1
|
Hasan M, He Z, Jia M, Leung AC, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
Collapse
Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C.F. Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| |
Collapse
|
2
|
Rao B, Wang L, Yang M, Luo H, Sun J, Liu S, Wang H, Wang X, Li L, Yuan C, Yu Z, Ren Z. Safety and immunogenicity of CoronaVac in healthy adults: A prospective observational multicenter real-world study in Henan Province, China. Virulence 2024; 15:2310450. [PMID: 38326274 PMCID: PMC10854291 DOI: 10.1080/21505594.2024.2310450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Vaccination has emerged as the primar approach for managing the COVID-19 pandemic. Despite certain clinical trials reporting the safety and immunogenicity of CoronaVac, additional multicenter real-world studies are still necessary. In this study, we recruited 506 healthy volunteers who were not infected with COVID-19 or vaccinated. Each participant provided peripheral blood samples three times: prior to the first dose of vaccine, prior to the second dose, and 8 weeks following the second dose. Ultimately, 388 participants completed the entire follow-up process. No serious adverse events were observed among any of the participants. Within 1 week of vaccination, 13.4% of participants experienced systemic adverse reactions, with fatigue (5.93%) and dizziness (3.35%) being the most frequent. Although some clinical indicators, including creatinine, significantly changed after vaccination (p < 0.05), the mean of all altered indicators remained within the normal range. The positive rates of neutralizing antibodies (NAb), IgG, and IgM were 12.3%, 18.85%, and 5.24% prior to the second dose, respectively; and 57.99%, 86.34%, and 2.32% at 8 weeks following the second dose, respectively. Additionally, seven indicators, such as sex, age, and BMI, were significantly correlated with NAb (p < 0.05). Finally, a prediction model was developed based on age, monocytes, and alanine aminotransferase (ALT) with an AUC value of 87.56% in the train set and 80.71% in the test set. This study demonstrated that safety and immunogenicity of CoronaVac were good. The prediction model based on the baseline clinical characteristics prior to vaccination can help to develop more suitable vaccination strategies.
Collapse
Affiliation(s)
- Benchen Rao
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province/Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Ling Wang
- Department of Laboratory Medicine, Henan Provincial Chest Hospital, Zhengzhou, China
| | - Mengzhao Yang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province/Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Hong Luo
- Department of Laboratory Medicine, Guangshan County People’s Hospital, Xinyang, Henan, China
| | - Junyi Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province/Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Shanshuo Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province/Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province/Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Xuemei Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province/Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Lei Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province/Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Chengyu Yuan
- Department of Laboratory Medicine, Guangshan County People’s Hospital, Xinyang, Henan, China
| | - Zujiang Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province/Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province/Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| |
Collapse
|
3
|
Santisteban Celis IC, Matoba N. Lectibodies as antivirals. Antiviral Res 2024; 227:105901. [PMID: 38734211 DOI: 10.1016/j.antiviral.2024.105901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Growing concerns regarding the emergence of highly transmissible viral diseases highlight the urgent need to expand the repertoire of antiviral therapeutics. For this reason, new strategies for neutralizing and inhibiting these viruses are necessary. A promising approach involves targeting the glycans present on the surfaces of enveloped viruses. Lectins, known for their ability to recognize specific carbohydrate molecules, offer the potential for glycan-targeted antiviral strategies. Indeed, numerous studies have reported the antiviral effects of various lectins of both endogenous and exogenous origins. However, many lectins in their natural forms, are not suitable for use as antiviral therapeutics due to toxicity, other unfavorable pharmacological effects, and/or unreliable manufacturing sources. Therefore, improvements are crucial for employing lectins as effective antiviral therapeutics. A novel approach to enhance lectins' suitability as pharmaceuticals could be the generation of recombinant lectin-Fc fusion proteins, termed "lectibodies." In this review, we discuss the scientific rationale behind lectin-based antiviral strategies and explore how lectibodies could facilitate the development of new antiviral therapeutics. We will also share our perspective on the potential of these molecules to transcend their potential use as antiviral agents.
Collapse
Affiliation(s)
- Ian Carlosalberto Santisteban Celis
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, USA; Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville, KY, USA
| | - Nobuyuki Matoba
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, USA; Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville, KY, USA; UofL Health - Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA.
| |
Collapse
|
4
|
Liu X, Sun Y, Song H, Zhang W, Liu T, Chu Z, Gu X, Ma Z, Jin W. Nanomaterials-based electrochemical biosensors for diagnosis of COVID-19. Talanta 2024; 274:125994. [PMID: 38547841 DOI: 10.1016/j.talanta.2024.125994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/15/2024] [Accepted: 03/24/2024] [Indexed: 05/04/2024]
Abstract
Since the outbreak of corona virus disease 2019 (COVID-19), this pandemic has caused severe death and infection worldwide. Owing to its strong infectivity, long incubation period, and nonspecific symptoms, the early diagnosis is essential to reduce risk of the severe illness. The electrochemical biosensor, as a fast and sensitive technique for quantitative analysis of body fluids, has been widely studied to diagnose different biomarkers caused at different infective stages of COVID-19 virus (SARS-CoV-2). Recently, many reports have proved that nanomaterials with special architectures and size effects can effectively promote the biosensing performance on the COVID-19 diagnosis, there are few comprehensive summary reports yet. Therefore, in this review, we will pay efforts on recent progress of advanced nanomaterials-facilitated electrochemical biosensors for the COVID-19 detections. The process of SARS-CoV-2 infection in humans will be briefly described, as well as summarizing the types of sensors that should be designed for different infection processes. Emphasis will be supplied to various functional nanomaterials which dominate the biosensing performance for comparison, expecting to provide a rational guidance on the material selection of biosensor construction for people. Finally, we will conclude the perspective on the design of superior nanomaterials-based biosensors facing the unknown virus in future.
Collapse
Affiliation(s)
- Xinxin Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, NO.30 Puzhu Road(S), Nanjing, 211816, PR China
| | - Yifan Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, NO.30 Puzhu Road(S), Nanjing, 211816, PR China
| | - Huaiyu Song
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, NO.30 Puzhu Road(S), Nanjing, 211816, PR China
| | - Wei Zhang
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, PR China
| | - Tao Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, NO.30 Puzhu Road(S), Nanjing, 211816, PR China.
| | - Zhenyu Chu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, NO.30 Puzhu Road(S), Nanjing, 211816, PR China
| | - Xiaoping Gu
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, PR China.
| | - Zhengliang Ma
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, PR China
| | - Wanqin Jin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, NO.30 Puzhu Road(S), Nanjing, 211816, PR China.
| |
Collapse
|
5
|
Gao J, Lei P, Su X, Liang J, Ren B, Ma X, Zhang Y, Zhang Y, Ma W. In vitro pharmacokinetic behavior in lung of harringtonine, an antagonist of SARS-CoV-2 associated proteins: New insights of inhalation therapy for COVID-19. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 129:155582. [PMID: 38608595 DOI: 10.1016/j.phymed.2024.155582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/11/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND Recent studies have shown that harringtonine (HT) could specifically bind with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein and host cell transmembrane serine protease 2 (TMPRSS2) to block membrane fusion, which is an effective antagonist for SARS-CoV-2. PURPOSE Our study focused on in-depth exploration of in vitro pharmacokinetic characteristics of HT in lung. METHODS HPLC-fluorescence detection method was used to detect changes of HT content. Incubation systems of lung microsomes for phase I metabolism and UGT incubation systems for phase II metabolism were performed to elucidate metabolites and metabolic mechanisms of HT, and then the metabolic enzyme phenotypes for HT were clarified by chemical inhibition method and recombinant enzyme method. Through metabolomics, we comprehensively evaluated the physiological dynamic changes in SD rat and human lung microsomes, and revealed the relationship between metabolomics and pharmacological activity of HT. RESULTS HPLC-fluorescence detection method showed strong specificity, high accuracy, and good stability for rapid quantification of HT. We confirmed that HT mainly underwent phase I metabolism, and the metabolites of HT in different species were all identified as 4'-demethyl HT, with metabolic pathway being hydrolysis reaction. CYP1A2 and CYP2E1 participated in HT metabolism, but as HT metabolism was not NADPH dependent, the esterase HCES1 in lung also played a role. The main KEGG pathways in SD rat and human lung microsomes were cortisol synthesis and secretion, steroid hormone biosynthesis and linoleic acid metabolism, respectively. The downregulated key biomarkers of 11-deoxycortisol, 21-deoxycortisol and 9(10)-EpOME suggested that HT could prevent immunosuppression and interfere with infection and replication of SARS-CoV-2. CONCLUSION HT was mainly metabolized into 4'-demethyl HT through phase I reactions, which was mediated by CYP1A2, CYP2E1, and HCES1. The downregulation of 11-deoxycortisol, 21-deoxycortisol and 9(10)-EpOME were key ways of HT against SARS-CoV-2. Our study was of great significance for development and clinical application of HT in the treatment of COVID-19.
Collapse
Affiliation(s)
- Jiapan Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Panpan Lei
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xinyue Su
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jinna Liang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Bingxi Ren
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xiaoyu Ma
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yuxiu Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yongjing Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China; Department of Medical Oncology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Weina Ma
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| |
Collapse
|
6
|
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2-based structural ensembles and molecular dynamics simulations. Phys Chem Chem Phys 2024. [PMID: 38869513 DOI: 10.1039/d4cp01372g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
In this study, we combined AlphaFold-based approaches for atomistic modeling of multiple protein states and microsecond molecular simulations to accurately characterize conformational ensembles evolution and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variants BA.1, BA.2, BA.2.75, BA.3, BA.4/BA.5 and BQ.1.1. We employed and validated several different adaptations of the AlphaFold methodology for modeling of conformational ensembles including the introduced randomized full sequence scanning for manipulation of sequence variations to systematically explore conformational dynamics of Omicron spike protein complexes with the ACE2 receptor. Microsecond atomistic molecular dynamics (MD) simulations provide a detailed characterization of the conformational landscapes and thermodynamic stability of the Omicron variant complexes. By integrating the predictions of conformational ensembles from different AlphaFold adaptations and applying statistical confidence metrics we can expand characterization of the conformational ensembles and identify functional protein conformations that determine the equilibrium dynamics for the Omicron spike complexes with the ACE2. Conformational ensembles of the Omicron RBD-ACE2 complexes obtained using AlphaFold-based approaches for modeling protein states and MD simulations are employed for accurate comparative prediction of the binding energetics revealing an excellent agreement with the experimental data. In particular, the results demonstrated that AlphaFold-generated extended conformational ensembles can produce accurate binding energies for the Omicron RBD-ACE2 complexes. The results of this study suggested complementarities and potential synergies between AlphaFold predictions of protein conformational ensembles and MD simulations showing that integrating information from both methods can potentially yield a more adequate characterization of the conformational landscapes for the Omicron RBD-ACE2 complexes. This study provides insights in the interplay between conformational dynamics and binding, showing that evolution of Omicron variants through acquisition of convergent mutational sites may leverage conformational adaptability and dynamic couplings between key binding energy hotspots to optimize ACE2 binding affinity and enable immune evasion.
Collapse
Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| |
Collapse
|
7
|
Liang L, Wang B, Zhang Q, Zhang S, Zhang S. Antibody drugs targeting SARS-CoV-2: Time for a rethink? Biomed Pharmacother 2024; 176:116900. [PMID: 38861858 DOI: 10.1016/j.biopha.2024.116900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/20/2024] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) heavily burdens human health. Multiple neutralizing antibodies (nAbs) have been issued for emergency use or tested for treating infected patients in the clinic. However, SARS-CoV-2 variants of concern (VOC) carrying mutations reduce the effectiveness of nAbs by preventing neutralization. Uncoding the mutation profile and immune evasion mechanism of SARS-CoV-2 can improve the outcome of Ab-mediated therapies. In this review, we first outline the development status of anti-SARS-CoV-2 Ab drugs and provide an overview of SARS-CoV-2 variants and their prevalence. We next focus on the failure causes of anti-SARS-CoV-2 Ab drugs and rethink the design strategy for developing new Ab drugs against COVID-19. This review provides updated information for the development of therapeutic Ab drugs against SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Likeng Liang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Bo Wang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Qing Zhang
- Department of Laboratory Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Nankai University, Tianjin 300121, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China.
| |
Collapse
|
8
|
Hills FR, Eruera AR, Hodgkinson-Bean J, Jorge F, Easingwood R, Brown SHJ, Bouwer JC, Li YP, Burga LN, Bostina M. Variation in structural motifs within SARS-related coronavirus spike proteins. PLoS Pathog 2024; 20:e1012158. [PMID: 38805567 DOI: 10.1371/journal.ppat.1012158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species within the SARS-related coronaviruses. Here, we present three novel SARS-related CoV spike protein structures solved by single particle cryo-electron microscopy analysis derived from bat (bat SL-CoV WIV1) and civet (cCoV-SZ3, cCoV-007) hosts. We report complex glycan trees that decorate the glycoproteins and density for water molecules which facilitated modeling of the water molecule coordination networks within structurally important regions. We note structural conservation of the fatty acid binding pocket and presence of a linoleic acid molecule which are associated with stabilization of the receptor binding domains in the "down" conformation. Additionally, the N-terminal biliverdin binding pocket is occupied by a density in all the structures. Finally, we analyzed structural differences in a loop of the receptor binding motif between coronaviruses known to infect humans and the animal coronaviruses described in this study, which regulate binding to the human angiotensin converting enzyme 2 receptor. This study offers a structural framework to evaluate the close relatives of SARS-CoV-2, the ability to inform pandemic prevention, and aid in the development of pan-neutralizing treatments.
Collapse
Affiliation(s)
- Francesca R Hills
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alice-Roza Eruera
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James Hodgkinson-Bean
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Fátima Jorge
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Richard Easingwood
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| | - Simon H J Brown
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - James C Bouwer
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, University of Wollongong, Wollongong, New South Wales, Australia
| | - Yi-Ping Li
- Institute of Human Virology and Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Laura N Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Otago Microscopy and Nano Imaging Unit, University of Otago, Dunedin, New Zealand
| |
Collapse
|
9
|
Wang S, Ran W, Sun L, Fan Q, Zhao Y, Wang B, Yang J, He Y, Wu Y, Wang Y, Chen L, Chuchuay A, You Y, Zhu X, Wang X, Chen Y, Wang Y, Chen YQ, Yuan Y, Zhao J, Mao Y. Sequential glycosylations at the multibasic cleavage site of SARS-CoV-2 spike protein regulate viral activity. Nat Commun 2024; 15:4162. [PMID: 38755139 PMCID: PMC11099032 DOI: 10.1038/s41467-024-48503-x] [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: 05/18/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
The multibasic furin cleavage site at the S1/S2 boundary of the spike protein is a hallmark of SARS-CoV-2 and plays a crucial role in viral infection. However, the mechanism underlying furin activation and its regulation remain poorly understood. Here, we show that GalNAc-T3 and T7 jointly initiate clustered O-glycosylations in the furin cleavage site of the SARS-CoV-2 spike protein, which inhibit furin processing, suppress the incorporation of the spike protein into virus-like-particles and affect viral infection. Mechanistic analysis reveals that the assembly of the spike protein into virus-like particles relies on interactions between the furin-cleaved spike protein and the membrane protein of SARS-CoV-2, suggesting a possible mechanism for furin activation. Interestingly, mutations in the spike protein of the alpha and delta variants of the virus confer resistance against glycosylation by GalNAc-T3 and T7. In the omicron variant, additional mutations reverse this resistance, making the spike protein susceptible to glycosylation in vitro and sensitive to GalNAc-T3 and T7 expression in human lung cells. Our findings highlight the role of glycosylation as a defense mechanism employed by host cells against SARS-CoV-2 and shed light on the evolutionary interplay between the host and the virus.
Collapse
Affiliation(s)
- Shengjun Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Wei Ran
- 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, China
| | - Lingyu Sun
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingchi Fan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanqi Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Foshan Institute for Food and Drug Control, Foshan, China
| | - Bowen Wang
- College of Life Science, Northwest University, Xi'an, China
| | - Jinghong 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, China
| | - Yuqi He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Luoyi Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Arpaporn Chuchuay
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuyu You
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinhai Zhu
- Instrumental Analysis & Research Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaojuan Wang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ye Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanqun Wang
- 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, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yanqiu Yuan
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jincun Zhao
- 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, China.
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou Laboratory, Bio-island, Guangzhou, China.
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
| | - Yang Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou, China.
| |
Collapse
|
10
|
Ishimaru H, Nishimura M, Shigematsu H, Marini MI, Hasegawa N, Takamiya R, Iwata S, Mori Y. Epitopes of an antibody that neutralizes a wide range of SARS-CoV-2 variants in a conserved subdomain 1 of the spike protein. J Virol 2024; 98:e0041624. [PMID: 38624232 PMCID: PMC11092320 DOI: 10.1128/jvi.00416-24] [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: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 04/17/2024] Open
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued, enabling the virus to escape from host immunity by changing its spike antigen, while biased toward the receptor-binding domain and N-terminal domain. Here, we isolated a novel pan-SARS-CoV-2 neutralizing antibody (which we named MO11) for even the recent dominators XBB.1.16 and EG.5.1, from a convalescent patient who had received three doses of an original mRNA COVID-19 vaccination. A cryo-electron microscopy analysis of the spike-MO11 complex at 2.3 Å atomic resolution revealed that it recognizes a conserved epitope hidden behind a glycan shield at N331 on subdomain 1 (SD1), holding both the N- and C-terminal segments comprising SD1. Our identification of MO11 unveiled the functional importance of SD1 for the spike's function, and we discuss the potential availability of a novel common epitope among the SARS-CoV-2 variants.IMPORTANCENovel severe acute respiratory syndrome coronavirus 2 variants with immune evasion ability are still repeatedly emerging, nonetheless, a part of immunity developed in responding to the antigen of earlier variants retains efficacy against recent variants irrespective of the numerous mutations. In exploration for the broadly effective antibodies, we identified a cross-neutralizing antibody, named MO11, from the B cells of the convalescent patient. MO11 targets a novel epitope in subdomain 1 (SD1) and was effective against all emerging variants including XBB.1.16 and EG.5.1. The neutralizing activity covering from D614G to EG.5.1 variants was explained by the conservation of the epitope, and it revealed the importance of the subdomain on regulating the function of the antigen for viral infection. Demonstrated identification of the neutralizing antibody that recognizes a conserved epitope implies basal contribution of such group of antibodies for prophylaxis against COVID-19.
Collapse
Affiliation(s)
- Hanako Ishimaru
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Mitsuhiro Nishimura
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Hideki Shigematsu
- Structural Biology Division, Japan Synchrotron Radiation Research Institute SPring-8, Sayo, Hyogo, Japan
| | - Maria Istiqomah Marini
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Natsumi Hasegawa
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Rei Takamiya
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Sachiyo Iwata
- Division of Cardiovascular Medicine, Hyogo Prefectural Kakogawa Medical Center, Kakogawa, Hyogo, Japan
| | - Yasuko Mori
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| |
Collapse
|
11
|
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity. J Phys Chem B 2024. [PMID: 38696745 DOI: 10.1021/acs.jpcb.4c01341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
In this study, we combined AlphaFold-based atomistic structural modeling, microsecond molecular simulations, mutational profiling, and network analysis to characterize binding mechanisms of the SARS-CoV-2 spike protein with the host receptor ACE2 for a series of Omicron XBB variants including XBB.1.5, XBB.1.5+L455F, XBB.1.5+F456L, and XBB.1.5+L455F+F456L. AlphaFold-based structural and dynamic modeling of SARS-CoV-2 Spike XBB lineages can accurately predict the experimental structures and characterize conformational ensembles of the spike protein complexes with the ACE2. Microsecond molecular dynamics simulations identified important differences in the conformational landscapes and equilibrium ensembles of the XBB variants, suggesting that combining AlphaFold predictions of multiple conformations with molecular dynamics simulations can provide a complementary approach for the characterization of functional protein states and binding mechanisms. Using the ensemble-based mutational profiling of protein residues and physics-based rigorous calculations of binding affinities, we identified binding energy hotspots and characterized the molecular basis underlying epistatic couplings between convergent mutational hotspots. Consistent with the experiments, the results revealed the mediating role of the Q493 hotspot in the synchronization of epistatic couplings between L455F and F456L mutations, providing a quantitative insight into the energetic determinants underlying binding differences between XBB lineages. We also proposed a network-based perturbation approach for mutational profiling of allosteric communications and uncovered the important relationships between allosteric centers mediating long-range communication and binding hotspots of epistatic couplings. The results of this study support a mechanism in which the binding mechanisms of the XBB variants may be determined by epistatic effects between convergent evolutionary hotspots that control ACE2 binding.
Collapse
Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| |
Collapse
|
12
|
Gu T, Wang M, Fu X, Tian X, Bi J, Lu N, Chen C, Yan S, Li A, Wang L, Li X, Liu K, Dong Z. Intratumoural delivery of TRAIL mRNA induces colon cancer cell apoptosis. Biomed Pharmacother 2024; 174:116603. [PMID: 38636395 DOI: 10.1016/j.biopha.2024.116603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024] Open
Abstract
Novel strategies in intratumoral injection and emerging immunotherapies have heralded a new era of precise cancer treatments. The affinity of SARS-CoV-2 to ACE2 receptors, a feature which facilitates virulent human infection, is leveraged in this research. Colon cancer cells, with their high ACE2 expression, provide a potentially strategic target for using this SARS-CoV-2 feature. While the highly expression of ACE2 is observed in several cancer types, the idea of using the viral spike protein for targeting colon cancer cells offers a novel approach in cancer treatment. Intratumoral delivery of nucleic acid-based drugs is a promising alternative to overcoming the limitations of existing therapies. The increasing importance of nucleic acids in this realm, and the use of Lipid Nanoparticles (LNPs) for local delivery of nucleic acid therapeutics, are important breakthroughs. LNPs protect nucleic acid drugs from degradation and enhance cellular uptake, making them a rapidly evolving nano delivery system with high precision and adaptability. Our study leveraged a tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) combined with a receptor-binding domain from the SARS-CoV-2 spike protein, encapsulated in LNPs, to target colon cancer cells. Our results indicated that the TRAIL fusion-mRNA induced apoptosis in vitro and in vivo. Collectively, our findings highlight LNP-encapsulated TRAIL fusion-mRNA as a potential colon cancer therapy.
Collapse
Affiliation(s)
- Tingxuan Gu
- Tianjian Laboratory of advanced Biomedical Sciences, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Mengqiao Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Xiaorong Fu
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Xueli Tian
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China; Medical Research Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Juanjuan Bi
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Ning Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Chen Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Shijia Yan
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Ang Li
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Luyun Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Xiang Li
- Tianjian Laboratory of advanced Biomedical Sciences, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Kangdong Liu
- Tianjian Laboratory of advanced Biomedical Sciences, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
| | - Zigang Dong
- Tianjian Laboratory of advanced Biomedical Sciences, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China.
| |
Collapse
|
13
|
Gupta G, Verkhivker G. Exploring Binding Pockets in the Conformational States of the SARS-CoV-2 Spike Trimers for the Screening of Allosteric Inhibitors Using Molecular Simulations and Ensemble-Based Ligand Docking. Int J Mol Sci 2024; 25:4955. [PMID: 38732174 PMCID: PMC11084335 DOI: 10.3390/ijms25094955] [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: 03/19/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Understanding mechanisms of allosteric regulation remains elusive for the SARS-CoV-2 spike protein, despite the increasing interest and effort in discovering allosteric inhibitors of the viral activity and interactions with the host receptor ACE2. The challenges of discovering allosteric modulators of the SARS-CoV-2 spike proteins are associated with the diversity of cryptic allosteric sites and complex molecular mechanisms that can be employed by allosteric ligands, including the alteration of the conformational equilibrium of spike protein and preferential stabilization of specific functional states. In the current study, we combine conformational dynamics analysis of distinct forms of the full-length spike protein trimers and machine-learning-based binding pocket detection with the ensemble-based ligand docking and binding free energy analysis to characterize the potential allosteric binding sites and determine structural and energetic determinants of allosteric inhibition for a series of experimentally validated allosteric molecules. The results demonstrate a good agreement between computational and experimental binding affinities, providing support to the predicted binding modes and suggesting key interactions formed by the allosteric ligands to elicit the experimentally observed inhibition. We establish structural and energetic determinants of allosteric binding for the experimentally known allosteric molecules, indicating a potential mechanism of allosteric modulation by targeting the hinges of the inter-protomer movements and blocking conformational changes between the closed and open spike trimer forms. The results of this study demonstrate that combining ensemble-based ligand docking with conformational states of spike protein and rigorous binding energy analysis enables robust characterization of the ligand binding modes, the identification of allosteric binding hotspots, and the prediction of binding affinities for validated allosteric modulators, which is consistent with the experimental data. This study suggested that the conformational adaptability of the protein allosteric sites and the diversity of ligand bound conformations are both in play to enable efficient targeting of allosteric binding sites and interfere with the conformational changes.
Collapse
Affiliation(s)
- Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA;
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA;
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| |
Collapse
|
14
|
Ogger PP, Martín MG, Jang S, Zhou J, Brown J, Sukhova K, Furnon W, Patel AH, Cowton V, Palmarini M, Barclay WS, Johansson C. SARS-CoV-2 strains bearing Omicron BA.1 spike replicate in C57BL/6 mice. Front Immunol 2024; 15:1383612. [PMID: 38742107 PMCID: PMC11089223 DOI: 10.3389/fimmu.2024.1383612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction SARS-CoV-2, the cause of the COVID pandemic, is an RNA virus with a high propensity to mutate. Successive virus variants, including variants of concern (VOC), have emerged with increased transmission or immune escape. The original pandemic virus and early variants replicated poorly, if at all, in mice at least partly due to a mismatch between the receptor binding domain on the viral spike protein and the murine angiotensin converting enzyme 2 (ACE2). Omicron VOC emerged in late 2021 harboring > 50 new mutations, 35 of them in the spike protein. This variant resulted in a very large wave of infections, even in the face of prior immunity, albeit being inherently less severe than earlier variants. Reflecting the lower severity reported in humans, Omicron displayed attenuated infection in hamsters and also in the K18-hACE2 mouse model. K18-hACE2 mice express both the human ACE2 as well as the endogenous mouse ACE2. Methods Here we infected hACE2 knock-in mice that express only human ACE2 and no murine ACE2, or C57BL/6 wildtype mice with SARS-CoV-2 D614G (first-wave isolate), Delta or Omicron BA.1 variants and assessed infectivity and downstream innate immune responses. Results While replication of SARS-CoV-2 Omicron was lower in the lungs of hACE2 knock-in mice compared with SARS-CoV-2 D614G and VOC Delta, it replicated more efficiently than the earlier variants in C57BL/6 wildtype mice. This opens the opportunity to test the effect of host genetics on SARS-CoV-2 infections in wildtype mice. As a proof of principle, we tested Omicron infection in mice lacking expression of the interferon-alpha receptor-1 (IFNAR1). In these mice we found that loss of type I IFN receptor signaling resulted in higher viral loads in the lungs were detected. Finally, using a chimeric virus of first wave SARS-CoV-2 harboring the Omicron spike protein, we show that Omicron spike increase infection of C57BL/6 wildtype mice, but non-spike genes of Omicron confer attenuation of viral replication. Discussion Since this chimeric virus efficiently infected C57BL/6 wildtype mice, and replicated in their lungs, our findings illustrate a pathway for genetic mapping of virushost interactions during SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Patricia P. Ogger
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Minerva Garcia Martín
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Soyeon Jang
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jonathan Brown
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Cecilia Johansson
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| |
Collapse
|
15
|
Khare S, Villalba MI, Canul-Tec JC, Cajiao AB, Kumar A, Backovic M, Rey FA, Pardon E, Steyaert J, Perez C, Reyes N. Receptor-recognition and antiviral mechanisms of retrovirus-derived human proteins. Nat Struct Mol Biol 2024:10.1038/s41594-024-01295-6. [PMID: 38671230 DOI: 10.1038/s41594-024-01295-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Human syncytin-1 and suppressyn are cellular proteins of retroviral origin involved in cell-cell fusion events to establish the maternal-fetal interface in the placenta. In cell culture, they restrict infections from members of the largest interference group of vertebrate retroviruses, and are regarded as host immunity factors expressed during development. At the core of the syncytin-1 and suppressyn functions are poorly understood mechanisms to recognize a common cellular receptor, the membrane transporter ASCT2. Here, we present cryo-electron microscopy structures of human ASCT2 in complexes with the receptor-binding domains of syncytin-1 and suppressyn. Despite their evolutionary divergence, the two placental proteins occupy similar positions in ASCT2, and are stabilized by the formation of a hybrid β-sheet or 'clamp' with the receptor. Structural predictions of the receptor-binding domains of extant retroviruses indicate overlapping binding interfaces and clamping sites with ASCT2, revealing a competition mechanism between the placental proteins and the retroviruses. Our work uncovers a common ASCT2 recognition mechanism by a large group of endogenous and disease-causing retroviruses, and provides high-resolution views on how placental human proteins exert morphological and immunological functions.
Collapse
Affiliation(s)
- Shashank Khare
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | - Miryam I Villalba
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | - Juan C Canul-Tec
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | | | - Anand Kumar
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Felix A Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Camilo Perez
- Biozentrum, University of Basel, Basel, Switzerland.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Nicolas Reyes
- Fundamental Microbiology and Pathogenicity Unit, CNRS, Université de Bordeaux, IECB, Bordeaux, France.
| |
Collapse
|
16
|
Yang YL, Wang B, Li W, Cai HL, Qian QY, Qin Y, Shi FS, Bosch BJ, Huang YW. Functional dissection of the spike glycoprotein S1 subunit and identification of cellular cofactors for regulation of swine acute diarrhea syndrome coronavirus entry. J Virol 2024; 98:e0013924. [PMID: 38501663 PMCID: PMC11019839 DOI: 10.1128/jvi.00139-24] [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: 01/19/2024] [Accepted: 03/02/2024] [Indexed: 03/20/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel porcine enteric coronavirus, and the broad interspecies infection of SADS-CoV poses a potential threat to human health. This study provides experimental evidence to dissect the roles of distinct domains within the SADS-CoV spike S1 subunit in cellular entry. Specifically, we expressed the S1 and its subdomains, S1A and S1B. Cell binding and invasion inhibition assays revealed a preference for the S1B subdomain in binding to the receptors on the cell surface, and this unknown receptor is not utilized by the porcine epidemic diarrhea virus. Nanoparticle display demonstrated hemagglutination of erythrocytes from pigs, humans, and mice, linking the S1A subdomain to the binding of sialic acid (Sia) involved in virus attachment. We successfully rescued GFP-labeled SADS-CoV (rSADS-GFP) from a recombinant cDNA clone to track viral infection. Antisera raised against S1, S1A, or S1B contained highly potent neutralizing antibodies, with anti-S1B showing better efficiency in neutralizing rSADS-GFP infection compared to anti-S1A. Furthermore, depletion of heparan sulfate (HS) by heparinase treatment or pre-incubation of rSADS-GFP with HS or constituent monosaccharides could inhibit SADS-CoV entry. Finally, we demonstrated that active furin cleavage of S glycoprotein and the presence of type II transmembrane serine protease (TMPRSS2) are essential for SADS-CoV infection. These combined observations suggest that the wide cell tropism of SADS-CoV may be related to the distribution of Sia or HS on the cell surface, whereas the S1B contains the main protein receptor binding site. Specific host proteases also play important roles in facilitating SADS-CoV entry.IMPORTANCESwine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel pathogen infecting piglet, and its unique genetic evolution characteristics and broad species tropism suggest the potential for cross-species transmission. The virus enters cells through its spike (S) glycoprotein. In this study, we identify the receptor binding domain on the C-terminal part of the S1 subunit (S1B) of SADS-CoV, whereas the sugar-binding domain located at the S1 N-terminal part of S1 (S1A). Sialic acid, heparan sulfate, and specific host proteases play essential roles in viral attachment and entry. The dissection of SADS-CoV S1 subunit's functional domains and identification of cellular entry cofactors will help to explore the receptors used by SADS-CoV, which may contribute to exploring the mechanisms behind cross-species transmission and host tropism.
Collapse
Affiliation(s)
- Yong-Le Yang
- Xianghu Laboratory, Hangzhou, China
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Bin Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Wentao Li
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Qian-Yu Qian
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yu Qin
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Fang-Shu Shi
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases & Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Yao-Wei Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, China
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
17
|
Garg P, Hsueh SCC, Plotkin SS. Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein. Biophys J 2024; 123:992-1005. [PMID: 38491772 PMCID: PMC11052916 DOI: 10.1016/j.bpj.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/02/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
The efficacy of vaccines against the SARS-CoV-2 virus significantly declines with the emergence of mutant strains, prompting investigation into the feasibility of targeting highly conserved but often cryptic regions on the S2 domain of spike protein. Using tools from molecular dynamics, we find that exposure of a conserved S2 epitope located in the central helices below the receptor binding domains would require large-scale motion beyond receptor binding domain up-down motion, but, along the reaction coordinates we explored, it is unlikely to be exposed by such large-scale dynamic fluctuations of the S1 domain without any external facilitating factors, despite some previous computational evidence suggesting transient exposure of this region. Furthermore, glycans, particularly those on N165 and N234, hinder S2-exposing opening dynamics, and thus stabilize spike in addition to immunologically shielding the protein surface. Although the S2 epitope region examined here is central to large-scale conformational changes during viral entry, free energy landscape analysis obtained using the path coordinate formalism reveals no inherent "loaded spring" effect, suggesting that a vaccine immunogen would tend to present the epitope in a prefusion-like conformation and may be effective in neutralization. These findings contribute to a deeper understanding of the dynamic origins of the function of the spike protein, as well as further characterizing the feasibility of the S2 epitope as a therapeutic target.
Collapse
Affiliation(s)
- Pranav Garg
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shawn C C Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada; Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
18
|
Wang J, Shi B, Chen H, Yu M, Wang P, Qian Z, Hu K, Wang J. Engineered Multivalent Nanobodies Efficiently Neutralize SARS-CoV-2 Omicron Subvariants BA.1, BA.4/5, XBB.1 and BQ.1.1. Vaccines (Basel) 2024; 12:417. [PMID: 38675799 PMCID: PMC11054741 DOI: 10.3390/vaccines12040417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Most available neutralizing antibodies are ineffective against highly mutated SARS-CoV-2 Omicron subvariants. Therefore, it is crucial to develop potent and broad-spectrum alternatives to effectively manage Omicron subvariants. Here, we constructed a high-diversity nanobody phage display library and identified nine nanobodies specific to the SARS-CoV-2 receptor-binding domain (RBD). Five of them exhibited cross-neutralization activity against the SARS-CoV-2 wild-type (WT) strain and the Omicron subvariants BA.1 and BA.4/5, and one nanobody demonstrated marked efficacy even against the Omicron subvariants BQ.1.1 and XBB.1. To enhance the therapeutic potential, we engineered a panel of multivalent nanobodies with increased neutralizing potency and breadth. The most potent multivalent nanobody, B13-B13-B13, cross-neutralized all tested pseudoviruses, with a geometric mean of the 50% inhibitory concentration (GM IC50) value of 20.83 ng/mL. An analysis of the mechanism underlying the enhancement of neutralization breadth by representative multivalent nanobodies demonstrated that the strategic engineering approach of combining two or three nanobodies into a multivalent molecule could improve the affinity between a single nanobody and spike, and could enhance tolerance toward escape mutations such as R346T and N460K. Our engineered multivalent nanobodies may be promising drug candidates for treating and preventing infection with Omicron subvariants and even future variants.
Collapse
Affiliation(s)
- Jiali Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Bingjie Shi
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Hanyi Chen
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Mengyuan Yu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Peipei Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Keping Hu
- The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Andes Antibody Technology Hengshui LL Company, Hengshui 053000, China
| | - Jianxun Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
- Shenzhen Research Institute, Beijing University of Chinese Medicine, Shenzhen 518118, China
| |
Collapse
|
19
|
Raisinghani N, Alshahrani M, Gupta G, Verkhivker G. Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape. Int J Mol Sci 2024; 25:4281. [PMID: 38673865 PMCID: PMC11049863 DOI: 10.3390/ijms25084281] [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: 03/13/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we performed a computational study of binding mechanisms for the SARS-CoV-2 spike Omicron XBB lineages with the host cell receptor ACE2 and a panel of diverse class one antibodies. The central objective of this investigation was to examine the molecular factors underlying epistatic couplings among convergent evolution hotspots that enable optimal balancing of ACE2 binding and antibody evasion for Omicron variants BA.1, BA2, BA.3, BA.4/BA.5, BQ.1.1, XBB.1, XBB.1.5, and XBB.1.5 + L455F/F456L. By combining evolutionary analysis, molecular dynamics simulations, and ensemble-based mutational scanning of spike protein residues in complexes with ACE2, we identified structural stability and binding affinity hotspots that are consistent with the results of biochemical studies. In agreement with the results of deep mutational scanning experiments, our quantitative analysis correctly reproduced strong and variant-specific epistatic effects in the XBB.1.5 and BA.2 variants. It was shown that Y453W and F456L mutations can enhance ACE2 binding when coupled with Q493 in XBB.1.5, while these mutations become destabilized when coupled with the R493 position in the BA.2 variant. The results provided a molecular rationale of the epistatic mechanism in Omicron variants, showing a central role of the Q493/R493 hotspot in modulating epistatic couplings between convergent mutational sites L455F and F456L in XBB lineages. The results of mutational scanning and binding analysis of the Omicron XBB spike variants with ACE2 receptors and a panel of class one antibodies provide a quantitative rationale for the experimental evidence that epistatic interactions of the physically proximal binding hotspots Y501, R498, Q493, L455F, and F456L can determine strong ACE2 binding, while convergent mutational sites F456L and F486P are instrumental in mediating broad antibody resistance. The study supports a mechanism in which the impact on ACE2 binding affinity is mediated through a small group of universal binding hotspots, while the effect of immune evasion could be more variant-dependent and modulated by convergent mutational sites in the conformationally adaptable spike regions.
Collapse
Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (N.R.); (M.A.); (G.G.)
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (N.R.); (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (N.R.); (M.A.); (G.G.)
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (N.R.); (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| |
Collapse
|
20
|
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587850. [PMID: 38617283 PMCID: PMC11014522 DOI: 10.1101/2024.04.02.587850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
In this study, we combined AlphaFold-based approaches for atomistic modeling of multiple protein states and microsecond molecular simulations to accurately characterize conformational ensembles and binding mechanisms of convergent evolution for the SARS-CoV-2 Spike Omicron variants BA.1, BA.2, BA.2.75, BA.3, BA.4/BA.5 and BQ.1.1. We employed and validated several different adaptations of the AlphaFold methodology for modeling of conformational ensembles including the introduced randomized full sequence scanning for manipulation of sequence variations to systematically explore conformational dynamics of Omicron Spike protein complexes with the ACE2 receptor. Microsecond atomistic molecular dynamic simulations provide a detailed characterization of the conformational landscapes and thermodynamic stability of the Omicron variant complexes. By integrating the predictions of conformational ensembles from different AlphaFold adaptations and applying statistical confidence metrics we can expand characterization of the conformational ensembles and identify functional protein conformations that determine the equilibrium dynamics for the Omicron Spike complexes with the ACE2. Conformational ensembles of the Omicron RBD-ACE2 complexes obtained using AlphaFold-based approaches for modeling protein states and molecular dynamics simulations are employed for accurate comparative prediction of the binding energetics revealing an excellent agreement with the experimental data. In particular, the results demonstrated that AlphaFold-generated extended conformational ensembles can produce accurate binding energies for the Omicron RBD-ACE2 complexes. The results of this study suggested complementarities and potential synergies between AlphaFold predictions of protein conformational ensembles and molecular dynamics simulations showing that integrating information from both methods can potentially yield a more adequate characterization of the conformational landscapes for the Omicron RBD-ACE2 complexes. This study provides insights in the interplay between conformational dynamics and binding, showing that evolution of Omicron variants through acquisition of convergent mutational sites may leverage conformational adaptability and dynamic couplings between key binding energy hotspots to optimize ACE2 binding affinity and enable immune evasion.
Collapse
|
21
|
Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
Collapse
Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
| |
Collapse
|
22
|
Sun YK, Wang C, Lin PQ, Hu L, Ye J, Gao ZG, Lin R, Li HM, Shu Q, Huang LS, Tan LH. Severe pediatric COVID-19: a review from the clinical and immunopathophysiological perspectives. World J Pediatr 2024; 20:307-324. [PMID: 38321331 PMCID: PMC11052880 DOI: 10.1007/s12519-023-00790-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/14/2023] [Indexed: 02/08/2024]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) tends to have mild presentations in children. However, severe and critical cases do arise in the pediatric population with debilitating systemic impacts and can be fatal at times, meriting further attention from clinicians. Meanwhile, the intricate interactions between the pathogen virulence factors and host defense mechanisms are believed to play indispensable roles in severe COVID-19 pathophysiology but remain incompletely understood. DATA SOURCES A comprehensive literature review was conducted for pertinent publications by reviewers independently using the PubMed, Embase, and Wanfang databases. Searched keywords included "COVID-19 in children", "severe pediatric COVID-19", and "critical illness in children with COVID-19". RESULTS Risks of developing severe COVID-19 in children escalate with increasing numbers of co-morbidities and an unvaccinated status. Acute respiratory distress stress and necrotizing pneumonia are prominent pulmonary manifestations, while various forms of cardiovascular and neurological involvement may also be seen. Multiple immunological processes are implicated in the host response to COVID-19 including the type I interferon and inflammasome pathways, whose dysregulation in severe and critical diseases translates into adverse clinical manifestations. Multisystem inflammatory syndrome in children (MIS-C), a potentially life-threatening immune-mediated condition chronologically associated with COVID-19 exposure, denotes another scientific and clinical conundrum that exemplifies the complexity of pediatric immunity. Despite the considerable dissimilarities between the pediatric and adult immune systems, clinical trials dedicated to children are lacking and current management recommendations are largely adapted from adult guidelines. CONCLUSIONS Severe pediatric COVID-19 can affect multiple organ systems. The dysregulated immune pathways in severe COVID-19 shape the disease course, epitomize the vast functional diversity of the pediatric immune system and highlight the immunophenotypical differences between children and adults. Consequently, further research may be warranted to adequately address them in pediatric-specific clinical practice guidelines.
Collapse
Affiliation(s)
- Yi-Kan Sun
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, China
| | - Can Wang
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Pei-Quan Lin
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Lei Hu
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Jing Ye
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Zhi-Gang Gao
- Department of General Surgery, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Ru Lin
- Department of Cardiopulmonary and Extracorporeal Life Support, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Hao-Min Li
- Clinical Data Center, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Qiang Shu
- Department of Cardiac Surgery, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Li-Su Huang
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China.
- Department of Infectious Diseases, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China.
| | - Lin-Hua Tan
- Surgical Intensive Care Unit, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, China.
| |
Collapse
|
23
|
Tam EH, Peng Y, Cheah MXY, Yan C, Xiao T. Neutralizing antibodies to block viral entry and for identification of entry inhibitors. Antiviral Res 2024; 224:105834. [PMID: 38369246 DOI: 10.1016/j.antiviral.2024.105834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Neutralizing antibodies (NAbs) are naturally produced by our immune system to combat viral infections. Clinically, neutralizing antibodies with potent efficacy and high specificity have been extensively used to prevent and treat a wide variety of viral infections, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Human Immunodeficiency Virus (HIV), Dengue Virus (DENV) and Hepatitis B Virus (HBV). An overwhelmingly large subset of clinically effective NAbs operates by targeting viral envelope proteins to inhibit viral entry into the host cell. Binding of viral envelope protein to the host receptor is a critical rate limiting step triggering a cascade of downstream events, including endocytosis, membrane fusion and pore formation to allow viral entry. In recent years, improved structural knowledge on these processes have allowed researchers to also leverage NAbs as an indispensable tool in guiding discovery of novel antiviral entry inhibitors, providing drug candidates with high efficacy and pan-genus specificity. This review will summarize the latest progresses on the applications of NAbs as effective entry inhibitors and as important tools to develop antiviral therapeutics by high-throughput drug screenings, rational design of peptidic entry inhibitor mimicking NAbs and in silico computational modeling approaches.
Collapse
Affiliation(s)
- Ee Hong Tam
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore
| | - Yu Peng
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore
| | - Megan Xin Yan Cheah
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research) 138673, Singapore
| | - Chuan Yan
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research) 138673, Singapore
| | - Tianshu Xiao
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore.
| |
Collapse
|
24
|
Naidu AS, Wang CK, Rao P, Mancini F, Clemens RA, Wirakartakusumah A, Chiu HF, Yen CH, Porretta S, Mathai I, Naidu SAG. Precision nutrition to reset virus-induced human metabolic reprogramming and dysregulation (HMRD) in long-COVID. NPJ Sci Food 2024; 8:19. [PMID: 38555403 PMCID: PMC10981760 DOI: 10.1038/s41538-024-00261-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
SARS-CoV-2, the etiological agent of COVID-19, is devoid of any metabolic capacity; therefore, it is critical for the viral pathogen to hijack host cellular metabolic machinery for its replication and propagation. This single-stranded RNA virus with a 29.9 kb genome encodes 14 open reading frames (ORFs) and initiates a plethora of virus-host protein-protein interactions in the human body. These extensive viral protein interactions with host-specific cellular targets could trigger severe human metabolic reprogramming/dysregulation (HMRD), a rewiring of sugar-, amino acid-, lipid-, and nucleotide-metabolism(s), as well as altered or impaired bioenergetics, immune dysfunction, and redox imbalance in the body. In the infectious process, the viral pathogen hijacks two major human receptors, angiotensin-converting enzyme (ACE)-2 and/or neuropilin (NRP)-1, for initial adhesion to cell surface; then utilizes two major host proteases, TMPRSS2 and/or furin, to gain cellular entry; and finally employs an endosomal enzyme, cathepsin L (CTSL) for fusogenic release of its viral genome. The virus-induced HMRD results in 5 possible infectious outcomes: asymptomatic, mild, moderate, severe to fatal episodes; while the symptomatic acute COVID-19 condition could manifest into 3 clinical phases: (i) hypoxia and hypoxemia (Warburg effect), (ii) hyperferritinemia ('cytokine storm'), and (iii) thrombocytosis (coagulopathy). The mean incubation period for COVID-19 onset was estimated to be 5.1 days, and most cases develop symptoms after 14 days. The mean viral clearance times were 24, 30, and 39 days for acute, severe, and ICU-admitted COVID-19 patients, respectively. However, about 25-70% of virus-free COVID-19 survivors continue to sustain virus-induced HMRD and exhibit a wide range of symptoms that are persistent, exacerbated, or new 'onset' clinical incidents, collectively termed as post-acute sequelae of COVID-19 (PASC) or long COVID. PASC patients experience several debilitating clinical condition(s) with >200 different and overlapping symptoms that may last for weeks to months. Chronic PASC is a cumulative outcome of at least 10 different HMRD-related pathophysiological mechanisms involving both virus-derived virulence factors and a multitude of innate host responses. Based on HMRD and virus-free clinical impairments of different human organs/systems, PASC patients can be categorized into 4 different clusters or sub-phenotypes: sub-phenotype-1 (33.8%) with cardiac and renal manifestations; sub-phenotype-2 (32.8%) with respiratory, sleep and anxiety disorders; sub-phenotype-3 (23.4%) with skeleto-muscular and nervous disorders; and sub-phenotype-4 (10.1%) with digestive and pulmonary dysfunctions. This narrative review elucidates the effects of viral hijack on host cellular machinery during SARS-CoV-2 infection, ensuing detrimental effect(s) of virus-induced HMRD on human metabolism, consequential symptomatic clinical implications, and damage to multiple organ systems; as well as chronic pathophysiological sequelae in virus-free PASC patients. We have also provided a few evidence-based, human randomized controlled trial (RCT)-tested, precision nutrients to reset HMRD for health recovery of PASC patients.
Collapse
Affiliation(s)
- A Satyanarayan Naidu
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA.
- N-terminus Research Laboratory, 232659 Via del Rio, Yorba Linda, CA, 92887, USA.
| | - Chin-Kun Wang
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- School of Nutrition, Chung Shan Medical University, 110, Section 1, Jianguo North Road, Taichung, 40201, Taiwan
| | - Pingfan Rao
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- College of Food and Bioengineering, Fujian Polytechnic Normal University, No.1, Campus New Village, Longjiang Street, Fuqing City, Fujian, China
| | - Fabrizio Mancini
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- President-Emeritus, Parker University, 2540 Walnut Hill Lane, Dallas, TX, 75229, USA
| | - Roger A Clemens
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- University of Southern California, Alfred E. Mann School of Pharmacy/D. K. Kim International Center for Regulatory & Quality Sciences, 1540 Alcazar St., CHP 140, Los Angeles, CA, 90089, USA
| | - Aman Wirakartakusumah
- International Union of Food Science and Technology (IUFoST), Guelph, ON, Canada
- IPMI International Business School Jakarta; South East Asian Food and Agriculture Science and Technology, IPB University, Bogor, Indonesia
| | - Hui-Fang Chiu
- Department of Chinese Medicine, Taichung Hospital, Ministry of Health & Well-being, Taichung, Taiwan
| | - Chi-Hua Yen
- Department of Family and Community Medicine, Chung Shan Medical University Hospital; School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Sebastiano Porretta
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- President, Italian Association of Food Technology (AITA), Milan, Italy
- Experimental Station for the Food Preserving Industry, Department of Consumer Science, Viale Tanara 31/a, I-43121, Parma, Italy
| | - Issac Mathai
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- Soukya International Holistic Health Center, Whitefield, Bengaluru, India
| | - Sreus A G Naidu
- Global Nutrition Healthcare Council (GNHC) Mission-COVID, Yorba Linda, CA, USA
- N-terminus Research Laboratory, 232659 Via del Rio, Yorba Linda, CA, 92887, USA
| |
Collapse
|
25
|
Bridge HN, Leiter W, Frazier CL, Weeks AM. An N terminomics toolbox combining 2-pyridinecarboxaldehyde probes and click chemistry for profiling protease specificity. Cell Chem Biol 2024; 31:534-549.e8. [PMID: 37816350 PMCID: PMC10960722 DOI: 10.1016/j.chembiol.2023.09.009] [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: 02/22/2023] [Revised: 07/10/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023]
Abstract
Proteomic profiling of protease-generated N termini provides key insights into protease function and specificity. However, current technologies have sequence limitations or require specialized synthetic reagents for N-terminal peptide isolation. Here, we introduce an N terminomics toolbox that combines selective N-terminal biotinylation using 2-pyridinecarboxaldehyde (2PCA) reagents with chemically cleavable linkers to enable efficient enrichment of protein N termini. By incorporating a commercially available alkyne-modified 2PCA in combination with Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), our strategy eliminates the need for chemical synthesis of N-terminal probes. Using these reagents, we developed PICS2 (Proteomic Identification of Cleavage Sites with 2PCA) to profile the specificity of subtilisin/kexin-type proprotein convertases (PCSKs). We also implemented CHOPPER (chemical enrichment of protease substrates with purchasable, elutable reagents) for global sequencing of apoptotic proteolytic cleavage sites. Based on their broad applicability and ease of implementation, PICS2 and CHOPPER are useful tools that will advance our understanding of protease biology.
Collapse
Affiliation(s)
- Haley N Bridge
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - William Leiter
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Clara L Frazier
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Amy M Weeks
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA.
| |
Collapse
|
26
|
Park C, Hwang IY, Yan SLS, Vimonpatranon S, Wei D, Van Ryk D, Girard A, Cicala C, Arthos J, Kehrl JH. Murine alveolar macrophages rapidly accumulate intranasally administered SARS-CoV-2 Spike protein leading to neutrophil recruitment and damage. eLife 2024; 12:RP86764. [PMID: 38507462 PMCID: PMC10954308 DOI: 10.7554/elife.86764] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
The trimeric SARS-CoV-2 Spike protein mediates viral attachment facilitating cell entry. Most COVID-19 vaccines direct mammalian cells to express the Spike protein or deliver it directly via inoculation to engender a protective immune response. The trafficking and cellular tropism of the Spike protein in vivo and its impact on immune cells remains incompletely elucidated. In this study, we inoculated mice intranasally, intravenously, and subcutaneously with fluorescently labeled recombinant SARS-CoV-2 Spike protein. Using flow cytometry and imaging techniques, we analyzed its localization, immune cell tropism, and acute functional impact. Intranasal administration led to rapid lung alveolar macrophage uptake, pulmonary vascular leakage, and neutrophil recruitment and damage. When injected near the inguinal lymph node medullary, but not subcapsular macrophages, captured the protein, while scrotal injection recruited and fragmented neutrophils. Widespread endothelial and liver Kupffer cell uptake followed intravenous administration. Human peripheral blood cells B cells, neutrophils, monocytes, and myeloid dendritic cells all efficiently bound Spike protein. Exposure to the Spike protein enhanced neutrophil NETosis and augmented human macrophage TNF-α (tumor necrosis factor-α) and IL-6 production. Human and murine immune cells employed C-type lectin receptors and Siglecs to help capture the Spike protein. This study highlights the potential toxicity of the SARS-CoV-2 Spike protein for mammalian cells and illustrates the central role for alveolar macrophage in pathogenic protein uptake.
Collapse
Affiliation(s)
- Chung Park
- B-Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Il-Young Hwang
- B-Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Serena Li-Sue Yan
- B-Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Sinmanus Vimonpatranon
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious DiseasesBethesdaUnited States
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences – United States ComponentBangkokThailand
| | - Danlan Wei
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Don Van Ryk
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Alexandre Girard
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Claudia Cicala
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - James Arthos
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - John H Kehrl
- B-Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| |
Collapse
|
27
|
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape. J Chem Inf Model 2024; 64:1657-1681. [PMID: 38373700 DOI: 10.1021/acs.jcim.3c01857] [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: 02/21/2024]
Abstract
The latest wave of SARS-CoV-2 Omicron variants displayed a growth advantage and increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with atomistic simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both the structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that the AlphaFold2-predicted structural ensemble of the BA.2.86 spike protein complex with ACE2 can accurately capture the main conformational states of the Omicron variant. Complementary to AlphaFold2 structural predictions, microsecond molecular dynamics simulations reveal the details of the conformational landscape and produced equilibrium ensembles of the BA.2.86 structures that are used to perform mutational scanning of spike residues and characterize structural stability and binding energy hotspots. The ensemble-based mutational profiling of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 revealed a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 convergent mutational hotspots R403K, F486P, and R493Q. To examine the immune evasion properties of BA.2.86 in atomistic detail, we performed structure-based mutational profiling of the spike protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against the BA.2.86 variant. The results revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have evolved to outcompete other Omicron subvariants by improving immune evasion while preserving binding affinity with ACE2 via through a compensatory effect of R493Q and F486P convergent mutational hotspots. This study demonstrated that an integrative approach combining AlphaFold2 predictions with complementary atomistic molecular dynamics simulations and robust ensemble-based mutational profiling of spike residues can enable accurate and comprehensive characterization of structure, dynamics, and binding mechanisms of newly emerging Omicron variants.
Collapse
Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States of America
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States of America
| |
Collapse
|
28
|
Kumar S, Dasgupta S, Sajadi MM, Snyder GA, DeVico AL, Ray K. Discordant Antigenic Properties of Soluble and Virion SARS-CoV-2 Spike Proteins. Viruses 2024; 16:407. [PMID: 38543772 PMCID: PMC10974403 DOI: 10.3390/v16030407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 04/01/2024] Open
Abstract
Efforts to develop vaccine and immunotherapeutic countermeasures against the COVID-19 pandemic focus on targeting the trimeric spike (S) proteins of SARS-CoV-2. Vaccines and therapeutic design strategies must impart the characteristics of virion S from historical and emerging variants onto practical constructs such as soluble, stabilized trimers. The virus spike is a heterotrimer of two subunits: S1, which includes the receptor binding domain (RBD) that binds the cell surface receptor ACE2, and S2, which mediates membrane fusion. Previous studies suggest that the antigenic, structural, and functional characteristics of virion S may differ from current soluble surrogates. For example, it was reported that certain anti-glycan, HIV-1 neutralizing monoclonal antibodies bind soluble SARS-CoV-2 S but do not neutralize SARS-CoV-2 virions. In this study, we used single-molecule fluorescence correlation spectroscopy (FCS) under physiologically relevant conditions to examine the reactivity of broadly neutralizing and non-neutralizing anti-S human monoclonal antibodies (mAbs) isolated in 2020. Binding efficiency was assessed by FCS with soluble S trimers, pseudoviruses and inactivated wild-type virions representing variants emerging from 2020 to date. Anti-glycan mAbs were tested and compared. We find that both anti-S specific and anti-glycan mAbs exhibit variable but efficient binding to a range of stabilized, soluble trimers. Across mAbs, the efficiencies of soluble S binding were positively correlated with reactivity against inactivated virions but not pseudoviruses. Binding efficiencies with pseudoviruses were generally lower than with soluble S or inactivated virions. Among neutralizing mAbs, potency did not correlate with binding efficiencies on any target. No neutralizing activity was detected with anti-glycan antibodies. Notably, the virion S released from membranes by detergent treatment gained more efficient reactivity with anti-glycan, HIV-neutralizing antibodies but lost reactivity with all anti-S mAbs. Collectively, the FCS binding data suggest that virion surfaces present appreciable amounts of both functional and nonfunctional trimers, with neutralizing anti-S favoring the former structures and non-neutralizing anti-glycan mAbs binding the latter. S released from solubilized virions represents a nonfunctional structure bound by anti-glycan mAbs, while engineered soluble trimers present a composite structure that is broadly reactive with both mAb types. The detection of disparate antigenicity and immunoreactivity profiles in engineered and virion-associated S highlight the value of single-virus analyses in designing future antiviral strategies against SARS-CoV-2.
Collapse
Affiliation(s)
- Sameer Kumar
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Souradip Dasgupta
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Mohammad M. Sajadi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Division of Clinical Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Greg A. Snyder
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Anthony L. DeVico
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Medicine, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| | - Krishanu Ray
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
| |
Collapse
|
29
|
Pasala C, Sharma S, Roychowdhury T, Moroni E, Colombo G, Chiosis G. N-Glycosylation as a Modulator of Protein Conformation and Assembly in Disease. Biomolecules 2024; 14:282. [PMID: 38540703 PMCID: PMC10968129 DOI: 10.3390/biom14030282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 05/01/2024] Open
Abstract
Glycosylation, a prevalent post-translational modification, plays a pivotal role in regulating intricate cellular processes by covalently attaching glycans to macromolecules. Dysregulated glycosylation is linked to a spectrum of diseases, encompassing cancer, neurodegenerative disorders, congenital disorders, infections, and inflammation. This review delves into the intricate interplay between glycosylation and protein conformation, with a specific focus on the profound impact of N-glycans on the selection of distinct protein conformations characterized by distinct interactomes-namely, protein assemblies-under normal and pathological conditions across various diseases. We begin by examining the spike protein of the SARS virus, illustrating how N-glycans regulate the infectivity of pathogenic agents. Subsequently, we utilize the prion protein and the chaperone glucose-regulated protein 94 as examples, exploring instances where N-glycosylation transforms physiological protein structures into disease-associated forms. Unraveling these connections provides valuable insights into potential therapeutic avenues and a deeper comprehension of the molecular intricacies that underlie disease conditions. This exploration of glycosylation's influence on protein conformation effectively bridges the gap between the glycome and disease, offering a comprehensive perspective on the therapeutic implications of targeting conformational mutants and their pathologic assemblies in various diseases. The goal is to unravel the nuances of these post-translational modifications, shedding light on how they contribute to the intricate interplay between protein conformation, assembly, and disease.
Collapse
Affiliation(s)
- Chiranjeevi Pasala
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (C.P.); (S.S.); (T.R.)
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (C.P.); (S.S.); (T.R.)
| | - Tanaya Roychowdhury
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (C.P.); (S.S.); (T.R.)
| | - Elisabetta Moroni
- The Institute of Chemical Sciences and Technologies (SCITEC), Italian National Research Council (CNR), 20131 Milano, Italy; (E.M.); (G.C.)
| | - Giorgio Colombo
- The Institute of Chemical Sciences and Technologies (SCITEC), Italian National Research Council (CNR), 20131 Milano, Italy; (E.M.); (G.C.)
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (C.P.); (S.S.); (T.R.)
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
30
|
Liu HY, Hu Y, Yu C, Wang ZG, Liu SL, Pang DW. Quantitative single-virus tracking for revealing the dynamics of SARS-CoV-2 fusion with plasma membrane. Sci Bull (Beijing) 2024; 69:502-511. [PMID: 37993331 DOI: 10.1016/j.scib.2023.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023]
Abstract
Viral envelope fusion with the host plasma membrane (PM) for genome release is a hallmark step in the life cycle of many enveloped viruses. This process is regulated by a complex network of biomolecules on the PM, but robust tools to precisely elucidate the dynamic mechanisms of virus-PM fusion events are still lacking. Here, we developed a quantitative single-virus tracking approach based on highly efficient dual-color labelling of viruses and batch trajectory analysis to achieve the spatiotemporal quantification of fusion events. This approach allows us to comprehensively analyze the membrane fusion mechanism utilized by pseudotyped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the single-virus level and precisely elucidate how the relevant biomolecules synergistically regulate the fusion process. Our results revealed that SARS-CoV-2 may promote the formation of supersaturated clusters of cholesterol to facilitate the initiation of the membrane fusion process and accelerate the viral genome release.
Collapse
Affiliation(s)
- Hao-Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
| | - Yusi Hu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
| | - Cong Yu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China; Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China.
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, Frontiers Science Center for Cell Responses, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, China; Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China.
| |
Collapse
|
31
|
Bi W, Tang K, Chen G, Xie Y, Polizzi NF, DeGrado WF, Yuan S, Dang B. An enhanced broad-spectrum peptide inhibits Omicron variants in vivo. Cell Rep Med 2024; 5:101418. [PMID: 38340726 PMCID: PMC10897629 DOI: 10.1016/j.xcrm.2024.101418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 11/29/2023] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
The continual emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) poses a major challenge to vaccines and antiviral therapeutics due to their extensive evasion of immunity. Aiming to develop potent and broad-spectrum anticoronavirus inhibitors, we generated A1-(GGGGS)7-HR2m (A1L35HR2m) by introducing an angiotensin-converting enzyme 2 (ACE2)-derived peptide A1 to the N terminus of the viral HR2-derived peptide HR2m through a long flexible linker, which showed significantly improved antiviral activity. Further cholesterol (Chol) modification at the C terminus of A1L35HR2m greatly enhanced the inhibitory activities against SARS-CoV-2, SARS-CoV-2 VOCs, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) pseudoviruses, with IC50 values ranging from 0.16 to 5.53 nM. A1L35HR2m-Chol also potently inhibits spike-protein-mediated cell-cell fusion and the replication of authentic Omicron BA.2.12.1, BA.5, and EG.5.1. Importantly, A1L35HR2m-Chol distributed widely in respiratory tract tissue and had a long half-life (>10 h) in vivo. Intranasal administration of A1L35HR2m-Chol to K18-hACE2 transgenic mice potently inhibited Omicron BA.5 and EG.5.1 infection both prophylactically and therapeutically.
Collapse
Affiliation(s)
- Wenwen Bi
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, Zhejiang, China; Frontier Biotechnology Laboratory, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310030, China.
| | - Kaiming Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Guilin Chen
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310030, China
| | - Yubin Xie
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Nicholas F Polizzi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Bobo Dang
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310030, Zhejiang, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310030, China.
| |
Collapse
|
32
|
Matveev EV, Ponomarev GV, Kazanov MD. Genome-wide bioinformatics analysis of human protease capacity for proteolytic cleavage of the SARS-CoV-2 spike glycoprotein. Microbiol Spectr 2024; 12:e0353023. [PMID: 38189333 PMCID: PMC10846095 DOI: 10.1128/spectrum.03530-23] [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: 10/03/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) primarily enters the cell by binding the virus's spike (S) glycoprotein to the angiotensin-converting enzyme 2 receptor on the cell surface, followed by proteolytic cleavage by host proteases. Studies have identified furin and transmembrane protease serine 2 proteases in priming and triggering cleavages of the S glycoprotein, converting it into a fusion-competent form and initiating membrane fusion, respectively. Alternatively, SARS-CoV-2 can enter the cell through the endocytic pathway, where activation is triggered by lysosomal cathepsin L. However, other proteases are also suspected to be involved in both entry routes. In this study, we conducted a genome-wide bioinformatics analysis to explore the capacity of human proteases in hydrolyzing peptide bonds of the S glycoprotein. Predictive models of sequence specificity for 169 human proteases were constructed and applied to the S glycoprotein together with the method for predicting structural susceptibility to proteolysis of protein regions. After validating our approach on extensively studied S2' and S1/S2 cleavage sites, we applied our method to each peptide bond of the S glycoprotein across all 169 proteases. Our results indicate that various members of the proprotein convertase subtilisin/kexin type, type II transmembrane family serine protease, and kallikrein families, as well as specific coagulation factors, are capable of cleaving S2' or S1/S2 sites. We have also identified a potential cleavage site of cathepsin L at the K790 position within the S2' loop. Structural analysis suggests that cleavage of this site induces conformational changes similar to the cleavage at the R815 (S2') position, leading to the exposure of the fusion peptide and subsequent fusion with the membrane. Other potential cleavage sites and the influence of mutations in common SARS-CoV-2 variants on proteolytic efficiency are discussed.IMPORTANCEThe entry of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) into the cell, activated by host proteases, is considerably more complex in coronaviruses than in most other viruses and is not fully understood. There is evidence that other proteases beyond the known furin and transmembrane protease serine 2 can activate the spike protein. Another example of uncertainty is the cleavage site for the alternative endocytic route of SARS-CoV-2 entrance, which is still unknown. Bioinformatics methods, modeling protease specificity and estimating the structural susceptibility of protein regions to proteolysis, can aid in studying this topic by predicting the involved proteases and their cleavage sites, thereby substantially reducing the amount of experimental work. Elucidating the mechanisms of spike protein activation is crucial for preventing possible future coronavirus pandemics and developing antiviral drugs.
Collapse
Affiliation(s)
- Evgenii V. Matveev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Research and Training Center on Bioinformatics, A.A.Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Laboratory of Cytogenetics and Molecular Genetics, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Gennady V. Ponomarev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Research and Training Center on Bioinformatics, A.A.Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Marat D. Kazanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Research and Training Center on Bioinformatics, A.A.Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Laboratory of Cytogenetics and Molecular Genetics, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| |
Collapse
|
33
|
Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
Collapse
Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
| |
Collapse
|
34
|
Hu X, Chi H, Fu X, Chen J, Dong L, Jiang S, Li Y, Chen J, Cheng M, Min Q, Tian Y, Zhang P. Tunable Multivalent Aptamer-Based DNA Nanostructures To Regulate Multiheteroreceptor-Mediated Tumor Recognition. J Am Chem Soc 2024; 146:2514-2523. [PMID: 38247135 DOI: 10.1021/jacs.3c10704] [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: 01/23/2024]
Abstract
Precise mapping and regulation of cell surface receptors hold immense significance in disease treatment, such as cancer, infection, and neurodisorders, but also face enormous challenges. In this study, we designed a series of adjustable multivalent aptamer-based DNA nanostructures to precisely control their interaction with receptors in tumor cells. By profiling surface receptors on 12 cell lines using 10 different aptamers, we generated a heatmap that accurately distinguished between various tumor types based on multiple markers. We then incorporated these aptamers onto DNA origami structures to regulate receptor recognition, with patch-like structures demonstrating a tendency to be trapped on the cell surface and with tube-like structures showing a preference for internalization. Through precise control of aptamer species, valence, and geometric patterns, we found that multiheteroreceptor-mediated recognition not only favored the specific binding of nanostructures to tumor cells but also greatly enhanced intracellular uptake by promoting clathrin-dependent endocytosis. Specifically, we achieved over 5-fold uptake in different tumor cells versus normal cells using tube-like structures modified with different diheteroaptamer pairs, facilitating targeted drug delivery. Moreover, patch-like structures with triheteroaptamers guided specific interactions between macrophages and tumor cells, leading to effective immune clearance. This programmable multivalent system allows for the precise regulation of cell recognition using multiple parameters, demonstrating great potential for personalized tumor treatment.
Collapse
Affiliation(s)
- Xiaoxue Hu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Hongli Chi
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Xiaoyi Fu
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jinling Chen
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Linying Dong
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Shiqi Jiang
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Yan Li
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jingyi Chen
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Ming Cheng
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Qianhao Min
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Penghui Zhang
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| |
Collapse
|
35
|
Zan F, Zhou Y, Chen T, Chen Y, Mu Z, Qian Z, Ou X. Stabilization of the Metastable Pre-Fusion Conformation of the SARS-CoV-2 Spike Glycoprotein through N-Linked Glycosylation of the S2 Subunit. Viruses 2024; 16:223. [PMID: 38399999 PMCID: PMC10891965 DOI: 10.3390/v16020223] [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: 12/15/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic, represents a serious threat to public health. The spike (S) glycoprotein of SARS-CoV-2 mediates viral entry into host cells and is heavily glycosylated. In this study, we systemically analyzed the roles of 22 putative N-linked glycans in SARS-CoV-2 S protein expression, membrane fusion, viral entry, and stability. Using the α-glycosidase inhibitors castanospermine and NB-DNJ, we confirmed that disruption of N-linked glycosylation blocked the maturation of the S protein, leading to the impairment of S protein-mediated membrane fusion. Single-amino-acid substitution of each of the 22 N-linked glycosylation sites with glutamine revealed that 9 out of the 22 N-linked glycosylation sites were critical for S protein folding and maturation. Thus, substitution at these sites resulted in reduced S protein-mediated cell-cell fusion and viral entry. Notably, the N1074Q mutation markedly affected S protein stability and induced significant receptor-independent syncytium (RIS) formation in HEK293T/hACE2-KO cells. Additionally, the removal of the furin cleavage site partially compensated for the instability induced by the N1074Q mutation. Although the corresponding mutation in the SARS-CoV S protein (N1056Q) did not induce RIS in HEK293T cells, the N669Q and N1080Q mutants exhibited increased fusogenic activity and did induce syncytium formation in HEK293T cells. Therefore, N-glycans on the SARS-CoV and SARS-CoV-2 S2 subunits are highly important for maintaining the pre-fusion state of the S protein. This study revealed the critical roles of N-glycans in S protein maturation and stability, information that has implications for the design of vaccines and antiviral strategies.
Collapse
Affiliation(s)
- Fuwen Zan
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yao Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Ting Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yahan Chen
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Zhixia Mu
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Xiuyuan Ou
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China (Y.Z.)
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| |
Collapse
|
36
|
Zhao X, Gao F. Novel Omicron Variants Enhance Anchored Recognition of TMEM106B: A New Pathway for SARS-CoV-2 Cellular Invasion. J Phys Chem Lett 2024; 15:671-680. [PMID: 38206837 DOI: 10.1021/acs.jpclett.3c03296] [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: 01/13/2024]
Abstract
The recent discovery that TMEM106B serves as a receptor mediating ACE2-independent SARS-CoV-2 entry into cells deserves attention, especially in the background of the frequent emergence of mutant strains. Here, the structure-dynamic features of this novel pathway are dissected deeply. Our investigation revealed that the large loop (RBD@471-491) could anchor TMEM106B, which was then firmly locked by another loop (RBD@444-451). The novel and widely disseminated Omicron variants (BA.2.86/EG.5.1) affect the anchoring recognition of proteins, with BA.2.86 being more likely to impact cells with limited or undetectable ACE2 expression. The large loop of the EG.5.1 variant captures TMEM106B poorly due to impaired electrostatic complementarity. Furthermore, we emphasize that antibody design against these two loops could enhance the protection of ACE2 low-expressing cells according to the alanine scanning mutagenesis of multiple antibodies. We hope this study will provide a novel perspective for the prevention and treatment against this new viral invasion pathway.
Collapse
Affiliation(s)
- Xiaoyu Zhao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| |
Collapse
|
37
|
Zech F, Jung C, Jacob T, Kirchhoff F. Causes and Consequences of Coronavirus Spike Protein Variability. Viruses 2024; 16:177. [PMID: 38399953 PMCID: PMC10892391 DOI: 10.3390/v16020177] [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: 12/28/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Coronaviruses are a large family of enveloped RNA viruses found in numerous animal species. They are well known for their ability to cross species barriers and have been transmitted from bats or intermediate hosts to humans on several occasions. Four of the seven human coronaviruses (hCoVs) are responsible for approximately 20% of common colds (hCoV-229E, -NL63, -OC43, -HKU1). Two others (SARS-CoV-1 and MERS-CoV) cause severe and frequently lethal respiratory syndromes but have only spread to very limited extents in the human population. In contrast the most recent human hCoV, SARS-CoV-2, while exhibiting intermediate pathogenicity, has a profound impact on public health due to its enormous spread. In this review, we discuss which initial features of the SARS-CoV-2 Spike protein and subsequent adaptations to the new human host may have helped this pathogen to cause the COVID-19 pandemic. Our focus is on host forces driving changes in the Spike protein and their consequences for virus infectivity, pathogenicity, immune evasion and resistance to preventive or therapeutic agents. In addition, we briefly address the significance and perspectives of broad-spectrum therapeutics and vaccines.
Collapse
Affiliation(s)
- Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany; (C.J.); (T.J.)
- Helmholtz-Institute Ulm (HIU) Electrochemical Energy Storage, 89081 Ulm, Germany
- Karlsruhe Institute of Technology (KIT), 76021 Karlsruhe, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| |
Collapse
|
38
|
Bedding MJ, Franck C, Johansen-Leete J, Aggarwal A, Maxwell JWC, Patel K, Hawkins PME, Low JKK, Siddiquee R, Sani HM, Ford DJ, Turville S, Mackay JP, Passioura T, Christie M, Payne RJ. Discovery of High Affinity Cyclic Peptide Ligands for Human ACE2 with SARS-CoV-2 Entry Inhibitory Activity. ACS Chem Biol 2024; 19:141-152. [PMID: 38085789 DOI: 10.1021/acschembio.3c00568] [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: 01/23/2024]
Abstract
The development of effective antiviral compounds is essential for mitigating the effects of the COVID-19 pandemic. Entry of SARS-CoV-2 virions into host cells is mediated by the interaction between the viral spike (S) protein and membrane-bound angiotensin-converting enzyme 2 (ACE2) on the surface of epithelial cells. Inhibition of this viral protein-host protein interaction is an attractive avenue for the development of antiviral molecules with numerous spike-binding molecules generated to date. Herein, we describe an alternative approach to inhibit the spike-ACE2 interaction by targeting the spike-binding interface of human ACE2 via mRNA display. Two consecutive display selections were performed to direct cyclic peptide ligand binding toward the spike binding interface of ACE2. Through this process, potent cyclic peptide binders of human ACE2 (with affinities in the picomolar to nanomolar range) were identified, two of which neutralized SARS-CoV-2 entry. This work demonstrates the potential of targeting ACE2 for the generation of anti-SARS-CoV-2 therapeutics as well as broad spectrum antivirals for the treatment of SARS-like betacoronavirus infection.
Collapse
Affiliation(s)
- Max J Bedding
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Charlotte Franck
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason Johansen-Leete
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paige M E Hawkins
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Rezwan Siddiquee
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Hakimeh Moghaddas Sani
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Daniel J Ford
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Toby Passioura
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mary Christie
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| |
Collapse
|
39
|
Gavilán E, Medina-Guzman R, Bahatyrevich-Kharitonik B, Ruano D. Protein Quality Control Systems and ER Stress as Key Players in SARS-CoV-2-Induced Neurodegeneration. Cells 2024; 13:123. [PMID: 38247815 PMCID: PMC10814689 DOI: 10.3390/cells13020123] [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: 11/29/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
The COVID-19 pandemic has brought to the forefront the intricate relationship between SARS-CoV-2 and its impact on neurological complications, including potential links to neurodegenerative processes, characterized by a dysfunction of the protein quality control systems and ER stress. This review article explores the role of protein quality control systems, such as the Unfolded Protein Response (UPR), the Endoplasmic Reticulum-Associated Degradation (ERAD), the Ubiquitin-Proteasome System (UPS), autophagy and the molecular chaperones, in SARS-CoV-2 infection. Our hypothesis suggests that SARS-CoV-2 produces ER stress and exploits the protein quality control systems, leading to a disruption in proteostasis that cannot be solved by the host cell. This disruption culminates in cell death and may represent a link between SARS-CoV-2 and neurodegeneration.
Collapse
Affiliation(s)
- Elena Gavilán
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Rafael Medina-Guzman
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
| | - Bazhena Bahatyrevich-Kharitonik
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| | - Diego Ruano
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla (US), 41012 Sevilla, Spain; (R.M.-G.); (B.B.-K.); (D.R.)
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Junta de Andalucía, CSIC, University of Seville (US), 41013 Sevilla, Spain
| |
Collapse
|
40
|
Biskupek I, Gieldon A. Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2). Int J Mol Sci 2024; 25:679. [PMID: 38203850 PMCID: PMC10779479 DOI: 10.3390/ijms25010679] [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: 11/02/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
The SARS-CoV-2 virus, commonly known as COVID-19, occurred in 2019. It is a highly contagious illness with effects ranging from mild symptoms to severe illness. It is also one of the best-known pathogens since more than 200,000 scientific papers occurred in the last few years. With the publication of the SARS-CoV-2 (SARS-CoV-2-CTD) spike (S) protein in a complex with human ACE2 (hACE2) (PDB (6LZG)), the molecular analysis of one of the most crucial steps on the infection pathway was possible. The aim of this manuscript is to simulate the most widely spread mutants of SARS-CoV-2, namely Alpha, Beta, Gamma, Delta, Omicron, and the first recognized variant (natural wild type). With the wide search of the hypersurface of the potential energy performed using the UNRES force field, the intermediate state of the ACE2-RBD complex was found. R403, K/N/T417, L455, F486, Y489, F495, Y501, and Y505 played a crucial role in the protein recognition mechanism. The intermediate state cannot be very stable since it will prevent the infection cascade.
Collapse
Affiliation(s)
| | - Artur Gieldon
- Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdansk, Poland;
| |
Collapse
|
41
|
Khan I, Li S, Tao L, Wang C, Ye B, Li H, Liu X, Ahmad I, Su W, Zhong G, Wen Z, Wang J, Hua RH, Ma A, Liang J, Wan XP, Bu ZG, Zheng YH. Tubeimosides are pan-coronavirus and filovirus inhibitors that can block their fusion protein binding to Niemann-Pick C1. Nat Commun 2024; 15:162. [PMID: 38167417 PMCID: PMC10762260 DOI: 10.1038/s41467-023-44504-4] [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: 07/03/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
SARS-CoV-2 and filovirus enter cells via the cell surface angiotensin-converting enzyme 2 (ACE2) or the late-endosome Niemann-Pick C1 (NPC1) as a receptor. Here, we screened 974 natural compounds and identified Tubeimosides I, II, and III as pan-coronavirus and filovirus entry inhibitors that target NPC1. Using in-silico, biochemical, and genomic approaches, we provide evidence that NPC1 also binds SARS-CoV-2 spike (S) protein on the receptor-binding domain (RBD), which is blocked by Tubeimosides. Importantly, NPC1 strongly promotes productive SARS-CoV-2 entry, which we propose is due to its influence on fusion in late endosomes. The Tubeimosides' antiviral activity and NPC1 function are further confirmed by infection with SARS-CoV-2 variants of concern (VOC), SARS-CoV, and MERS-CoV. Thus, NPC1 is a critical entry co-factor for highly pathogenic human coronaviruses (HCoVs) in the late endosomes, and Tubeimosides hold promise as a new countermeasure for these HCoVs and filoviruses.
Collapse
Affiliation(s)
- Ilyas Khan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Sunan Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lihong Tao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chong Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Bowei Ye
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Huiyu Li
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Xiaoyang Liu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Iqbal Ahmad
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wenqiang Su
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Gongxun Zhong
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhiyuan Wen
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jinliang Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Rong-Hong Hua
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ao Ma
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Jie Liang
- Center for Bioinformatics and Quantitative Biology, Richard and Loan Hill Department of Biomedical Engineering, The University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Xiao-Peng Wan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Zhi-Gao Bu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Yong-Hui Zheng
- Department of Microbiology and Immunology, The University of Illinois Chicago, Chicago, IL, 60612, USA.
| |
Collapse
|
42
|
Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
Collapse
Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
| |
Collapse
|
43
|
Nawaz S, Janiad S, Fatima A, Saleem M, Fatima U, Ali A. Rapidly Evolving SARS-CoV-2: A Brief Review Regarding the Variants and their Effects on Vaccine Efficacies. Infect Disord Drug Targets 2024; 24:58-66. [PMID: 38178666 DOI: 10.2174/0118715265271109231129112515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/14/2023] [Accepted: 10/26/2023] [Indexed: 01/06/2024]
Abstract
Since the commencement of Corona Virus Disease 2019 (COVID-19) pandemic, which has resulted in millions of mortalities globally, the efforts to minimize the damages have equally been up to the task. One of those efforts includes the mass vaccine development initiative targeting the deadly Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). So far, vaccines have tremendously decreased the rate of transmission and infection in most parts of the world. However, the repeated resurgence of different types of mutated versions of the virus, also known as variants, has somehow created uncertainties about the efficacies of different types of vaccines. This review discusses some of the interesting SARS-CoV-2 features, including general structure, genomics, and mechanisms of variants development and their consequent immune escape. This review also focuses very briefly on antigenic drift, shift, and vaccine-developing platforms.
Collapse
Affiliation(s)
- Shahid Nawaz
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Sara Janiad
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Pakistan
| | - Aiman Fatima
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Maira Saleem
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Urooj Fatima
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Pakistan
| | - Asad Ali
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
44
|
Liang JJ, Pitsillou E, Hung A, Karagiannis TC. A repository of COVID-19 related molecular dynamics simulations and utilisation in the context of nsp10-nsp16 antivirals. J Mol Graph Model 2024; 126:108666. [PMID: 37976980 DOI: 10.1016/j.jmgm.2023.108666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of establishing systems and infrastructure to develop vaccines, antiviral drugs, and therapeutic antibodies against emerging pathogens. Typical drug discovery processes involve targeting suitable proteins to effect pathogen replication or to attenuate host responses, by examining either large chemical databases or protein-protein interactions. Following initial screens, molecular dynamics (MD) simulations are critical for gaining further insight into molecular interactions. During the COVID-19 pandemic, many research groups made their simulations widely available, as highlighted by the comprehensive D.E. Shaw Research trajectory database. To investigate protein target sites and evaluate potential lead compounds, we performed over 300 MD simulations relating to COVID-19. We organised our simulations into a repository, which is publicly available at https://epimedlab.org/trajectories/. The trajectories cover a large part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome, and the majority of our MD simulations focused on the identification of potential antivirals. For example, we focused on the S-adenosyl-l-methionine binding site of the nsp10-nsp16 complex, a critical component of viral replication, revealing verbascoside as a potential lead. Moreover, we utilised MD trajectories to explore the interface between the spike protein receptor binding domain and human angiotensin-converting enzyme 2 receptor, with the ultimate aim being investigation of new variants in real-time. Overall, MD simulations are a critical component of the in silico drug discovery process and as highlighted throughout the pandemic, data sharing enables accelerated progress. We have organised our extensive collection of COVID-19 related MD trajectories into an easily accessible repository.
Collapse
Affiliation(s)
- Julia J Liang
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
45
|
Len JS, Koh CWT, Chan KR. The Functional Roles of MDSCs in Severe COVID-19 Pathogenesis. Viruses 2023; 16:27. [PMID: 38257728 PMCID: PMC10821470 DOI: 10.3390/v16010027] [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: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Severe COVID-19 is a major cause of morbidity and mortality worldwide, especially among those with co-morbidities, the elderly, and the immunocompromised. However, the molecular determinants critical for severe COVID-19 progression remain to be fully elucidated. Meta-analyses of transcriptomic RNAseq and single-cell sequencing datasets comparing severe and mild COVID-19 patients have demonstrated that the early expansion of myeloid-derived suppressor cells (MDSCs) could be a key feature of severe COVID-19 progression. Besides serving as potential early prognostic biomarkers for severe COVID-19 progression, several studies have also indicated the functional roles of MDSCs in severe COVID-19 pathogenesis and possibly even long COVID. Given the potential links between MDSCs and severe COVID-19, we examine the existing literature summarizing the characteristics of MDSCs, provide evidence of MDSCs in facilitating severe COVID-19 pathogenesis, and discuss the potential therapeutic avenues that can be explored to reduce the risk and burden of severe COVID-19. We also provide a web app where users can visualize the temporal changes in specific genes or MDSC-related gene sets during severe COVID-19 progression and disease resolution, based on our previous study.
Collapse
Affiliation(s)
- Jia Soon Len
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Clara W. T. Koh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore;
| | - Kuan Rong Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore;
| |
Collapse
|
46
|
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] [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.
Collapse
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
| |
Collapse
|
47
|
Baboo S, Diedrich JK, Torres JL, Copps J, Singh B, Garrett PT, Ward AB, Paulson JC, Yates JR. Evolving spike-protein N-glycosylation in SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539897. [PMID: 37214937 PMCID: PMC10197516 DOI: 10.1101/2023.05.08.539897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Since >3 years, SARS-CoV-2 has plunged humans into a colossal pandemic. Henceforth, multiple waves of infection have swept through the human population, led by variants that were able to partially evade acquired immunity. The co-evolution of SARS-CoV-2 variants with human immunity provides an excellent opportunity to study the interaction between viral pathogens and their human hosts. The heavily N-glycosylated spike-protein of SARS-CoV-2 plays a pivotal role in initiating infection and is the target for host immune-response, both of which are impacted by host-installed N-glycans. Using highly-sensitive DeGlyPHER approach, we compared the N-glycan landscape on spikes of the SARS-CoV-2 Wuhan-Hu-1 strain to seven WHO-defined variants of concern/interest, using recombinantly expressed, soluble spike-protein trimers, sharing same stabilizing-mutations. We found that N-glycan processing is conserved at most sites. However, in multiple variants, processing of N-glycans from high mannose- to complex-type is reduced at sites N165, N343 and N616, implicated in spike-protein function.
Collapse
Affiliation(s)
- Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Bhavya Singh
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Patrick T. Garrett
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - James C. Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| |
Collapse
|
48
|
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571185. [PMID: 38168257 PMCID: PMC10760024 DOI: 10.1101/2023.12.11.571185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In this study, we combined AI-based atomistic structural modeling and microsecond molecular simulations of the SARS-CoV-2 Spike complexes with the host receptor ACE2 for XBB.1.5+L455F, XBB.1.5+F456L(EG.5) and XBB.1.5+L455F/F456L (FLip) lineages to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and physics-based rigorous computations of binding affinities, we identified binding energy hotspots and characterized molecular basis underlying epistatic couplings between convergent mutational hotspots. Consistent with the experiments, the results revealed the mediating role of Q493 hotspot in synchronization of epistatic couplings between L455F and F456L mutations providing a quantitative insight into the mechanism underlying differences between XBB lineages. Mutational profiling is combined with network-based model of epistatic couplings showing that the Q493, L455 and F456 sites mediate stable communities at the binding interface with ACE2 and can serve as stable mediators of non-additive couplings. Structure-based mutational analysis of Spike protein binding with the class 1 antibodies quantified the critical role of F456L and F486P mutations in eliciting strong immune evasion response. The results of this analysis support a mechanism in which the emergence of EG.5 and FLip variants may have been dictated by leveraging strong epistatic effects between several convergent revolutionary hotspots that provide synergy between the improved ACE2 binding and broad neutralization resistance. This interpretation is consistent with the notion that functionally balanced substitutions which simultaneously optimize immune evasion and high ACE2 affinity may continue to emerge through lineages with beneficial pair or triplet combinations of RBD mutations involving mediators of epistatic couplings and sites in highly adaptable RBD regions.
Collapse
|
49
|
Kibria MG, Lavine CL, Tang W, Wang S, Gao H, Shi W, Zhu H, Voyer J, Rits‐Volloch S, Keerti, Bi C, Peng H, Wesemann DR, Lu J, Xie H, Seaman MS, Chen B. Antibody-mediated SARS-CoV-2 entry in cultured cells. EMBO Rep 2023; 24:e57724. [PMID: 38277394 PMCID: PMC10702815 DOI: 10.15252/embr.202357724] [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: 06/27/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 01/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells by first engaging its cellular receptor angiotensin converting enzyme 2 (ACE2) to induce conformational changes in the virus-encoded spike protein and fusion between the viral and target cell membranes. Here, we report that certain monoclonal neutralizing antibodies against distinct epitopic regions of the receptor-binding domain of the spike can replace ACE2 to serve as a receptor and efficiently support membrane fusion and viral infectivity in vitro. These receptor-like antibodies can function in the form of a complex of their soluble immunoglobulin G with Fc-gamma receptor I, a chimera of their antigen-binding fragment with the transmembrane domain of ACE2 or a membrane-bound B cell receptor, indicating that ACE2 and its specific interaction with the spike protein are dispensable for SARS-CoV-2 entry. These results suggest that antibody responses against SARS-CoV-2 may help expand the viral tropism to otherwise nonpermissive cell types with potential implications for viral transmission and pathogenesis.
Collapse
Affiliation(s)
- Md Golam Kibria
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| | - Christy L Lavine
- Center for Virology and Vaccine ResearchBeth Israel Deaconess Medical CenterBostonMAUSA
| | - Weichun Tang
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMDUSA
| | | | - Hailong Gao
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| | - Wei Shi
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of MedicineBostonMAUSA
| | - Jewel Voyer
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
| | | | - Keerti
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's HospitalRagon Institute of MGH, MIT and HarvardBostonMAUSA
| | - Caihong Bi
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's HospitalRagon Institute of MGH, MIT and HarvardBostonMAUSA
| | - Hanqin Peng
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
| | - Duane R Wesemann
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's HospitalRagon Institute of MGH, MIT and HarvardBostonMAUSA
| | - Jianming Lu
- Codex BioSolutions, Inc.RockvilleMDUSA
- Department of Biochemistry and Molecular and Cellular BiologyGeorgetown UniversityWashingtonDCUSA
| | - Hang Xie
- Laboratory of Pediatric and Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMDUSA
| | - Michael S Seaman
- Center for Virology and Vaccine ResearchBeth Israel Deaconess Medical CenterBostonMAUSA
| | - Bing Chen
- Division of Molecular MedicineBoston Children's HospitalBostonMAUSA
- Department of PediatricsHarvard Medical SchoolBostonMAUSA
| |
Collapse
|
50
|
Park C, Hwang IY, Yan SLS, Vimonpatranon S, Wei D, Van Ryk D, Girard A, Cicala C, Arthos J, Kehrl JH. Murine Alveolar Macrophages Rapidly Accumulate Intranasally Administered SARS-CoV-2 Spike Protein leading to Neutrophil Recruitment and Damage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532446. [PMID: 37090605 PMCID: PMC10120727 DOI: 10.1101/2023.03.13.532446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The trimeric SARS-CoV-2 Spike protein mediates viral attachment facilitating cell entry. Most COVID-19 vaccines direct mammalian cells to express the Spike protein or deliver it directly via inoculation to engender a protective immune response. The trafficking and cellular tropism of the Spike protein in vivo and its impact on immune cells remains incompletely elucidated. In this study we inoculated mice intranasally, intravenously, and subcutaneously with fluorescently labeled recombinant SARS-CoV-2 Spike protein. Using flow cytometry and imaging techniques we analyzed its localization, immune cell tropism, and acute functional impact. Intranasal administration led to rapid lung alveolar macrophage uptake, pulmonary vascular leakage, and neutrophil recruitment and damage. When injected near the inguinal lymph node medullary, but not subcapsular macrophages, captured the protein, while scrotal injection recruited and fragmented neutrophils. Wide-spread endothelial and liver Kupffer cell uptake followed intravenous administration. Human peripheral blood cells B cells, neutrophils, monocytes, and myeloid dendritic cells all efficiently bound Spike protein. Exposure to the Spike protein enhanced neutrophil NETosis and augmented human macrophage TNF-α and IL-6 production. Human and murine immune cells employed C-type lectin receptors and Siglecs to help capture the Spike protein. This study highlights the potential toxicity of the SARS-CoV-2 Spike protein for mammalian cells and illustrates the central role for alveolar macrophage in pathogenic protein uptake.
Collapse
Affiliation(s)
- Chung Park
- B-cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Il-Young Hwang
- B-cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Serena Li-Sue Yan
- B-cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Sinmanus Vimonpatranon
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences – United States Component, Bangkok, Thailand
| | - Danlan Wei
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Don Van Ryk
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Alexandre Girard
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Claudia Cicala
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - James Arthos
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - John H. Kehrl
- B-cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| |
Collapse
|