1
|
Miranda MC, Kepl E, Navarro MJ, Chen C, Johnson M, Sprouse KR, Stewart C, Palser A, Valdez A, Pettie D, Sydeman C, Ogohara C, Kraft JC, Pham M, Murphy M, Wrenn S, Fiala B, Ravichandran R, Ellis D, Carter L, Corti D, Kellam P, Lee K, Walls AC, Veesler D, King NP. Potent neutralization of SARS-CoV-2 variants by RBD nanoparticle and prefusion-stabilized spike immunogens. NPJ Vaccines 2024; 9:184. [PMID: 39379400 PMCID: PMC11461925 DOI: 10.1038/s41541-024-00982-1] [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: 01/18/2024] [Accepted: 09/25/2024] [Indexed: 10/10/2024] Open
Abstract
We previously described a two-component protein nanoparticle vaccine platform that displays 60 copies of the SARS-CoV-2 spike protein RBD (RBD-NP). The vaccine, when adjuvanted with AS03, was shown to elicit robust neutralizing antibody and CD4 T cell responses in Phase I/II clinical trials, met its primary co-endpoints in a Phase III trial, and has been licensed by multiple regulatory authorities under the brand name SKYCovioneTM. Here we characterize the biophysical properties, stability, antigenicity, and immunogenicity of RBD-NP immunogens incorporating mutations from the B.1.351 (β) and P.1 (γ) variants of concern (VOCs) that emerged in 2020. We also show that the RBD-NP platform can be adapted to the Omicron strains BA.5 and XBB.1.5. We compare β and γ variant and E484K point mutant nanoparticle immunogens to the nanoparticle displaying the Wu-1 RBD, as well as to soluble prefusion-stabilized (HexaPro) spike trimers harboring VOC-derived mutations. We find the properties of immunogens based on different SARS-CoV-2 variants can differ substantially, which could affect the viability of variant vaccine development. Introducing stabilizing mutations in the linoleic acid binding site of the RBD-NPs resulted in increased physical stability compared to versions lacking the stabilizing mutations without deleteriously affecting immunogenicity. The RBD-NP immunogens and HexaPro trimers, as well as combinations of VOC-based immunogens, elicited comparable levels of neutralizing antibodies against distinct VOCs. Our results demonstrate that RBD-NP-based vaccines can elicit neutralizing antibody responses against SARS-CoV-2 variants and can be rapidly designed and stabilized, demonstrating the potential of two-component RBD-NPs as a platform for the development of broadly protective coronavirus vaccines.
Collapse
Affiliation(s)
- Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Elizabeth Kepl
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mary Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Chengbo Chen
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA, USA
| | - Max Johnson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anne Palser
- Kymab Ltd., Babraham Research Campus, Cambridge, UK
| | - Adian Valdez
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Cassandra Ogohara
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John C Kraft
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Minh Pham
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sam Wrenn
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Rashmi Ravichandran
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Paul Kellam
- Kymab Ltd., Babraham Research Campus, Cambridge, UK
- Department of Infectious Disease, Imperial College, London, UK
| | - Kelly Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| |
Collapse
|
2
|
Ganesan S, Mittal N, Bhat A, Adiga RS, Ganesan A, Nagarajan D, Varadarajan R. Improved Prediction of Stabilizing Mutations in Proteins by Incorporation of Mutational Effects on Ligand Binding. Proteins 2024. [PMID: 39166462 DOI: 10.1002/prot.26738] [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: 04/11/2024] [Revised: 07/18/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
While many computational methods accurately predict destabilizing mutations, identifying stabilizing mutations has remained a challenge, because of their relative rarity. We tested ΔΔG0 predictions from computational predictors such as Rosetta, ThermoMPNN, RaSP, and DeepDDG, using 82 mutants of the bacterial toxin CcdB as a test case. On this dataset, the best computational predictor is ThermoMPNN, which identifies stabilizing mutations with a precision of 68%. However, the average increase in Tm for these predicted mutations was only 1°C for CcdB, and predictions were poorer for a more challenging target, influenza neuraminidase. Using data from multiple previously described yeast surface display libraries and in vitro thermal stability measurements, we trained logistic regression models to identify stabilizing mutations with a precision of 90% and an average increase in Tm of 3°C for CcdB. When such libraries contain a population of mutants with significantly enhanced binding relative to the corresponding wild type, there is no benefit in using computational predictors. It is then possible to predict stabilizing mutations without any training, simply by examining the distribution of mutational binding scores. This avoids laborious steps of in vitro expression, purification, and stability characterization. When this is not the case, combining data from computational predictors with high-throughput experimental binding data enhances the prediction of stabilizing mutations. However, this requires training on stability data measured in vitro with known stabilized mutants. It is thus feasible to predict stabilizing mutations rapidly and accurately for any system of interest that can be subjected to a binding selection or screen.
Collapse
Affiliation(s)
- Srivarshini Ganesan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Nidhi Mittal
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, India
| | - Akash Bhat
- Department of Biotechnology, M.S. Ramaiah University of Applied Sciences, Bengaluru, India
| | - Rachana S Adiga
- Department of Biotechnology, M.S. Ramaiah University of Applied Sciences, Bengaluru, India
| | - Ananthakrishnan Ganesan
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California, USA
| | - Deepesh Nagarajan
- Department of Biotechnology, M.S. Ramaiah University of Applied Sciences, Bengaluru, India
| | | |
Collapse
|
3
|
Jitender, Vikram Kumar B, Singh S, Verma G, Kumar R, Mishra PM, Kumar S, Nagaraj SK, Nag J, Joy CM, Nikam B, Singh D, Pooja, Kalidas N, Singh S, Mumtaz, Bhardwaj AK, Mankotia DS, Ringe RP, Gupta N, Tripathi S, Mishra RPN. Mammalian cell expressed recombinant trimeric spike protein is a potent vaccine antigen and confers near-complete protection against SARS-CoV-2 infection in Hamster. Vaccine 2024; 42:126099. [PMID: 38981743 DOI: 10.1016/j.vaccine.2024.06.066] [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: 03/13/2024] [Revised: 06/20/2024] [Accepted: 06/30/2024] [Indexed: 07/11/2024]
Abstract
Numerous vaccine candidates have emerged in the fight against SARS-CoV-2, yet the challenges posed by viral evolution and the evasion of vaccine-induced immunity persist. The development of broadly protective vaccines is essential in countering the threat posed by variants of concern (VoC) capable of eluding existing vaccine defenses. Among the diverse SARS-CoV-2 vaccine candidates, detailed characterization of those based on the expression of the entire spike protein in mammalian cells have been limited. In our study, we engineered a recombinant prefusion-stabilized trimeric spike protein antigen, IMT-CVAX, encoded by the IMT-C20 gene. This antigen was expressed utilizing a suspension mammalian cell line (CHO-S). The establishment of a stable cell line expressing IMT-CVAX involved the integration of the gene into the CHO genome, followed by the expression, purification, and characterization of the protein. To gauge the vaccine potential of adjuvanted IMT-CVAX, we conducted assessments in small animals. Analyses of blood collected from immunized animals included measurements of anti-spike IgG, SARS-CoV-2 neutralization, and responses from GC-B and Tfh cells. Furthermore, the protective efficacy of IMT-CVAX was evaluated using a Hamster challenge model. Our findings indicate that adjuvanted IMT-CVAX elicits an excellent immune response in both mice and hamsters. Notably, sera from animals immunized with IMT-CVAX effectively neutralize a diverse range of SARS-CoV-2 variants. Moreover, IMT-CVAX immunization conferred complete protection to hamsters against SARS-CoV-2 infection. In hACE2 transgenic mice, IMT-CVAX vaccination induced a robust response from GC-B and Tfh cells. Based on our preclinical model assessments, adjuvanted IMT-CVAX emerges as a highly efficacious vaccine candidate. This protein-subunit-based vaccine exhibits promise for clinical development, offering an affordable solution for both primary and heterologous immunization against SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Jitender
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - B Vikram Kumar
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sneha Singh
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Geetika Verma
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Reetesh Kumar
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Pranaya M Mishra
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sahil Kumar
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Santhosh K Nagaraj
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Joydeep Nag
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Christy M Joy
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | | | | | - Pooja
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Nidhi Kalidas
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Shubham Singh
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Mumtaz
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ashwani K Bhardwaj
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Dhananjay S Mankotia
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Rajesh P Ringe
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Nimesh Gupta
- National Institute of Immunology, New Delhi, India
| | - Shashank Tripathi
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India; Microbiology & Cell Biology Department, Indian Institute of Science, Bengaluru, India
| | - Ravi P N Mishra
- Vaccine & Biotherapeutics Research Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
| |
Collapse
|
4
|
Khan MS, Jakob V, Singh R, Rajmani RS, Kumar S, Lemoine C, Kleanthous H, Ringe RP, Dubois PM, Varadarajan R. Enhancing Immunogenicity of a Thermostable, Efficacious SARS-CoV-2 Vaccine Formulation through Oligomerization and Adjuvant Choice. Pharmaceutics 2023; 15:2759. [PMID: 38140101 PMCID: PMC10747592 DOI: 10.3390/pharmaceutics15122759] [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: 10/25/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Currently deployed SARS-CoV-2 vaccines all require storage at refrigerated or sub-zero temperatures. We demonstrate that after month-long incubation at 37 °C, solubilization, and formulation with squalene-in-water emulsion adjuvant, a stabilized receptor binding domain retains immunogenicity and protective efficacy. We also examine the effects of trimerization of the stabilized RBD, as well as of additional adjuvants, on both B and T-cell responses. The additional emulsion or liposome-based adjuvants contained a synthetic TLR-4 ligand and/or the saponin QS-21. Trimerization enhanced immunogenicity, with significant antibody titers detectable after a single immunization. Saponin-containing adjuvants elicited enhanced immunogenicity relative to both emulsion and aluminum hydroxide adjuvanted formulations lacking these immunostimulants. Trimeric RBD formulated with liposomal based adjuvant containing both TLR-4 ligand and saponin elicited a strongly Th1 biased response, with ~10-fold higher neutralization titers than the corresponding aluminum hydroxide adjuvanted formulation. The SARS-CoV-2 virus is now endemic in humans, and it is likely that periodic updating of vaccine formulations in response to viral evolution will continue to be required to protect vulnerable individuals. In this context, it is desirable to have efficacious, thermostable vaccine formulations to facilitate widespread vaccine coverage, including in low- and middle-income countries, where global access rights to clinically de-risked adjuvants will be important moving forward.
Collapse
Affiliation(s)
- Mohammad Suhail Khan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (M.S.K.); (R.S.R.)
| | - Virginie Jakob
- Vaccine Formulation Institute, Rue du Champ-Blanchot 4, 1228 Plan-les-Ouates, Switzerland; (V.J.); (C.L.)
| | - Randhir Singh
- Mynvax Private Limited, 3rd Floor, Brigade MLR Centre, No. 50, Vani Vilas Road, Basavanagudi, Bengaluru 560004, India;
| | - Raju S. Rajmani
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (M.S.K.); (R.S.R.)
| | - Sahil Kumar
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh 160036, India; (S.K.); (R.P.R.)
| | - Céline Lemoine
- Vaccine Formulation Institute, Rue du Champ-Blanchot 4, 1228 Plan-les-Ouates, Switzerland; (V.J.); (C.L.)
| | | | - Rajesh P. Ringe
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh 160036, India; (S.K.); (R.P.R.)
| | - Patrice M. Dubois
- Vaccine Formulation Institute, Rue du Champ-Blanchot 4, 1228 Plan-les-Ouates, Switzerland; (V.J.); (C.L.)
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (M.S.K.); (R.S.R.)
| |
Collapse
|
5
|
Kumar S, Delipan R, Chakraborty D, Kanjo K, Singh R, Singh N, Siddiqui S, Tyagi A, Jha V, Thakur KG, Pandey R, Varadarajan R, Ringe RP. Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity, and neutralization sensitivity. J Virol 2023; 97:e0092223. [PMID: 37861334 PMCID: PMC10688319 DOI: 10.1128/jvi.00922-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE The Omicron subvariants have substantially evaded host-neutralizing antibodies and adopted an endosomal route of entry. The virus has acquired several mutations in the receptor binding domain and N-terminal domain of S1 subunit, but remarkably, also incorporated mutations in S2 which are fixed in Omicron sub-lineage. Here, we found that the mutations in the S2 subunit affect the structural and biological properties such as neutralization escape, entry route, fusogenicity, and protease requirement. In vivo, these mutations may have significant roles in tropism and replication. A detailed understanding of the effects of S2 mutations on Spike function, immune evasion, and viral entry would inform the vaccine design, as well as therapeutic interventions aiming to block the essential proteases for virus entry. Thus, our study has identified the crucial role of S2 mutations in stabilizing the Omicron spike and modulating neutralization resistance to antibodies targeting the S1 subunit.
Collapse
Affiliation(s)
- Sahil Kumar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rathina Delipan
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | | | - Kawkab Kanjo
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | | | - Nittu Singh
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Samreen Siddiqui
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Akansha Tyagi
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Vinitaa Jha
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Krishan G. Thakur
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Rajesh P. Ringe
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| |
Collapse
|
6
|
Mittal N, Kumar S, Rajmani RS, Singh R, Lemoine C, Jakob V, Bj S, Jagannath N, Bhat M, Chakraborty D, Pandey S, Jory A, Sa SS, Kleanthous H, Dubois P, Ringe RP, Varadarajan R. Enhanced protective efficacy of a thermostable RBD-S2 vaccine formulation against SARS-CoV-2 and its variants. NPJ Vaccines 2023; 8:161. [PMID: 37880298 PMCID: PMC10600342 DOI: 10.1038/s41541-023-00755-2] [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: 04/16/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023] Open
Abstract
With the rapid emergence of variants of concern (VOC), the efficacy of currently licensed vaccines has reduced drastically. VOC mutations largely occur in the S1 subunit of Spike. The S2 subunit of SARS-CoV-2 is conserved and thus more likely to elicit broadly reactive immune responses that could improve protection. However, the contribution of the S2 subunit in improving the overall efficacy of vaccines remains unclear. Therefore, we designed, and evaluated the immunogenicity and protective potential of a stabilized SARS-CoV-2 Receptor Binding Domain (RBD) fused to a stabilized S2. Immunogens were expressed as soluble proteins with approximately fivefold higher purified yield than the Spike ectodomain and formulated along with Squalene-in-water emulsion (SWE) adjuvant. Immunization with S2 alone failed to elicit a neutralizing immune response, but significantly reduced lung viral titers in mice challenged with the heterologous Beta variant. In hamsters, SWE-formulated RS2 (a genetic fusion of stabilized RBD with S2) showed enhanced immunogenicity and efficacy relative to corresponding RBD and Spike formulations. Despite being based on the ancestral Wuhan strain of SARS-CoV-2, RS2 elicited broad neutralization, including against Omicron variants (BA.1, BA.5 and BF.7), and the clade 1a WIV-1 and SARS-CoV-1 strains. RS2 elicited sera showed enhanced competition with both S2 directed and RBD Class 4 directed broadly neutralizing antibodies, relative to RBD and Spike elicited sera. When lyophilized, RS2 retained antigenicity and immunogenicity even after incubation at 37 °C for a month. The data collectively suggest that the RS2 immunogen is a promising modality to combat SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Nidhi Mittal
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, 560012, India
| | - Sahil Kumar
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, 160036, India
| | - Raju S Rajmani
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, 560012, India
| | - Randhir Singh
- Mynvax Private Limited; 3rd Floor, Brigade MLR Centre, No.50, Vani Vilas Road, Basavanagudi, Bengaluru, 560004, India
| | - Céline Lemoine
- Vaccine Formulation Institute; Rue du Champ-Blanchod 4, 1228, Plan-les-Ouates, Switzerland
| | - Virginie Jakob
- Vaccine Formulation Institute; Rue du Champ-Blanchod 4, 1228, Plan-les-Ouates, Switzerland
| | - Sowrabha Bj
- Mynvax Private Limited; 3rd Floor, Brigade MLR Centre, No.50, Vani Vilas Road, Basavanagudi, Bengaluru, 560004, India
| | - Nayana Jagannath
- Mynvax Private Limited; 3rd Floor, Brigade MLR Centre, No.50, Vani Vilas Road, Basavanagudi, Bengaluru, 560004, India
| | - Madhuraj Bhat
- Mynvax Private Limited; 3rd Floor, Brigade MLR Centre, No.50, Vani Vilas Road, Basavanagudi, Bengaluru, 560004, India
| | - Debajyoti Chakraborty
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, 560012, India
| | - Suman Pandey
- Mynvax Private Limited; 3rd Floor, Brigade MLR Centre, No.50, Vani Vilas Road, Basavanagudi, Bengaluru, 560004, India
| | - Aurélie Jory
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Suba Soundarya Sa
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | | | - Patrice Dubois
- Vaccine Formulation Institute; Rue du Champ-Blanchod 4, 1228, Plan-les-Ouates, Switzerland
| | - Rajesh P Ringe
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, 160036, India.
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru, 560012, India.
| |
Collapse
|
7
|
UVC-Based Air Disinfection Systems for Rapid Inactivation of SARS-CoV-2 Present in the Air. Pathogens 2023; 12:pathogens12030419. [PMID: 36986341 PMCID: PMC10053150 DOI: 10.3390/pathogens12030419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 03/09/2023] Open
Abstract
The World Health Organization (WHO) declared in May 2021 that SARS-CoV-2 is transmitted not only by close contact with infectious respiratory fluids from infected people or contaminated materials but also indirectly through air. Airborne transmission has serious implications for the control measures we can deploy, given the emergence of more transmissible variants. This emphasizes the need to deploy a mechanism to reduce the viral load in the air, especially in closed and crowded places such as hospitals, public transport buses, etc. In this study, we explored ultraviolet C (UVC) radiation for its ability to inactivate the SARS-CoV-2 particles present in aerosols and designed an air disinfection system to eliminate infectious viruses. We studied the virus inactivation kinetics to identify the UVC dosage required to achieve maximum virus inactivation. Based on the experimental data, UVC-based devices were designed for the sanitization of air through HVAC systems in closed spaces. Further, a risk assessment model to estimate the risk reduction was applied which showed that the use of UVC radiation could result in the reduction of the risk of infection in occupied spaces by up to 90%.
Collapse
|
8
|
Raoufi E, Hosseini F, Onagh B, Salehi-Shadkami M, Mehrali M, Mohsenzadegan M, Ho JQ, Bigdelou B, Sepand MR, Webster TJ, Zanganeh S, Farajollahi MM. Designing and developing a sensitive and specific SARS-CoV-2 RBD IgG detection kit for identifying positive human samples. Clin Chim Acta 2023; 542:117279. [PMID: 36871661 PMCID: PMC9985519 DOI: 10.1016/j.cca.2023.117279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/07/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND More than 3 y into the coronavirus 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to undergo mutations. In this context, the Receptor Binding Domain (RBD) is the most antigenic region among the SARS-CoV-2 Spike protein and has emerged as a promising candidate for immunological development. We designed an IgG-based indirect enzyme-linked immunoassay (ELISA) kit based on recombinant RBD, which was produced from the laboratory to 10 L industry scales in Pichia pastoris. METHODS A recombinant-RBD comprising 283 residues (31 kDa) was constructed after epitope analyses. The target gene was initially cloned into an Escherichia coli TOP10 genotype and transformed into Pichia pastoris CBS7435 muts for protein production. Production was scaled up in a 10 L fermenter after a 1 L shake-flask cultivation. The product was ultrafiltered and purified using ion-exchange chromatography. IgG-positive human sera for SARS-CoV-2 were employed by an ELISA test to evaluate the antigenicity and specific binding of the produced protein. RESULTS Bioreactor cultivation yielded 4 g/l of the target protein after 160 h of fermentation, and ion-exchange chromatography indicated a purity > 95%. A human serum ELISA test was performed in 4 parts, and the ROC area under the curve (AUC) was > 0.96 for each part. The mean specificity and sensitivity of each part was 100% and 91.5%, respectively. CONCLUSION A highly specific and sensitive IgG-based serologic kit was developed for improved diagnostic purposes in patients with COVID-19 after generating an RBD antigen in Pichia pastoris at laboratory and 10 L fermentation scales.
Collapse
Affiliation(s)
- Ehsan Raoufi
- Department of Medical Biotechnology, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Hosseini
- Department of Medical Biotechnology, Iran University of Medical Sciences, Tehran, Iran
| | - Bahman Onagh
- Department of Biochemistry, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Marjan Mehrali
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Monireh Mohsenzadegan
- Department of Medical Laboratory Science, Iran University of Medical Sciences, Tehran, Iran
| | - Jim Q Ho
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Banafsheh Bigdelou
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States
| | - Mohammad Reza Sepand
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States
| | - Thomas J Webster
- School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, China; School of Engineering, Saveetha University, Chennai, India; Program in Materials Science, UFPI, Teresina, Brazil
| | - Steven Zanganeh
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States.
| | | |
Collapse
|
9
|
Kanjo K, Chattopadhyay G, Malladi SK, Singh R, Jayatheertha S, Varadarajan R. Biophysical Correlates of Enhanced Immunogenicity of a Stabilized Variant of the Receptor Binding Domain of SARS-CoV-2. J Phys Chem B 2023; 127:1704-1714. [PMID: 36790910 PMCID: PMC9942533 DOI: 10.1021/acs.jpcb.2c07262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The receptor binding domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We have previously reported the design and characterization of a mammalian cell expressed RBD derivative, mRBD1-3.2, that has higher thermal stability and greatly enhanced immunogenicity relative to the wild type mRBD. The protein is highly thermotolerant and immunogenic and is being explored for use in room temperature stable Covid-19 vaccine formulations. In the current study, we have investigated the folding pathway of both WT and stabilized RBD. It was found that chemical denaturation of RBD proceeds through a stable equilibrium intermediate. Thermal and chemical denaturation is reversible, as assayed by binding to the receptor ACE2. Unusually, in its native state, RBD binds to the hydrophobic probe ANS, and enhanced ANS binding is observed for the equilibrium intermediate state. Further characterization of the folding of mRBD1-3.2, both in solution and after reconstitution of lyophilized protein stored for a month at 37 °C, revealed a higher stability represented by higher Cm, faster refolding, slower unfolding, and enhanced resistance to proteolytic cleavage relative to WT. In contrast to WT RBD, the mutant showed decreased interaction with the hydrophobic moiety linoleic acid. Collectively, these data suggest that the enhanced immunogenicity results from reduced conformational fluctuations that likely enhance in vivo half-life as well as reduce the exposure of irrelevant non-neutralizing epitopes to the immune system.
Collapse
Affiliation(s)
- Kawkab Kanjo
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India
| | | | - Sameer Kumar Malladi
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India
| | - Randhir Singh
- Mynvax Private Limited, Fourth Floor, Brigade MLR Center, 50, Vanivilas Rd, Gandhi Bazaar, Basavanagudi, Bangalore, Karnataka 560004, India
| | - Sowrabha Jayatheertha
- Mynvax Private Limited, Fourth Floor, Brigade MLR Center, 50, Vanivilas Rd, Gandhi Bazaar, Basavanagudi, Bangalore, Karnataka 560004, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India.,Mynvax Private Limited, Fourth Floor, Brigade MLR Center, 50, Vanivilas Rd, Gandhi Bazaar, Basavanagudi, Bangalore, Karnataka 560004, India
| |
Collapse
|
10
|
Rodriguez-Aponte SA, Dalvie NC, Wong TY, Johnston RS, Naranjo CA, Bajoria S, Kumru OS, Kaur K, Russ BP, Lee KS, Cyphert HA, Barbier M, Rao HD, Rajurkar MP, Lothe RR, Shaligram US, Batwal S, Chandrasekaran R, Nagar G, Kleanthous H, Biswas S, Bevere JR, Joshi SB, Volkin DB, Damron FH, Love JC. Molecular engineering of a cryptic epitope in Spike RBD improves manufacturability and neutralizing breadth against SARS-CoV-2 variants. Vaccine 2023; 41:1108-1118. [PMID: 36610932 PMCID: PMC9797419 DOI: 10.1016/j.vaccine.2022.12.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022]
Abstract
There is a continued need for sarbecovirus vaccines that can be manufactured and distributed in low- and middle-income countries (LMICs). Subunit protein vaccines are manufactured at large scales at low costs, have less stringent temperature requirements for distribution in LMICs, and several candidates have shown protection against SARS-CoV-2. We previously reported an engineered variant of the SARS-CoV-2 Spike protein receptor binding domain antigen (RBD-L452K-F490W; RBD-J) with enhanced manufacturability and immunogenicity compared to the ancestral RBD. Here, we report a second-generation engineered RBD antigen (RBD-J6) with two additional mutations to a hydrophobic cryptic epitope in the RBD core, S383D and L518D, that further improved expression titers and biophysical stability. RBD-J6 retained binding affinity to human convalescent sera and to all tested neutralizing antibodies except antibodies that target the class IV epitope on the RBD core. K18-hACE2 transgenic mice immunized with three doses of a Beta variant of RBD-J6 displayed on a virus-like particle (VLP) generated neutralizing antibodies (nAb) to nine SARS-CoV-2 variants of concern at similar levels as two doses of Comirnaty. The vaccinated mice were also protected from challenge with Alpha or Beta SARS-CoV-2. This engineered antigen could be useful for modular RBD-based subunit vaccines to enhance manufacturability and global access, or for further development of variant-specific or broadly acting booster vaccines.
Collapse
Affiliation(s)
- Sergio A Rodriguez-Aponte
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil C Dalvie
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ting Y Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Ryan S Johnston
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Naranjo
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sakshi Bajoria
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Ozan S Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Brynnan P Russ
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Katherine S Lee
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Holly A Cyphert
- Department of Biological Sciences, Marshall University, Huntington, WV 26506, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Harish D Rao
- Serum Institute of India Pvt. Ltd., Pune 411028, India
| | | | | | | | | | | | - Gaurav Nagar
- Serum Institute of India Pvt. Ltd., Pune 411028, India
| | | | - Sumi Biswas
- SpyBiotech Limited, Oxford Business Park North, Oxford OX4 2JZ, UK
| | - Justin R Bevere
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Sangeeta B Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - J Christopher Love
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
| |
Collapse
|
11
|
Khaleeq S, Sengupta N, Kumar S, Patel UR, Rajmani RS, Reddy P, Pandey S, Singh R, Dutta S, Ringe RP, Varadarajan R. Neutralizing Efficacy of Encapsulin Nanoparticles against SARS-CoV2 Variants of Concern. Viruses 2023; 15:346. [PMID: 36851560 PMCID: PMC9961482 DOI: 10.3390/v15020346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Rapid emergence of the SARS-CoV-2 variants has dampened the protective efficacy of existing authorized vaccines. Nanoparticle platforms offer a means to improve vaccine immunogenicity by presenting multiple copies of desired antigens in a repetitive manner which closely mimics natural infection. We have applied nanoparticle display combined with the SpyTag-SpyCatcher system to design encapsulin-mRBD, a nanoparticle vaccine displaying 180 copies of the monomeric SARS-CoV-2 spike receptor-binding domain (RBD). Here we show that encapsulin-mRBD is strongly antigenic and thermotolerant for long durations. After two immunizations, squalene-in-water emulsion (SWE)-adjuvanted encapsulin-mRBD in mice induces potent and comparable neutralizing antibody titers of 105 against wild-type (B.1), alpha, beta, and delta variants of concern. Sera also neutralizes the recent Omicron with appreciable neutralization titers, and significant neutralization is observed even after a single immunization.
Collapse
Affiliation(s)
- Sara Khaleeq
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India
| | - Nayanika Sengupta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India
| | - Sahil Kumar
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh 160036, India
| | - Unnatiben Rajeshbhai Patel
- Mynvax Private Limited, 3rd Floor, Brigade MLR Centre, No. 50, Vani Vilas Road, Basavanagudi, Bengaluru 560004, India
| | - Raju S. Rajmani
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India
| | - Poorvi Reddy
- Mynvax Private Limited, 3rd Floor, Brigade MLR Centre, No. 50, Vani Vilas Road, Basavanagudi, Bengaluru 560004, India
| | - Suman Pandey
- Mynvax Private Limited, 3rd Floor, Brigade MLR Centre, No. 50, Vani Vilas Road, Basavanagudi, Bengaluru 560004, India
| | - Randhir Singh
- Mynvax Private Limited, 3rd Floor, Brigade MLR Centre, No. 50, Vani Vilas Road, Basavanagudi, Bengaluru 560004, India
| | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India
| | - Rajesh P. Ringe
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh 160036, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India
| |
Collapse
|
12
|
Chattopadhyay G, Bhowmick J, Manjunath K, Ahmed S, Goyal P, Varadarajan R. Mechanistic insights into global suppressors of protein folding defects. PLoS Genet 2022; 18:e1010334. [PMID: 36037221 PMCID: PMC9491731 DOI: 10.1371/journal.pgen.1010334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/09/2022] [Accepted: 07/11/2022] [Indexed: 01/14/2023] Open
Abstract
Most amino acid substitutions in a protein either lead to partial loss-of-function or are near neutral. Several studies have shown the existence of second-site mutations that can rescue defects caused by diverse loss-of-function mutations. Such global suppressor mutations are key drivers of protein evolution. However, the mechanisms responsible for such suppression remain poorly understood. To address this, we characterized multiple suppressor mutations both in isolation and in combination with inactive mutants. We examined six global suppressors of the bacterial toxin CcdB, the known M182T global suppressor of TEM-1 β-lactamase, the N239Y global suppressor of p53-DBD and three suppressors of the SARS-CoV-2 spike Receptor Binding Domain. When coupled to inactive mutants, they promote increased in-vivo solubilities as well as regain-of-function phenotypes. In the case of CcdB, where novel suppressors were isolated, we determined the crystal structures of three such suppressors to obtain insight into the specific molecular interactions responsible for the observed effects. While most individual suppressors result in small stability enhancements relative to wildtype, which can be combined to yield significant stability increments, thermodynamic stabilisation is neither necessary nor sufficient for suppressor action. Instead, in diverse systems, we observe that individual global suppressors greatly enhance the foldability of buried site mutants, primarily through increase in refolding rate parameters measured in vitro. In the crowded intracellular environment, mutations that slow down folding likely facilitate off-pathway aggregation. We suggest that suppressor mutations that accelerate refolding can counteract this, enhancing the yield of properly folded, functional protein in vivo.
Collapse
Affiliation(s)
| | - Jayantika Bhowmick
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore,
India
| | - Kavyashree Manjunath
- Centre for Chemical Biology and Therapeutics, Institute For Stem Cell
Science and Regenerative Medicine, Bangalore, India
| | - Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore,
India
| | - Parveen Goyal
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore,
India
| | | |
Collapse
|
13
|
Lim HX, Masomian M, Khalid K, Kumar AU, MacAry PA, Poh CL. Identification of B-Cell Epitopes for Eliciting Neutralizing Antibodies against the SARS-CoV-2 Spike Protein through Bioinformatics and Monoclonal Antibody Targeting. Int J Mol Sci 2022; 23:ijms23084341. [PMID: 35457159 PMCID: PMC9029629 DOI: 10.3390/ijms23084341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 03/24/2022] [Accepted: 04/06/2022] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global public health crisis. Effective COVID-19 vaccines developed by Pfizer-BioNTech, Moderna, and Astra Zeneca have made significant impacts in controlling the COVID-19 burden, especially in reducing the transmission of SARS-CoV-2 and hospitalization incidences. In view of the emergence of new SARS-CoV-2 variants, vaccines developed against the Wuhan strain were less effective against the variants. Neutralizing antibodies produced by B cells are a critical component of adaptive immunity, particularly in neutralizing viruses by blocking virus attachment and entry into cells. Therefore, the identification of protective linear B-cell epitopes can guide epitope-based peptide designs. This study reviews the identification of SARS-CoV-2 B-cell epitopes within the spike, membrane and nucleocapsid proteins that can be incorporated as potent B-cell epitopes into peptide vaccine constructs. The bioinformatic approach offers a new in silico strategy for the mapping and identification of potential B-cell epitopes and, upon in vivo validation, would be useful for the rapid development of effective multi-epitope-based vaccines. Potent B-cell epitopes were identified from the analysis of three-dimensional structures of monoclonal antibodies in a complex with SARS-CoV-2 from literature mining. This review provides significant insights into the elicitation of potential neutralizing antibodies by potent B-cell epitopes, which could advance the development of multi-epitope peptide vaccines against SARS-CoV-2.
Collapse
Affiliation(s)
- Hui Xuan Lim
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
| | - Malihe Masomian
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
| | - Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
| | - Asqwin Uthaya Kumar
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
| | - Paul A. MacAry
- Life Sciences Institute, National University of Singapore, Singapore 119077, Singapore;
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Petaling Jaya 47500, Selangor, Malaysia; (H.X.L.); (M.M.); (K.K.); (A.U.K.)
- Correspondence:
| |
Collapse
|
14
|
Jansen van Vuren P, McAuley AJ, Kuiper MJ, Singanallur NB, Bruce MP, Riddell S, Goldie S, Mangalaganesh S, Chahal S, Drew TW, Blasdell KR, Tachedjian M, Caly L, Druce JD, Ahmed S, Khan MS, Malladi SK, Singh R, Pandey S, Varadarajan R, Vasan SS. Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. Viruses 2022; 14:800. [PMID: 35458530 PMCID: PMC9031315 DOI: 10.3390/v14040800] [Citation(s) in RCA: 4] [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: 03/08/2022] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 02/06/2023] Open
Abstract
As existing vaccines fail to completely prevent COVID-19 infections or community transmission, there is an unmet need for vaccines that can better combat SARS-CoV-2 variants of concern (VOC). We previously developed highly thermo-tolerant monomeric and trimeric receptor-binding domain derivatives that can withstand 100 °C for 90 min and 37 °C for four weeks and help eliminate cold-chain requirements. We show that mice immunised with these vaccine formulations elicit high titres of antibodies that neutralise SARS-CoV-2 variants VIC31 (with Spike: D614G mutation), Delta and Omicron (BA.1.1) VOC. Compared to VIC31, there was an average 14.4-fold reduction in neutralisation against BA.1.1 for the three monomeric antigen-adjuvant combinations and a 16.5-fold reduction for the three trimeric antigen-adjuvant combinations; the corresponding values against Delta were 2.5 and 3.0. Our findings suggest that monomeric formulations are suitable for upcoming Phase I human clinical trials and that there is potential for increasing the efficacy with vaccine matching to improve the responses against emerging variants. These findings are consistent with in silico modelling and AlphaFold predictions, which show that, while oligomeric presentation can be generally beneficial, it can make important epitopes inaccessible and also carries the risk of eliciting unwanted antibodies against the oligomerisation domain.
Collapse
Affiliation(s)
- Petrus Jansen van Vuren
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Alexander J. McAuley
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Michael J. Kuiper
- Data61, Commonwealth Scientific and Industrial Research Organisation, Docklands, VIC 3008, Australia;
| | - Nagendrakumar Balasubramanian Singanallur
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Matthew P. Bruce
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Shane Riddell
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Sarah Goldie
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Shruthi Mangalaganesh
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Simran Chahal
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Trevor W. Drew
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Kim R. Blasdell
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Mary Tachedjian
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital and The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (J.D.D.)
| | - Julian D. Druce
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital and The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (J.D.D.)
| | - Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India; (S.A.); (M.S.K.); (S.K.M.); (R.V.)
| | - Mohammad Suhail Khan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India; (S.A.); (M.S.K.); (S.K.M.); (R.V.)
| | - Sameer Kumar Malladi
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India; (S.A.); (M.S.K.); (S.K.M.); (R.V.)
| | - Randhir Singh
- Mynvax Private Limited, ES-12, Incubation Centre, Society for Innovation and Development, Indian Institute of Science, Bengaluru 560012, India; (R.S.); (S.P.)
| | - Suman Pandey
- Mynvax Private Limited, ES-12, Incubation Centre, Society for Innovation and Development, Indian Institute of Science, Bengaluru 560012, India; (R.S.); (S.P.)
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India; (S.A.); (M.S.K.); (S.K.M.); (R.V.)
| | - Seshadri S. Vasan
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC 3220, Australia; (P.J.v.V.); (A.J.M.); (N.B.S.); (M.P.B.); (S.R.); (S.G.); (S.M.); (S.C.); (T.W.D.); (K.R.B.); (M.T.)
- Department of Health Sciences, University of York, York YO10 5DD, UK
| |
Collapse
|
15
|
Ahmed S, Manjunath K, Chattopadhyay G, Varadarajan R. Identification of stabilizing point mutations through mutagenesis of destabilized protein libraries. J Biol Chem 2022; 298:101785. [PMID: 35247389 PMCID: PMC8971944 DOI: 10.1016/j.jbc.2022.101785] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/18/2022] [Accepted: 02/26/2022] [Indexed: 01/22/2023] Open
Abstract
Although there have been recent transformative advances in the area of protein structure prediction, prediction of point mutations that improve protein stability remains challenging. It is possible to construct and screen large mutant libraries for improved activity or ligand binding. However, reliable screens for mutants that improve protein stability do not yet exist, especially for proteins that are well folded and relatively stable. Here, we demonstrate that incorporation of a single, specific, destabilizing mutation termed parent inactivating mutation into each member of a single-site saturation mutagenesis library, followed by screening for suppressors, allows for robust and accurate identification of stabilizing mutations. We carried out fluorescence-activated cell sorting of such a yeast surface display, saturation suppressor library of the bacterial toxin CcdB, followed by deep sequencing of sorted populations. We found that multiple stabilizing mutations could be identified after a single round of sorting. In addition, multiple libraries with different parent inactivating mutations could be pooled and simultaneously screened to further enhance the accuracy of identification of stabilizing mutations. Finally, we show that individual stabilizing mutations could be combined to result in a multi-mutant that demonstrated an increase in thermal melting temperature of about 20 °C, and that displayed enhanced tolerance to high temperature exposure. We conclude that as this method is robust and employs small library sizes, it can be readily extended to other display and screening formats to rapidly isolate stabilized protein mutants.
Collapse
Affiliation(s)
- Shahbaz Ahmed
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology and Therapeutics, Institute of Stem Cell Science and Regenerative Medicine, Bangalore, India
| | | | | |
Collapse
|