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Chew CWY, Young BE, Tambyah PA, Vasoo S, Chan CEZ. Bidirectional Evolution of SARS-CoV-2 Virus in Immunocompromised Hosts. Influenza Other Respir Viruses 2024; 18:e13266. [PMID: 38462553 PMCID: PMC10925721 DOI: 10.1111/irv.13266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/04/2024] [Indexed: 03/12/2024] Open
Affiliation(s)
| | - Barnaby E. Young
- National Centre for Infectious DiseasesSingaporeSingapore
- Tan Tock Seng HospitalSingaporeSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
| | - Paul A. Tambyah
- Division of Infectious Diseases, Department of MedicineNational University HospitalSingaporeSingapore
- Infectious Diseases Translational Research ProgramNational University of SingaporeSingaporeSingapore
| | - Shawn Vasoo
- National Centre for Infectious DiseasesSingaporeSingapore
- Tan Tock Seng HospitalSingaporeSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
| | - Conrad E. Z. Chan
- National Centre for Infectious DiseasesSingaporeSingapore
- Defence Medical and Environmental Research InstituteDSO National LaboratoriesSingaporeSingapore
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2
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Chye DH, Chew CWY, Yeo HP, Tambyah PA, Young BE, Tan GGY, Tan BH, Vasoo S, Chan CEZ. Neutralization escape of emerging subvariants XBB.1.5/1.9.1 and XBB.2.3 from current therapeutic monoclonal antibodies. J Med Virol 2023; 95:e29074. [PMID: 37665160 DOI: 10.1002/jmv.29074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Affiliation(s)
- De Hoe Chye
- DSO National Laboratories, Defence Medical and Environmental Research Institute, Singapore, Singapore
| | | | - He Ping Yeo
- National Centre for Infectious Diseases, Singapore, Singapore
| | - Paul A Tambyah
- Department of Medicine, Infectious Diseases Translational Research Program, Division of Infectious Diseases, National University Hospital, National University of Singapore, Singapore, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Gladys G Y Tan
- DSO National Laboratories, Defence Medical and Environmental Research Institute, Singapore, Singapore
| | - Boon Huan Tan
- DSO National Laboratories, Defence Medical and Environmental Research Institute, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Conrad E Z Chan
- DSO National Laboratories, Defence Medical and Environmental Research Institute, Singapore, Singapore
- National Centre for Infectious Diseases, Singapore, Singapore
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3
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Chan CEZ, Wong SKK, Yazid NBM, Ng OT, Marimuthu K, Chan M, Howe HS, Leo YS, Leung BP, Vasoo SS, Young BE. Residual humoral immunity sustained over decades in a cohort of vaccinia-vaccinated individuals. J Infect Dis 2022; 227:1002-1006. [PMID: 36200239 DOI: 10.1093/infdis/jiac409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/14/2022] Open
Abstract
In 2019, Singapore experienced a case of imported Monkeypox. As with smallpox, disease can be prevented through vaccination, which was mandatory for Singaporean infants until 1981. However, the degree of residual immunity in older vaccinated Singaporeans remains unknown. Sera from individuals born from 1946-1984 were therefore tested and those born prior to 1981 were found to have higher anti-vaccinia IgG and neutralizing activity titres. This suggests that protective humoral immunity remains which could reduce disease severity in an orthopoxvirus outbreak. Correlation between IgG and neutralizing titres was observed indicating that serology could be used as a surrogate marker for immunity.
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Affiliation(s)
- Conrad E Z Chan
- National Centre for Infectious Diseases, Singapore 308442, Singapore.,Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
| | - Steven K K Wong
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
| | | | - Oon Tek Ng
- National Centre for Infectious Diseases, Singapore 308442, Singapore.,Tan Tock Seng Hospital, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore 308442, Singapore.,Tan Tock Seng Hospital, Singapore 308433, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Monica Chan
- National Centre for Infectious Diseases, Singapore 308442, Singapore.,Tan Tock Seng Hospital, Singapore 308433, Singapore
| | - Hwee Siew Howe
- National Centre for Infectious Diseases, Singapore 308442, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, Singapore 308442, Singapore.,Tan Tock Seng Hospital, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Bernard P Leung
- Tan Tock Seng Hospital, Singapore 308433, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Health and Social Sciences, Singapore Institute of Technology, Singapore 138683, Singapore
| | - Shawn S Vasoo
- National Centre for Infectious Diseases, Singapore 308442, Singapore.,Tan Tock Seng Hospital, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Barnaby E Young
- National Centre for Infectious Diseases, Singapore 308442, Singapore.,Tan Tock Seng Hospital, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
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4
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Blasiak A, Truong ATL, Wang P, Hooi L, Chye DH, Tan SB, You K, Remus A, Allen DM, Chai LYA, Chan CEZ, Lye DCB, Tan GYG, Seah SGK, Chow EKH, Ho D. IDentif.AI-Omicron: Harnessing an AI-Derived and Disease-Agnostic Platform to Pinpoint Combinatorial Therapies for Clinically Actionable Anti-SARS-CoV-2 Intervention. ACS Nano 2022; 16:15141-15154. [PMID: 35977379 DOI: 10.1021/acsnano.2c06366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanomedicine-based and unmodified drug interventions to address COVID-19 have evolved over the course of the pandemic as more information is gleaned and virus variants continue to emerge. For example, some early therapies (e.g., antibodies) have experienced markedly decreased efficacy. Due to a growing concern of future drug resistant variants, current drug development strategies are seeking to find effective drug combinations. In this study, we used IDentif.AI, an artificial intelligence-derived platform, to investigate the drug-drug and drug-dose interaction space of six promising experimental or currently deployed therapies at various concentrations: EIDD-1931, YH-53, nirmatrelvir, AT-511, favipiravir, and auranofin. The drugs were tested in vitro against a live B.1.1.529 (Omicron) virus first in monotherapy and then in 50 strategic combinations designed to interrogate the interaction space of 729 possible combinations. Key findings and interactions were then further explored and validated in an additional experimental round using an expanded concentration range. Overall, we found that few of the tested drugs showed moderate efficacy as monotherapies in the actionable concentration range, but combinatorial drug testing revealed significant dose-dependent drug-drug interactions, specifically between EIDD-1931 and YH-53, as well as nirmatrelvir and YH-53. Checkerboard validation analysis confirmed these synergistic interactions and also identified an interaction between EIDD-1931 and favipiravir in an expanded range. Based on the platform nature of IDentif.AI, these findings may support further explorations of the dose-dependent drug interactions between different drug classes in further pre-clinical and clinical trials as possible combinatorial therapies consisting of unmodified and nanomedicine-enabled drugs, to combat current and future COVID-19 strains and other emerging pathogens.
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Affiliation(s)
- Agata Blasiak
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 117583, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
| | - Anh T L Truong
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 117583, Singapore
| | - Peter Wang
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 117583, Singapore
| | - Lissa Hooi
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - De Hoe Chye
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 117510, Singapore
| | - Shi-Bei Tan
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 117583, Singapore
| | - Kui You
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 117583, Singapore
| | - Alexandria Remus
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 117583, Singapore
| | - David Michael Allen
- Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 119228, Singapore
- Division of Infectious Disease, Department of Medicine, National University Hospital, 119074, Singapore
| | - Louis Yi Ann Chai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 119228, Singapore
- Division of Infectious Disease, Department of Medicine, National University Hospital, 119074, Singapore
| | - Conrad E Z Chan
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 117510, Singapore
- National Centre for Infectious Diseases (NCID), Jalan Tan Tock Seng, 308442, Singapore
| | - David C B Lye
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 119228, Singapore
- National Centre for Infectious Diseases (NCID), Jalan Tan Tock Seng, 308442, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 308232, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, 308433, Singapore
| | - Gek-Yen G Tan
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 117510, Singapore
| | - Shirley G K Seah
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 117510, Singapore
| | - Edward Kai-Hua Chow
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 117583, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Dean Ho
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 117583, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
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5
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Prativadibhayankaram VS, Lee LSU, Lye D, Xiaoying X, Nellore R, Pendharkar V, Hentze H, Guan S, Ayers BJ, Seah SGK, Chye DH, Talib NSN, Kaliaperumal N, Ong WY, Wong ZX, Au VB, Alok A, Connolly JE, Boyd-Kirkup JD, Ingram PJ, Hanson BJ, Ethirajulu K, O'Connell D, Chan CEZ. First-in-Human Study to Evaluate Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of a Rapidly Developed SARS-CoV-2 Therapeutic Antibody, AOD01, in Healthy Adults. Infect Dis Ther 2022; 11:1999-2015. [PMID: 36058990 PMCID: PMC9441134 DOI: 10.1007/s40121-022-00681-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction AOD01 is a novel, fully human immunoglobulin (Ig) G1 neutralizing monoclonal antibody that was developed as a therapeutic against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). This first-in-human study assessed safety, tolerability, pharmacokinetics (PK), and pharmacodynamics of AOD01 in healthy volunteers. Methods Intravenous doses of AOD01 were evaluated in escalating cohorts [four single-dose cohorts (2, 5, 10, and 20 mg/kg) and one two-dose cohort (two doses of 20 mg/kg, 24 h apart)]. Results Twenty-three subjects were randomized to receive AOD01 or a placebo in blinded fashion. A total of 34 treatment-emergent adverse events (TEAEs) were reported; all were mild in severity. Related events (headache and diarrhea) were reported in one subject each. No event of infusion reactions, serious adverse event (SAE), or discontinuation due to AE were reported. The changes in laboratory parameters, vital signs, and electrocardiograms were minimal. Dose-related exposure was seen from doses 2 to 20 mg/kg as confirmed by Cmax and AUC0–tlast. The median Tmax was 1.5–3 h. Clearance was dose independent. Study results revealed long half-lives (163–465 h). Antidrug antibodies (ADA) to AOD01 were not detected among subjects, except in one subject of the two-dose cohort on day 92. Sustained ex vivo neutralization of SARS-CoV-2 was recorded until day 29 with single doses from 2 to 20 mg/kg and until day 43 with two doses of 20 mg/kg. Conclusions AOD01 was safe and well tolerated, demonstrated dose-related PK, non-immunogenic status, and sustained ex vivo neutralization of SARS-CoV-2 after single intravenous dose ranging from 2 to 20 mg/kg and two doses of 20 mg/kg and show good potential for treatment of SARS-CoV-2 infection. (Health Sciences Authority identifier number CTA2000119). Supplementary Information The online version contains supplementary material available at 10.1007/s40121-022-00681-1.
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Affiliation(s)
| | - Lawrence Soon-U Lee
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore
| | - David Lye
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore.,Yong Loo Lin School of Medicine, Singapore, Singapore.,Lee Kong Chian School of Medicine, Singapore, Singapore
| | - Xu Xiaoying
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore
| | - Ranjani Nellore
- Experimental Drug Development Centre, A*STAR Research Entities (ARES), Singapore, Singapore
| | - Vishal Pendharkar
- Experimental Drug Development Centre, A*STAR Research Entities (ARES), Singapore, Singapore
| | - Hannes Hentze
- Experimental Drug Development Centre, A*STAR Research Entities (ARES), Singapore, Singapore
| | - Siyu Guan
- Hummingbird Bioscience, Singapore, Singapore
| | | | - Shirley G K Seah
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - De Hoe Chye
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - Najwa S N Talib
- Institute of Molecular and Cell Biology (IMCB), A*STAR Research Entities (ARES), Singapore, Singapore
| | - Nivashini Kaliaperumal
- Institute of Molecular and Cell Biology (IMCB), A*STAR Research Entities (ARES), Singapore, Singapore
| | - Wei Yee Ong
- Institute of Molecular and Cell Biology (IMCB), A*STAR Research Entities (ARES), Singapore, Singapore
| | - Zi Xin Wong
- Institute of Molecular and Cell Biology (IMCB), A*STAR Research Entities (ARES), Singapore, Singapore
| | - Veonice B Au
- Institute of Molecular and Cell Biology (IMCB), A*STAR Research Entities (ARES), Singapore, Singapore
| | - Anshula Alok
- Institute of Molecular and Cell Biology (IMCB), A*STAR Research Entities (ARES), Singapore, Singapore
| | - John E Connolly
- Institute of Molecular and Cell Biology (IMCB), A*STAR Research Entities (ARES), Singapore, Singapore.,Institute of Biomedical Studies, Baylor University, Waco, TX, USA
| | | | | | | | - Kantharaj Ethirajulu
- Experimental Drug Development Centre, A*STAR Research Entities (ARES), Singapore, Singapore
| | - Damian O'Connell
- Experimental Drug Development Centre, A*STAR Research Entities (ARES), Singapore, Singapore
| | - Conrad E Z Chan
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, 16 Jalan Tan Tock Seng, Singapore, 308442, Singapore. .,Biological Defence Programme, DSO National Laboratories, Singapore, Singapore.
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6
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Chan CEZ, Seah SGK, Chye DH, Massey S, Torres M, Lim APC, Wong SKK, Neo JJY, Wong PS, Lim JH, Loh GSL, Wang D, Boyd-Kirkup JD, Guan S, Thakkar D, Teo GH, Purushotorman K, Hutchinson PE, Young BE, Low JG, MacAry PA, Hentze H, Prativadibhayankara VS, Ethirajulu K, Comer JE, Tseng CTK, Barrett ADT, Ingram PJ, Brasel T, Hanson BJ. The Fc-mediated effector functions of a potent SARS-CoV-2 neutralizing antibody, SC31, isolated from an early convalescent COVID-19 patient, are essential for the optimal therapeutic efficacy of the antibody. PLoS One 2021; 16:e0253487. [PMID: 34161386 PMCID: PMC8221499 DOI: 10.1371/journal.pone.0253487] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
Although SARS-CoV-2-neutralizing antibodies are promising therapeutics against COVID-19, little is known about their mechanism(s) of action or effective dosing windows. We report the generation and development of SC31, a potent SARS-CoV-2 neutralizing antibody, isolated from a convalescent patient. Antibody-mediated neutralization occurs via an epitope within the receptor-binding domain of the SARS-CoV-2 Spike protein. SC31 exhibited potent anti-SARS-CoV-2 activities in multiple animal models. In SARS-CoV-2 infected K18-human ACE2 transgenic mice, treatment with SC31 greatly reduced viral loads and attenuated pro-inflammatory responses linked to the severity of COVID-19. Importantly, a comparison of the efficacies of SC31 and its Fc-null LALA variant revealed that the optimal therapeutic efficacy of SC31 requires Fc-mediated effector functions that promote IFNγ-driven anti-viral immune responses, in addition to its neutralization ability. A dose-dependent efficacy of SC31 was observed down to 5mg/kg when administered before viral-induced lung inflammatory responses. In addition, antibody-dependent enhancement was not observed even when infected mice were treated with SC31 at sub-therapeutic doses. In SARS-CoV-2-infected hamsters, SC31 treatment significantly prevented weight loss, reduced viral loads, and attenuated the histopathology of the lungs. In rhesus macaques, the therapeutic potential of SC31 was evidenced through the reduction of viral loads in both upper and lower respiratory tracts to undetectable levels. Together, the results of our preclinical studies demonstrated the therapeutic efficacy of SC31 in three different models and its potential as a COVID-19 therapeutic candidate.
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Affiliation(s)
- Conrad E. Z. Chan
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - Shirley G. K. Seah
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - De Hoe Chye
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - Shane Massey
- Department of Microbiology & Immunology and Office of Regulated Nonclinical Studies, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Maricela Torres
- Department of Microbiology & Immunology and Office of Regulated Nonclinical Studies, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Angeline P. C. Lim
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - Steven K. K. Wong
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - Jacklyn J. Y. Neo
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - Pui San Wong
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - Jie Hui Lim
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - Gary S. L. Loh
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | - Dongling Wang
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
| | | | - Siyu Guan
- Hummingbird Bioscience, Singapore, Singapore
| | | | - Guo Hui Teo
- Life Science Institute, National University of Singapore, Singapore, Singapore
| | - Kiren Purushotorman
- Life Science Institute, National University of Singapore, Singapore, Singapore
| | - Paul E. Hutchinson
- Life Science Institute, National University of Singapore, Singapore, Singapore
| | | | - Jenny G. Low
- Singapore General Hospital, Singapore, Singapore
- Programme in Emerging Infectious Disease, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Paul A. MacAry
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hannes Hentze
- Experimental Drug Development Centre, Therapeutics Development, A*STAR Research Entities (ARES), Singapore, Singapore
| | | | - Kantharaj Ethirajulu
- Experimental Drug Development Centre, Therapeutics Development, A*STAR Research Entities (ARES), Singapore, Singapore
| | - Jason E. Comer
- Department of Microbiology & Immunology and Office of Regulated Nonclinical Studies, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Chien-Te K. Tseng
- Department of Microbiology & Immunology and Center of Biodefense and Emerging Disease, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Alan D. T. Barrett
- Department of Pathology and Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, United States of America
| | | | - Trevor Brasel
- Department of Microbiology & Immunology and Office of Regulated Nonclinical Studies, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Brendon John Hanson
- Biological Defence Programme, DSO National Laboratories, Singapore, Singapore
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7
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Blasiak A, Lim JJ, Seah SGK, Kee T, Remus A, Chye DH, Wong PS, Hooi L, Truong ATL, Le N, Chan CEZ, Desai R, Ding X, Hanson BJ, Chow EK, Ho D. IDentif.AI: Rapidly optimizing combination therapy design against severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Cov-2) with digital drug development. Bioeng Transl Med 2021; 6:e10196. [PMID: 33532594 PMCID: PMC7823122 DOI: 10.1002/btm2.10196] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to multiple drug repurposing clinical trials that have yielded largely uncertain outcomes. To overcome this challenge, we used IDentif.AI, a platform that pairs experimental validation with artificial intelligence (AI) and digital drug development to rapidly pinpoint unpredictable drug interactions and optimize infectious disease combination therapy design with clinically relevant dosages. IDentif.AI was paired with a 12-drug candidate therapy set representing over 530,000 drug combinations against the SARS-CoV-2 live virus collected from a patient sample. IDentif.AI pinpointed the optimal combination as remdesivir, ritonavir, and lopinavir, which was experimentally validated to mediate a 6.5-fold enhanced efficacy over remdesivir alone. Additionally, it showed hydroxychloroquine and azithromycin to be relatively ineffective. The study was completed within 2 weeks, with a three-order of magnitude reduction in the number of tests needed. IDentif.AI independently mirrored clinical trial outcomes to date without any data from these trials. The robustness of this digital drug development approach paired with in vitro experimentation and AI-driven optimization suggests that IDentif.AI may be clinically actionable toward current and future outbreaks.
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Affiliation(s)
- Agata Blasiak
- The N.1 Institute for Health (N.1)National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Biomedical Engineering, NUS EngineeringNational University of SingaporeSingaporeSingapore
| | - Jhin Jieh Lim
- Cancer Science Institute of SingaporeNational University of SingaporeSingaporeSingapore
| | - Shirley Gek Kheng Seah
- Defence Medical and Environmental Research InstituteDSO National LaboratoriesSingaporeSingapore
| | - Theodore Kee
- The N.1 Institute for Health (N.1)National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Biomedical Engineering, NUS EngineeringNational University of SingaporeSingaporeSingapore
| | - Alexandria Remus
- The N.1 Institute for Health (N.1)National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Biomedical Engineering, NUS EngineeringNational University of SingaporeSingaporeSingapore
| | - De Hoe Chye
- Defence Medical and Environmental Research InstituteDSO National LaboratoriesSingaporeSingapore
| | - Pui San Wong
- Defence Medical and Environmental Research InstituteDSO National LaboratoriesSingaporeSingapore
| | - Lissa Hooi
- Cancer Science Institute of SingaporeNational University of SingaporeSingaporeSingapore
| | - Anh T. L. Truong
- The N.1 Institute for Health (N.1)National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Biomedical Engineering, NUS EngineeringNational University of SingaporeSingaporeSingapore
| | - Nguyen Le
- The N.1 Institute for Health (N.1)National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Biomedical Engineering, NUS EngineeringNational University of SingaporeSingaporeSingapore
| | - Conrad E. Z. Chan
- Defence Medical and Environmental Research InstituteDSO National LaboratoriesSingaporeSingapore
| | | | - Xianting Ding
- Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Brendon J. Hanson
- Defence Medical and Environmental Research InstituteDSO National LaboratoriesSingaporeSingapore
| | - Edward Kai‐Hua Chow
- The N.1 Institute for Health (N.1)National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Biomedical Engineering, NUS EngineeringNational University of SingaporeSingaporeSingapore
- Cancer Science Institute of SingaporeNational University of SingaporeSingaporeSingapore
- Department of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Dean Ho
- The N.1 Institute for Health (N.1)National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Biomedical Engineering, NUS EngineeringNational University of SingaporeSingaporeSingapore
- Department of Pharmacology, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
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8
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Lim SY, Chan CEZ, Lisowska MM, Hanson BJ, MacAry PA. The Molecular Engineering of an Anti-Idiotypic Antibody for Pharmacokinetic Analysis of a Fully Human Anti-Infective. PLoS One 2015; 10:e0145381. [PMID: 26700297 PMCID: PMC4689483 DOI: 10.1371/journal.pone.0145381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 12/01/2015] [Indexed: 11/19/2022] Open
Abstract
Anti-idiotype monoclonal antibodies represent a class of reagents that are potentially optimal for analyzing the pharmacokinetics of fully human, anti-infective antibodies that have been developed as therapeutic candidates. This is particularly important where direct pathogen binding assays are complicated by requirements for biosafety level III or IV for pathogen handling. In this study, we describe the development of a recombinant, anti-idiotype monoclonal antibody termed E1 for the detection of a fully human, serotype-specific, therapeutic antibody candidate for the BSLIII pathogen Dengue virus termed 14c10 hG1. E1 was generated by naïve human Fab phage library panning technology and subsequently engineered as a monoclonal antibody. We show that E1 is highly specific for the fully-folded form of 14c10 hG1 and can be employed for the detection of this antibody in healthy human subjects' serum by enzyme linked immunosorbent assay. In addition, we show that E1 is capable of blocking the binding of 14c10 hG1 to dengue virus serotype 1. Finally, we show that E1 can detect 14c10 hG1 in mouse serum after the administration of the therapeutic antibody in vivo. E1 represents an important new form of ancillary reagent that can be utilized in the clinical development of a therapeutic human antibody candidate.
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Affiliation(s)
- She Yah Lim
- Department of Microbiology, National University of Singapore, Singapore, Singapore
- Immunology Program, Centre for Life Sciences, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, Singapore, Singapore
| | - Conrad E. Z. Chan
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Singapore
| | - Malgorzata M. Lisowska
- Department of Microbiology, National University of Singapore, Singapore, Singapore
- Immunology Program, Centre for Life Sciences, National University of Singapore, Singapore, Singapore
| | - Brendon J. Hanson
- Department of Microbiology, National University of Singapore, Singapore, Singapore
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Singapore
| | - Paul A. MacAry
- Department of Microbiology, National University of Singapore, Singapore, Singapore
- Immunology Program, Centre for Life Sciences, National University of Singapore, Singapore, Singapore
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Abstract
Phage display involves the expression of selected proteins on the surface of filamentous phage through fusion with phage coat protein, with the genetic sequence packaged within, linking phenotype to genotype selection. When combined with antibody libraries, phage display allows for rapid in vitro selection of antigen-specific antibodies and recovery of their corresponding coding sequence. Large non-immune and synthetic human libraries have been constructed as well as smaller immune libraries based on capturing a single individual’s immune repertoire. This completely in vitro process allows for isolation of antibodies against poorly immunogenic targets as well as those that cannot be obtained by animal immunization, thus further expanding the utility of the approach. Phage antibody display represents the first developed methodology for high throughput screening for human therapeutic antibody candidates. Recently, other methods have been developed for generation of fully human therapeutic antibodies, such as single B-cell screening, next-generation genome sequencing and transgenic mice with human germline B-cell genes. While each of these have their particular advantages, phage display has remained a key methodology for human antibody discovery due its in vitro process. Here, we review the continuing role of this technique alongside other developing technologies for therapeutic antibody discovery.
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Affiliation(s)
- Conrad E Z Chan
- Biological Defence Program, Defense Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore
| | - Angeline P C Lim
- Biological Defence Program, Defense Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore
| | - Paul A MacAry
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore Immunology Program, Centre for Life Sciences, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Brendon J Hanson
- Biological Defence Program, Defense Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, Singapore 117510, Singapore Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
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Chan CEZ, Chan AHY, Lim APC, Hanson BJ. Comparison of the efficiency of antibody selection from semi-synthetic scFv and non-immune Fab phage display libraries against protein targets for rapid development of diagnostic immunoassays. J Immunol Methods 2011; 373:79-88. [PMID: 21856306 PMCID: PMC7094349 DOI: 10.1016/j.jim.2011.08.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/03/2011] [Accepted: 08/03/2011] [Indexed: 12/05/2022]
Abstract
Rapid development of diagnostic immunoassays against novel emerging or genetically modified pathogens in an emergency situation is dependent on the timely isolation of specific antibodies. Non-immune antibody phage display libraries are an efficient in vitro method for selecting monoclonal antibodies and hence ideal in these circumstances. Such libraries can be constructed from a variety of sources e.g. B cell cDNA or synthetically generated, and use a variety of antibody formats, typically scFv or Fab. However, antibody source and format can impact on the quality of antibodies generated and hence the effectiveness of this methodology for the timely production of antibodies. We have carried out a comparative screening of two antibody libraries, a semi-synthetic scFv library and a human-derived Fab library against the protective antigen toxin component of Bacillus anthracis and the epsilon toxin of Clostridium botulinum. We have shown that while the synthetic library produced a diverse collection of specific scFv-phage, these contained a high frequency of unnatural amber stops and glycosylation sites which limited their conversion to IgG, and also a high number which lost specificity when expressed as IgG. In contrast, these limitations were overcome by the use of a natural human library. Antibodies from both libraries could be used to develop sandwich ELISA assays with similar sensitivity. However, the ease and speed with which full-length IgG could be generated from the human-derived Fab library makes screening this type of library the preferable method for rapid antibody generation for diagnostic assay development.
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Affiliation(s)
- Conrad E Z Chan
- Biodefence Therapeutics Laboratory, Defence Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive, #13-00, S(117510), Singapore
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Chan CEZ, Chan AHY, Hanson BJ, Ooi EE. The use of antibodies in the treatment of infectious diseases. Singapore Med J 2009; 50:663-673. [PMID: 19644620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
There is a long history of the use of antibodies in the treatment and prophylaxis of infectious diseases, because these molecules play a critical role in directing the effector mechanisms of the immune system against the pathogens they recognise. However, the widespread application of this therapy has been hampered by allergic reactions, production costs and the availability of alternative drugs such as antibiotics. Some of these obstacles can now be overcome with advances in biotechnology, which has enabled the development of antibody-based drugs for use first in treating cancer, and recently, for treating infectious diseases. The efficacy of such antibodies has been demonstrated in various in vitro studies, animal models and clinical trials for a variety of both viral and bacterial pathogens. Antibodies appear to hold great promise as a new class of drugs against infectious diseases.
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Affiliation(s)
- C E Z Chan
- DSO National Laboratories, #13-00, 27 Medical Drive, Singapore.
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Lim APC, Chan CEZ, Wong SKK, Chan AHY, Ooi EE, Hanson BJ. Neutralizing human monoclonal antibody against H5N1 influenza HA selected from a Fab-phage display library. Virol J 2008; 5:130. [PMID: 18957074 PMCID: PMC2582236 DOI: 10.1186/1743-422x-5-130] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 10/28/2008] [Indexed: 11/19/2022] Open
Abstract
Identification of neutralizing antibodies with specificity away from the traditional mutation prone antigenic regions, against the conserved regions of hemagglutinin from H5N1 influenza virus has the potential to provide a therapeutic option which can be developed ahead of time in preparation for a possible pandemic due to H5N1 viruses. In this study, we used a combination of panning strategies against the hemagglutinin (HA) of several antigenic distinct H5N1 isolates to bias selection of Fab-phage from a naïve human library away from the antigenic regions of HA, toward the more conserved portions of the protein. All of the identified Fab clones which showed binding to multiple antigenically distinct HA were converted to fully human IgG, and tested for their ability to neutralize the uptake of H5N1-virus like particles (VLP) into MDCK cells. Five of the antibodies which showed binding to the relatively conserved HA2 subunit of HA, exhibited neutralization of H5N1-VLP uptake in a dose dependant manner. The inhibitory effects of these five antibodies were similar to those observed with a previously described neutralizing antibody specific for the 140s antigenic loop present within HA1 and highlight the exciting possibility that these antibodies may be efficacious against multiple H5N1 strains.
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Affiliation(s)
- Angeline P C Lim
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Dr, 117510, Singapore.
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Lim APC, Wong SKK, Chan AHY, Chan CEZ, Ooi EE, Hanson BJ. Epitope characterization of the protective monoclonal antibody VN04-2 shows broadly neutralizing activity against highly pathogenic H5N1. Virol J 2008; 5:80. [PMID: 18616831 PMCID: PMC2481255 DOI: 10.1186/1743-422x-5-80] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 07/11/2008] [Indexed: 11/10/2022] Open
Abstract
The monoclonal antibody VN04-2 was previously shown to protect mice against lethal A/Vietnam/1203/04 H5N1 virus challenge when administered pre- and post-infection. In this study, we characterized the binding requirements of this antibody using direct binding to hemagglutinin and neutralization assays with H5N1 virus-like particles (H5N1-VLP) of eight recent H5N1 strains representing the major mutations within the 140s antigenic loop. Binding was clade independent and 3 mutations within this antigenic region are required before escape is possible, suggesting that apart from the H5N1 viruses circulating in Indonesia, VN04-2 may provide protection against H5N1 viruses from all other regions.
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Affiliation(s)
- Angeline P C Lim
- Defence Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Dr, 117510, Singapore.
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