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Sarker A, Dhama N, Gupta RD. Dengue virus neutralizing antibody: a review of targets, cross-reactivity, and antibody-dependent enhancement. Front Immunol 2023; 14:1200195. [PMID: 37334355 PMCID: PMC10272415 DOI: 10.3389/fimmu.2023.1200195] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/19/2023] [Indexed: 06/20/2023] Open
Abstract
Dengue is the most common viral infection spread by mosquitoes, prevalent in tropical countries. The acute dengue virus (DENV) infection is a benign and primarily febrile illness. However, secondary infection with alternative serotypes can worsen the condition, leading to severe and potentially fatal dengue. The antibody raised by the vaccine or the primary infections are frequently cross-reactive; however, weakly neutralizing, and during subsequent infection, they may increase the odds of antibody-dependent enhancement (ADE). Despite that, many neutralizing antibodies have been identified against the DENV, which are thought to be useful in reducing dengue severity. Indeed, an antibody must be free from ADE for therapeutic application, as it is pretty common in dengue infection and escalates disease severity. Therefore, this review has described the critical characteristics of DENV and the potential immune targets in general. The primary emphasis is given to the envelope protein of DENV, where potential epitopes targeted for generating serotype-specific and cross-reactive antibodies have critically been described. In addition, a novel class of highly neutralizing antibodies targeted to the quaternary structure, similar to viral particles, has also been described. Lastly, we have discussed different aspects of the pathogenesis and ADE, which would provide significant insights into developing safe and effective antibody therapeutics and equivalent protein subunit vaccines.
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Meng JX, Hu QM, Zhang LM, Li N, He YW, Yang ZX, Sun Y, Wang JL. Isolation and Genetic Evolution of Dengue Virus from the 2019 Outbreak in Xishuangbanna, Yunnan Province, China. Vector Borne Zoonotic Dis 2023. [PMID: 37184906 DOI: 10.1089/vbz.2022.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Background: Dengue virus (DENV) can be divided into four serotypes-DENV-1, DENV-2, DENV-3, and DENV-4. In humans, infection leads to dengue fever (DF), dengue hemorrhagic fever, and dengue shock syndrome, both widely prevalent in tropical and subtropical regions. In 2019, a severe outbreak of DF occurred in Xishuangbanna, Yunnan province. Objective: To investigate the etiology and genotype of the causative agents of this severe dengue outbreak in Xishuangbanna. Methods: Between October and November 2019, the sera of patients clinically diagnosed with DF were collected in the first People's Hospital of Xishuangbanna. RNA was extracted from the sera and amplified by RT-PCR with flavivirus primers. Flavivirus-positive sera were then used to inoculate Aedes albopictus cells (C6/36); viral RNA was extracted from these cells, amplified, and sequenced with DENV E gene-specific primers. Sequence splicing and nucleotide homology genetic evolution analysis were carried out by biological software (DNAStar). Unique mutations in the E genes of isolated DENV were analyzed by SWISS-MODEL and PyMOL. Results: Of the 60 samples collected from DF patients, 39 tested positively with flavivirus primers. The DENV was isolated from 25 of the 39 positive seras, of which 20 showed cytopathic effects (CPE) and 5 were no CPE. In these 25 isolated nucleic acids, 21 strains of DENV-1, 3 strains of DENV-2, and 1 strain of DENV-3 were identified according to the sequence of E protein. In the four unique mutations (D52, Y149, L312, T386), D52 and Y149 in the E protein of DENV-1 were predicted to be exposed on the surface of the prefusion conformation. Conclusion: The 2019 outbreak of DF in Xishuangbanna area of Yunnan Province consists of at least three serotypes of DENV-1, DENV-2, and DENV-3, and the sources of these virus strains are of mixed and complicated origin.
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Affiliation(s)
- Jin-Xin Meng
- Yunnan Tropical and Subtropical Animal Virus Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Qiu-Ming Hu
- People's Hospital of Jinghong City, Jinghong, China
| | - Li-Ming Zhang
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Nan Li
- Yunnan Tropical and Subtropical Animal Virus Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yu-Wen He
- Yunnan Tropical and Subtropical Animal Virus Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Zhen-Xing Yang
- Yunnan Tropical and Subtropical Animal Virus Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yi Sun
- The First People's Hospital of Yunnan Province, Kunming, China
| | - Jing-Lin Wang
- Yunnan Tropical and Subtropical Animal Virus Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming, China
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3
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Monoclonal antibody therapeutics for infectious diseases: Beyond normal human immunoglobulin. Pharmacol Ther 2022; 240:108233. [PMID: 35738431 PMCID: PMC9212443 DOI: 10.1016/j.pharmthera.2022.108233] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/30/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022]
Abstract
Antibody therapy is effective for treating infectious diseases. Due to the coronavirus disease 2019 (COVID-19) pandemic and the rise of drug-resistant bacteria, rapid development of neutralizing monoclonal antibodies (mAbs) to treat infectious diseases is urgently needed. Using a therapeutic human mAb with the lowest immunogenicity is recommended, because chimera and humanized mAbs are occasionally immunogenic. In order to directly obtain naïve human mAbs, there are three methods: phage display, B cell receptor (BCR) cDNA sequencing of a single cell, and antibody-encoding gene and amino acid sequencing of immortalized cells using memory B cells, which are isolated from human peripheral blood mononuclear cells of healthy, vaccinated, infected, or recovered individuals. After screening against the antigen and performing neutralization assays, a human neutralizing mAb is constructed from the antibody-encoding DNA sequences of these memory B cells. This review describes examples of obtaining human neutralizing mAbs against various infectious diseases using these methods. However, a few of these mAbs have been approved for therapy. Therefore, antigen characterization and evaluation of neutralization activity in vitro and in vivo are indispensable for the development of therapeutic mAbs. These results will accelerate the development of antibody drug as therapeutic agents.
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4
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Generation of soluble, cleaved, well-ordered, native-like dimers of dengue virus 4 envelope protein ectodomain (sE) suitable for vaccine immunogen design. Int J Biol Macromol 2022; 217:19-26. [PMID: 35817240 DOI: 10.1016/j.ijbiomac.2022.07.028] [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: 09/03/2021] [Revised: 11/12/2021] [Accepted: 07/04/2022] [Indexed: 11/24/2022]
Abstract
Dengue virus is transmitted by Aedes mosquitoes and dengue is endemic in many regions of the world. Severe dengue results in complications that may lead to death. Although some vaccine candidates are in clinical trials and one vaccine Dengvaxia, with restricted efficacy, is available, there are currently no specific therapies to completely prevent or treat dengue. The dengue virus structural protein E (envelope) exists as a head-to-tail dimer on mature virus, is targeted by broadly neutralizing antibodies and is suitable for developing vaccine immunogens. Here, we have used a redesigned dengue prME expression construct and immunoaffinity chromatography with conformational/quaternary antibody A11 to purify soluble DENV4 sE(A259C) (E ectodomain) dimers from mammalian expression system to ~99 % purity. These dimers retain glycosylation reported for native DENV E, display the three major broadly neutralizing antibody epitopes, and form well-ordered structure. This strategy can be used for developing subunit vaccine candidates against dengue and other flaviviruses.
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Hou J, Ye W, Chen J. Current Development and Challenges of Tetravalent Live-Attenuated Dengue Vaccines. Front Immunol 2022; 13:840104. [PMID: 35281026 PMCID: PMC8907379 DOI: 10.3389/fimmu.2022.840104] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/03/2022] [Indexed: 01/26/2023] Open
Abstract
Dengue is the most common arboviral disease caused by one of four distinct but closely related dengue viruses (DENV) and places significant economic and public health burdens in the endemic areas. A dengue vaccine will be important in advancing disease control. However, the effort has been challenged by the requirement to induce effective protection against all four DENV serotypes and the potential adverse effect due to the phenomenon that partial immunity to DENV may worsen the symptoms upon subsequent heterotypic infection. Currently, the most advanced dengue vaccines are all tetravalent and based on recombinant live attenuated viruses. CYD-TDV, developed by Sanofi Pasteur, has been approved but is limited for use in individuals with prior dengue infection. Two other tetravalent live attenuated vaccine candidates: TAK-003 by Takeda and TV003 by National Institute of Allergy and Infectious Diseases, have completed phase 3 and phase 2 clinical trials, respectively. This review focuses on the designs and evaluation of TAK-003 and TV003 vaccine candidates in humans in comparison to the licensed CYD-TDV vaccine. We highlight specific lessons from existing studies and challenges that must be overcome in order to develop a dengue vaccine that confers effective and balanced protection against all four DENV serotypes but with minimal adverse effects.
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Affiliation(s)
- Jue Hou
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology (SMART), Singapore, Singapore
| | - Weijian Ye
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology (SMART), Singapore, Singapore
| | - Jianzhu Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology (SMART), Singapore, Singapore.,Department of Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
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6
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Yu Y, Si L, Meng Y. Flavivirus Entry Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:171-197. [PMID: 35412141 DOI: 10.1007/978-981-16-8702-0_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Flaviviruses, including Dengue virus, Zika virus, Yellow fever virus, Japanese encephalitis virus, West Nile virus, cause thousands of deaths and millions of illnesses each year. The large outbreak of ZIKV in 2016 reminds us that flaviviruses can pose a serious threat to human safety and public health as emerging and re-emerging viruses. However, there are no specific drugs approved for the treatment of flavivirus infections. Due to no need to enter the cells, viral entry inhibitors have the unique advantage in suppressing viral infections. Flaviviruses bind to receptors and attach to the cell surface, then enter the endosome in a clathrin-dependent manner and finalizes the viral entry process after fusion with the cell membrane in a low pH environment. Small molecules, antibodies or peptides can inhibit flavivirus entry by targeting the above processes. Here, we focus on flavivirus entry inhibitors with well-defined target and antiviral activity. We hope that our review will provide a theoretical basis for flavivirus treatment and drug research and help to accelerate the clinical application of flavivirus entry inhibitors.
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Affiliation(s)
- Yufeng Yu
- Medical School, Nanjing University, Nanjing, Jiangsu, China.
| | - Lulu Si
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yu Meng
- Department of Microbiology and Immunology, College of Basic Medical Sciences, Dali University, Dali, Yunnan, China
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7
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Charged Residue Implantation Improves the Affinity of a Cross-Reactive Dengue Virus Antibody. Int J Mol Sci 2022; 23:ijms23084197. [PMID: 35457015 PMCID: PMC9027083 DOI: 10.3390/ijms23084197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 11/23/2022] Open
Abstract
Dengue virus (DENV) has four serotypes that complicate vaccine development. Envelope protein domain III (EDIII) of DENV is a promising target for therapeutic antibody development. One EDIII-specific antibody, dubbed 1A1D-2, cross-reacts with DENV 1, 2, and 3 but not 4. To improve the affinity of 1A1D-2, in this study, we analyzed the previously solved structure of 1A1D-2-DENV2 EDIII complex. Mutations were designed, including A54E and Y105R in the heavy chain, with charges complementary to the epitope. Molecular dynamics simulation was then used to validate the formation of predicted salt bridges. Interestingly, a surface plasmon resonance experiment showed that both mutations increased affinities of 1A1D-2 toward EDIII of DENV1, 2, and 3 regardless of their sequence variation. Results also revealed that A54E improved affinities through both a faster association and slower dissociation, whereas Y105R improved affinities through a slower dissociation. Further simulation suggested that the same mutants interacted with different residues in different serotypes. Remarkably, combination of the two mutations additively improved 1A1D-2 affinity by 8, 36, and 13-fold toward DENV1, 2, and 3, respectively. In summary, this study demonstrated the utility of tweaking antibody-antigen charge complementarity for affinity maturation and emphasized the complexity of improving antibody affinity toward multiple antigens.
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8
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A novel and effective approach to generate germline-like monoclonal antibodies by integration of phage and mammalian cell display platforms. Acta Pharmacol Sin 2022; 43:954-962. [PMID: 34234269 PMCID: PMC8975860 DOI: 10.1038/s41401-021-00707-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Phage display technology allows for rapid selection of antibodies from the large repertoire of human antibody fragments displayed on phages. However, antibody fragments should be converted to IgG for biological characterizations and affinity of antibodies obtained from phage display library is frequently not sufficient for efficient use in clinical settings. Here, we describe a new approach that combines phage and mammalian cell display, enabling simultaneous affinity screening of full-length IgG antibodies. Using this strategy, we successfully obtained a novel germline-like anti-TIM-3 monoclonal antibody named m101, which was revealed to be a potent anti-TIM-3 therapeutic monoclonal antibody via in vitro and in vivo experiments, indicating its effectiveness and power. Thus, this platform can help develop new monoclonal antibody therapeutics with high affinity and low immunogenicity.
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9
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Santiago HC, Pereira-Neto TA, Gonçalves-Pereira MH, Terzian ACB, Durbin AP. Peculiarities of Zika Immunity and Vaccine Development: Lessons from Dengue and the Contribution from Controlled Human Infection Model. Pathogens 2022; 11:pathogens11030294. [PMID: 35335618 PMCID: PMC8951202 DOI: 10.3390/pathogens11030294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 01/27/2023] Open
Abstract
The Zika virus (ZIKV) was first isolated from a rhesus macaque in the Zika forest of Uganda in 1947. Isolated cases were reported until 2007, when the first major outbreaks of Zika infection were reported from the Island of Yap in Micronesia and from French Polynesia in 2013. In 2015, ZIKV started to circulate in Latin America, and in 2016, ZIKV was considered by WHO to be a Public Health Emergency of International Concern due to cases of Congenital Zika Syndrome (CZS), a ZIKV-associated complication never observed before. After a peak of cases in 2016, the infection incidence dropped dramatically but still causes concern because of the associated microcephaly cases, especially in regions where the dengue virus (DENV) is endemic and co-circulates with ZIKV. A vaccine could be an important tool to mitigate CZS in endemic countries. However, the immunological relationship between ZIKV and other flaviviruses, especially DENV, and the low numbers of ZIKV infections are potential challenges for developing and testing a vaccine against ZIKV. Here, we discuss ZIKV vaccine development with the perspective of the immunological concerns implicated by DENV-ZIKV cross-reactivity and the use of a controlled human infection model (CHIM) as a tool to accelerate vaccine development.
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Affiliation(s)
- Helton C. Santiago
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 30270-901, MG, Brazil; (T.A.P.-N.); (M.H.G.-P.)
- Correspondence: ; Tel.: +55-31-3409-2664
| | - Tertuliano A. Pereira-Neto
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 30270-901, MG, Brazil; (T.A.P.-N.); (M.H.G.-P.)
| | - Marcela H. Gonçalves-Pereira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 30270-901, MG, Brazil; (T.A.P.-N.); (M.H.G.-P.)
| | - Ana C. B. Terzian
- Laboratory of Cellular Immunology, Rene Rachou Institute, Fiocruz, Belo Horizonte 30190-002, MG, Brazil;
| | - Anna P. Durbin
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA;
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10
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Anasir MI, Poh CL. Discovery of B-cell epitopes for development of dengue vaccines and antibody therapeutics. Med Microbiol Immunol 2022; 211:1-18. [PMID: 35059822 DOI: 10.1007/s00430-021-00726-1] [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: 07/21/2021] [Accepted: 12/04/2021] [Indexed: 10/19/2022]
Abstract
Dengue is one of the most frequently transmitted viral infections globally which creates a serious burden to the healthcare system in many countries in the tropical and subtropical regions. To date, no vaccine has demonstrated balanced protection against the four dengue serotypes. Dengvaxia as the only vaccine that has been licensed for use in endemic areas has shown an increased risk in dengue-naïve vaccines to develop severe dengue. A crucial element in protection from dengue infection is the neutralizing antibody responses. Therefore, the identification of protective linear B-cell epitopes can guide vaccine design and facilitate the development of monoclonal antibodies as dengue therapeutics. This review summarizes the identification of dengue B-cell epitopes within the envelope (E) protein of dengue that can be incorporated into peptide vaccine constructs. These epitopes have been identified through approaches such as bioinformatics, three-dimensional structure analysis of antibody-dengue complexes, mutagenesis/alanine scanning and escape mutant studies. Additionally, the therapeutic potential of monoclonal antibodies targeting the E protein of dengue is reviewed. This can provide a basis for the design of future dengue therapies.
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Affiliation(s)
- Mohd Ishtiaq Anasir
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Shah Alam, Selangor, Malaysia
- Centre for Virus and Vaccine Research, Sunway University, 5, Jalan Universiti, 47500, Bandar Sunway, Selangor, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, Sunway University, 5, Jalan Universiti, 47500, Bandar Sunway, Selangor, Malaysia.
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11
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Murin CD, Gilchuk P, Crowe JE, Ward AB. Structural Biology Illuminates Molecular Determinants of Broad Ebolavirus Neutralization by Human Antibodies for Pan-Ebolavirus Therapeutic Development. Front Immunol 2022; 12:808047. [PMID: 35082794 PMCID: PMC8784787 DOI: 10.3389/fimmu.2021.808047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 01/13/2023] Open
Abstract
Monoclonal antibodies (mAbs) have proven effective for the treatment of ebolavirus infection in humans, with two mAb-based drugs Inmazeb™ and Ebanga™ receiving FDA approval in 2020. While these drugs represent a major advance in the field of filoviral therapeutics, they are composed of antibodies with single-species specificity for Zaire ebolavirus. The Ebolavirus genus includes five additional species, two of which, Bundibugyo ebolavirus and Sudan ebolavirus, have caused severe disease and significant outbreaks in the past. There are several recently identified broadly neutralizing ebolavirus antibodies, including some in the clinical development pipeline, that have demonstrated broad protection in preclinical studies. In this review, we describe how structural biology has illuminated the molecular basis of broad ebolavirus neutralization, including details of common antigenic sites of vulnerability on the glycoprotein surface. We begin with a discussion outlining the history of monoclonal antibody therapeutics for ebolaviruses, with an emphasis on how structural biology has contributed to these efforts. Next, we highlight key structural studies that have advanced our understanding of ebolavirus glycoprotein structures and mechanisms of antibody-mediated neutralization. Finally, we offer examples of how structural biology has contributed to advances in anti-viral medicines and discuss what opportunities the future holds, including rationally designed next-generation therapeutics with increased potency, breadth, and specificity against ebolaviruses.
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MESH Headings
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antiviral Agents/immunology
- Antiviral Agents/therapeutic use
- Drug Combinations
- Ebolavirus/drug effects
- Ebolavirus/immunology
- Ebolavirus/physiology
- Epitopes/chemistry
- Epitopes/immunology
- Glycoproteins/chemistry
- Glycoproteins/immunology
- Hemorrhagic Fever, Ebola/drug therapy
- Hemorrhagic Fever, Ebola/immunology
- Hemorrhagic Fever, Ebola/virology
- Humans
- Models, Molecular
- Protein Domains/immunology
- Viral Proteins/chemistry
- Viral Proteins/immunology
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Affiliation(s)
- Charles D. Murin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
| | - Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States
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12
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Carrara SC, Bogen JP, Grzeschik J, Hock B, Kolmar H. Antibody Library Screening Using Yeast Biopanning and Fluorescence-Activated Cell Sorting. Methods Mol Biol 2022; 2491:177-193. [PMID: 35482191 DOI: 10.1007/978-1-0716-2285-8_10] [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] [Indexed: 06/14/2023]
Abstract
Yeast surface display (YSD) emerged as a prominent screening methodology for the isolation of monoclonal antibodies (mAbs) against various antigens. However, phage display remains the gold standard in cell panning-based screenings to isolate mAbs against difficult-to-screen targets, such as G-protein coupled receptors (GPCR) and ion channels. Herein we describe a step-by-step protocol to establish and perform the isolation of mAbs using YSD in a fluorescence-activated cell sorting (FACS)-assisted biopanning manner, yielding a variety of antibodies binding their antigen with high affinity in the natural environment of the cell. Upon mixing antibody-displaying yeast cells with antigen-displaying mammalian cells, complexes are specifically formed and isolated for enrichment of yeast cells encoding binders against the antigen. The utilization of mammalian cells expressing the respective target accounts for accessibility of the epitope and the correct conformation of the antigen. Furthermore, critical characterization methods mandatory for this kind of antibodies are illuminated.
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Affiliation(s)
- Stefania C Carrara
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Jan P Bogen
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Julius Grzeschik
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Björn Hock
- Ferring International Center S.A., Saint-Prex, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
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13
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Linciano S, Wong EL, Mazzocato Y, Chinellato M, Scaravetti T, Caregnato A, Cacco V, Romanyuk Z, Angelini A. Guidelines, Strategies, and Principles for the Directed Evolution of Cross-Reactive Antibodies Using Yeast Surface Display Technology. Methods Mol Biol 2022; 2491:251-262. [PMID: 35482195 DOI: 10.1007/978-1-0716-2285-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The ability of cross-reactive antibodies to bind multiple related or unrelated targets derived from different species provides not only superior therapeutic efficacy but also a better assessment of treatment toxicity, thereby facilitating the transition from preclinical models to human clinical studies. This chapter provides some guidelines for the directed evolution of cross-reactive antibodies using yeast surface display technology. Cross-reactive antibodies are initially isolated from a naïve library by combining highly avid magnetic bead separations followed by multiple cycles of flow cytometry sorting. Once initial cross-reactive clones are identified, sequential rounds of mutagenesis and two-pressure selection strategies are applied to engineer cross-reactive antibodies with improved affinity and yet retained or superior cross-reactivity.
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Affiliation(s)
- Sara Linciano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ee Lin Wong
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Ylenia Mazzocato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Monica Chinellato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
- Department of Medicine (DIMED), University of Padua, Padua, Italy
| | - Tiziano Scaravetti
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alberto Caregnato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Veronica Cacco
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Zhanna Romanyuk
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Mestre, Italy.
- European Centre for Living Technology (ECLT), Ca' Bottacin, Venice, Italy.
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14
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Horst A, Smakaj E, Natali EN, Tosoni D, Babrak LM, Meier P, Miho E. Machine Learning Detects Anti-DENV Signatures in Antibody Repertoire Sequences. Front Artif Intell 2021; 4:715462. [PMID: 34708197 PMCID: PMC8542978 DOI: 10.3389/frai.2021.715462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Dengue infection is a global threat. As of today, there is no universal dengue fever treatment or vaccines unreservedly recommended by the World Health Organization. The investigation of the specific immune response to dengue virus would support antibody discovery as therapeutics for passive immunization and vaccine design. High-throughput sequencing enables the identification of the multitude of antibodies elicited in response to dengue infection at the sequence level. Artificial intelligence can mine the complex data generated and has the potential to uncover patterns in entire antibody repertoires and detect signatures distinctive of single virus-binding antibodies. However, these machine learning have not been harnessed to determine the immune response to dengue virus. In order to enable the application of machine learning, we have benchmarked existing methods for encoding biological and chemical knowledge as inputs and have investigated novel encoding techniques. We have applied different machine learning methods such as neural networks, random forests, and support vector machines and have investigated the parameter space to determine best performing algorithms for the detection and prediction of antibody patterns at the repertoire and antibody sequence levels in dengue-infected individuals. Our results show that immune response signatures to dengue are detectable both at the antibody repertoire and at the antibody sequence levels. By combining machine learning with phylogenies and network analysis, we generated novel sequences that present dengue-binding specific signatures. These results might aid further antibody discovery and support vaccine design.
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Affiliation(s)
- Alexander Horst
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Erand Smakaj
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Eriberto Noel Natali
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Deniz Tosoni
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Lmar Marie Babrak
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Patrick Meier
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Enkelejda Miho
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,aiNET GmbH, Basel, Switzerland
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15
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Near-germline human monoclonal antibodies neutralize and protect against multiple arthritogenic alphaviruses. Proc Natl Acad Sci U S A 2021; 118:2100104118. [PMID: 34507983 DOI: 10.1073/pnas.2100104118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 12/11/2022] Open
Abstract
Arthritogenic alphaviruses are globally distributed, mosquito-transmitted viruses that cause rheumatological disease in humans and include Chikungunya virus (CHIKV), Mayaro virus (MAYV), and others. Although serological evidence suggests that some antibody-mediated heterologous immunity may be afforded by alphavirus infection, the extent to which broadly neutralizing antibodies that protect against multiple arthritogenic alphaviruses are elicited during natural infection remains unknown. Here, we describe the isolation and characterization of MAYV-reactive alphavirus monoclonal antibodies (mAbs) from a CHIKV-convalescent donor. We characterized 33 human mAbs that cross-reacted with CHIKV and MAYV and engaged multiple epitopes on the E1 and E2 glycoproteins. We identified five mAbs that target distinct regions of the B domain of E2 and potently neutralize multiple alphaviruses with differential breadth of inhibition. These broadly neutralizing mAbs (bNAbs) contain few somatic mutations and inferred germline-revertants retained neutralizing capacity. Two bNAbs, DC2.M16 and DC2.M357, protected against both CHIKV- and MAYV-induced musculoskeletal disease in mice. These findings enhance our understanding of the cross-reactive and cross-protective antibody response to human alphavirus infections.
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16
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Kotaki T, Kurosu T, Grinyo-Escuer A, Davidson E, Churrotin S, Okabayashi T, Puiprom O, Mulyatno KC, Sucipto TH, Doranz BJ, Ono KI, Soegijanto S, Kameoka M. An affinity-matured human monoclonal antibody targeting fusion loop epitope of dengue virus with in vivo therapeutic potency. Sci Rep 2021; 11:12987. [PMID: 34155267 PMCID: PMC8217507 DOI: 10.1038/s41598-021-92403-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 06/08/2021] [Indexed: 11/26/2022] Open
Abstract
Dengue virus (DENV), from the genus flavivirus of the family flaviviridae, causes serious health problems globally. Human monoclonal antibodies (HuMAb) can be used to elucidate the mechanisms of neutralization and antibody-dependent enhancement (ADE) of DENV infections, leading to the development of a vaccine or therapeutic antibodies. Here, we generated eight HuMAb clones from an Indonesian patient infected with DENV. These HuMAbs exhibited the typical characteristics of weak neutralizing antibodies including high cross-reactivity with other flaviviruses and targeting of the fusion loop epitope (FLE). However, one of the HuMAbs, 3G9, exhibited strong neutralization (NT50 < 0.1 μg/ml) and possessed a high somatic hyper-mutation rate of the variable region, indicating affinity-maturation. Administration of this antibody significantly prolonged the survival of interferon-α/β/γ receptor knockout C57BL/6 mice after a lethal DENV challenge. Additionally, Fc-modified 3G9 that had lost their in vitro ADE activity showed enhanced therapeutic potency in vivo and competed strongly with an ADE-prone antibody in vitro. Taken together, the affinity-matured FLE-targeting antibody 3G9 exhibits promising features for therapeutic application including a low NT50 value, potential for treatment of various kinds of mosquito-borne flavivirus infection, and suppression of ADE. This study demonstrates the therapeutic potency of affinity-matured FLE-targeting antibodies.
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Affiliation(s)
- Tomohiro Kotaki
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan.
- Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia.
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
| | - Takeshi Kurosu
- Department of Virology I, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | | | | | - Siti Churrotin
- Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Tamaki Okabayashi
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Orapim Puiprom
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kris Cahyo Mulyatno
- Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Teguh Hari Sucipto
- Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | | | - Ken-Ichiro Ono
- Medical & Biological Laboratories Co., Ltd., Tokyo, Japan
| | - Soegeng Soegijanto
- Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Masanori Kameoka
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan.
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17
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Natali EN, Babrak LM, Miho E. Prospective Artificial Intelligence to Dissect the Dengue Immune Response and Discover Therapeutics. Front Immunol 2021; 12:574411. [PMID: 34211454 PMCID: PMC8239437 DOI: 10.3389/fimmu.2021.574411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Dengue virus (DENV) poses a serious threat to global health as the causative agent of dengue fever. The virus is endemic in more than 128 countries resulting in approximately 390 million infection cases each year. Currently, there is no approved therapeutic for treatment nor a fully efficacious vaccine. The development of therapeutics is confounded and hampered by the complexity of the immune response to DENV, in particular to sequential infection with different DENV serotypes (DENV1-5). Researchers have shown that the DENV envelope (E) antigen is primarily responsible for the interaction and subsequent invasion of host cells for all serotypes and can elicit neutralizing antibodies in humans. The advent of high-throughput sequencing and the rapid advancements in computational analysis of complex data, has provided tools for the deconvolution of the DENV immune response. Several types of complex statistical analyses, machine learning models and complex visualizations can be applied to begin answering questions about the B- and T-cell immune responses to multiple infections, antibody-dependent enhancement, identification of novel therapeutics and advance vaccine research.
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Affiliation(s)
- Eriberto N. Natali
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Lmar M. Babrak
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
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18
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Larson PA, Bartlett ML, Garcia K, Chitty J, Balkema-Buschmann A, Towner J, Kugelman J, Palacios G, Sanchez-Lockhart M. Genomic features of humoral immunity support tolerance model in Egyptian rousette bats. Cell Rep 2021; 35:109140. [PMID: 34010652 DOI: 10.1016/j.celrep.2021.109140] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 10/08/2020] [Accepted: 04/26/2021] [Indexed: 01/05/2023] Open
Abstract
Bats asymptomatically harbor many viruses that can cause severe human diseases. The Egyptian rousette bat (ERB) is the only known reservoir for Marburgviruses and Sosuga virus, making it an exceptional animal model to study antiviral mechanisms in an asymptomatic host. With this goal in mind, we constructed and annotated the immunoglobulin heavy chain locus, finding an expansion on immunoglobulin variable genes associated with protective human antibodies to different viruses. We also annotated two functional and distinct immunoglobulin epsilon genes and four distinctive functional immunoglobulin gamma genes. We described the Fc receptor repertoire in ERBs, including features that may affect activation potential, and discovered the lack of evolutionary conserved short pentraxins. These findings reinforce the hypothesis that a differential threshold of regulation and/or absence of key immune mediators may promote tolerance and decrease inflammation in ERBs.
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Affiliation(s)
- Peter A Larson
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Maggie L Bartlett
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Karla Garcia
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Joseph Chitty
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | | | - Jonathan Towner
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jeffrey Kugelman
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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19
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Zhu X, Yu F, Wu Y, Ying T. Potent germline-like monoclonal antibodies: rapid identification of promising candidates for antibody-based antiviral therapy. Antib Ther 2021; 4:89-98. [PMID: 34104872 PMCID: PMC8178282 DOI: 10.1093/abt/tbab008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/14/2021] [Indexed: 11/20/2022] Open
Abstract
In recent years, fully human monoclonal antibodies (mAbs) are making up an increasing share of the pharmaceutical market. However, to improve affinity and efficacy of antibodies, many somatic hypermutations could be introduced during affinity maturation, which cause several issues including safety and efficacy and limit their application in clinic. Here, we propose a special class of human mAbs with limited level of somatic mutations, referred to as germline-like mAbs. Remarkably, germline-like mAbs could have high affinity and potent neutralizing activity in vitro and in various animal models, despite lacking of extensive affinity maturation. Furthermore, the germline nature of these mAbs implies that they exhibit lower immunogenicity and can be elicited relatively fast in vivo compared with highly somatically mutated antibodies. In this review, we summarize germline-like mAbs with strong therapeutic and protection activity against various viruses that caused large-scale outbreaks in the last decade, including influenza virus H7N9, Zika virus, Dengue virus, Middle East respiratory syndrome coronavirus and severe acute respiratory syndrome coronavirus 2. We also illustrate underlying molecular mechanisms of these germline-like antibodies against viral infections from the structural and genetic perspective, thus providing insight into further development as therapeutic agents for the treatment of infectious diseases and implication for rational design of effective vaccines.
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Affiliation(s)
- Xiaoyi Zhu
- MOE/NHC Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding 071001, China
| | - Yanling Wu
- MOE/NHC Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Tianlei Ying
- MOE/NHC Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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20
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A potent neutralizing mouse monoclonal antibody specific to dengue virus type 1 Mochizuki strain recognized a novel epitope around the N-67 glycan on the envelope protein: A possible explanation of dengue virus evolution regarding the acquisition of N-67 glycan. Virus Res 2020; 294:198278. [PMID: 33388392 DOI: 10.1016/j.virusres.2020.198278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022]
Abstract
The analysis of neutralizing epitope of dengue virus (DENV) is important for the development of an effective dengue vaccine. A potent neutralizing mouse monoclonal antibody named 7F4 was previously reported and, here, we further analyzed the detailed epitope of this antibody. 7F4 recognized a novel conformational epitope close to the N-67 glycan on the envelope protein. This antibody was specific to the DENV that lacks N-67 glycan, including the Mochizuki strain. Interestingly, the Mochizuki strain acquired N-67 glycan by 7F4 selective pressure. Considering that most of the currently circulating DENVs possess N-67 glycan, DENVs may have evolved to escape from antibodies targeting 7F4 epitope, suggesting the potency of this neutralizing epitope. In addition, this study demonstrated the existence of the epitopes close to 7F4 epitope and their crucial role in neutralization. In conclusion, the epitopes close to the N-67 glycan are attractive targets for the dengue vaccine antigen. Further analysis of this epitope is warranted.
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21
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Li W, Chen C, Drelich A, Martinez DR, Gralinski LE, Sun Z, Schäfer A, Kulkarni SS, Liu X, Leist SR, Zhelev DV, Zhang L, Kim YJ, Peterson EC, Conard A, Mellors JW, Tseng CTK, Falzarano D, Baric RS, Dimitrov DS. Rapid identification of a human antibody with high prophylactic and therapeutic efficacy in three animal models of SARS-CoV-2 infection. Proc Natl Acad Sci U S A 2020; 117:29832-29838. [PMID: 33139569 PMCID: PMC7703590 DOI: 10.1073/pnas.2010197117] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Effective therapies are urgently needed for the SARS-CoV-2/COVID-19 pandemic. We identified panels of fully human monoclonal antibodies (mAbs) from large phage-displayed Fab, scFv, and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. A high-affinity Fab was selected from one of the libraries and converted to a full-size antibody, IgG1 ab1, which competed with human ACE2 for binding to RBD. It potently neutralized replication-competent SARS-CoV-2 but not SARS-CoV, as measured by two different tissue culture assays, as well as a replication-competent mouse ACE2-adapted SARS-CoV-2 in BALB/c mice and native virus in hACE2-expressing transgenic mice showing activity at the lowest tested dose of 2 mg/kg. IgG1 ab1 also exhibited high prophylactic and therapeutic efficacy in a hamster model of SARS-CoV-2 infection. The mechanism of neutralization is by competition with ACE2 but could involve antibody-dependent cellular cytotoxicity (ADCC) as IgG1 ab1 had ADCC activity in vitro. The ab1 sequence has a relatively low number of somatic mutations, indicating that ab1-like antibodies could be quickly elicited during natural SARS-CoV-2 infection or by RBD-based vaccines. IgG1 ab1 did not aggregate, did not exhibit other developability liabilities, and did not bind to any of the 5,300 human membrane-associated proteins tested. These results suggest that IgG1 ab1 has potential for therapy and prophylaxis of SARS-CoV-2 infections. The rapid identification (within 6 d of availability of antigen for panning) of potent mAbs shows the value of large antibody libraries for response to public health threats from emerging microbes.
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Affiliation(s)
- Wei Li
- Department of Medicine, Division of Infectious Diseases, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, PA 15261;
| | - Chuan Chen
- Department of Medicine, Division of Infectious Diseases, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, PA 15261
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, Centers for Biodefense and Emerging Diseases, Galveston National Laboratory, Galveston, TX 77550
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Zehua Sun
- Department of Medicine, Division of Infectious Diseases, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, PA 15261
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Swarali S Kulkarni
- Department of Veterinary Microbiology, Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Xianglei Liu
- Department of Medicine, Division of Infectious Diseases, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, PA 15261
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Doncho V Zhelev
- Department of Medicine, Division of Infectious Diseases, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, PA 15261
| | - Liyong Zhang
- Department of Medicine, Division of Infectious Diseases, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, PA 15261
| | - Ye-Jin Kim
- Department of Medicine, Division of Infectious Diseases, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, PA 15261
| | | | | | - John W Mellors
- Department of Medicine, Division of Infectious Diseases, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, PA 15261
- Abound Bio, Pittsburgh, PA 15219
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, Centers for Biodefense and Emerging Diseases, Galveston National Laboratory, Galveston, TX 77550
| | - Darryl Falzarano
- Department of Veterinary Microbiology, Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Dimiter S Dimitrov
- Department of Medicine, Division of Infectious Diseases, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, PA 15261;
- Abound Bio, Pittsburgh, PA 15219
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22
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Mohapatra RK, Pintilie L, Kandi V, Sarangi AK, Das D, Sahu R, Perekhoda L. The recent challenges of highly contagious COVID-19, causing respiratory infections: Symptoms, diagnosis, transmission, possible vaccines, animal models, and immunotherapy. Chem Biol Drug Des 2020. [PMID: 32654267 DOI: 10.1111/cbdd.v96.510.1111/cbdd.13761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
COVID-19 is highly contagious pathogenic viral infection initiated from Wuhan seafood wholesale market of China on December 2019 and spread rapidly around the whole world due to onward transmission. This recent outbreak of novel coronavirus (CoV) was believed to be originated from bats and causing respiratory infections such as common cold, dry cough, fever, headache, dyspnea, pneumonia, and finally Severe Acute Respiratory Syndrome (SARS) in humans. For this widespread zoonotic virus, human-to-human transmission has resulted in nearly 83 lakh cases in 213 countries and territories with 4,50,686 deaths as on 19 June 2020. This review presents a report on the origin, transmission, symptoms, diagnosis, possible vaccines, animal models, and immunotherapy for this novel virus and will provide ample references for the researchers toward the ongoing development of therapeutic agents and vaccines and also preventing the spread of this disease.
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Affiliation(s)
- Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, Odisha, India
| | - Lucia Pintilie
- Department of Synthesis of Bioactive Substances and Pharmaceutical Technologies, National Institute for Chemical and Pharmaceutical Research and Development, Bucharest, Romania
| | - Venkataramana Kandi
- Department of Microbiology, Pratima Institute of Medical Sciences, Karimnagar, Hyderabad, India
| | - Ashish K Sarangi
- Department of Chemistry, School of Applied Sciences, Centurion University of Technology and Management, Odisha, India
| | - Debadutta Das
- Department of Chemistry, Sukanti Degree College, Subarnapur, Odisha, India
| | - Raghaba Sahu
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Lina Perekhoda
- Department of medicinal chemistry, National University of Pharmacy, Kharkiv, Ukraine
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23
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Mohapatra RK, Pintilie L, Kandi V, Sarangi AK, Das D, Sahu R, Perekhoda L. The recent challenges of highly contagious COVID-19, causing respiratory infections: Symptoms, diagnosis, transmission, possible vaccines, animal models, and immunotherapy. Chem Biol Drug Des 2020; 96:1187-1208. [PMID: 32654267 PMCID: PMC7405220 DOI: 10.1111/cbdd.13761] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/20/2020] [Accepted: 06/28/2020] [Indexed: 01/07/2023]
Abstract
COVID-19 is highly contagious pathogenic viral infection initiated from Wuhan seafood wholesale market of China on December 2019 and spread rapidly around the whole world due to onward transmission. This recent outbreak of novel coronavirus (CoV) was believed to be originated from bats and causing respiratory infections such as common cold, dry cough, fever, headache, dyspnea, pneumonia, and finally Severe Acute Respiratory Syndrome (SARS) in humans. For this widespread zoonotic virus, human-to-human transmission has resulted in nearly 83 lakh cases in 213 countries and territories with 4,50,686 deaths as on 19 June 2020. This review presents a report on the origin, transmission, symptoms, diagnosis, possible vaccines, animal models, and immunotherapy for this novel virus and will provide ample references for the researchers toward the ongoing development of therapeutic agents and vaccines and also preventing the spread of this disease.
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Affiliation(s)
| | - Lucia Pintilie
- Department of Synthesis of Bioactive Substances and Pharmaceutical TechnologiesNational Institute for Chemical and Pharmaceutical Research and DevelopmentBucharestRomania
| | - Venkataramana Kandi
- Department of MicrobiologyPratima Institute of Medical SciencesKarimnagarHyderabadIndia
| | - Ashish K. Sarangi
- Department of ChemistrySchool of Applied Sciences, Centurion University of Technology and ManagementOdishaIndia
| | - Debadutta Das
- Department of ChemistrySukanti Degree CollegeSubarnapurOdishaIndia
| | - Raghaba Sahu
- College of PharmacySeoul National UniversitySeoulSouth Korea
| | - Lina Perekhoda
- Department of medicinal chemistryNational University of PharmacyKharkivUkraine
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24
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Bogen JP, Storka J, Yanakieva D, Fiebig D, Grzeschik J, Hock B, Kolmar H. Isolation of Common Light Chain Antibodies from Immunized Chickens Using Yeast Biopanning and Fluorescence-Activated Cell Sorting. Biotechnol J 2020; 16:e2000240. [PMID: 32914549 DOI: 10.1002/biot.202000240] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/31/2020] [Indexed: 12/19/2022]
Abstract
The phylogenetic distance between chickens and humans accounts for a strong immune response and a broader epitope coverage compared to rodent immunization approaches. Here the authors report the isolation of common light chain (cLC)-based chicken monoclonal antibodies from an anti-epidermal growth factor receptor (EGFR) immune library utilizing yeast surface display in combination with yeast biopanning and fluorescence-activated cell sorting (FACS). For the selection of high-affinity antibodies, a yeast cell library presenting cLC-comprising fragment antigen binding (Fab) fragments is panned against hEGFR-overexpressing A431 cells. The resulting cell-cell-complexes are sorted by FACS resulting in gradual enrichment of EGFR-binding Fabs in three sorting rounds. The isolated antibodies share the same light chain and show high specificity for EGFR, resulting in selective binding to A431 cells with notable EC50 values. All identified antibodies show very good aggregation propensity profiles and thermostabilities. Additionally, epitope binning demonstrates that these cLC antibodies cover a broad epitope space. Isolation of antibodies from immunized chickens by yeast cell biopanning makes an addition to the repertoire of methods for antibody library screening, paving the way for the generation of cLC-based bispecific antibodies against native mammalian receptors.
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Affiliation(s)
- Jan P Bogen
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, Darmstadt, D-64287, Germany.,Ferring Darmstadt Laboratory, Biologics Technology and Development, Alarich-Weiss-Straße 4, Darmstadt, D-64287, Germany
| | - Juliana Storka
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, Darmstadt, D-64287, Germany.,Ferring Darmstadt Laboratory, Biologics Technology and Development, Alarich-Weiss-Straße 4, Darmstadt, D-64287, Germany
| | - Desislava Yanakieva
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, Darmstadt, D-64287, Germany
| | - David Fiebig
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, Darmstadt, D-64287, Germany.,Ferring Darmstadt Laboratory, Biologics Technology and Development, Alarich-Weiss-Straße 4, Darmstadt, D-64287, Germany
| | - Julius Grzeschik
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Alarich-Weiss-Straße 4, Darmstadt, D-64287, Germany
| | - Björn Hock
- Ferring International Center S.A., Chemin de la Vergognausaz 50, Saint-Prex, CH-1162, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, Darmstadt, D-64287, Germany
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Valentine KM, Croft M, Shresta S. Protection against dengue virus requires a sustained balance of antibody and T cell responses. Curr Opin Virol 2020; 43:22-27. [PMID: 32798886 PMCID: PMC7655611 DOI: 10.1016/j.coviro.2020.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Pre-existing immunity to dengue virus (DENV) can either protect against or exacerbate, a phenomenon known as antibody dependent enhancement (ADE), a secondary DENV infection. DENV, as an escalating health problem worldwide, has increased the urgency to understand the precise parameters shaping the anti-DENV antibody (Ab) and T cell responses, thereby tipping the balance towards protection versus pathogenesis. Herein, we present the current state of knowledge of about the interplay between the Ab and T cell responses that dictate the outcome of DENV infection and discuss how this newfound knowledge is reshaping strategies for developing safe and effective DENV vaccines.
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Affiliation(s)
- Kristen M Valentine
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Michael Croft
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
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26
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Chen RE, Diamond MS. Dengue mouse models for evaluating pathogenesis and countermeasures. Curr Opin Virol 2020; 43:50-58. [PMID: 32950933 PMCID: PMC7774505 DOI: 10.1016/j.coviro.2020.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/01/2020] [Indexed: 12/14/2022]
Abstract
Dengue virus (DENV) causes the most prevalent arbovirus illness worldwide and is responsible for many debilitating epidemics. The four circulating DENV serotypes infect humans and can cause asymptomatic, mild, moderate, or severe Dengue. Because of the global morbidity and mortality due to Dengue, deployment of a safe and effective tetravalent vaccine has been a high priority, and to date, a partially realized goal. The study of pathogenesis and development of DENV therapeutics and vaccines has been limited by few animal models that recapitulate key features of human disease. Over the past two decades, mouse models of DENV infection have evolved with increasing success. Here, we review the utilization and limitations of mice for studying DENV pathogenesis and evaluating countermeasures.
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Affiliation(s)
- Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA.
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27
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Durham ND, Agrawal A, Waltari E, Croote D, Zanini F, Fouch M, Davidson E, Smith O, Carabajal E, Pak JE, Doranz BJ, Robinson M, Sanz AM, Albornoz LL, Rosso F, Einav S, Quake SR, McCutcheon KM, Goo L. Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics. eLife 2019; 8:e52384. [PMID: 31820734 PMCID: PMC6927745 DOI: 10.7554/elife.52384] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/09/2019] [Indexed: 12/23/2022] Open
Abstract
Eliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To define bNAb targets, we characterized 28 antibodies belonging to expanded and hypermutated clonal families identified by transcriptomic analysis of single plasmablasts from DENV-infected individuals. Among these, we identified J9 and J8, two somatically related bNAbs that potently neutralized DENV1-4. Mutagenesis studies showed that the major recognition determinants of these bNAbs are in E protein domain I, distinct from the only known class of human bNAbs against DENV with a well-defined epitope. B cell repertoire analysis from acute-phase peripheral blood suggested that J9 and J8 followed divergent somatic hypermutation pathways, and that a limited number of mutations was sufficient for neutralizing activity. Our study suggests multiple B cell evolutionary pathways leading to DENV bNAbs targeting a new epitope that can be exploited for vaccine design.
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Affiliation(s)
| | | | - Eric Waltari
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Derek Croote
- Department of BioengineeringStanford UniversityStanfordUnited States
| | - Fabio Zanini
- Department of BioengineeringStanford UniversityStanfordUnited States
| | | | | | - Olivia Smith
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | | | - John E Pak
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | | | - Makeda Robinson
- Division of Infectious Diseases and Geographic Medicine, Department of MedicineStanford University School of MedicineStanfordUnited States
- Department of Microbiology and ImmunologyStanford University School of MedicineStanfordUnited States
| | - Ana M Sanz
- Clinical Research CenterFundación Valle del LiliCaliColombia
| | - Ludwig L Albornoz
- Pathology and Laboratory DepartmentFundación Valle del LiliCaliColombia
| | - Fernando Rosso
- Clinical Research CenterFundación Valle del LiliCaliColombia
- Department of Internal Medicine, Division of Infectious DiseasesFundación Valle del LiliCaliColombia
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of MedicineStanford University School of MedicineStanfordUnited States
- Department of Microbiology and ImmunologyStanford University School of MedicineStanfordUnited States
| | - Stephen R Quake
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Department of BioengineeringStanford UniversityStanfordUnited States
| | | | - Leslie Goo
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
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Engineering a Novel Antibody-Peptide Bispecific Fusion Protein Against MERS-CoV. Antibodies (Basel) 2019; 8:antib8040053. [PMID: 31690009 PMCID: PMC6963733 DOI: 10.3390/antib8040053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 01/01/2023] Open
Abstract
In recent years, tremendous efforts have been made in the engineering of bispecific or multi-specific antibody-based therapeutics by combining two or more functional antigen-recognizing elements into a single construct. However, to the best of our knowledge there has been no reported cases of effective antiviral antibody-peptide bispecific fusion proteins. We previously developed potent fully human monoclonal antibodies and inhibitory peptides against Middle East Respiratory Syndrome Coronavirus (MERS-CoV), a novel coronavirus that causes severe acute respiratory illness with high mortality. Here, we describe the generation of antibody-peptide bispecific fusion proteins, each of which contains an anti-MERS-CoV single-chain antibody m336 (or normal human IgG1 CH3 domain as a control) linked with, or without, a MERS-CoV fusion inhibitory peptide HR2P. We found that one of these fusion proteins, designated as m336 diabody-pep, exhibited more potent inhibitory activity than the antibody or the peptide alone against pseudotyped MERS-CoV infection and MERS-CoV S protein-mediated cell-cell fusion, suggesting its potential to be developed as an effective bispecific immunotherapeutic for clinical use.
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