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An K, Yang X, Luo M, Yan J, Xu P, Zhang H, Li Y, Wu S, Warshel A, Bai C. Mechanistic study of the transmission pattern of the SARS-CoV-2 omicron variant. Proteins 2024; 92:705-719. [PMID: 38183172 PMCID: PMC11059747 DOI: 10.1002/prot.26663] [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: 10/18/2023] [Revised: 11/25/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024]
Abstract
The omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) characterized by 30 mutations in its spike protein, has rapidly spread worldwide since November 2021, significantly exacerbating the ongoing COVID-19 pandemic. In order to investigate the relationship between these mutations and the variant's high transmissibility, we conducted a systematic analysis of the mutational effect on spike-angiotensin-converting enzyme-2 (ACE2) interactions and explored the structural/energy correlation of key mutations, utilizing a reliable coarse-grained model. Our study extended beyond the receptor-binding domain (RBD) of spike trimer through comprehensive modeling of the full-length spike trimer rather than just the RBD. Our free-energy calculation revealed that the enhanced binding affinity between the spike protein and the ACE2 receptor is correlated with the increased structural stability of the isolated spike protein, thus explaining the omicron variant's heightened transmissibility. The conclusion was supported by our experimental analyses involving the expression and purification of the full-length spike trimer. Furthermore, the energy decomposition analysis established those electrostatic interactions make major contributions to this effect. We categorized the mutations into four groups and established an analytical framework that can be employed in studying future mutations. Additionally, our calculations rationalized the reduced affinity of the omicron variant towards most available therapeutic neutralizing antibodies, when compared with the wild type. By providing concrete experimental data and offering a solid explanation, this study contributes to a better understanding of the relationship between theories and observations and lays the foundation for future investigations.
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Affiliation(s)
- Ke An
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang, 310005, P.R. China
| | - Xianzhi Yang
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen 518000, China
| | - Mengqi Luo
- College of Management, Shenzhen University, Shenzhen, 518060, China
| | - Junfang Yan
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
| | - Peiyi Xu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
| | - Honghui Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
| | - Yuqing Li
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518116, China
| | - Song Wu
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518116, China
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
- Warshel Institute for Computational Biology
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang, 310005, P.R. China
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Rai P, Marano JM, Kang L, Coutermarsh-Ott S, Daamen AR, Lipsky PE, Weger-Lucarelli J. Obesity fosters severe disease outcomes in a mouse model of coronavirus infection associated with transcriptomic abnormalities. J Med Virol 2024; 96:e29587. [PMID: 38587204 DOI: 10.1002/jmv.29587] [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: 02/01/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
Obesity has been identified as an independent risk factor for severe outcomes in humans with coronavirus disease 2019 (COVID-19) and other infectious diseases. Here, we established a mouse model of COVID-19 using the murine betacoronavirus, mouse hepatitis virus 1 (MHV-1). C57BL/6 and C3H/HeJ mice exposed to MHV-1 developed mild and severe disease, respectively. Obese C57BL/6 mice developed clinical manifestations similar to those of lean controls. In contrast, all obese C3H/HeJ mice succumbed by 8 days postinfection, compared to a 50% mortality rate in lean controls. Notably, both lean and obese C3H/HeJ mice exposed to MHV-1 developed lung lesions consistent with severe human COVID-19, with marked evidence of diffuse alveolar damage (DAD). To identify early predictive biomarkers of worsened disease outcomes in obese C3H/HeJ mice, we sequenced RNA from whole blood 2 days postinfection and assessed changes in gene and pathway expression. Many pathways uniquely altered in obese C3H/HeJ mice postinfection aligned with those found in humans with severe COVID-19. Furthermore, we observed altered gene expression related to the unfolded protein response and lipid metabolism in infected obese mice compared to their lean counterparts, suggesting a role in the severity of disease outcomes. This study presents a novel model for studying COVID-19 and elucidating the mechanisms underlying severe disease outcomes in obese and other hosts.
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Affiliation(s)
- Pallavi Rai
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA
| | - Jeffrey M Marano
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, Virginia, USA
| | - Lin Kang
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
- Biomedical Affairs and Research, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, USA
- College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana, USA
| | - Sheryl Coutermarsh-Ott
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
| | | | | | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA
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Wang F, Ma X, Ye J, Shi C, Chen Y, Yu Z, Li T, Yang D, Li M, Wang P. Precise Detection of Viral RNA by Programming Multiplex Rolling Circle Amplification and Strand Displacement. Anal Chem 2023; 95:17699-17707. [PMID: 37971750 DOI: 10.1021/acs.analchem.3c03548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Detection of viral infections (e.g., SARS-CoV-2) with high precision is critical to disease control and treatment. There is an urgent need to develop point-of-care detection methods to complement the gold standard laboratory-based PCR assay with comparable sensitivity and specificity. Herein, we developed a method termed mCAD to achieve ultraspecific point-of-care detection of SARS-CoV-2 RNA while maintaining high sensitivity by programming multiplex rolling circle amplification and toehold-mediated strand displacement reactions. RCA offers sufficient amplification of RNA targets for subsequent detection. Most importantly, a multilayer of detection specificity is implemented into mCAD via sequence-specific hybridization of nucleic acids across serial steps of this protocol to fully eliminate potential false-positive detections. Using mCAD, we demonstrated a highly specific, sensitive, and convenient visual detection of SARS-CoV-2 RNA from both synthetic and clinical samples, exhibiting performance comparable to qPCR. We envision that mCAD will find its broad applications in clinical prospects for nucleic acid detections readily beyond SARS-CoV-2 RNA.
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Affiliation(s)
- Fukai Wang
- College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200233, China
| | - Xiaowei Ma
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jing Ye
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chenzhi Shi
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yun Chen
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhicai Yu
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Tianming Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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Luo Y, Liu S, Xue J, Yang Y, Zhao J, Sun Y, Wang B, Yin S, Li J, Xia Y, Ge F, Dong J, Guo L, Ye B, Huang W, Wang Y, Xi JJ. High-throughput screening of spike variants uncovers the key residues that alter the affinity and antigenicity of SARS-CoV-2. Cell Discov 2023; 9:40. [PMID: 37041132 PMCID: PMC10088716 DOI: 10.1038/s41421-023-00534-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/03/2023] [Indexed: 04/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has elicited a worldwide pandemic since late 2019. There has been ~675 million confirmed coronavirus disease 2019 (COVID-19) cases, leading to more than 6.8 million deaths as of March 1, 2023. Five SARS-CoV-2 variants of concern (VOCs) were tracked as they emerged and were subsequently characterized. However, it is still difficult to predict the next dominant variant due to the rapid evolution of its spike (S) glycoprotein, which affects the binding activity between cellular receptor angiotensin-converting enzyme 2 (ACE2) and blocks the presenting epitope from humoral monoclonal antibody (mAb) recognition. Here, we established a robust mammalian cell-surface-display platform to study the interactions of S-ACE2 and S-mAb on a large scale. A lentivirus library of S variants was generated via in silico chip synthesis followed by site-directed saturation mutagenesis, after which the enriched candidates were acquired through single-cell fluorescence sorting and analyzed by third-generation DNA sequencing technologies. The mutational landscape provides a blueprint for understanding the key residues of the S protein binding affinity to ACE2 and mAb evasion. It was found that S205F, Y453F, Q493A, Q493M, Q498H, Q498Y, N501F, and N501T showed a 3-12-fold increase in infectivity, of which Y453F, Q493A, and Q498Y exhibited at least a 10-fold resistance to mAbs REGN10933, LY-CoV555, and REGN10987, respectively. These methods for mammalian cells may assist in the precise control of SARS-CoV-2 in the future.
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Affiliation(s)
- Yufeng Luo
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Shuo Liu
- Graduate School of Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Jiguo Xue
- Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Ye Yang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Junxuan Zhao
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Ying Sun
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bolun Wang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Shenyi Yin
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Juan Li
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Yuchao Xia
- GeneX Health Co. Ltd, Beijing, China
- College of Science, Beijing Information Science and Technology University, Beijing, China
| | - Feixiang Ge
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | | | - Lvze Guo
- GeneX Health Co. Ltd, Beijing, China
| | - Buqing Ye
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Youchun Wang
- Graduate School of Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China.
| | - Jianzhong Jeff Xi
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China.
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An K, Zhu X, Yan J, Xu P, Hu L, Bai C. A systematic study on the binding affinity of SARS-CoV-2 spike protein to antibodies. AIMS Microbiol 2022; 8:595-611. [PMID: 36694585 PMCID: PMC9834082 DOI: 10.3934/microbiol.2022038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
The COVID-19 pandemic has caused a worldwide health crisis and economic recession. Effective prevention and treatment methods are urgently required to control the pandemic. However, the emergence of novel SARS-CoV-2 variants challenges the effectiveness of currently available vaccines and therapeutic antibodies. In this study, through the assessment of binding free energies, we analyzed the mutational effects on the binding affinity of the coronavirus spike protein to neutralizing antibodies, patient-derived antibodies, and artificially designed antibody mimics. We designed a scoring method to assess the immune evasion ability of viral variants. We also evaluated the differences between several targeting sites on the spike protein of antibodies. The results presented herein might prove helpful in the development of more effective therapies in the future.
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Affiliation(s)
- Ke An
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, 518172, Guangdong, People's Republic of China,School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xiaohong Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, 518172, Guangdong, People's Republic of China,School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Junfang Yan
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, 518172, Guangdong, People's Republic of China
| | - Peiyi Xu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, 518172, Guangdong, People's Republic of China
| | - Linfeng Hu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, 518172, Guangdong, People's Republic of China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, 518172, Guangdong, People's Republic of China,Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang, 310005, P.R. China,* Correspondence:
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6
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Chavda VP, Bezbaruah R, Deka K, Nongrang L, Kalita T. The Delta and Omicron Variants of SARS-CoV-2: What We Know So Far. Vaccines (Basel) 2022; 10:1926. [PMID: 36423021 PMCID: PMC9698608 DOI: 10.3390/vaccines10111926] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 07/30/2023] Open
Abstract
The world has not yet completely overcome the fear of the havoc brought by SARS-CoV-2. The virus has undergone several mutations since its initial appearance in China in December 2019. Several variations (i.e., B.1.616.1 (Kappa variant), B.1.617.2 (Delta variant), B.1.617.3, and BA.2.75 (Omicron variant)) have emerged throughout the pandemic, altering the virus's capacity to spread, risk profile, and even symptoms. Humanity faces a serious threat as long as the virus keeps adapting and changing its fundamental function to evade the immune system. The Delta variant has two escape alterations, E484Q and L452R, as well as other mutations; the most notable of these is P681R, which is expected to boost infectivity, whereas the Omicron has about 60 mutations with certain deletions and insertions. The Delta variant is 40-60% more contagious in comparison to the Alpha variant. Additionally, the AY.1 lineage, also known as the "Delta plus" variant, surfaced as a result of a mutation in the Delta variant, which was one of the causes of the life-threatening second wave of coronavirus disease 2019 (COVID-19). Nevertheless, the recent Omicron variants represent a reminder that the COVID-19 epidemic is far from ending. The wave has sparked a fervor of investigation on why the variant initially appeared to propagate so much more rapidly than the other three variants of concerns (VOCs), whether it is more threatening in those other ways, and how its type of mutations, which induce minor changes in its proteins, can wreck trouble. This review sheds light on the pathogenicity, mutations, treatments, and impact on the vaccine efficacy of the Delta and Omicron variants of SARS-CoV-2.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380008, Gujarat, India
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Kangkan Deka
- NETES Institute of Pharmaceutical Science, Mirza, Guwahati 781125, Assam, India
| | - Lawandashisha Nongrang
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Tutumoni Kalita
- Girijananda Chowdhury Institute of Pharmaceutical Science, Azara, Guwahati 781017, Assam, India
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Chen X, Han J, Cai X, Wang S. Antimicrobial peptides: Sustainable application informed by evolutionary constraints. Biotechnol Adv 2022; 60:108012. [PMID: 35752270 DOI: 10.1016/j.biotechadv.2022.108012] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/02/2022] [Accepted: 06/19/2022] [Indexed: 01/10/2023]
Abstract
The proliferation and global expansion of multidrug-resistant (MDR) bacteria have deepened the need to develop novel antimicrobials. Antimicrobial peptides (AMPs) are regarded as promising antibacterial agents because of their broad-spectrum antibacterial activity and multifaceted mechanisms of action with non-specific targets. However, if AMPs are to be applied sustainably, knowledge of how they induce resistance in pathogenic bacteria must be mastered to avoid repeating the traditional antibiotic resistance mistakes currently faced. Furthermore, the evolutionary constraints on the acquisition of AMP resistance by microorganisms in the natural environment, such as functional compatibility and fitness trade-offs, inform the translational application of AMPs. Consequently, the shortcut to achieve sustainable utilization of AMPs is to uncover the evolutionary constraints of bacteria on AMP resistance in nature and find the tricks to exploit these constraints, such as applying AMP cocktails to minimize the efficacy of selection for resistance or combining nanomaterials to maximize the costs of AMP resistance. Altogether, this review dissects the benefits, challenges, and opportunities of utilizing AMPs against disease-causing bacteria, and highlights the use of AMP cocktails or nanomaterials to proactively address potential AMP resistance crises in the future.
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Affiliation(s)
- Xuan Chen
- College of Chemical Engineering, Fuzhou University, Fuzhou, Fujian 350108, China; College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jinzhi Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xixi Cai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Shaoyun Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, China.
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8
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Xu Z, Zou Y, Gao X, Niu MM, Li J, Xue L, Jiang S. Dual-targeting cyclic peptides of receptor-binding domain (RBD) and main protease (Mpro) as potential drug leads for the treatment of SARS-CoV-2 infection. Front Pharmacol 2022; 13:1041331. [PMID: 36339564 PMCID: PMC9627161 DOI: 10.3389/fphar.2022.1041331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/10/2022] [Indexed: 12/01/2023] Open
Abstract
The receptor-binding domain (RBD) and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) play a crucial role in the entry and replication of viral particles, and co-targeting both of them could be an attractive approach for the treatment of SARS-CoV-2 infection by setting up a "double lock" in the viral lifecycle. However, few dual RBD/Mpro-targeting agents have been reported. Here, four novel RBD/Mpro dual-targeting peptides, termed as MRs 1-4, were discovered by an integrated virtual screening scheme combining molecular docking-based screening and molecular dynamics simulation. All of them possessed nanomolar binding affinities to both RBD and Mpro ranging from 14.4 to 39.2 nM and 22.5-40.4 nM, respectively. Further pseudovirus infection assay revealed that the four selected peptides showed >50% inhibition against SARS-CoV-2 pseudovirus at a concentration of 5 µM without significant cytotoxicity to host cells. This study leads to the identification of a class of dual RBD/Mpro-targeting agents, which may be developed as potential and effective SARS-CoV-2 therapeutics.
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Affiliation(s)
- Zhen Xu
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yunting Zou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Xi Gao
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Jindong Li
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Lu Xue
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Su Jiang
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
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9
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Morgan RW, Atkins DL, Hsu A, Kamath-Rayne BD, Aziz K, Berg RA, Bhanji F, Chan M, Cheng A, Chiotos K, de Caen A, Duff JP, Fuchs S, Joyner BL, Kleinman M, Lasa JJ, Lee HC, Lehotzky RE, Levy A, McBride ME, Meckler G, Nadkarni V, Raymond T, Roberts K, Schexnayder SM, Sutton RM, Terry M, Walsh B, Zelop CM, Sasson C, Topjian A. Guidance for Cardiopulmonary Resuscitation of Children With Suspected or Confirmed COVID-19. Pediatrics 2022; 150:188494. [PMID: 35818123 DOI: 10.1542/peds.2021-056043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/22/2022] [Indexed: 11/24/2022] Open
Abstract
This article aims to provide guidance to health care workers for the provision of basic and advanced life support to children and neonates with suspected or confirmed coronavirus disease 2019 (COVID-19). It aligns with the 2020 American Heart Association Guidelines for Cardiopulmonary Resuscitation (CPR) and Emergency Cardiovascular care while providing strategies for reducing risk of transmission of severe acute respiratory syndrome coronavirus 2 to health care providers. Patients with suspected or confirmed COVID-19 and cardiac arrest should receive chest compressions and defibrillation, when indicated, as soon as possible. Because of the importance of ventilation during pediatric and neonatal resuscitation, oxygenation and ventilation should be prioritized. All CPR events should therefore be considered aerosol-generating procedures. Thus, personal protective equipment (PPE) appropriate for aerosol-generating procedures (including N95 respirators or an equivalent) should be donned before resuscitation, and high-efficiency particulate air filters should be used. Any personnel without appropriate PPE should be immediately excused by providers wearing appropriate PPE. Neonatal resuscitation guidance is unchanged from standard algorithms, except for specific attention to infection prevention and control. In summary, health care personnel should continue to reduce the risk of severe acute respiratory syndrome coronavirus 2 transmission through vaccination and use of appropriate PPE during pediatric resuscitations. Health care organizations should ensure the availability and appropriate use of PPE. Because delays or withheld CPR increases the risk to patients for poor clinical outcomes, children and neonates with suspected or confirmed COVID-19 should receive prompt, high-quality CPR in accordance with evidence-based guidelines.
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Affiliation(s)
- Ryan W Morgan
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Dianne L Atkins
- Stead Family Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Antony Hsu
- Department of Emergency Medicine, St. Joseph Mercy Ann Arbor Hospital, Superior Township, Michigan
| | - Beena D Kamath-Rayne
- Global Newborn and Child Health, American Academy of Pediatrics, Itasca, Illinois
| | - Khalid Aziz
- Department of Pediatrics, Division of Newborn Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Robert A Berg
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Farhan Bhanji
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Melissa Chan
- Departments of Pediatrics and Pediatric Emergency Medicine, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adam Cheng
- Department of Paediatrics, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - Kathleen Chiotos
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Allan de Caen
- Department of Pediatrics, Division of Critical Care, Stollery Children's Hospital, University of Alberta, Edmonton, Alberta, Canada
| | - Jonathan P Duff
- Department of Pediatrics, Division of Critical Care, Stollery Children's Hospital, University of Alberta, Edmonton, Alberta, Canada
| | | | - Benny L Joyner
- Departments of Pediatrics, Anesthesiology & Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Monica Kleinman
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Javier J Lasa
- Cardiovascular ICU, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Henry C Lee
- Division of Neonatology, Stanford University, Stanford, California
| | | | - Arielle Levy
- Departments of Pediatrics and Pediatric Emergency Medicine, Sainte-Justine Hospital University Center, University of Montreal, Montreal, Quebec, Canada
| | - Mary E McBride
- Cardiology, and Critical Care Medicine, Northwestern University, Ann & Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Garth Meckler
- Departments of Pediatrics and Pediatric Emergency Medicine, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vinay Nadkarni
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Tia Raymond
- Department of Pediatric Cardiac Critical Care, Medical City Children's Hospital, Dallas, Texas
| | - Kathryn Roberts
- Center for Nursing Excellence, Education & Innovation, Joe DiMaggio Children's Hospital, Hollywood, Florida
| | - Stephen M Schexnayder
- Departments of Critical Care Medicine and Emergency Medicine, Arkansas Children's Hospital, Springdale, Arkansas
| | - Robert M Sutton
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Mark Terry
- National Registry of Emergency Medical Technicians, Columbus, Ohio
| | - Brian Walsh
- Respiratory Care, Children's Hospital Colorado, Aurora, Colorado
| | - Carolyn M Zelop
- Department of Obstetrics and Gynecology, NYU School of Medicine and The Valley Hospital, New York City, New York
| | - Comilla Sasson
- ECC Science & Innovation, American Heart Association, Dallas, Texas
| | - Alexis Topjian
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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10
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Joshi N, Shukla S, Narayan RJ. Novel photonic methods for diagnosis of
SARS‐CoV
‐2 infection. TRANSLATIONAL BIOPHOTONICS 2022; 4:e202200001. [PMID: 35602265 PMCID: PMC9111306 DOI: 10.1002/tbio.202200001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Naveen Joshi
- Department of Materials Science and Engineering North Carolina State University Raleigh NC USA
| | - Shubhangi Shukla
- Joint Department of Biomedical Engineering, North Carolina State University Raleigh NC USA
| | - Roger J. Narayan
- Joint Department of Biomedical Engineering, North Carolina State University Raleigh NC USA
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11
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Atkins DL, Sasson C, Hsu A, Aziz K, Becker LB, Berg RA, Bhanji F, Bradley SM, Brooks SC, Chan M, Chan PS, Cheng A, Clemency BM, de Caen A, Duff JP, Edelson DP, Flores GE, Fuchs S, Girotra S, Hinkson C, Joyner BL, Kamath-Rayne BD, Kleinman M, Kudenchuk PJ, Lasa JJ, Lavonas EJ, Lee HC, Lehotzky RE, Levy A, McBride ME, Meckler G, Merchant RM, Moitra VK, Nadkarni V, Panchal AR, Ann Peberdy M, Raymond T, Roberts K, Sayre MR, Schexnayder SM, Sutton RM, Terry M, Topjian A, Walsh B, Wang DS, Zelop CM, Morgan RW. 2022 Interim Guidance to Health Care Providers for Basic and Advanced Cardiac Life Support in Adults, Children, and Neonates With Suspected or Confirmed COVID-19: From the Emergency Cardiovascular Care Committee and Get With The Guidelines-Resuscitation Adult and Pediatric Task Forces of the American Heart Association in Collaboration With the American Academy of Pediatrics, American Association for Respiratory Care, the Society of Critical Care Anesthesiologists, and American Society of Anesthesiologists. Circ Cardiovasc Qual Outcomes 2022; 15:e008900. [PMID: 35072519 DOI: 10.1161/circoutcomes.122.008900] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dianne L Atkins
- Carver College of Medicine, University of Iowa (D.L.A., S.G.)
| | | | - Antony Hsu
- St Joseph Mercy Hospital, Ann Arbor, MI (A.H.)
| | - Khalid Aziz
- University of Alberta, Edmonton, Canada (K.A.)
| | - Lance B Becker
- Donald and Barbara Zucker School of Medicine at Hofstra Northwell, Hempstead, NY (L.B.B.)
| | - Robert A Berg
- The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine (R.A.B., V.N., A.T., R.W.M., R.M.S.)
| | | | - Steven M Bradley
- Minneapolis Heart Institute, Healthcare Delivery Innovation Center, MN (S.M.B.)
| | | | - Melissa Chan
- University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada (M.C., G.M.)
| | - Paul S Chan
- Mid America Heart Institute and the University of Missouri-Kansas City, MO (P.S.C.)
| | - Adam Cheng
- Alberta Children's Hospital, University of Calgary, AB, Canada (A.C.)
| | | | - Allan de Caen
- Stollery Children's Hospital, University of Alberta, Edmonton, Canada (A.d.C., J.P.D.)
| | - Jonathan P Duff
- Stollery Children's Hospital, University of Alberta, Edmonton, Canada (A.d.C., J.P.D.)
| | | | - Gustavo E Flores
- Emergency & Critical Care Trainings, San Juan, Puerto Rico (G.E.F.)
| | - Susan Fuchs
- Ann & Robert H. Lurie Children's Hospital, Chicago, IL (S.F., M.E.M.)
| | - Saket Girotra
- Carver College of Medicine, University of Iowa (D.L.A., S.G.)
| | - Carl Hinkson
- Providence Regional Medical Center, Everett, WA (C.H.)
| | - Benny L Joyner
- University of North Carolina at Chapel Hill, NC (B.L.J.)
| | - Beena D Kamath-Rayne
- Global Newborn and Child Health, American Academy of Pediatrics, Itasca, IL (B.D.K.-R.)
| | | | | | | | | | | | | | - Arielle Levy
- Sainte-Justine Hospital University Center, University of Montreal, QC, Canada (A.L.)
| | - Mary E McBride
- Ann & Robert H. Lurie Children's Hospital, Chicago, IL (S.F., M.E.M.)
| | - Garth Meckler
- University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada (M.C., G.M.)
| | - Raina M Merchant
- The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine (R.A.B., V.N., A.T., R.W.M., R.M.S.).,University of Pennsylvania, Philadelphia, PA (R.M.M.)
| | - Vivek K Moitra
- College of Physicians & Surgeons of Columbia University, NY (V.K.M.)
| | - Vinay Nadkarni
- The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine (R.A.B., V.N., A.T., R.W.M., R.M.S.)
| | - Ashish R Panchal
- The Ohio State University Wexner Medical Center, Columbus, OH (A.R.P.)
| | | | - Tia Raymond
- Medical City Children's Hospital, Dallas, TX (T.R.)
| | | | | | | | - Robert M Sutton
- The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine (R.A.B., V.N., A.T., R.W.M., R.M.S.)
| | - Mark Terry
- National Registry of Emergency Medical Technicians, Columbus, OH (M.T.)
| | - Alexis Topjian
- Donald and Barbara Zucker School of Medicine at Hofstra Northwell, Hempstead, NY (L.B.B.)
| | - Brian Walsh
- Children's Hospital Colorado, Aurora, CO (B.W.)
| | - David S Wang
- Columbia University Irving Medical Center, NY (D.S.W.)
| | | | - Ryan W Morgan
- The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine (R.A.B., V.N., A.T., R.W.M., R.M.S.)
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