1 Recombinant protein vaccines, a proven approach against coronavirus pandemics Jafar Amani 2 Introduction • In December 2019, a cluster of patients with pneumonia surfaced in Wuhan, China. • SARS-CoV-2 is a positive-strand RNA virus that belongs to the group of Betacoronaviruses. • The genome of SARS-CoV-2 is approximately 29,700 nucleotides long and shares 79.5% sequence identity with SARS-CoV. • The 3end of the genome encodes 4 major structural proteins, including the spike (S) protein, nucleocapsid (N) protein, membrane (M) protein, and the envelope (E) protein 3 4 Introduction • SARS-CoV-2 binds to the receptor angiotensin converting enzyme 2 (ACE2) on host cell for the virus entry and subsequent pathogenesis. • resulting in severe respiratory illness with symptoms of fever, cough, and shortness of breath, and severe cases can be fatal. 5 6 SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1),B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. 7 Structural features of coronavirus SARS-CoV-2 spike protein: Targets for vaccination • Fig. 1. Structural features of the SARS-CoV-2 spike (S) protein. (A) Ribbon diagram of the homotrimeric S, adopted from [19], (with permission from Elsevier Inc.). (B) Side view of the prefusion structure of S, with a single RBD in open (“up”) conformation (green), adopted from [18], (with permission from Science.org). (C) Top view of the prefusion structure of S, with two single RBDs in closed (“down”) conformation (white and grey) and one single RBD in open (“up”) conformation (green), adopted from [18], (with permission from Science.org). (D) Single monomer of S, with the RBD in closed (“down”) conformation (green), adopted from [18], (with permission from Science.org). (E) Single monomer of S, with the RBD in open (“up”) conformation (green), adopted from [18], (with permission from Science.org). (For interpretation of the references to colour in this figure legend, the reader is referred to • 8 9 SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications Notable non-synonymous mutations and deletions (D) in S, envelope (E), ORF8, nucleocapsid (N) proteins of SARS-CoV-2 501Y.V1, 501Y.V2 (*) and P.1 (#) variants. Co-occurring mutations other than D614G (S protein) and P323L (ORF1ab) are shown here. Protein names are shown in parenthesis. Table adapted from Portelli et al. and the Public Health England report. References for modulation in hACE2 affinity or antibody resistance (shown as superscripts) are provided in supplementary information. 10 MD Simulation Analysis of S Protein with ACE2 Receptors Binding interactions and energy of Spike proteins with ACE-2. (A) The number of hydrogen bonds between the wild type and mutant (N501Y and N440K) spike protein and ACE2 during the simulation. (B) Wild type spike–ACE2 interactions in the average structure extracted from MD simulations, N501 (circled) making hydrophobic contact (hydrogen bonds are shown with green dots and non-polar interactions with magenta and brick semicircle). (C) N501Y–ACE2 interactions in the average structure. (D) Molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM/GBSA) binding free energy of spike proteins with ACE2. 11 Different Types of SARS-CoV-2 Vaccines under Development 12 DRAFT landscape of COVID-19 candidate vaccines – 14 May 2021 13 Subunit Vaccines Vaccine antigen candidate • Full-length S-protein based vaccines • RBD-based vaccines • Multi-epitope vaccines Protein production technologies • Escherichia coli • Yeasts • Mammalian cell culture expression systems • Insect cells 14 Subunit Vaccines • the University of Queensland is developing a subunit • vaccine based on the “molecular clamp” technology. • Clover Biopharmaceuticals Inc. revealed that • they are developing a vaccine candidate against SARS- CoV-2 using the “Trimer-Tag” technology, • and the trimeric S protein subunit vaccine candidate was produced via a mammalian cell expression • system. Novavax, Inc. announced that they had produced multiple nanoparticle vaccine candidates • based on S protein, and now is assessing efficacy in animal models to identify an optimal vaccine candidate for human testing. • Besides, Johnson & Johnson, Pasteur Institute, and Chongqing Zhifei Biological Products Co., Ltd. also started subunit vaccine development against SARS-CoV- 2. 15 . Spike Protein (S Protein) • S protein is currently the most promising antigen formulation for SARS-CoV-2 vaccine research. • First, it is surface exposure and thus is able to be directly recognized by host immune system . • Second, it mediates the interaction with host cell by binding to the receptor ACE2, which is essential for subsequent virus entry to target cells and causing subsequent pathogenicity. Finally, the homologue proteins were already used for vaccine development against SARS- CoV and MERS-CoV, and were proved to be effective. 16 . Spike Protein (S Protein) • The monomer of S protein from SARS-CoV-2 contains 1273 amino acids, with a molecular weight of about 140 kDa. The S protein contains two subunits (S1 and S2). The S1 subunit can be further defined with two domains termed the N-terminal domain (NTD) and the C-terminal domain (CTD). The receptor binding domain (RBD) located in the CTD. • S2 subunit contains the basic elements required for membrane fusion, including an internal membrane fusion peptide (FP), So far, the potential fragments of S protein for use as antigens in vaccine development include the full-length S protein, the RBD domain, the S1 subunit, NTD, and FP. 17 Subunit COVID-19 vaccine (Spike Protein) SARS-CoV-2 rS/Matrix M1-Adjuvant (Full length recombinant SARS CoV-2 Phase glycoprotein nanoparticle vaccine 2 Day 0 + 21 IM Novavax 3 adjuvanted with Matrix M) SARS-CoV-2 vaccine formulation 1 with adjuvant 1 (S protein (baculovirus Phase 2 Day 0 + 21 IM Sanofi Pasteur + GSK production) 1/2 SCB-2019 + AS03 or CpG 1018 adjuvant plus Alum adjuvant (Native like Clover Biopharmaceuticals Phase 2 Day 0 + 21 IM Trimeric subunit Spike Protein vaccine) Inc./GSK/Dynavax 2/3 Medigen Vaccine Biologics + MVC-COV1901 (S-2P protein + CpG Dynavax + National Institute Phase 2 Day 0 + 28 IM 1018) of Allergy and Infectious 2 Diseases (NIAID) COVAX-19® Recombinant spike Phase 1 Day 0 IM Vaxine Pty Ltd. protein + adjuvant 1 IM Razi Cov Pars, recombinant spike Day 0 + 21 Razi Vaccine and Serum Phase 3 and protein +51 Research Institute 1 IN 18 RBD • Since the RBD of S protein directly interacts with the ACE2 receptor on host cells, RBD immunization induced specific antibodies may block this recognition and thus effectively prevent the invasion of the virus. As a matter of fact, most of SARS-CoV-2 subunit vaccines currently under development use RBD as the antigen. Moreover, the RBD domain was also used in the development of SARS-CoV and MERS-CoV vaccines. 19 Subunit COVID-19 vaccine (RBD Protein) Day 0 + 28 or Anhui Zhifei Longcom Biopharmaceutical Recombinant SARS-CoV-2 vaccine 2-3 Day 0 + 28 + IM + Institute of Microbiology, Chinese Phase 3 (CHO Cell) 56 Academy of Sciences Phase KBP-COVID-19 (RBD-based) 2 Day 0 + 21 IM Kentucky Bioprocessing Inc. 1/2 FINLAY-FR anti-SARS-CoV-2 Vaccine 2 Day 0 + 28 IM Instituto Finlay de Vacunas Phase 2 (RBD + adjuvant) RBD (baculovirus production expressed in Sf9 cells) 2 Day 0 + 28 IM West China Hospital + Sichuan University Phase 2 Recombinant SARS-CoV-2 vaccine (Sf9 Cell) AdimrSC-2f (recombinant RBD +/- ND ND ND Adimmune Corporation Phase 1 Aluminium) Day 0 + 14 + Center for Genetic Engineering and Phase CIGB-669 (RBD+AgnHB) 3 28 or Day 0 IN Biotechnology (CIGB) 1/2 +28 + 56 Day 0 + 14 + CIGB-66 (RBD+aluminium Center for Genetic Engineering and Phase 3 28 or Day 0 IM hydroxide) Biotechnology (CIGB) 1/2 +28 + 56 University Medical Center Groningen + Phase SARS-CoV-2-RBD-Fc fusion protein SC or IM Akston Biosciences Inc. 1/2 20 NTD • Similar to RBD, the N-terminal domains (NTD) of S protein from several coronaviruses were • reported to show carbohydrate receptor- binding activity. For example, the NTD of spike protein form transmissible gastroenteritis virus (TGEV) was reported to bind sialic acid via NTD. The carbohydrate-binding properties of IBV M41 strain are also related to the NTD of the S protein. Thus, this domain is also a candidate antigen for vaccine development. 21 S1 Subunit • The S1 subunit, which contains both RBD and NTD described above, is mainly involved in the S • protein binding to the host receptor. It is also widely used in vaccine development. • Wang et al. reported that MERS-CoV S1 protein formulated with MF59 adjuvant protected hDPP4 transgenic mice against lethal virus challenge, and the protection correlated well with the neutralizing antibody titer. • Adney et al. confirmed that immunization with adjuvanted S1 protein reduced and delayed virus • shedding in the upper respiratory tract of dromedary camels and complete protection was observed in alpaca against MERS-CoV challenge. 22 FP • The FP domain of the S2 subunit is involved in the membrane fusion of the virus, which is also a key step in viral pathogenicity [32]. Therefore, it may also serve as a vaccine candidate antigen. At present, Tianjin University has constructed an RBD-FP fusion protein, and high titer of antibodies was detected in mice immunized with this fusion protein, and the effcacy is under evaluation. 23 Nucleocapsid Protein (N Protein) • The N protein is the most abundant protein in coronavirus, and it is normally highly conserved, • with a molecular weight of about 50 kDa. N protein has multiple functions including formation of nucleocapsids, signal transduction virus budding, RNA replication, and mRNA transcription.