1
|
Wegman AD, Kalimuddin S, Marques ETA, Adams LE, Rothman AL, Gromowski GD, Wang TT, Weiskopf D, Hibberd ML, Alex Perkins T, Christofferson RC, Gunale B, Kulkarni PS, Rosas A, Macareo L, Yacoub S, Eong Ooi E, Paz-Bailey G, Thomas SJ, Waickman AT. Proceedings of the dengue endgame summit: Imagining a world with dengue control. Vaccine 2024; 42:126071. [PMID: 38890105 DOI: 10.1016/j.vaccine.2024.06.038] [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: 11/20/2023] [Revised: 05/22/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
The first dengue "endgame" summit was held in Syracuse, NY over August 9 and 10, 2023. Organized and hosted by the Institute for Global Health and Translational Sciences at SUNY Upstate Medical University, the gathering brought together researchers, clinicians, drug and vaccine developers, government officials, and other key stakeholders in the dengue field for a highly collaborative and discussion-oriented event. The objective of the gathering was to discuss the current state of dengue around the world, what dengue "control" might look like, and what a potential roadmap might look like to achieve functional dengue control. Over the course of 7 sessions, speakers with a diverse array of expertise highlighted both current and historic challenges associated with dengue control, the state of dengue countermeasure development and deployment, as well as fundamental virologic, immunologic, and medical barriers to achieving dengue control. While sustained eradication of dengue was considered challenging, attendees were optimistic that significant reduction in the burden of dengue can be achieved by integration of vector control with effective application of therapeutics and vaccines.
Collapse
Affiliation(s)
- Adam D Wegman
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | - Shirin Kalimuddin
- Department of Infectious Diseases, Singapore General Hospital, Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Ernesto T A Marques
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Laura E Adams
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico, USA
| | - Alan L Rothman
- Department of Cell and Molecular Biology, Institute for Immunology and Informatics, University of Rhode Island, Providence, RI, USA
| | - Gregory D Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Taia T Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Daniela Weiskopf
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Martin L Hibberd
- London School of Hygiene & Tropical Medicine Department of Infection Biology, Keppel Street, London WC1E 7HT, England; Associate Faculty, National Institutes of Health, University of the Philippines, Philippines
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Rebecca C Christofferson
- Department of Pathobiological Sciences, Louisiana School of Veterinary Medicine, Baton Rouge, LA, USA
| | | | | | - Angel Rosas
- Takeda Pharmaceuticals, Inc, Boston, MA, USA
| | | | - Sophie Yacoub
- Oxford University Clinical Research Unit (OUCRU) Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, University of Oxford, UK
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Gabriela Paz-Bailey
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico, USA
| | - Stephen J Thomas
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA; Institute for Global Health and Translational Sciences, State University of New York Upstate Medical University, Syracuse, NY 13210, USA.
| | - Adam T Waickman
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA; Institute for Global Health and Translational Sciences, State University of New York Upstate Medical University, Syracuse, NY 13210, USA.
| |
Collapse
|
2
|
Nilchan N, Kraivong R, Luangaram P, Phungsom A, Tantiwatcharakunthon M, Traewachiwiphak S, Prommool T, Punyadee N, Avirutnan P, Duangchinda T, Malasit P, Puttikhunt C. An Engineered N-Glycosylated Dengue Envelope Protein Domain III Facilitates Epitope-Directed Selection of Potently Neutralizing and Minimally Enhancing Antibodies. ACS Infect Dis 2024; 10:2690-2704. [PMID: 38943594 PMCID: PMC11320570 DOI: 10.1021/acsinfecdis.4c00058] [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] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024]
Abstract
The envelope protein of dengue virus (DENV) is a primary target of the humoral immune response. The domain III of the DENV envelope protein (EDIII) is known to be the target of multiple potently neutralizing antibodies. One such antibody is 3H5, a mouse antibody that binds strongly to EDIII and potently neutralizes DENV serotype 2 (DENV-2) with unusually minimal antibody-dependent enhancement (ADE). To selectively display the binding epitope of 3H5, we strategically modified DENV-2 EDIII by shielding other known epitopes with engineered N-glycosylation sites. The modifications resulted in a glycosylated EDIII antigen termed "EDIII mutant N". This antigen was successfully used to sift through a dengue-immune scFv-phage library to select for scFv antibodies that bind to or closely surround the 3H5 epitope. The selected scFv antibodies were expressed as full-length human antibodies and showed potent neutralization activity to DENV-2 with low or negligible ADE resembling 3H5. These findings not only demonstrate the capability of the N-glycosylated EDIII mutant N as a tool to drive an epitope-directed antibody selection campaign but also highlight its potential as a dengue immunogen. This glycosylated antigen shows promise in focusing the antibody response toward a potently neutralizing epitope while reducing the risk of antibody-dependent enhancement.
Collapse
Affiliation(s)
- Napon Nilchan
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
| | - Romchat Kraivong
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
| | - Prasit Luangaram
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
| | - Anunyaporn Phungsom
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
| | - Mongkhonphan Tantiwatcharakunthon
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
| | - Somchoke Traewachiwiphak
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
| | - Tanapan Prommool
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
| | - Nuntaya Punyadee
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
- Division
of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj
Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Panisadee Avirutnan
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
- Division
of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj
Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Thaneeya Duangchinda
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Medical
Biotechnology Research Unit, National Center for Genetic Engineering
and Biotechnology (BIOTEC), National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Prida Malasit
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Siriraj
Center of Research Excellence in Dengue and Emerging Pathogens Mahidol University, Bangkok 10700, Thailand
- Division
of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj
Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chunya Puttikhunt
- Molecular
Biology of Dengue and Flaviviruses Research Team, Medical Molecular
Biotechnology Research Group National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Medical
Biotechnology Research Unit, National Center for Genetic Engineering
and Biotechnology (BIOTEC), National Science
and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| |
Collapse
|
3
|
Ooi EE, Chan YF. Is a therapeutic dengue monoclonal antibody on the way? THE LANCET. INFECTIOUS DISEASES 2024; 24:567-568. [PMID: 38408456 DOI: 10.1016/s1473-3099(24)00083-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/28/2024]
Affiliation(s)
- Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857; Viral Research and Experimental Medicine Centre, SingHealth Duke-NUS Academic Medical Centre, Singapore; Department of Translational Clinical Research, Singapore General Hospital, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
| | - Yvonne Fz Chan
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| |
Collapse
|
4
|
Gunale B, Farinola N, Kamat CD, Poonawalla CS, Pisal SS, Dhere RM, Miller C, Kulkarni PS. An observer-blind, randomised, placebo-controlled, phase 1, single ascending dose study of dengue monoclonal antibody in healthy adults in Australia. THE LANCET. INFECTIOUS DISEASES 2024; 24:639-649. [PMID: 38408457 DOI: 10.1016/s1473-3099(24)00030-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Dengue is highly prevalent in Asia and Latin America and has no specific dengue antiviral treatment. A recombinant monoclonal antibody (VIS513) that neutralises all four serotypes of the dengue virus has been developed in India. After confirmation of safety and efficacy in preclinical studies, it was tested in a first-in-human study to assess the safety and pharmacokinetics. METHODS This was a partially blind (observer-blind), randomised, placebo-controlled, phase 1, single ascending dose study in Australia. Participants were dengue naive, healthy adults (aged 18-45 years) with no clinically significant disorders or immunosuppressive conditions. Four dose levels of dengue monoclonal antibody (ie, 1 mg/kg, 3 mg/kg, 7 mg/kg, and 12 mg/kg; n=4 for 1 mg/kg and n=10 each for 3 mg/kg, 7 mg/kg, and 12 mg/kg doses) were assessed in a dose-ascending way with a placebo control (n=2 for each dose cohort, total n=6) for each cohort except for 1 mg/kg. Within each cohort, participants were first randomly assigned (1:1) in a sentinel sub-cohort and then randomly assigned (9:1) in an expansion sub-cohort to dengue monoclonal antibody or placebo except for the 1 mg/kg cohort. Participants, investigators, and outcome assessors were masked and treatment administrators were not masked. 40 participants received a single intravenous injection or infusion of either dengue monoclonal antibody or placebo over a period of 3 min to 2 h and were followed up until day 85. The primary outcomes were proportion of participants with adverse events and serious adverse events (SAEs) up to 84 days after dosing whereas the secondary outcomes were to assess the pharmacokinetic profile of dengue monoclonal antibody and to assess the presence of anti-drug antibody (ADA) to dengue monoclonal antibody. All participants were included in the safety analysis and the pharmacokinetic population involved participants receiving dengue monoclonal antibody. This study is registered with ClinicalTrials.gov, NCT03883620. FINDINGS Between March 22 and Dec 23, 2019, 40 healthy adults were randomly assigned and all completed the study. There were no SAEs reported. None of the placebo recipients (n=6) reported any adverse events. 31 (91%) of 34 participants receiving dengue monoclonal antibody reported 143 adverse events (1 mg/kg: four [100%] of four participants; 3 mg/kg: ten [100%] of ten participants; 7 mg/kg: seven [70%] of ten participants; 12 mg/kg: ten [100%] of ten participants). Of these 143 adverse events, 80 were treatment-related adverse events in 28 (82%) of 34 participants. Headache (16 [47%] of 34), infusion reaction (11 [32%] of 34), lymphopenia (seven [21%] of 34), fatigue (five [15%] of 34), and pyrexia (four [12%] of 34) were the most common reactions. Infusion reactions were reduced in the 7 mg/kg (two [20%] of ten participants) and 12 mg/kg (three [30%] of ten) cohorts with paracetamol premedication compared with the 3 mg/kg cohort (five [50%] of ten). The majority of adverse events were grade 1 or grade 2 in severity, and resolved completely. Median maximum serum concentrations ranged from 28 μg/mL (1 mg/kg) to 525 μg/mL (12 mg/kg). The median elimination half-life ranged from 775 h (1 mg/kg) to 878 h (12 mg/kg). No ADA against dengue monoclonal antibody was detected. INTERPRETATION Dengue monoclonal antibody was safe and well tolerated. It showed a dose-proportionate increase in pharmacokinetic exposure. These data support further evaluation of dengue monoclonal antibody in patients with dengue for safety and efficacy. FUNDING Serum Institute of India.
Collapse
|
5
|
Severa M, Etna MP, Andreano E, Ricci D, Cairo G, Fiore S, Canitano A, Cara A, Stefanelli P, Rappuoli R, Palamara AT, Coccia EM. Functional diversification of innate and inflammatory immune responses mediated by antibody fragment crystallizable activities against SARS-CoV-2. iScience 2024; 27:109703. [PMID: 38706870 PMCID: PMC11068556 DOI: 10.1016/j.isci.2024.109703] [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: 08/08/2023] [Revised: 01/25/2024] [Accepted: 04/06/2024] [Indexed: 05/07/2024] Open
Abstract
Monoclonal antibodies (mAb) targeting the SARS-CoV-2 Spike (S) glycoprotein have been exploited for the treatment of severe COVID-19. In this study, we evaluated the immune-regulatory features of two neutralizing anti-S mAbs (nAbs), named J08 and F05, with wild-type (WT) conformation or silenced Fc functions. In the presence of D614G SARS-CoV-2, WT nAbs enhance intracellular viral uptake in immune cells and amplify antiviral type I Interferon and inflammatory cytokine and chemokine production without viral replication, promoting the differentiation of CD16+ inflammatory monocytes and innate/adaptive PD-L1+ and PD-L1+CD80+ plasmacytoid Dendritic Cells. In spite of a reduced neutralizing property, WT J08 nAb still promotes the IL-6 production and differentiation of CD16+ monocytes once binding Omicron BA.1 variant. Fc-mediated regulation of antiviral and inflammatory responses, in the absence of viral replication, highlighted in this study, might positively tune immune response during SARS-CoV-2 infection and be exploited also in mAb-based therapeutic and prophylactic strategies against viral infections.
Collapse
Affiliation(s)
- Martina Severa
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Marilena Paola Etna
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Emanuele Andreano
- Monoclonal Antibody Discovery Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | - Daniela Ricci
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
- Department of Sciences, Roma Tre University, 00154 Rome, Italy
| | - Giada Cairo
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Stefano Fiore
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Andrea Canitano
- National Center for Global Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Andrea Cara
- National Center for Global Health, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Rino Rappuoli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Fondazione Biotecnopolo di Siena, 53100 Siena, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Eliana Marina Coccia
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| |
Collapse
|
6
|
Marković V, Szczepańska A, Berlicki Ł. Antiviral Protein-Protein Interaction Inhibitors. J Med Chem 2024; 67:3205-3231. [PMID: 38394369 PMCID: PMC10945500 DOI: 10.1021/acs.jmedchem.3c01543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/04/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024]
Abstract
Continually repeating outbreaks of pathogenic viruses necessitate the construction of effective antiviral strategies. Therefore, the development of new specific antiviral drugs in a well-established and efficient manner is crucial. Taking into account the strong ability of viruses to change, therapies with diversified molecular targets must be sought. In addition to the widely explored viral enzyme inhibitor approach, inhibition of protein-protein interactions is a very valuable strategy. In this Perspective, protein-protein interaction inhibitors targeting HIV, SARS-CoV-2, HCV, Ebola, Dengue, and Chikungunya viruses are reviewed and discussed. Antibodies, peptides/peptidomimetics, and small molecules constitute three classes of compounds that have been explored, and each of them has some advantages and disadvantages for drug development.
Collapse
Affiliation(s)
- Violeta Marković
- Wrocław
University of Science and Technology, Department
of Bioorganic Chemistry, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
- University
of Kragujevac, Faculty of Science,
Department of Chemistry, R. Domanovića 12, 34000 Kragujevac, Serbia
| | - Anna Szczepańska
- Wrocław
University of Science and Technology, Department
of Bioorganic Chemistry, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Łukasz Berlicki
- Wrocław
University of Science and Technology, Department
of Bioorganic Chemistry, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| |
Collapse
|
7
|
Efe O, Gassen RB, Morena L, Ganchiku Y, Al Jurdi A, Lape IT, Ventura-Aguiar P, LeGuern C, Madsen JC, Shriver Z, Babcock GJ, Borges TJ, Riella LV. A humanized IL-2 mutein expands Tregs and prolongs transplant survival in preclinical models. J Clin Invest 2024; 134:e173107. [PMID: 38426492 PMCID: PMC10904054 DOI: 10.1172/jci173107] [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: 06/15/2023] [Accepted: 01/05/2024] [Indexed: 03/02/2024] Open
Abstract
Long-term organ transplant survival remains suboptimal, and life-long immunosuppression predisposes transplant recipients to an increased risk of infection, malignancy, and kidney toxicity. Promoting the regulatory arm of the immune system by expanding Tregs may allow immunosuppression minimization and improve long-term graft outcomes. While low-dose IL-2 treatment can expand Tregs, it has a short half-life and off-target expansion of NK and effector T cells, limiting its clinical applicability. Here, we designed a humanized mutein IL-2 with high Treg selectivity and a prolonged half-life due to the fusion of an Fc domain, which we termed mIL-2. We showed selective and sustainable Treg expansion by mIL-2 in 2 murine models of skin transplantation. This expansion led to donor-specific tolerance through robust increases in polyclonal and antigen-specific Tregs, along with enhanced Treg-suppressive function. We also showed that Treg expansion by mIL-2 could overcome the failure of calcineurin inhibitors or costimulation blockade to prolong the survival of major-mismatched skin grafts. Validating its translational potential, mIL-2 induced a selective and sustainable in vivo Treg expansion in cynomolgus monkeys and showed selectivity for human Tregs in vitro and in a humanized mouse model. This work demonstrated that mIL-2 can enhance immune regulation and promote long-term allograft survival, potentially minimizing immunosuppression.
Collapse
Affiliation(s)
- Orhan Efe
- Center for Transplantation Sciences, Department of Surgery
- Division of Nephrology, Department of Medicine, and
| | | | - Leela Morena
- Center for Transplantation Sciences, Department of Surgery
| | | | - Ayman Al Jurdi
- Center for Transplantation Sciences, Department of Surgery
- Division of Nephrology, Department of Medicine, and
| | | | | | | | - Joren C. Madsen
- Center for Transplantation Sciences, Department of Surgery
- Division of Cardiac Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Leonardo V. Riella
- Center for Transplantation Sciences, Department of Surgery
- Division of Nephrology, Department of Medicine, and
| |
Collapse
|
8
|
Gallo E. Revolutionizing Synthetic Antibody Design: Harnessing Artificial Intelligence and Deep Sequencing Big Data for Unprecedented Advances. Mol Biotechnol 2024:10.1007/s12033-024-01064-2. [PMID: 38308755 DOI: 10.1007/s12033-024-01064-2] [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: 11/03/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
Abstract
Synthetic antibodies (Abs) represent a category of engineered proteins meticulously crafted to replicate the functions of their natural counterparts. Such Abs are generated in vitro, enabling advanced molecular alterations associated with antigen recognition, paratope site engineering, and biochemical refinements. In a parallel realm, deep sequencing has brought about a paradigm shift in molecular biology. It facilitates the prompt and cost-effective high-throughput sequencing of DNA and RNA molecules, enabling the comprehensive big data analysis of Ab transcriptomes, including specific regions of interest. Significantly, the integration of artificial intelligence (AI), based on machine- and deep- learning approaches, has fundamentally transformed our capacity to discern patterns hidden within deep sequencing big data, including distinctive Ab features and protein folding free energy landscapes. Ultimately, current AI advances can generate approximations of the most stable Ab structural configurations, enabling the prediction of de novo synthetic Abs. As a result, this manuscript comprehensively examines the latest and relevant literature concerning the intersection of deep sequencing big data and AI methodologies for the design and development of synthetic Abs. Together, these advancements have accelerated the exploration of antibody repertoires, contributing to the refinement of synthetic Ab engineering and optimizations, and facilitating advancements in the lead identification process.
Collapse
Affiliation(s)
- Eugenio Gallo
- Avance Biologicals, Department of Medicinal Chemistry, 950 Dupont Street, Toronto, ON, M6H 1Z2, Canada.
- RevivAb, Department of Protein Engineering, Av. Ipiranga, 6681, Partenon, Porto Alegre, RS, 90619-900, Brazil.
| |
Collapse
|
9
|
Minatel VM, Prudencio CR, Barraviera B, Ferreira RS. Nanobodies: a promising approach to treatment of viral diseases. Front Immunol 2024; 14:1303353. [PMID: 38322011 PMCID: PMC10844482 DOI: 10.3389/fimmu.2023.1303353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/12/2023] [Indexed: 02/08/2024] Open
Abstract
Since their discovery in the 1990s, heavy chain antibodies have garnered significant interest in the scientific community. These antibodies, found in camelids such as llamas and alpacas, exhibit distinct characteristics from conventional antibodies due to the absence of a light chain in their structure. Furthermore, they possess a single antigen-binding domain known as VHH or Nanobody (Nb). With a small size of approximately 15 kDa, these Nbs demonstrate improved characteristics compared to conventional antibodies, including greater physicochemical stability and enhanced biodistribution, enabling them to bind inaccessible epitopes more effectively. As a result, Nbs have found numerous applications in various medical and veterinary fields, particularly in diagnostics and therapeutics. Advances in biotechnology have made the production of recombinant antibodies feasible and compatible with large-scale manufacturing. Through the construction of immune phage libraries that display VHHs and subsequent selection through biopanning, it has become possible to isolate specific Nbs targeting pharmaceutical targets of interest, such as viruses. This review describes the processes involved in nanobody production, from hyperimmunization to purification, with the aim of their application in the pharmaceutical industry.
Collapse
Affiliation(s)
- Vitória Meneghetti Minatel
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
| | | | - Benedito Barraviera
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
| | - Rui Seabra Ferreira
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
| |
Collapse
|
10
|
Keelapang P, Ketloy C, Puttikhunt C, Sriburi R, Prompetchara E, Sae-Lim M, Siridechadilok B, Duangchinda T, Noisakran S, Charoensri N, Suriyaphol P, Suparattanagool P, Utaipat U, Masrinoul P, Avirutnan P, Mongkolsapaya J, Screaton G, Auewarakul P, Malaivijitnond S, Yoksan S, Malasit P, Ruxrungtham K, Pulmanausahakul R, Sittisombut N. Heterologous prime-boost immunization induces protection against dengue virus infection in cynomolgus macaques. J Virol 2023; 97:e0096323. [PMID: 37846984 PMCID: PMC10688363 DOI: 10.1128/jvi.00963-23] [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: 07/03/2023] [Accepted: 09/06/2023] [Indexed: 10/18/2023] Open
Abstract
IMPORTANCE Currently licensed dengue vaccines do not induce long-term protection in children without previous exposure to dengue viruses in nature. These vaccines are based on selected attenuated strains of the four dengue serotypes and employed in combination for two or three consecutive doses. In our search for a better dengue vaccine candidate, live attenuated strains were followed by non-infectious virus-like particles or the plasmids that generate these particles upon injection into the body. This heterologous prime-boost immunization induced elevated levels of virus-specific antibodies and helped to prevent dengue virus infection in a high proportion of vaccinated macaques. In macaques that remained susceptible to dengue virus, distinct mechanisms were found to account for the immunization failures, providing a better understanding of vaccine actions. Additional studies in humans in the future may help to establish whether this combination approach represents a more effective means of preventing dengue by vaccination.
Collapse
Affiliation(s)
- Poonsook Keelapang
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Chutitorn Ketloy
- Center of Excellence in Vaccine Research and Development, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chunya Puttikhunt
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
- Division of Dengue Hemorrhagic Fever Research, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rungtawan Sriburi
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Eakachai Prompetchara
- Center of Excellence in Vaccine Research and Development, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Malinee Sae-Lim
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Bunpote Siridechadilok
- Division of Dengue Hemorrhagic Fever Research, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Frontier Biodesign and Bioengineering Research Team, National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand
| | - Thaneeya Duangchinda
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
- Division of Dengue Hemorrhagic Fever Research, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sansanee Noisakran
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
- Division of Dengue Hemorrhagic Fever Research, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nicha Charoensri
- Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Prapat Suriyaphol
- Siriraj Informatics and Data Innovation Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Utaiwan Utaipat
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Promsin Masrinoul
- Center for Vaccine Development, Institute of Molecular Biosciences, Mahidol University at Salaya, Nakhon Pathom, Thailand
| | - Panisadee Avirutnan
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
- Division of Dengue Hemorrhagic Fever Research, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Juthathip Mongkolsapaya
- Division of Dengue Hemorrhagic Fever Research, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gavin Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Sutee Yoksan
- Center for Vaccine Development, Institute of Molecular Biosciences, Mahidol University at Salaya, Nakhon Pathom, Thailand
| | - Prida Malasit
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
- Division of Dengue Hemorrhagic Fever Research, Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kiat Ruxrungtham
- Center of Excellence in Vaccine Research and Development, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Nopporn Sittisombut
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| |
Collapse
|
11
|
Clark T, Subramanian V, Jayaraman A, Fitzpatrick E, Gopal R, Pentakota N, Rurak T, Anand S, Viglione A, Raman R, Tharakaraman K, Sasisekharan R. Enhancing antibody affinity through experimental sampling of non-deleterious CDR mutations predicted by machine learning. Commun Chem 2023; 6:244. [PMID: 37945793 PMCID: PMC10636138 DOI: 10.1038/s42004-023-01037-7] [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: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
The application of machine learning (ML) models to optimize antibody affinity to an antigen is gaining prominence. Unfortunately, the small and biased nature of the publicly available antibody-antigen interaction datasets makes it challenging to build an ML model that can accurately predict binding affinity changes due to mutations (ΔΔG). Recognizing these inherent limitations, we reformulated the problem to ask whether an ML model capable of classifying deleterious vs non-deleterious mutations can guide antibody affinity maturation in a practical setting. To test this hypothesis, we developed a Random Forest classifier (Antibody Random Forest Classifier or AbRFC) with expert-guided features and integrated it into a computational-experimental workflow. AbRFC effectively predicted non-deleterious mutations on an in-house validation dataset that is free of biases seen in the publicly available training datasets. Furthermore, experimental screening of a limited number of predictions from the model (<10^2 designs) identified affinity-enhancing mutations in two unrelated SARS-CoV-2 antibodies, resulting in constructs with up to 1000-fold increased binding to the SARS-COV-2 RBD. Our findings indicate that accurate prediction and screening of non-deleterious mutations using machine learning offers a powerful approach to improving antibody affinity.
Collapse
Affiliation(s)
- Thomas Clark
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Akila Jayaraman
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Ranjani Gopal
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Troy Rurak
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | - Shweta Anand
- Altus Enterprises, 900 Middlesex Turnpike, Billerica, MA, USA
| | | | - Rahul Raman
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | | | - Ram Sasisekharan
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| |
Collapse
|
12
|
Ormundo LF, Barreto CT, Tsuruta LR. Development of Therapeutic Monoclonal Antibodies for Emerging Arbovirus Infections. Viruses 2023; 15:2177. [PMID: 38005854 PMCID: PMC10675117 DOI: 10.3390/v15112177] [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: 09/11/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Antibody-based passive immunotherapy has been used effectively in the treatment and prophylaxis of infectious diseases. Outbreaks of emerging viral infections from arthropod-borne viruses (arboviruses) represent a global public health problem due to their rapid spread, urging measures and the treatment of infected individuals to combat them. Preparedness in advances in developing antivirals and relevant epidemiological studies protect us from damage and losses. Immunotherapy based on monoclonal antibodies (mAbs) has been shown to be very specific in combating infectious diseases and various other illnesses. Recent advances in mAb discovery techniques have allowed the development and approval of a wide number of therapeutic mAbs. This review focuses on the technological approaches available to select neutralizing mAbs for emerging arbovirus infections and the next-generation strategies to obtain highly effective and potent mAbs. The characteristics of mAbs developed as prophylactic and therapeutic antiviral agents for dengue, Zika, chikungunya, West Nile and tick-borne encephalitis virus are presented, as well as the protective effect demonstrated in animal model studies.
Collapse
Affiliation(s)
- Leonardo F. Ormundo
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo 05503-900, Brazil; (L.F.O.); (C.T.B.)
- The Interunits Graduate Program in Biotechnology, University of São Paulo, São Paulo 05503-900, Brazil
| | - Carolina T. Barreto
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo 05503-900, Brazil; (L.F.O.); (C.T.B.)
- The Interunits Graduate Program in Biotechnology, University of São Paulo, São Paulo 05503-900, Brazil
| | - Lilian R. Tsuruta
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo 05503-900, Brazil; (L.F.O.); (C.T.B.)
| |
Collapse
|
13
|
Diani E, Lagni A, Lotti V, Tonon E, Cecchetto R, Gibellini D. Vector-Transmitted Flaviviruses: An Antiviral Molecules Overview. Microorganisms 2023; 11:2427. [PMID: 37894085 PMCID: PMC10608811 DOI: 10.3390/microorganisms11102427] [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: 08/17/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
Flaviviruses cause numerous pathologies in humans across a broad clinical spectrum with potentially severe clinical manifestations, including hemorrhagic and neurological disorders. Among human flaviviruses, some viral proteins show high conservation and are good candidates as targets for drug design. From an epidemiological point of view, flaviviruses cause more than 400 million cases of infection worldwide each year. In particular, the Yellow Fever, dengue, West Nile, and Zika viruses have high morbidity and mortality-about an estimated 20,000 deaths per year. As they depend on human vectors, they have expanded their geographical range in recent years due to altered climatic and social conditions. Despite these epidemiological and clinical premises, there are limited antiviral treatments for these infections. In this review, we describe the major compounds that are currently under evaluation for the treatment of flavivirus infections and the challenges faced during clinical trials, outlining their mechanisms of action in order to present an overview of ongoing studies. According to our review, the absence of approved antivirals for flaviviruses led to in vitro and in vivo experiments aimed at identifying compounds that can interfere with one or more viral cycle steps. Still, the currently unavailability of approved antivirals poses a significant public health issue.
Collapse
Affiliation(s)
- Erica Diani
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (A.L.); (V.L.); (R.C.)
| | - Anna Lagni
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (A.L.); (V.L.); (R.C.)
| | - Virginia Lotti
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (A.L.); (V.L.); (R.C.)
| | - Emil Tonon
- Unit of Microbiology, Azienda Ospedaliera Universitaria Integrata Verona, 37134 Verona, Italy;
| | - Riccardo Cecchetto
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (A.L.); (V.L.); (R.C.)
- Unit of Microbiology, Azienda Ospedaliera Universitaria Integrata Verona, 37134 Verona, Italy;
| | - Davide Gibellini
- Department of Diagnostic and Public Health, Microbiology Section, University of Verona, 37134 Verona, Italy; (A.L.); (V.L.); (R.C.)
- Unit of Microbiology, Azienda Ospedaliera Universitaria Integrata Verona, 37134 Verona, Italy;
| |
Collapse
|
14
|
Keelapang P, Kraivong R, Pulmanausahakul R, Sriburi R, Prompetchara E, Kaewmaneephong J, Charoensri N, Pakchotanon P, Duangchinda T, Suparattanagool P, Luangaram P, Masrinoul P, Mongkolsapaya J, Screaton G, Ruxrungtham K, Auewarakul P, Yoksan S, Malasit P, Puttikhunt C, Ketloy C, Sittisombut N. Blockade-of-Binding Activities toward Envelope-Associated, Type-Specific Epitopes as a Correlative Marker for Dengue Virus-Neutralizing Antibody. Microbiol Spectr 2023; 11:e0091823. [PMID: 37409936 PMCID: PMC10433959 DOI: 10.1128/spectrum.00918-23] [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: 03/02/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Humans infected with dengue virus (DENV) acquire long-term protection against the infecting serotype, whereas cross-protection against other serotypes is short-lived. Long-term protection induced by low levels of type-specific neutralizing antibodies can be assessed using the virus-neutralizing antibody test. However, this test is laborious and time-consuming. In this study, a blockade-of-binding enzyme-linked immunoassay was developed to assess antibody activity by using a set of neutralizing anti-E monoclonal antibodies and blood samples from dengue virus-infected or -immunized macaques. Diluted blood samples were incubated with plate-bound dengue virus particles before the addition of an enzyme-conjugated antibody specific to the epitope of interest. Based on blocking reference curves constructed using autologous purified antibodies, sample blocking activity was determined as the relative concentration of unconjugated antibody that resulted in the same percent signal reduction. In separate DENV-1-, -2-, -3-, and -4-related sets of samples, moderate to strong correlations of the blocking activity with neutralizing antibody titers were found with the four type-specific antibodies 1F4, 3H5, 8A1, and 5H2, respectively. Significant correlations were observed for single samples taken 1 month after infection as well as samples drawn before and at various time points after infection/immunization. Similar testing using a cross-reactive EDE-1 antibody revealed a moderate correlation between the blocking activity and the neutralizing antibody titer only for the DENV-2-related set. The potential usefulness of the blockade-of-binding activity as a correlative marker of neutralizing antibodies against dengue viruses needs to be validated in humans. IMPORTANCE This study describes a blockade-of-binding assay for the determination of antibodies that recognize a selected set of serotype-specific or group-reactive epitopes in the envelope of dengue virus. By employing blood samples collected from dengue virus-infected or -immunized macaques, moderate to strong correlations of the epitope-blocking activities with the virus-neutralizing antibody titers were observed with serotype-specific blocking activities for each of the four dengue serotypes. This simple, rapid, and less laborious method should be useful for the evaluation of antibody responses to dengue virus infection and may serve as, or be a component of, an in vitro correlate of protection against dengue in the future.
Collapse
Affiliation(s)
- Poonsook Keelapang
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Medical Biotechnology Research Unit, BIOTEC, NSTDA, Bangkok, Thailand
| | - Romchat Kraivong
- Medical Biotechnology Research Unit, BIOTEC, NSTDA, Bangkok, Thailand
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
- Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Rungtawan Sriburi
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Medical Biotechnology Research Unit, BIOTEC, NSTDA, Bangkok, Thailand
| | - Eakachai Prompetchara
- Center of Excellence in Vaccine Research and Development (Chula-VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jutamart Kaewmaneephong
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nicha Charoensri
- Center for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Pattarakul Pakchotanon
- Medical Biotechnology Research Unit, BIOTEC, NSTDA, Bangkok, Thailand
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Thaneeya Duangchinda
- Medical Biotechnology Research Unit, BIOTEC, NSTDA, Bangkok, Thailand
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
- Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Prasit Luangaram
- Medical Biotechnology Research Unit, BIOTEC, NSTDA, Bangkok, Thailand
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Promsin Masrinoul
- Center for Vaccine Development, Institute of Molecular Biosciences, Mahidol University at Salaya, Nakhon Pathom, Thailand
| | - Juthathip Mongkolsapaya
- Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Science (CAMS), Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Gavin Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Science (CAMS), Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Kiat Ruxrungtham
- Center of Excellence in Vaccine Research and Development (Chula-VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sutee Yoksan
- Center for Vaccine Development, Institute of Molecular Biosciences, Mahidol University at Salaya, Nakhon Pathom, Thailand
| | - Prida Malasit
- Medical Biotechnology Research Unit, BIOTEC, NSTDA, Bangkok, Thailand
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
- Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chunya Puttikhunt
- Medical Biotechnology Research Unit, BIOTEC, NSTDA, Bangkok, Thailand
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
- Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutitorn Ketloy
- Center of Excellence in Vaccine Research and Development (Chula-VRC), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nopporn Sittisombut
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Medical Biotechnology Research Unit, BIOTEC, NSTDA, Bangkok, Thailand
| |
Collapse
|
15
|
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.
Collapse
|
16
|
Chen Q, Li R, Wu B, Zhang X, Zhang H, Chen R. A tetravalent nanoparticle vaccine elicits a balanced and potent immune response against dengue viruses without inducing antibody-dependent enhancement. Front Immunol 2023; 14:1193175. [PMID: 37275868 PMCID: PMC10235449 DOI: 10.3389/fimmu.2023.1193175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
Dengue fever is a global health threat caused by the dengue virus (DENV), a vector-borne and single-stranded RNA virus. Development of a safe and efficacious vaccine against DENV is a demanding challenge. The greatest pitfall in the development of vaccines is antibody-dependent enhancement (ADE), which is closely associated with disease exacerbation. We displayed the modified envelope proteins from the four serotypes of the DENV on a 24-mer ferritin nanoparticle, respectively. This tetravalent nanoparticle vaccine induced potent humoral and cellular immunity in mice without ADE and conferred efficient protection against the lethal challenge of DENV-2 and DENV-3 in AG6 mice. Further exploration of immunization strategies showed that even single-dose vaccination could reduce pathologic damage in BALB/c mice infected with high doses of DENV-2. Treatment with cyclic-di-guanosine monophosphate facilitated a higher titer of neutralizing antibodies and a stronger type-1 T-helper cell-biased immune response, thereby revealing it to be an effective adjuvant for dengue nanoparticle vaccines. These data suggest that a promising tetravalent nanoparticle vaccine could be produced to prevent DENV infection.
Collapse
Affiliation(s)
- Qier Chen
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Rong Li
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bolin Wu
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xu Zhang
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Zhang
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Bio-Island, Guangzhou, Guangdong, China
| | - Ran Chen
- Institute of Human Virology, Department of Pathogen Biology and Biosecurity, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| |
Collapse
|
17
|
Huang Z, Zhang Y, Li H, Zhu J, Song W, Chen K, Zhang Y, Lou Y. Vaccine development for mosquito-borne viral diseases. Front Immunol 2023; 14:1161149. [PMID: 37251387 PMCID: PMC10213220 DOI: 10.3389/fimmu.2023.1161149] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Mosquito-borne viral diseases are a group of viral illnesses that are predominantly transmitted by mosquitoes, including viruses from the Togaviridae and Flaviviridae families. In recent years, outbreaks caused by Dengue and Zika viruses from the Flaviviridae family, and Chikungunya virus from the Togaviridae family, have raised significant concerns for public health. However, there are currently no safe and effective vaccines available for these viruses, except for CYD-TDV, which has been licensed for Dengue virus. Efforts to control the transmission of COVID-19, such as home quarantine and travel restrictions, have somewhat limited the spread of mosquito-borne viral diseases. Several vaccine platforms, including inactivated vaccines, viral-vector vaccines, live attenuated vaccines, protein vaccines, and nucleic acid vaccines, are being developed to combat these viruses. This review analyzes the various vaccine platforms against Dengue, Zika, and Chikungunya viruses and provides valuable insights for responding to potential outbreaks.
Collapse
Affiliation(s)
- Zhiwei Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuxuan Zhang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Hongyu Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiajie Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Wanchen Song
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yanjun Zhang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yongliang Lou
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
18
|
Iwasaki YW, Tharakaraman K, Subramanian V, Khongmanee A, Hatas A, Fleischer E, Rurak TT, Ngok-ngam P, Tit-oon P, Ruchirawat M, Satayavivad J, Fuangthong M, Sasisekharan R. Generation of bispecific antibodies by structure-guided redesign of IgG constant regions. Front Immunol 2023; 13:1063002. [PMID: 36703993 PMCID: PMC9871890 DOI: 10.3389/fimmu.2022.1063002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/13/2022] [Indexed: 01/12/2023] Open
Abstract
Bispecific antibodies (BsAbs) form an exciting class of bio-therapeutics owing to their multispecificity. Although numerous formats have been developed, generation of hetero-tetrameric IgG1-like BsAbs having acceptable safety and pharmacokinetics profiles from a single cell culture system remains challenging due to the heterogeneous pairing between the four chains. Herein, we employed a structure-guided approach to engineer mutations in the constant domain interfaces (CH1-CL and CH3-CH3) of heavy and κ light chains to prevent heavy-light mispairing in the antigen binding fragment (Fab) region and heavy-heavy homodimerization in the Fc region. Transient co-transfection of mammalian cells with heavy and light chains of pre-existing antibodies carrying the engineered constant domains generates BsAbs with percentage purity ranging from 78% to 85%. The engineered BsAbs demonstrate simultaneous binding of both antigens, while retaining the thermal stability, Fc-mediated effector properties and FcRn binding properties of the parental antibodies. Importantly, since the variable domains were not modified, the mutations may enable BsAb formation from antibodies belonging to different germline origins and isotypes. The rationally designed mutations reported in this work could serve as a starting point for generating optimized solutions required for large scale production.
Collapse
Affiliation(s)
- Yordkhwan W. Iwasaki
- Program in Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok, Thailand
| | - Kannan Tharakaraman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Vidya Subramanian
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Amnart Khongmanee
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand
| | - Andrew Hatas
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Eduardo Fleischer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Troy T. Rurak
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Patchara Ngok-ngam
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand
| | - Phanthakarn Tit-oon
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand
| | - Mathuros Ruchirawat
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand,Center of Excellence on Environmental Health and Toxicology (EHT), Office of the Permanent Secretary (OPS), Ministry of Higher Education, Science, Research and Innovation (MHESI), Bangkok, Thailand
| | - Jutamaad Satayavivad
- Program in Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok, Thailand,Center of Excellence on Environmental Health and Toxicology (EHT), Office of the Permanent Secretary (OPS), Ministry of Higher Education, Science, Research and Innovation (MHESI), Bangkok, Thailand,Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Mayuree Fuangthong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, Thailand,Center of Excellence on Environmental Health and Toxicology (EHT), Office of the Permanent Secretary (OPS), Ministry of Higher Education, Science, Research and Innovation (MHESI), Bangkok, Thailand,Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand,*Correspondence: Mayuree Fuangthong, ; Ram Sasisekharan,
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States,*Correspondence: Mayuree Fuangthong, ; Ram Sasisekharan,
| |
Collapse
|
19
|
Biner DW, Grosch JS, Ortoleva PJ. B-cell epitope discovery: The first protein flexibility-based algorithm-Zika virus conserved epitope demonstration. PLoS One 2023; 18:e0262321. [PMID: 36920995 PMCID: PMC10016673 DOI: 10.1371/journal.pone.0262321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 12/22/2021] [Indexed: 03/16/2023] Open
Abstract
Antibody-antigen interaction-at antigenic local environments called B-cell epitopes-is a prominent mechanism for neutralization of infection. Effective mimicry, and display, of B-cell epitopes is key to vaccine design. Here, a physical approach is evaluated for the discovery of epitopes which evolve slowly over closely related pathogens (conserved epitopes). The approach is 1) protein flexibility-based and 2) demonstrated with clinically relevant enveloped viruses, simulated via molecular dynamics. The approach is validated against 1) seven structurally characterized enveloped virus epitopes which evolved the least (out of thirty-nine enveloped virus-antibody structures), 2) two structurally characterized non-enveloped virus epitopes which evolved slowly (out of eight non-enveloped virus-antibody structures), and 3) eight preexisting epitope and peptide discovery algorithms. Rationale for a new benchmarking scheme is presented. A data-driven epitope clustering algorithm is introduced. The prediction of five Zika virus epitopes (for future exploration on recombinant vaccine technologies) is demonstrated. For the first time, protein flexibility is shown to outperform solvent accessible surface area as an epitope discovery metric.
Collapse
Affiliation(s)
- Daniel W. Biner
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Jason S. Grosch
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Peter J. Ortoleva
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
| |
Collapse
|
20
|
Miller NL, Clark T, Raman R, Sasisekharan R. Learned features of antibody-antigen binding affinity. Front Mol Biosci 2023; 10:1112738. [PMID: 36895805 PMCID: PMC9989197 DOI: 10.3389/fmolb.2023.1112738] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
Defining predictors of antigen-binding affinity of antibodies is valuable for engineering therapeutic antibodies with high binding affinity to their targets. However, this task is challenging owing to the huge diversity in the conformations of the complementarity determining regions of antibodies and the mode of engagement between antibody and antigen. In this study, we used the structural antibody database (SAbDab) to identify features that can discriminate high- and low-binding affinity across a 5-log scale. First, we abstracted features based on previously learned representations of protein-protein interactions to derive 'complex' feature sets, which include energetic, statistical, network-based, and machine-learned features. Second, we contrasted these complex feature sets with additional 'simple' feature sets based on counts of contacts between antibody and antigen. By investigating the predictive potential of 700 features contained in the eight complex and simple feature sets, we observed that simple feature sets perform comparably to complex feature sets in classification of binding affinity. Moreover, combining features from all eight feature-sets provided the best classification performance (median cross-validation AUROC and F1-score of 0.72). Of note, classification performance is substantially improved when several sources of data leakage (e.g., homologous antibodies) are not removed from the dataset, emphasizing a potential pitfall in this task. We additionally observe a classification performance plateau across diverse featurization approaches, highlighting the need for additional affinity-labeled antibody-antigen structural data. The findings from our present study set the stage for future studies aimed at multiple-log enhancement of antibody affinity through feature-guided engineering.
Collapse
Affiliation(s)
- Nathaniel L Miller
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States.,Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
21
|
Waickman AT, Newell K, Endy TP, Thomas SJ. Biologics for dengue prevention: up-to-date. Expert Opin Biol Ther 2023; 23:73-87. [PMID: 36417290 DOI: 10.1080/14712598.2022.2151837] [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: 11/24/2022]
Abstract
INTRODUCTION Dengue is a worsening global public health problem. The vector-viral-host interactions driving the pathogenesis of dengue are multi-dimensional. Sequential dengue virus (DENV) infections with different DENV types significantly increase the risk of severe disease. Treatment is supportive in nature as there are no licensed anti-DENV antivirals or immuno-therapeutics. A single dengue vaccine has widely been licensed with two others in advanced clinical development. Dengvaxia® has been licensed in numerous countries but uptake has been slow as a result of safety signals noted in the youngest recipients and those who were dengue naïve at the time of vaccination. AREAS COVERED In this review, the current state of dengue vaccine and antiviral drug development will be discussed as well as new developments in controlled human infection models to support product development. EXPERT OPINION The world needs a safe and efficacious tetravalent dengue vaccine capable of protecting multiple different populations across a broad age range and different flavivirus immunologic backgrounds. Safe and effective antivirals are also needed to prevent or attenuate dengue disease in the unvaccinated, in cases of vaccine failure, or in high-risk populations.
Collapse
Affiliation(s)
- Adam T Waickman
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY USA
| | - Krista Newell
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY USA
| | - Timothy P Endy
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY USA
| | - Stephen J Thomas
- Department of Microbiology and Immunology, State University of New York Upstate Medical University, Syracuse, NY USA
| |
Collapse
|
22
|
Conti S, Karplus M. A Computational Framework for Determining the Breadth of Antibodies Against Highly Mutable Pathogens. Methods Mol Biol 2023; 2552:399-408. [PMID: 36346605 DOI: 10.1007/978-1-0716-2609-2_22] [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: 06/16/2023]
Abstract
Highly mutable pathogens pose daunting challenges for antibody design. The usual criteria of high potency and specificity are often insufficient to design antibodies that provide long-lasting protection. This is due, in part, to the ability of the pathogen to rapidly acquire mutations that permit them to evade the designed antibodies. To overcome these limitations, design of antibodies with a larger neutralizing breadth can be pursued. Such broadly neutralizing antibodies (bnAbs) should remain targeted to a specific epitope, yet show robustness against pathogen mutability, thereby neutralizing a higher number of antigens. This is particularly important for highly mutable pathogens, like the influenza virus and the human immunodeficiency virus (HIV). The protocol describes a method for computing the "breadth" of a given antibody, an essential aspect of antibody design.
Collapse
Affiliation(s)
- Simone Conti
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France.
| |
Collapse
|
23
|
Troisi M, Marini E, Abbiento V, Stazzoni S, Andreano E, Rappuoli R. A new dawn for monoclonal antibodies against antimicrobial resistant bacteria. Front Microbiol 2022; 13:1080059. [PMID: 36590399 PMCID: PMC9795047 DOI: 10.3389/fmicb.2022.1080059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) is a quickly advancing threat for human health worldwide and almost 5 million deaths are already attributable to this phenomenon every year. Since antibiotics are failing to treat AMR-bacteria, new tools are needed, and human monoclonal antibodies (mAbs) can fill this role. In almost 50 years since the introduction of the first technology that led to mAb discovery, enormous leaps forward have been made to identify and develop extremely potent human mAbs. While their usefulness has been extensively proved against viral pathogens, human mAbs have yet to find their space in treating and preventing infections from AMR-bacteria and fully conquer the field of infectious diseases. The novel and most innovative technologies herein reviewed can support this goal and add powerful tools in the arsenal of weapons against AMR.
Collapse
Affiliation(s)
- Marco Troisi
- Monoclonal Antibody Discovery (MAD) Laboratory, Fondazione Toscana Life Sciences, Siena, Italy
| | - Eleonora Marini
- Monoclonal Antibody Discovery (MAD) Laboratory, Fondazione Toscana Life Sciences, Siena, Italy
| | - Valentina Abbiento
- Monoclonal Antibody Discovery (MAD) Laboratory, Fondazione Toscana Life Sciences, Siena, Italy
| | - Samuele Stazzoni
- Monoclonal Antibody Discovery (MAD) Laboratory, Fondazione Toscana Life Sciences, Siena, Italy
| | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Laboratory, Fondazione Toscana Life Sciences, Siena, Italy
| | - Rino Rappuoli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
- Fondazione Biotecnopolo di Siena, Siena, Italy
| |
Collapse
|
24
|
Gopal R, Fitzpatrick E, Pentakota N, Jayaraman A, Tharakaraman K, Capila I. Optimizing Antibody Affinity and Developability Using a Framework-CDR Shuffling Approach-Application to an Anti-SARS-CoV-2 Antibody. Viruses 2022; 14:2694. [PMID: 36560698 PMCID: PMC9784564 DOI: 10.3390/v14122694] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
The computational methods used for engineering antibodies for clinical development have undergone a transformation from three-dimensional structure-guided approaches to artificial-intelligence- and machine-learning-based approaches that leverage the large sequence data space of hundreds of millions of antibodies generated by next-generation sequencing (NGS) studies. Building on the wealth of available sequence data, we implemented a computational shuffling approach to antibody components, using the complementarity-determining region (CDR) and the framework region (FWR) to optimize an antibody for improved affinity and developability. This approach uses a set of rules to suitably combine the CDRs and FWRs derived from naturally occurring antibody sequences to engineer an antibody with high affinity and specificity. To illustrate this approach, we selected a representative SARS-CoV-2-neutralizing antibody, H4, which was identified and isolated previously based on the predominant germlines that were employed in a human host to target the SARS-CoV-2-human ACE2 receptor interaction. Compared to screening vast CDR libraries for affinity enhancements, our approach identified fewer than 100 antibody framework-CDR combinations, from which we screened and selected an antibody (CB79) that showed a reduced dissociation rate and improved affinity against the SARS-CoV-2 spike protein (7-fold) when compared to H4. The improved affinity also translated into improved neutralization (>75-fold improvement) of SARS-CoV-2. Our rapid and robust approach for optimizing antibodies from parts without the need for tedious structure-guided CDR optimization will have broad utility for biotechnological applications.
Collapse
Affiliation(s)
- Ranjani Gopal
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Emmett Fitzpatrick
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Niharika Pentakota
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Akila Jayaraman
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Kannan Tharakaraman
- Discovery and Diagnostics Division, Peritia Inc., 12 Gill Street, Woburn, MA 01801, USA
| | - Ishan Capila
- Celltas Biosciences, 900 Middlesex Turnpike, Billerica, MA 01821, USA
| |
Collapse
|
25
|
Lu J, Chen L, Du P, Guo J, Wang X, Jiang Y, Yu Y, Wang R, Yang Z. A human monoclonal antibody to neutralize all four serotypes of dengue virus derived from patients at the convalescent phase of infection. Virology 2022; 576:74-82. [PMID: 36183498 DOI: 10.1016/j.virol.2022.09.007] [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: 05/06/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 11/16/2022]
Abstract
Dengue virus (DENV) is a prevalent mosquito-transmitted human pathogen, causing about 100 million cases of acute dengue fever and 21,000 deaths annually worldwide. Therapeutic neutralizing antibodies against dengue virus might be effective to treat severe dengue fever. Here, we showed that human monoclonal antibody (HMAb) 9C7 bound to all four intact serotypes of DENV but not to the recombinant envelope protein, suggesting HMAb 9C7 recognized a conformational epitope of the envelope protein. Taken together our results suggested that HMAb 9C7 neutralized all four serotypes of DENV in vitro and, for DENV-1, indicated activity at the pre- and post-attachment steps in the viral life cycle. HMAb 9C7 potently protected suckling mice from lethal challenge with all four serotypes of DENV. FcγRII-mediated uptake of immune complexes and antibody-dependent enhancement at low doses of the antibody were abolished by two Leu-to-Ala (9C7-LALA) mutations or deletion of nine amino acids (9C7-9del) in HMAb 9C7 Fc. Therefore, HMAb 9C7 represented a promising prophylactic and therapeutic agent against all four serotypes of DENV.
Collapse
Affiliation(s)
- Jiansheng Lu
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Lei Chen
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Peng Du
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Jiazheng Guo
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xi Wang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Yujia Jiang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Yunzhou Yu
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China.
| | - Rong Wang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China.
| | - Zhixin Yang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China.
| |
Collapse
|
26
|
Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
Collapse
Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
| |
Collapse
|
27
|
Miller NL, Raman R, Clark T, Sasisekharan R. Complexity of Viral Epitope Surfaces as Evasive Targets for Vaccines and Therapeutic Antibodies. Front Immunol 2022; 13:904609. [PMID: 35784339 PMCID: PMC9247215 DOI: 10.3389/fimmu.2022.904609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022] Open
Abstract
The dynamic interplay between virus and host plays out across many interacting surfaces as virus and host evolve continually in response to one another. In particular, epitope-paratope interactions (EPIs) between viral antigen and host antibodies drive much of this evolutionary race. In this review, we describe a series of recent studies examining aspects of epitope complexity that go beyond two interacting protein surfaces as EPIs are typically understood. To structure our discussion, we present a framework for understanding epitope complexity as a spectrum along a series of axes, focusing primarily on 1) epitope biochemical complexity (e.g., epitopes involving N-glycans) and 2) antigen conformational/dynamic complexity (e.g., epitopes with differential properties depending on antigen state or fold-axis). We highlight additional epitope complexity factors including epitope tertiary/quaternary structure, which contribute to epistatic relationships between epitope residues within- or adjacent-to a given epitope, as well as epitope overlap resulting from polyclonal antibody responses, which is relevant when assessing antigenic pressure against a given epitope. Finally, we discuss how these different forms of epitope complexity can limit EPI analyses and therapeutic antibody development, as well as recent efforts to overcome these limitations.
Collapse
Affiliation(s)
- Nathaniel L. Miller
- Harvard Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
28
|
Finding a chink in the armor: Update, limitations, and challenges toward successful antivirals against flaviviruses. PLoS Negl Trop Dis 2022; 16:e0010291. [PMID: 35482672 PMCID: PMC9049358 DOI: 10.1371/journal.pntd.0010291] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Flaviviruses have caused large epidemics and ongoing outbreaks for centuries. They are now distributed in every continent infecting up to millions of people annually and may emerge to cause future epidemics. Some of the viruses from this group cause severe illnesses ranging from hemorrhagic to neurological manifestations. Despite decades of research, there are currently no approved antiviral drugs against flaviviruses, urging for new strategies and antiviral targets. In recent years, integrated omics data-based drug repurposing paired with novel drug validation methodologies and appropriate animal models has substantially aided in the discovery of new antiviral medicines. Here, we aim to review the latest progress in the development of both new and repurposed (i) direct-acting antivirals; (ii) host-targeting antivirals; and (iii) multitarget antivirals against flaviviruses, which have been evaluated both in vitro and in vivo, with an emphasis on their targets and mechanisms. The search yielded 37 compounds that have been evaluated for their efficacy against flaviviruses in animal models; 20 of them are repurposed drugs, and the majority of them exhibit broad-spectrum antiviral activity. The review also highlighted the major limitations and challenges faced in the current in vitro and in vivo evaluations that hamper the development of successful antiviral drugs for flaviviruses. We provided an analysis of what can be learned from some of the approved antiviral drugs as well as drugs that failed clinical trials. Potent in vitro and in vivo antiviral efficacy alone does not warrant successful antiviral drugs; current gaps in studies need to be addressed to improve efficacy and safety in clinical trials.
Collapse
|
29
|
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.
Collapse
|
30
|
Hruškovicová J, Bhide K, Petroušková P, Tkáčová Z, Mochnáčová E, Čurlík J, Bhide M, Kulkarni A. Engineering the Single Domain Antibodies Targeting Receptor Binding Motifs Within the Domain III of West Nile Virus Envelope Glycoprotein. Front Microbiol 2022; 13:801466. [PMID: 35432292 PMCID: PMC9012491 DOI: 10.3389/fmicb.2022.801466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
West Nile virus (WNV) is a mosquito-borne neurotrophic flavivirus causing mild febrile illness to severe encephalitis and acute flaccid paralysis with long-term or permanent neurological disorders. Due to the absence of targeted therapy or vaccines, there is a growing need to develop effective anti-WNV therapy. In this study, single-domain antibodies (sdAbs) were developed against the domain III (DIII) of WNV’s envelope glycoprotein to interrupt the interaction between DIII and the human brain microvascular endothelial cells (hBMEC). The peripheral blood mononuclear cells of the llama immunized with recombinant DIIIL297–S403 (rDIII) were used to generate a variable heavy chain only (VHH)-Escherichia coli library, and phage display was performed using the M13K07ΔpIII Hyperphages system. Phages displaying sdAbs against rDIII were panned with the synthetic analogs of the DIII receptor binding motifs, DIII-1G299–K307 and DIII-2V371–R388, and the VHH gene from the eluted phages was subcloned into E. coli SHuffle. Soluble sdAbs purified from 96 E. coli SHuffle clones were screened to identify 20 candidates strongly binding to the synthetic analogs of DIII-1G299–K307 and DIII-2V371–R388 on a dot blot assay. Among them, sdAbA1, sdAbA6, sdAbA9, and sdAbA10 blocked the interaction between rDIII and human brain microvascular endothelial cells (hBMECs) on Western blot and cell ELISA. However, optimum stability during the overexpression was noticed only for sdAbA10 and it also neutralized the WNV–like particles (WNV-VLP) in the Luciferase assay with an half maximal effective concentration (EC50) of 1.48 nm. Furthermore, the hemocompatibility and cytotoxicity of sdAbA10 were assessed by a hemolytic assay and XTT-based hBMEC proliferation assay resulting in 0.1% of hemolytic activity and 82% hBMEC viability, respectively. Therefore, the sdAbA10 targeting DIII-2V371–R388 of the WNV envelope glycoprotein is observed to be suitable for in vivo trials as a specific therapy for WNV–induced neuropathogenesis.
Collapse
Affiliation(s)
- Jana Hruškovicová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Košice, Slovakia
| | - Katarína Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Košice, Slovakia
| | - Patrícia Petroušková
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Košice, Slovakia
| | - Zuzana Tkáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Košice, Slovakia
| | - Evelína Mochnáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Košice, Slovakia
| | - Ján Čurlík
- Department of Breeding and Diseases of Game, Fish and Bees, Ecology and Cynology, The University of Veterinary Medicine and Pharmacy, Košice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Košice, Slovakia
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Amod Kulkarni
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Košice, Slovakia
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- *Correspondence: Amod Kulkarni,
| |
Collapse
|
31
|
Molecular dynamics simulations and Gaussian network model for designing antibody mimicking protein towards dengue envelope protein. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Miller NL, Clark T, Raman R, Sasisekharan R. An Antigenic Space Framework for Understanding Antibody Escape of SARS-CoV-2 Variants. Viruses 2021; 13:2009. [PMID: 34696440 PMCID: PMC8537311 DOI: 10.3390/v13102009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
The evolution of mutations in SARS-CoV-2 at antigenic sites that impact neutralizing antibody responses in humans poses a risk to immunity developed through vaccination and natural infection. The highly successful RNA-based vaccines have enabled rapid vaccine updates that incorporate mutations from current variants of concern (VOCs). It is therefore important to anticipate future antigenic mutations as the virus navigates the heterogeneous global landscape of host immunity. Toward this goal, we survey epitope-paratope interfaces of anti-SARS-CoV-2 antibodies to map an antigenic space that captures the role of each spike protein residue within the polyclonal antibody response directed against the ACE2-receptor binding domain (RBD) or the N-terminal domain (NTD). In particular, the antigenic space map builds on recently published epitope definitions by annotating epitope overlap and orthogonality at the residue level. We employ the antigenic space map as a framework to understand how mutations on nine major variants contribute to each variant's evasion of neutralizing antibodies. Further, we identify constellations of mutations that span the orthogonal epitope regions of the RBD and NTD on the variants with the greatest antibody escape. Finally, we apply the antigenic space map to predict which regions of antigenic space-should they mutate-may be most likely to complementarily augment antibody evasion for the most evasive and transmissible VOCs.
Collapse
Affiliation(s)
- Nathaniel L. Miller
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (T.C.); (R.R.)
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (T.C.); (R.R.)
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (T.C.); (R.R.)
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (T.C.); (R.R.)
| |
Collapse
|
34
|
Scott CAP, Amarilla AA, Bibby S, Newton ND, Hall RA, Hobson-Peters J, Muller DA, Chappell KJ, Young PR, Modhiran N, Watterson D. Implications of Dengue Virus Maturation on Vaccine Induced Humoral Immunity in Mice. Viruses 2021; 13:v13091843. [PMID: 34578424 PMCID: PMC8473161 DOI: 10.3390/v13091843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022] Open
Abstract
The use of dengue virus (DENV) vaccines has been hindered by the complexities of antibody dependent enhancement (ADE). Current late-stage vaccine candidates utilize attenuated and chimeric DENVs that produce particles of varying maturities. Antibodies that are elicited by preferentially exposed epitopes on immature virions have been linked to increased ADE. We aimed to further understand the humoral immunity promoted by DENV particles of varying maturities in an AG129 mouse model using a chimeric insect specific vaccine candidate, bDENV-2. We immunized mice with mature, partially mature, and immature bDENV-2 and found that immunization with partially mature bDENV-2 produced more robust and cross-neutralizing immune responses than immunization with immature or mature bDENV-2. Upon challenge with mouse adapted DENV-2 (D220), we observed 80% protection for mature bDENV-2 vaccinated mice and 100% for immature and partially mature vaccinated mice, suggesting that protection to homotypic challenge is not dependent on maturation. Finally, we found reduced in vitro ADE at subneutralising serum concentrations for mice immunized with mature bDENV-2. These results suggest that both immature and mature DENV particles play a role in homotypic protection; however, the increased risk of in vitro ADE from immature particles indicates potential safety benefits from mature DENV-based vaccines.
Collapse
Affiliation(s)
- Connor A. P. Scott
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
| | - Summa Bibby
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
| | - Natalee D. Newton
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
| | - Roy A. Hall
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Jody Hobson-Peters
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - David A. Muller
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
| | - Keith J. Chappell
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Paul R. Young
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
- Correspondence: (N.M.); (D.W.)
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.A.P.S.); (A.A.A.); (S.B.); (N.D.N.); (R.A.H.); (J.H.-P.); (D.A.M.); (K.J.C.); (P.R.Y.)
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD 4072, Australia
- Correspondence: (N.M.); (D.W.)
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Lee DCP, Raman R, Ghafar NA, Budigi Y. An antibody engineering platform using amino acid networks: A case study in development of antiviral therapeutics. Antiviral Res 2021; 192:105105. [PMID: 34111505 DOI: 10.1016/j.antiviral.2021.105105] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022]
Abstract
We present here a case study of an antibody-engineering platform that selects, modifies, and assembles antibody parts to construct novel antibodies. A salient feature of this platform includes the role of amino acid networks in optimizing framework regions (FRs) and complementarity determining regions (CDRs) to engineer new antibodies with desired structure-function relationships. The details of this approach are described in the context of its utility in engineering ZAb_FLEP, a potent anti-Zika virus antibody. ZAb_FLEP comprises of distinct parts, including heavy chain and light chain FRs and CDRs, with engineered features such as loop lengths and optimal epitope-paratope contacts. We demonstrate, with different test antibodies derived from different FR-CDR combinations, that despite these test antibodies sharing high overall sequence similarity, they yield diverse functional readouts. Furthermore, we show that strategies relying on one dimensional sequence similarity-based analyses of antibodies miss important structural nuances of the FR-CDR relationship, which is effectively addressed by the amino acid networks approach of this platform.
Collapse
Affiliation(s)
| | - Rahul Raman
- Department of Biological Engineering, And Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | |
Collapse
|
37
|
Miller NL, Clark T, Raman R, Sasisekharan R. Mapping Potential Antigenic Drift Sites (PADS) on SARS-CoV-2 Spike in Continuous Epitope-Paratope Space. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.06.07.446560. [PMID: 34127976 PMCID: PMC8202428 DOI: 10.1101/2021.06.07.446560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
SARS-CoV-2 mutations with antigenic effects pose a risk to immunity developed through vaccination and natural infection. While vaccine updates for current variants of concern (VOCs) are underway, it is likewise important to prepare for further antigenic mutations as the virus navigates the heterogeneous global landscape of host immunity. Toward this end, a wealth of data and tools exist that can augment existing genetic surveillance of VOC evolution. In this study, we integrate published datasets describing genetic, structural, and functional constraints on mutation along with computational analyses of antibody-spike co-crystal structures to identify a set of potential antigenic drift sites (PADS) within the receptor binding domain (RBD) and N-terminal domain (NTD) of SARS-CoV-2 spike protein. Further, we project the PADS set into a continuous epitope-paratope space to facilitate interpretation of the degree to which newly observed mutations might be antigenically synergistic with existing VOC mutations, and this representation suggests that functionally convergent and synergistic antigenic mutations are accruing across VOC NTDs. The PADS set and synergy visualization serve as a reference as new mutations are detected on VOCs, enable proactive investigation of potentially synergistic mutations, and offer guidance to antibody and vaccine design efforts.
Collapse
Affiliation(s)
- Nathaniel L. Miller
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
38
|
Yi HG, Kim H, Kwon J, Choi YJ, Jang J, Cho DW. Application of 3D bioprinting in the prevention and the therapy for human diseases. Signal Transduct Target Ther 2021; 6:177. [PMID: 33986257 PMCID: PMC8119699 DOI: 10.1038/s41392-021-00566-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/24/2021] [Accepted: 03/08/2021] [Indexed: 02/06/2023] Open
Abstract
Rapid development of vaccines and therapeutics is necessary to tackle the emergence of new pathogens and infectious diseases. To speed up the drug discovery process, the conventional development pipeline can be retooled by introducing advanced in vitro models as alternatives to conventional infectious disease models and by employing advanced technology for the production of medicine and cell/drug delivery systems. In this regard, layer-by-layer construction with a 3D bioprinting system or other technologies provides a beneficial method for developing highly biomimetic and reliable in vitro models for infectious disease research. In addition, the high flexibility and versatility of 3D bioprinting offer advantages in the effective production of vaccines, therapeutics, and relevant delivery systems. Herein, we discuss the potential of 3D bioprinting technologies for the control of infectious diseases. We also suggest that 3D bioprinting in infectious disease research and drug development could be a significant platform technology for the rapid and automated production of tissue/organ models and medicines in the near future.
Collapse
Affiliation(s)
- Hee-Gyeong Yi
- Department of Rural and Biosystems Engineering, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-Ro, Gwangju, 61186, Korea
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Pohang, Kyungbuk, 37673, Korea
| | - Hyeonji Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Pohang, Kyungbuk, 37673, Korea
| | - Junyoung Kwon
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Pohang, Kyungbuk, 37673, Korea
| | - Yeong-Jin Choi
- Department of Advanced Biomaterials Research, Korea Institute of Materials Science (KIMS), 797 Changwondaero, Changwon, Kyungnam, 51508, Korea
| | - Jinah Jang
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Pohang, Kyungbuk, 37673, Korea.
- Department of Convergence IT Engineering, POSTECH, 77 Cheongam-Ro, Pohang, Kyungbuk, 37673, Korea.
- Institute of Convergence Science, Yonsei University, 50 Yonsei-Ro, Seoul, 03722, Korea.
| | - Dong-Woo Cho
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Pohang, Kyungbuk, 37673, Korea.
- Institute of Convergence Science, Yonsei University, 50 Yonsei-Ro, Seoul, 03722, Korea.
| |
Collapse
|
39
|
On the irrationality of rational design of an HIV vaccine in light of protein intrinsic disorder. Arch Virol 2021; 166:1283-1296. [PMID: 33606110 PMCID: PMC7892713 DOI: 10.1007/s00705-021-04984-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/19/2020] [Indexed: 12/18/2022]
Abstract
The lack of progress in finding an efficient vaccine for a human immunodeficiency virus (HIV) is daunting. In fact, this search has spanned nearly four decades without much success. There are several objective reasons for such a failure, which include the highly glycosylated nature of HIV-1, the presence of neotopes, and high mutation rates. This article argues that the presence of highly flexible and intrinsically disordered regions in both human anti-HIV-1 antibodies and the major HIV-1immunogen, its surface glycoprotein gp120, represent one of the major causes for the lack of success in utilization of structure-based reverse vaccinology.
Collapse
|
40
|
Dey D, Poudyal S, Rehman A, Hasan SS. Structural and biochemical insights into flavivirus proteins. Virus Res 2021; 296:198343. [PMID: 33607183 DOI: 10.1016/j.virusres.2021.198343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/01/2023]
Abstract
Flaviviruses are the fastest spreading arthropod-borne viruses that cause severe symptoms such as hepatitis, hemorrhagic fever, encephalitis, and congenital deformities. Nearly 40 % of the entire human population is at risk of flavivirus epidemics. Yet, effective vaccination is restricted only to a few flaviviruses such as yellow fever and Japanese encephalitis viruses, and most recently for select cases of dengue virus infections. Despite the global spread of dengue virus, and emergence of new threats such as Zika virus and a new genotype of Japanese encephalitis virus, insights into flavivirus targets for potentially broad-spectrum vaccination are limited. In this review article, we highlight biochemical and structural differences in flavivirus proteins critical for virus assembly and host interactions. A comparative sequence analysis of pH-responsive properties of viral structural proteins identifies trends in conservation of complementary acidic-basic character between interacting viral structural proteins. This is highly relevant to the understanding of pH-sensitive differences in virus assembly in organelles such as neutral ER and acidic Golgi. Surface residues in viral interfaces identified by structural approaches are shown to demonstrate partial conservation, further reinforcing virus-specificity in assembly and interactions with host proteins. A comparative analysis of epitope conservation in emerging flaviviruses identifies therapeutic antibody candidates that have potential as broad spectrum anti-virals, thus providing a path towards development of vaccines.
Collapse
Affiliation(s)
- Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore MD 21201, USA
| | - Shishir Poudyal
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette IN 47907, USA
| | - Asma Rehman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore MD 21201, USA
| | - S Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, 22. S. Greene St. Baltimore MD 21201, USA; Center for Biomolecular Therapeutics, University of Maryland School of Medicine, 9600 Gudelsky Drive, Rockville MD 20850, USA.
| |
Collapse
|
41
|
Susantad T, Fuangthong M, Tharakaraman K, Tit-Oon P, Ruchirawat M, Sasisekharan R. Modified recombinant human erythropoietin with potentially reduced immunogenicity. Sci Rep 2021; 11:1491. [PMID: 33452310 PMCID: PMC7810742 DOI: 10.1038/s41598-020-80402-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 12/15/2020] [Indexed: 11/09/2022] Open
Abstract
Recombinant human erythropoietin (rHuEPO) is a biopharmaceutical drug given to patients who have a low hemoglobin related to chronic kidney disease, cancer or anemia. However, some patients repeatedly receiving rHuEPO develop anti-rHuEPO neutralizing antibodies leading to the development of pure red cell aplasia (PRCA). The immunogenic antibody response activated by rHuEPO is believed to be triggered by T-cells recognizing EPO epitopes bound to MHC molecules displayed on the cell surface of APCs. Previous studies have reported an association between the development of anti-rHuEpo-associated PRCA and the HLA-DRB1*09 gene, which is reported to be entrenched in the Thai population. In this study, we used computational design to screen for immunogenic hotspots recognized by HLA-DRB1*09, and predicted seventeen mutants having anywhere between one through four mutations that reduce affinity for the allele, without disrupting the structural integrity and bioactivity. Five out of seventeen mutants were less immunogenic in vitro while retaining similar or slightly reduced bioactivity than rHuEPO. These engineered proteins could be the potential candidates to treat patients who are rHuEpo-dependent and express the HLA-DRB1*09 allele.
Collapse
Affiliation(s)
- Thanutsorn Susantad
- Program in Environmental Toxicology, Chulabhorn Graduate Institute, Bangkok, 10210, Thailand.,Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Mayuree Fuangthong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Kannan Tharakaraman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Phanthakarn Tit-Oon
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Mathuros Ruchirawat
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand.
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
42
|
Subdominance in Antibody Responses: Implications for Vaccine Development. Microbiol Mol Biol Rev 2020; 85:85/1/e00078-20. [PMID: 33239435 DOI: 10.1128/mmbr.00078-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vaccines work primarily by eliciting antibodies, even when recovery from natural infection depends on cellular immunity. Large efforts have therefore been made to identify microbial antigens that elicit protective antibodies, but these endeavors have encountered major difficulties, as witnessed by the lack of vaccines against many pathogens. This review summarizes accumulating evidence that subdominant protein regions, i.e., surface-exposed regions that elicit relatively weak antibody responses, are of particular interest for vaccine development. This concept may seem counterintuitive, but subdominance may represent an immune evasion mechanism, implying that the corresponding region potentially is a key target for protective immunity. Following a presentation of the concepts of immunodominance and subdominance, the review will present work on subdominant regions in several major human pathogens: the protozoan Plasmodium falciparum, two species of pathogenic streptococci, and the dengue and influenza viruses. Later sections are devoted to the molecular basis of subdominance, its potential role in immune evasion, and general implications for vaccine development. Special emphasis will be placed on the fact that a whole surface-exposed protein domain can be subdominant, as demonstrated for all of the pathogens described here. Overall, the available data indicate that subdominant protein regions are of much interest for vaccine development, not least in bacterial and protozoal systems, for which antibody subdominance remains largely unexplored.
Collapse
|
43
|
Tit-Oon P, Tharakaraman K, Artpradit C, Godavarthi A, Sungkeeree P, Sasisekharan V, Kerdwong J, Miller NL, Mahajan B, Khongmanee A, Ruchirawat M, Sasisekharan R, Fuangthong M. Prediction of the binding interface between monoclonal antibody m102.4 and Nipah attachment glycoprotein using structure-guided alanine scanning and computational docking. Sci Rep 2020; 10:18256. [PMID: 33106487 PMCID: PMC7588459 DOI: 10.1038/s41598-020-75056-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022] Open
Abstract
Nipah Virus (NiV) has been designated as a priority disease with an urgent need for therapeutic development by World Health Organization. The monoclonal antibody m102.4 binds to the immunodominant NiV receptor-binding glycoprotein (GP), and potently neutralizes NiV, indicating its potential as a therapeutic agent. Although the co-crystal structure of m102.3, an m102.4 derivative, in complex with the GP of the related Hendra Virus (HeV) has been solved, the structural interaction between m102.4 and NiV is uncharacterized. Herein, we used structure-guided alanine-scanning mutagenesis to map the functional epitope and paratope residues that govern the antigen-antibody interaction. Our results revealed that the binding of m102.4 is mediated predominantly by two residues in the HCDR3 region, which is unusually small for an antibody-antigen interaction. We performed computational docking to generate a structural model of m102.4-NiV interaction. Our model indicates that m102.4 targets the common hydrophobic central cavity and a hydrophilic rim on the GP, as observed for the m102.3-HeV co-crystal, albeit with Fv orientation differences. In summary, our study provides insight into the m102.4-NiV interaction, demonstrating that structure-guided alanine-scanning and computational modeling can serve as the starting point for additional antibody reengineering (e.g. affinity maturation) to generate potential therapeutic candidates.
Collapse
Affiliation(s)
- Phanthakarn Tit-Oon
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Kannan Tharakaraman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Abhinav Godavarthi
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Yale University, New Haven, CT, 06520, USA
| | - Pareenart Sungkeeree
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Varun Sasisekharan
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Jarunee Kerdwong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Nathaniel Loren Miller
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Bhuvna Mahajan
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Amnart Khongmanee
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Mathuros Ruchirawat
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Mayuree Fuangthong
- Translational Research Unit, Chulabhorn Research Institute, Bangkok, 10210, Thailand.
| |
Collapse
|
44
|
Shukla R, Ramasamy V, Shanmugam RK, Ahuja R, Khanna N. Antibody-Dependent Enhancement: A Challenge for Developing a Safe Dengue Vaccine. Front Cell Infect Microbiol 2020; 10:572681. [PMID: 33194810 PMCID: PMC7642463 DOI: 10.3389/fcimb.2020.572681] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/15/2020] [Indexed: 01/05/2023] Open
Abstract
In 2019, the United States Food and Drug Administration accorded restricted approval to Sanofi Pasteur's Dengvaxia, a live attenuated vaccine (LAV) for dengue fever, a mosquito-borne viral disease, caused by four antigenically distinct dengue virus serotypes (DENV 1-4). The reason for this limited approval is the concern that this vaccine sensitized some of the dengue-naïve recipients to severe dengue fever. Recent knowledge about the nature of the immune response elicited by DENV viruses suggests that all LAVs have inherent capacity to predominantly elicit antibodies (Abs) against the pre-membrane (prM) and fusion loop epitope (FLE) of DENV. These antibodies are generally cross-reactive among DENV serotypes carrying a higher risk of promoting Antibody-Dependent Enhancement (ADE). ADE is a phenomenon in which suboptimal neutralizing or non-neutralizing cross-reactive antibodies bind to virus and facilitate Fcγ receptor mediated enhanced entry into host cells, followed by its replication, and thus increasing the cellular viral load. On the other hand, antibody responses directed against the host-cell receptor binding domain of DENV envelope domain-III (EDIII), exhibit a higher degree of type-specificity with lower potential of ADE. The challenges associated with whole DENV-based vaccine strategies necessitate re-focusing our attention toward the designed dengue vaccine candidates, capable of inducing predominantly type-specific immune responses. If the designed vaccines elicited predominantly EDIII-directed serotype specific antibodies in the absence of prM and FLE antibodies, this could avoid the ADE phenomenon largely associated with the prM and FLE antibodies. The generation of type-specific antibodies to each of the four DENV serotypes by the designed vaccines could avoid the immune evasion mechanisms of DENVs. For the enhanced vaccine safety, all dengue vaccine candidates should be assessed for the extent of type-specific (minimal ADE) vs. cross-reactive (ADE promoting) neutralizing antibodies. The type-specific EDIII antibodies may be more directly related to protection from disease in the absence of ADE promoted by the cross-reactive antibodies.
Collapse
Affiliation(s)
- Rahul Shukla
- Translational Health Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Viswanathan Ramasamy
- Translational Health Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rajgokul K Shanmugam
- Translational Health Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Richa Ahuja
- Translational Health Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Navin Khanna
- Translational Health Group, Molecular Medicine Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| |
Collapse
|
45
|
Silva NM, Santos NC, Martins IC. Dengue and Zika Viruses: Epidemiological History, Potential Therapies, and Promising Vaccines. Trop Med Infect Dis 2020; 5:E150. [PMID: 32977703 PMCID: PMC7709709 DOI: 10.3390/tropicalmed5040150] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/05/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022] Open
Abstract
Dengue virus (DENV), which can lead to fatal hemorrhagic fever, affects 390 million people worldwide. The closely related Zika virus (ZIKV) causes microcephaly in newborns and Guillain-Barré syndrome in adults. Both viruses are mostly transmitted by Aedes albopictus and Aedes aegypti mosquitoes, which, due to globalization of trade and travel alongside climate change, are spreading worldwide, paving the way to DENV and ZIKV transmission and the occurrence of new epidemics. Local outbreaks have already occurred in temperate climates, even in Europe. As there are no specific treatments, these viruses are an international public health concern. Here, we analyze and discuss DENV and ZIKV outbreaks history, clinical and pathogenesis features, and modes of transmission, supplementing with information on advances on potential therapies and restraining measures. Taking advantage of the knowledge of the structure and biological function of the capsid (C) protein, a relatively conserved protein among flaviviruses, within a genus that includes DENV and ZIKV, we designed and patented a new drug lead, pep14-23 (WO2008/028939A1). It was demonstrated that it inhibits the interaction of DENV C protein with the host lipid system, a process essential for viral replication. Such an approach can be used to develop new therapies for related viruses, such as ZIKV.
Collapse
Affiliation(s)
| | - Nuno C. Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal;
| | - Ivo C. Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal;
| |
Collapse
|
46
|
Remmel JL, Beauchemin KS, Mishra AK, Frei JC, Lai JR, Bailey-Kellogg C, Ackerman ME. Combinatorial Resurfacing of Dengue Envelope Protein Domain III Antigens Selectively Ablates Epitopes Associated with Serotype-Specific or Infection-Enhancing Antibody Responses. ACS COMBINATORIAL SCIENCE 2020; 22:446-456. [PMID: 32574486 DOI: 10.1021/acscombsci.0c00073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutagenesis of surface-exposed residues, or "resurfacing", is a protein engineering strategy that can be utilized to disrupt antibody recognition or modulate the capacity of a protein to elicit antibody responses. We apply resurfacing to engineer Dengue virus envelope protein domain III (DENV DIII) antigens with the goal of focusing humoral recognition on epitopes of interest by selective ablation of irrelevant and undesired epitopes. Cross-reactive but non-neutralizing antibodies have the potential to enhance Dengue virus (DENV) infection by a process called antibody-dependent enhancement, thought to be associated with severe secondary heterotypic infection. Thus, a focus on epitopes associated with broadly neutralizing antibodies is important both for understanding human antibody responses against DENV and for the development of a successful DENV vaccine. To engineer DENV DIII antigens focusing on the AG strand epitope associated with broadly neutralizing antibody responses, we generated yeast surface display libraries of DENV2 DIII where the AB loop (associated with cross-reactive but non-neutralizing antibody responses) and FG loop (associated with serotype-specific antibody responses) were mutagenized to allow for all possible amino acid substitutions. Loop variants that maintained the AG strand epitope and simultaneously disrupted the AB and FG loop epitopes exhibited high and diverse mutational loads that were amenable to loop exchange and transplantation into a DENV4 DIII background. Thus, several loop variants fulfill this antigenicity criteria regardless of serotype context. The resulting resurfaced DIII antigens may be utilized as AG strand epitope-focusing probes or immunogen candidates.
Collapse
Affiliation(s)
- Jennifer L. Remmel
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Kathryn S. Beauchemin
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Akaash K. Mishra
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Julia C. Frei
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, United States
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755, United States
| |
Collapse
|
47
|
Zhao H, Xu L, Bombardi R, Nargi R, Deng Z, Errico JM, Nelson CA, Dowd KA, Pierson TC, Crowe JE, Diamond MS, Fremont DH. Mechanism of differential Zika and dengue virus neutralization by a public antibody lineage targeting the DIII lateral ridge. J Exp Med 2020; 217:jem.20191792. [PMID: 31757867 PMCID: PMC7041715 DOI: 10.1084/jem.20191792] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/09/2019] [Accepted: 10/18/2019] [Indexed: 12/20/2022] Open
Abstract
Evaluation of the human antibody response to Zika virus has identified common germline-derived mAbs capable of cross flavivirus neutralization. Zhao et al. provide a detailed mechanistic understanding of how flavivirus infections are prevented in a strain-specific manner by a representative mAb. We previously generated a panel of human monoclonal antibodies (mAbs) against Zika virus (ZIKV) and identified one, ZIKV-116, that shares germline usage with mAbs identified in multiple donors. Here we show that ZIKV-116 interferes with ZIKV infection at a post-cellular attachment step by blocking viral fusion with host membranes. ZIKV-116 recognizes the lateral ridge of envelope protein domain III, with one critical residue varying between the Asian and African strains responsible for differential binding affinity and neutralization potency (E393D). ZIKV-116 also binds to and cross-neutralizes some dengue virus serotype 1 (DENV1) strains, with genotype-dependent inhibition explained by variation in a domain II residue (R204K) that potentially modulates exposure of the distally located, partially cryptic epitope. The V-J reverted germline configuration of ZIKV-116 preferentially binds to and neutralizes an Asian ZIKV strain, suggesting that this epitope may optimally induce related B cell clonotypes. Overall, these studies provide a structural and molecular mechanism for a cross-reactive mAb that uniquely neutralizes ZIKV and DENV1.
Collapse
Affiliation(s)
- Haiyan Zhao
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO
| | - Lily Xu
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO
| | - Robin Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN
| | - Rachel Nargi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN
| | - Zengqin Deng
- Department of Cell Biology & Physiology, Washington University School of Medicine, Saint Louis, MO
| | - John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO
| | - Christopher A Nelson
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO
| | - Kimberly A Dowd
- Viral Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Theodore C Pierson
- Viral Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Michael S Diamond
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO.,Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO.,Department of Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO.,Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO.,Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO
| |
Collapse
|
48
|
Pecetta S, Finco O, Seubert A. Quantum leap of monoclonal antibody (mAb) discovery and development in the COVID-19 era. Semin Immunol 2020; 50:101427. [PMID: 33277154 PMCID: PMC7670927 DOI: 10.1016/j.smim.2020.101427] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/16/2020] [Accepted: 11/16/2020] [Indexed: 01/08/2023]
Abstract
In recent years the global market for monoclonal antibodies (mAbs) became a multi-billion-dollar business. This success is mainly driven by treatments in the oncology and autoimmune space. Instead, development of effective mAbs against infectious diseases has been lagging behind. For years the high production cost and limited efficacy have blocked broader application of mAbs in the infectious disease space, which instead has been dominated for almost a century by effective and cheap antibiotics and vaccines. Only very few mAbs against RSV, anthrax, Clostridium difficile or rabies have reached the market. This is about to change. The development of urgently needed and highly effective mAbs as preventive and therapeutic treatments against a variety of pathogens is gaining traction. Vast advances in mAb isolation, engineering and production have entirely shifted the cost-efficacy balance. MAbs against devastating diseases like Ebola, HIV and other complex pathogens are now within reach. This trend is further accelerated by ongoing or imminent health crises like COVID-19 and antimicrobial resistance (AMR), where antibodies could be the last resort. In this review we will retrace the history of antibodies from the times of serum therapy to modern mAbs and lay out how the current run for effective treatments against COVID-19 will lead to a quantum leap in scientific, technological and health care system innovation around mAb treatments for infectious diseases.
Collapse
|
49
|
Tyagi A, Ahmed T, Shi J, Bhushan S. A complex between the Zika virion and the Fab of a broadly cross-reactive neutralizing monoclonal antibody revealed by cryo-EM and single particle analysis at 4.1 Å resolution. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100028. [PMID: 32647830 PMCID: PMC7337043 DOI: 10.1016/j.yjsbx.2020.100028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 11/30/2022]
Abstract
Zika virus (ZIKV) recently emerged as a major public health concern because it can cause fetal microcephaly and neurological disease such as the Guillain-Barré syndrome. A particularly potent class of broadly neutralizing antibodies (nAbs) targets a quaternary epitope located at the interface of two envelope proteins monomers, exposed at the surface of the mature virion. This “E-dimer-dependent epitope” (EDE), comprises the fusion loop of one monomer at the tip of domain II of E and a portion of the domains I and III of the adjacent monomer. Since this epitope largely overlaps with the binding site of the precursor membrane protein (prM) during Zika virion maturation, its molecular surface is evolutionary conserved in flaviviruses such as Dengue and Zika viruses, and can elicit antibodies that broadly neutralize various ZIKV strains. Here, we present a cryo-EM reconstruction at 4.1 Å resolution of the virion bound to the antigen binding fragment (Fab) of an antibody that targets this mutationally-constrained quaternary epitope. The Fab incompletely covers the surface of the virion as it does not bind next to its 5-fold icosahedral axes. The structure reveals details of the binding mode of this potent neutralizing class of antibodies and can inform the design of immunogens and vaccines targeting this conserved epitope.
Collapse
Affiliation(s)
- Anu Tyagi
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Tofayel Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jian Shi
- Center for Bio-Imaging Sciences, National University of Singapore, Singapore
| | - Shashi Bhushan
- School of Biological Sciences, Nanyang Technological University, Singapore
- Nanyang Institute of Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, 636921, Singapore
- Corresponding author at: School of Biological Sciences, Nanyang Technological University, Singapore.
| |
Collapse
|
50
|
Wilken L, Rimmelzwaan GF. Adaptive Immunity to Dengue Virus: Slippery Slope or Solid Ground for Rational Vaccine Design? Pathogens 2020; 9:pathogens9060470. [PMID: 32549226 PMCID: PMC7350362 DOI: 10.3390/pathogens9060470] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022] Open
Abstract
The four serotypes of dengue virus are the most widespread causes of arboviral disease, currently placing half of the human population at risk of infection. Pre-existing immunity to one dengue virus serotype can predispose to severe disease following secondary infection with a different serotype. The phenomenon of immune enhancement has complicated vaccine development and likely explains the poor long-term safety profile of a recently licenced dengue vaccine. Therefore, alternative vaccine strategies should be considered. This review summarises studies dissecting the adaptive immune responses to dengue virus infection and (experimental) vaccination. In particular, we discuss the roles of (i) neutralising antibodies, (ii) antibodies to non-structural protein 1, and (iii) T cells in protection and pathogenesis. We also address how these findings could translate into next-generation vaccine approaches that mitigate the risk of enhanced dengue disease. Finally, we argue that the development of a safe and efficacious dengue vaccine is an attainable goal.
Collapse
|