan R, Amperayani KR, Varadhi G, Dhanraj G, Athista M, Mahapatra S, Prakash S. Unraveling bioactive metabolites of mangroves as putative inhibitors of SARS-CoV-2 Mpro and RBD proteins: molecular dynamics and ADMET analysis. J Biomol Struct Dyn 2023:1-10. [PMID: 37897196 DOI: 10.1080/07391102.2023.2275185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023]
Abstract
COVID-19 is a deadly pandemic caused by Corona virus leading to millions of deaths worldwide. Till today no medicine was available to cure this disease. This study selected 262 potential bioactive natural products derived from mangroves to inhibit the main protease (Mpro) and receptor-binding domain (RBD) protein of the COVID-19 virus. All the ligands were subjected to Adsorption Digestion Metabolism Excretion and Toxicity (ADMET) predictions and docking studies using AutodockVina. Among all the ligands, NP_143 (Shearinine A) and NP_242 (Amentoflavone), having the highest docking score of 10.2 and 10.1 Kj/mole, respectively, were picked for 100 ns of Molecular Dynamics using GROMACS. The trajectories generated were used to estimate Root mean square deviation (RMSD), Root mean square fluctuations (RMSF), Radius of Gyrations (RG), Solvent accessible surface area (SASA), and Hydrogen bonds. From the data generated, both the ligands have good binding ability at the active site of Mpro protein and do not deviate much. They have strong interactions with the amino acids during the 100 ns of simulations and can thus be considered potential drug candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ramasamy Ramasubburayan
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Karteek Rao Amperayani
- Department of Organic Chemistry, Gayatri Vidya Parishad College for Degree and PG Courses (Autonomous), Andhra Pradesh, India
| | - Govinda Varadhi
- Department of Organic Chemistry, Gayatri Vidya Parishad College for Degree and PG Courses (Autonomous), Andhra Pradesh, India
| | - Ganapathy Dhanraj
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | - Manoharan Athista
- Department of Bioinformatics, Sathyabama Institute of Sciences and Technology, Chennai, Tamil Nadu, India
| | - Sonalismita Mahapatra
- Marine Biotechnology Research Laboratory, Department of Basic Sciences, Institute of Fisheries and Post Graduate Studies, Tamilnadu Dr. J. Jayalalitha Fisheries University, OMR Campus, Vaniyanchavadi, Chennai, Tamil Nadu, India
| | - Santhiyagu Prakash
- Marine Biotechnology Research Laboratory, Department of Basic Sciences, Institute of Fisheries and Post Graduate Studies, Tamilnadu Dr. J. Jayalalitha Fisheries University, OMR Campus, Vaniyanchavadi, Chennai, Tamil Nadu, India
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