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Havranek B, Lindsey GW, Higuchi Y, Itoh Y, Suzuki T, Okamoto T, Hoshino A, Procko E, Islam SM. A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo. Commun Biol 2023; 6:513. [PMID: 37173421 PMCID: PMC10177734 DOI: 10.1038/s42003-023-04860-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a 'decoy' to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.
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Affiliation(s)
- Brandon Havranek
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, USA
- ComputePharma, LLC., Chicago, IL, USA
| | | | - Yusuke Higuchi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801, USA
- Cyrus Biotechnology, Inc., Seattle, WA, USA
| | - Shahidul M Islam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- ComputePharma, LLC., Chicago, IL, USA.
- Department of Chemistry, Delaware State University, Dover, DE, 19901, USA.
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Hou N, Wang L, Li M, Xie B, He L, Guo M, Liu S, Wang M, Zhang R, Wang K. Do COVID-19 CT features vary between patients from within and outside mainland China? Findings from a meta-analysis. Front Public Health 2022; 10:939095. [PMID: 36311632 PMCID: PMC9616120 DOI: 10.3389/fpubh.2022.939095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 07/25/2022] [Indexed: 01/25/2023] Open
Abstract
Background Chest computerized tomography (CT) plays an important role in detecting patients with suspected coronavirus disease 2019 (COVID-19), however, there are no systematic summaries on whether the chest CT findings of patients within mainland China are applicable to those found in patients outside. Methods Relevant studies were retrieved comprehensively by searching PubMed, Embase, and Cochrane Library databases before 15 April 2022. Quality assessment of diagnostic accuracy studies (QUADAS) was used to evaluate the quality of the included studies, which were divided into two groups according to whether they were in mainland China or outside. Data on diagnostic performance, unilateral or bilateral lung involvement, and typical chest CT imaging appearances were extracted, and then, meta-analyses were performed with R software to compare the CT features of COVID-19 pneumonia between patients from within and outside mainland China. Results Of the 8,258 studies screened, 19 studies with 3,400 patients in mainland China and 14 studies with 554 outside mainland China were included. Overall, the risk of quality assessment and publication bias was low. The diagnostic value of chest CT is similar between patients from within and outside mainland China (93, 91%). The pooled incidence of unilateral lung involvement (15, 7%), the crazy-paving sign (31, 21%), mixed ground-glass opacities (GGO) and consolidations (51, 35%), air bronchogram (44, 25%), vascular engorgement (59, 33%), bronchial wall thickening (19, 12%), and septal thickening (39, 26%) in patients from mainland China were significantly higher than those from outside; however, the incidence rates of bilateral lung involvement (75, 84%), GGO (78, 87%), consolidations (45, 58%), nodules (12, 17%), and pleural effusion (9, 15%) were significantly lower. Conclusion Considering that the chest CT features of patients in mainland China may not reflect those of the patients abroad, radiologists and clinicians should be familiar with various CT presentations suggestive of COVID-19 in different regions.
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Affiliation(s)
- Nianzong Hou
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai, China,Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Lin Wang
- Department of Critical Care Medicine, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Mingzhe Li
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Bing Xie
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Lu He
- Department of Urology, Dongfeng Hospital, Hubei University of Medicine, Shiyan, China
| | - Mingyu Guo
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Shuo Liu
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Meiyu Wang
- Department of Cardiology, The People's Hospital of Zhangdian District, Zibo, China
| | - Rumin Zhang
- Department of Critical Care Medicine, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Kai Wang
- Department of Critical Care Medicine, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China,*Correspondence: Kai Wang
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3
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Abstract
The World Health Organisation has reported that the viral disease known as COVID-19, caused by SARS-CoV-2, is the leading cause of death by a single infectious agent. This narrative review examines certain components of the pandemic: its origins, early clinical data, global and UK-focussed epidemiology, vaccination, variants, and long COVID.
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Affiliation(s)
- A. D. Blann
- School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, United Kingdom
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4
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Han Y, Yang Z, Hu H, Zhang H, Chen L, Li K, Kong L, Wang Q, Liu B, Wang M, Lin J, Chen PR. Covalently Engineered Protein Minibinders with Enhanced Neutralization Efficacy against Escaping SARS-CoV-2 Variants. J Am Chem Soc 2022; 144:5702-5707. [PMID: 35212528 PMCID: PMC8905923 DOI: 10.1021/jacs.1c11554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/12/2022]
Abstract
The rapid emergence and spread of escaping mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has significantly challenged our efforts in fighting against the COVID-19 pandemic. A broadly neutralizing reagent against these concerning variants is thus highly desirable for the prophylactic and therapeutic treatments of SARS-CoV-2 infection. We herein report a covalent engineering strategy on protein minibinders for potent neutralization of the escaping variants such as B.1.617.2 (Delta), B.1.617.1 (Kappa), and B.1.1.529 (Omicron) through in situ cross-linking with the spike receptor binding domain (RBD). The resulting covalent minibinder (GlueBinder) exhibited enhanced blockage of RBD-human angiotensin-converting enzyme 2 (huACE2) interaction and more potent neutralization effect against the Delta variant than its noncovalent counterpart as demonstrated on authentic virus. By leveraging the covalent chemistry against escaping mutations, our strategy may be generally applicable for restoring and enhancing the potency of neutralizing antibodies to SARS-CoV-2 and other rapidly evolving viral targets.
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Affiliation(s)
- Yu Han
- Synthetic and Functional Biomolecules Center, Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education,
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871,
China
- Peking-Tsinghua Center for Life Sciences, Academy for
Advanced Interdisciplinary Studies, Peking University, Beijing
100871, China
| | - Zhenlin Yang
- Synthetic and Functional Biomolecules Center, Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education,
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871,
China
- Peking-Tsinghua Center for Life Sciences, Academy for
Advanced Interdisciplinary Studies, Peking University, Beijing
100871, China
| | - Hengrui Hu
- State Key Laboratory of Virology, Wuhan Institute of
Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei 430071, China
| | - Heng Zhang
- Synthetic and Functional Biomolecules Center, Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education,
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871,
China
- Shenzhen Bay Laboratory,
Shenzhen 518055, China
| | - Long Chen
- Synthetic and Functional Biomolecules Center, Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education,
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871,
China
| | - Kexin Li
- Peking-Tsinghua Center for Life Sciences, Academy for
Advanced Interdisciplinary Studies, Peking University, Beijing
100871, China
| | - Linghao Kong
- Peking-Tsinghua Center for Life Sciences, Academy for
Advanced Interdisciplinary Studies, Peking University, Beijing
100871, China
| | - Qianran Wang
- State Key Laboratory of Virology, Wuhan Institute of
Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei 430071, China
| | - Bo Liu
- Department of Microorganism Engineering,
Beijing Institute of Biotechnology, Beijing 100071,
China
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of
Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei 430071, China
| | - Jian Lin
- Synthetic and Functional Biomolecules Center, Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education,
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871,
China
- Department of Pharmacy, Peking University
Third Hospital, Beijing 100191, China
| | - Peng R. Chen
- Synthetic and Functional Biomolecules Center, Key
Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education,
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871,
China
- Peking-Tsinghua Center for Life Sciences, Academy for
Advanced Interdisciplinary Studies, Peking University, Beijing
100871, China
- Shenzhen Bay Laboratory,
Shenzhen 518055, China
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Papanikolaou V, Chrysovergis A, Ragos V, Tsiambas E, Katsinis S, Manoli A, Papouliakos S, Roukas D, Mastronikolis S, Peschos D, Batistatou A, Kyrodimos E, Mastronikolis N. From delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants. Gene 2022; 814:146134. [PMID: 34990799 PMCID: PMC8725615 DOI: 10.1016/j.gene.2021.146134] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
Abstract
Coronavirus-related Severe Acute Respiratory Syndrome (SARS-CoV) in 2002/2003, Middle-East Respiratory Syndrome (MERS-CoV) in 2012/2013, and especially the current 2019/2021 Severe Acute Respiratory Syndrome-2 (SARS-CoV-2) affected negatively the national health systems’ endurance worldwide. SARS-Cov-2 virus belongs to lineage b of beta-CoVs demonstrating a strong phylogenetic similarity with BatCoVRaTG13 type. Spike (S) glycoprotein projections -consisting of two subunits S1/S2- provide a unique crown-like formation (corona) on virion’s surface. Concerning their functional role, S1 represents the main receptor-binding domain (RBD), whereas S2 is involved in the virus-cell membrane fusion mechanism. On Nov 26th 2021, WHO designated the new SARS-CoV-2 strain – named Omicron, from letter ‘’όμικρον’’ in the Greek alphabet - as a variant of concern (B.1.1529 variant). Potentially this new variant is associated with high transmissibility leading to elevated infectivity and probably increased re-infection rates. Its impact on morbidity/mortality remains under investigation. In the current paper, analyzing and comparing the alterations of SARS-CoV-2 S RNA sequences in the defined variants (Alpha to Omicron), we observed some interesting findings regarding the S1-RBD/S2 mutation/deletion equilibrium that maybe affect and modify its activity.
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Affiliation(s)
| | - Aris Chrysovergis
- 1ST ENT Department, Hippocration Hospital, University of Athens, Athens, Greece
| | - Vasileios Ragos
- Dept of Maxillofacial, Medical School, University of Ioannina, Greece
| | - Evangelos Tsiambas
- Dept of Maxillofacial, Medical School, University of Ioannina, Greece; Department of Cytology, Molecular Unit, 417 Veterans Army Hospital (NIMTS), Athens, Greece.
| | - Spyros Katsinis
- Department of Otorhinolaryngology, Thoracic Diseases General Hospital "Sotiria", Athens, Greece
| | - Arezina Manoli
- Department of Otorhinolaryngology, Thoracic Diseases General Hospital "Sotiria", Athens, Greece
| | | | - Dimitrios Roukas
- Department of Psychiatry, 417 Veterans Army Hospital (NIMTS), Athens, Greece
| | | | - Dimitrios Peschos
- Department of Physiology, Medical School, University of Ioannina, Greece
| | - Anna Batistatou
- ENT Department, Medical School, University of Patras, Greece
| | - Efthimios Kyrodimos
- 1ST ENT Department, Hippocration Hospital, University of Athens, Athens, Greece
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Tran TX, Lien NTK, Thu HT, Duy ND, Duong BTT, Quyen DV. Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam-a molecular potential for the vaccine development? PeerJ 2021; 9:e12329. [PMID: 34721997 PMCID: PMC8530102 DOI: 10.7717/peerj.12329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/27/2021] [Indexed: 11/20/2022] Open
Abstract
Background Porcine epidemic diarrhea virus (PEDV) is a dangerous virus causing large piglet losses. PEDV spread rapidly between pig farms and caused the death of up to 90% of infected piglets. Current vaccines are only partially effective in providing immunity to suckling due to the rapid dissemination and ongoing evolution of PEDV. Methods In this study, the complete genome of a PEDV strain in Vietnam 2018 (IBT/VN/2018 strain) has been sequenced. The nucleotide sequence of each fragment was assembled to build a continuous complete sequence using the DNASTAR program. The complete nucleotide sequences and amino acid sequences of S, N, and ORF3 genes were aligned and analyzed to detect the mutations. Results The full-length genome was determined with 28,031 nucleotides in length which consisted of the 5'UTR, ORF1ab, S protein, ORF3, E protein, M protein, N protein, and 3'UTR region. The phylogenetic analysis showed that the IBT/VN/2018 strain was highly virulent belonged to the G2b subgroup along with the Northern American and Asian S-INDEL strains. Multiple sequence alignment of deduced amino acids revealed numerous mutations in the S, N, and ORF3 regions including one substitution 766P > L766 in the epitope SS6; two in the S0subdomain (135DN136 > 135SI136 and N144> D144); two in subdomain SHR1 at aa 1009L > M1009 and 1089S > L1089; one at aa 1279P > S1279 in subdomain SHR2 of the S protein; two at aa 364N > I364 and 378N > S378 in the N protein; four at aa 25L > S25, 70I > V70, 107C > F107, and 168D > N168 in the ORF3 protein. We identified two insertions (at aa 59NQGV62 and aa 145N) and one deletion (at aa 168DI169) in S protein. Remarkable, eight amino acid substitutions (294I > M294, 318A > S318, 335V > I335, 361A > T361, 497R > T497, 501SH502 > 501IY502, 506I > T506, 682V > I682, and 777P > L777) were found in SA subdomain. Besides, N- and O-glycosylation analysis of S, N, and ORF3 protein reveals three known sites (25G+, 123N+, and 62V+) and three novel sites (144D+, 1009M+, and 1279L+) in the IBT/VN/2018 strain compared with the vaccine strains. Taken together, the results showed that mutations in the S, N, and ORF3 genes can affect receptor specificity, viral pathogenicity, and the ability to evade the host immune system of the IBT/VN/2018 strain. Our results highlight the importance of molecular characterization of field strains of PEDV for the development of an effective vaccine to control PEDV infections in Vietnam.
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Affiliation(s)
- Thach Xuan Tran
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam
| | - Nguyen T K Lien
- Functional of Genomics Lab, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha T Thu
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam
| | - Nguyen Dinh Duy
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam
| | - Bui T T Duong
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam
| | - Dong Van Quyen
- Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam.,University of Science and Technology of Ha Noi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
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