Antibodies to combat viral infections: development strategies and progress

Abstract

Monoclonal antibodies (mAbs) are appealing as potential therapeutics and prophylactics for viral infections owing to characteristics such as their high specificity and their ability to enhance immune responses. Furthermore, antibody engineering can be used to strengthen effector function and prolong mAb half-life, and advances in structural biology have enabled the selection and optimization of potent neutralizing mAbs through identification of vulnerable regions in viral proteins, which can also be relevant for vaccine design. The COVID-19 pandemic has stimulated extensive efforts to develop neutralizing mAbs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with several mAbs now having received authorization for emergency use, providing not just an important component of strategies to combat COVID-19 but also a boost to efforts to harness mAbs in therapeutic and preventive settings for other infectious diseases. Here, we describe advances in antibody discovery and engineering that have led to the development of mAbs for use against infections caused by viruses including SARS-CoV-2, respiratory syncytial virus (RSV), Ebola virus (EBOV), human cytomegalovirus (HCMV) and influenza. We also discuss the rationale for moving from empirical to structure-guided strategies in vaccine development, based on identifying optimal candidate antigens and vulnerable regions within them that can be targeted by antibodies to result in a strong protective immune response.

Fig. 1. Mechanism of action of monoclonal antibodies during viral infection.

a | Overview of monoclonal antibody (mAb) structure; heavy chains shown in yellow and red, light chains in blue and green. b | Binding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the angiotensin-converting enzyme 2 (ACE2) receptor on host cells is mediated by the viral spike (S) protein, which comprises an S1 subunit (including a receptor-binding domain (RBD) and an amino-terminal domain (NTD)) and an S2 subunit. Priming of coronavirus spike proteins by host cell proteases such as the transmembrane serine protease TMPRSS2 through cleavage at S1/S2 and S2′ sites (see Fig. 3) is essential for viral entry. Therapeutic antibodies and antibodies elicited by vaccination that bind to the RBD or NTD can block viral binding to ACE2, or block fusion between viral and cellular membranes (see Fig. 3). c | Effector functions of antibodies. mAbs can facilitate target cell death via complement fixation and membrane attack complex (MAC) activation, which is known as complement-dependent cytotoxicity (CDC). Antibody-dependent cellular cytotoxicity (ADCC) is a mechanism of cell-mediated immune defence whereby an effector cell (natural killer cell, macrophage, neutrophil or eosinophil) of the immune system actively lyses a target cell, whose membrane has been bound by specific antibodies. Natural killer cells release cytotoxic factors (perforin and proteases known as granzymes) that cause death of the infected cell. Antibody-dependent cellular phagocytosis is the mechanism by which antibody-opsonized target cells activate Fcγ receptors (FcγRs) on the surface of macrophages to induce phagocytosis, resulting in internalization and degradation of the target cell through phagosome acidification. Fab, fragment antigen-binding domain; Fc, crystallizable fragment; Fv, variable fragment; VH, variable heavy; VL, variable light.

Fig. 2. Antibody discovery approaches.

a | Phage bio-panning is based on a library of phages that contain genes coding for variable heavy (VH)/variable light (VL) domains, leading to production of encoded antibodies on phage surfaces. Selection of antibodies produced by phages involves immobilization of the ligand of interest on a solid support (spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shown), followed by applying the phage display library to immobilized ligand to allow binding of specific variants. To eliminate adherent non-binders, multiple rounds of washing are usually performed, and remaining bound phages are eluted and re-amplified. b | Recombinant antigens conjugated to a fluorescent marker are incubated with class-switched memory B cells and sorted according to their capacity to bind the antigen of interest (such as the S protein of SARS-CoV-2) by fluorescence-activated flow cytometry, followed by identification of the antibodies they produce. c | Target-agnostic approaches using single B cell culture. Single B cells are seeded on a feeder layer in the presence of a cytokine mix and a Toll-like receptor (TLR) activator. Culture supernatant is screened for neutralization activity and clones of interest are retrieved and sequenced. d | Workflow for organoid reconstitution from human tonsils to develop an in vitro system that recapitulates key germinal centre features, including production of antigen-specific antibodies, somatic hypermutation and affinity maturation. e | Workflow for single cell immune profiling. B cells are encapsulated with barcoded gel beads in a single partition and undergo reverse transcription followed by PCR. Each cDNA is barcoded from its individual cell of origin and processed for next-generation sequencing. Fab, fragment antigen-binding domain; mAb, monoclonal antibody; scFv, single-chain variable fragment. Panel a is adapted from ref., under a Creative Commons license CC BY 3.0.

Fig. 3. The SARS-CoV-2 spike protein and neutralizing antibodies targeting the receptor-binding domain.

a | Structural representation of the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with modelled carboxy-terminal part. b | SARS-CoV-2 spike protein domain architecture. c | Structure of the receptor-binding domain (RBD) (grey) bound to angiotensin-converting enzyme 2 (ACE2) (forest green) [PDB:6M0J]. d | Neutralizing antibodies can prevent opening of the S protein to block RBD erection, block the RBD to prevent binding to ACE2, block the amino-terminal domain (NTD) or block the fusion step. e | Footprints of ACE2 (green) or footprints of different ultrapotent antibody neutralizer classes (blue) shown on the RBD (grey). To generate footprints, the ‘Clashes/Contacts’ tool in UCSF Chimera was used to identify residues on the RBD that contact monoclonal antibodies (mAbs). Default contact criteria with van der Waals overlap of ≥–0.4 Å or more were used. CH, central helix; CD, connector domain; FP, fusion peptide; HR1, heptad repeat 1; HR2, heptad repeat 2; SD1, subdomain 1; SD2, subdomain 2; SS, signal sequence; TM, transmembrane region.

Fig. 4. Neutralizing antibodies that bind to glycoproteins from various pathogens.

a | Antigenic sites of the fusion protein (F) of respiratory syncytial virus (RSV). Locations of six antigenic sites on pre-fusion structure shown on left [PDB:4MMU], with locations on post-fusion structure shown on right [PDB:6APB]. b | Crystal structure of Zaire Ebola virus (EBOV) glycoprotein [PDB:5JQ3]: GP2 in dark grey, GP1 head in blue, GP1 glycan cap in cyan and glycans in yellow. To the right, trimeric glycoprotein shown with the ZMapp antibody cocktail [PDB:5KEN and PDB:5KEL], with mAb114 [PDB:5FHC] or with three monoclonal antibodies (mAbs) that make up REGN-EB3. c | Glycoproteins of human cytomegalovirus (HCMV) and antibody-binding sites. Trimer gH/gL/gO structure [PDB:7LBE] shown with antibody footprint (orange) for MSL-109 and 13H11 mAb on gH (left) and gH/gL/UL128/UL130/UL131A pentamer [PDB:5VOD] (centre) shown with footprint of antigenic sites present on UL. On the right, structures of gB in pre-fusion [PDB:7KDP] shown with coloured antigenic sites (AD1 in orange, AD2 in red, AD4 in green and AD5 in blue). d | Influenza haemagglutinin (HA) consists of three homotrimers built from two chains, HA1 and HA2, that are linked via a disulfide bond. HA molecules are commonly divided into immunodominant head and immunosubdominant stem. Based on sequence variations of HA, influenza is divided into two phylogenetic groups that are further subdivided into a total of 18 strains. Colour-coded dots represent observed binding of various broadly neutralizing antibodies (bNAbs) against different HAs [PDB:3S12]. Footprints of several group 1-specific and group 2-specific antibodies as well as pan-group reactive antibodies on HA stem shown to right. CD, core domain.

Fig. 5. Reverse vaccinology 2.0.

Single cell cultures of plasma or memory B cells from a convalescent patient or vaccinated donor are used to screen for monoclonal antibodies (mAbs) with neutralizing activity against the target pathogen. Next, recombinant mAbs are used to identify the antigen and investigate the 3D structure of the antigen–mAb complex. This structural information is used to optimize a stabilized antigen for a vaccine. Fab, fragment antigen-binding domain; PBMC, peripheral blood mononuclear cell.