Cong Yao's group collaborated to develop neutralizing antibodies against coxsackievirus A16 and reveal its molecular mechanism

On December 21, the international academic journal Nature Communications published online the collaborative research paper "Molecular mechanism of antibody neutralization of" by Cong Yao's research group of the Center for Excellence in Molecular Cell Science (Institute of Biochemistry and Cell Biology) of the Chinese Academy of Sciences and Huang Zhong's research group of the Shanghai Pasteur Institute of the Chinese Academy of Sciences coxsackievirus A16”
。 This study developed two specific monoclonal antibodies 9B5 and 8C4 against coxsackievirus A16 (CVA16), based on cryo-EM and biochemical analysis, to clarify the functional and structural basis of neutralization mediated by the above specific antibodies, providing important information
for the design and development of CVA16 vaccines and antibody therapies.

CVA16 is a member of the genus Enteroviruses of the family Pibnucleoviridae and is one of
the leading pathogens of hand-foot-and-mouth disease (HFMD) in infants and young children.
CVA16 infection can lead to mild and self-limited symptoms, as well as serious clinical complications such as encephalitis, myocarditis, pneumonia, and even death
.
However, there are currently no vaccines and treatments
.
Neutralizing antibodies play a key role
in antiviral protective immunity.
Therefore, it is important to develop CVA16-specific neutralizing antibodies and determine their function, binding epitope, and mechanism of operation to aid in the development of
anti-CVA16 vaccines and drugs.

Huang's team prepared two CVA16-specific monoclonal antibodies, 9B5 and 8C4
.
The above antibodies not only have strong in vitro neutralizing activity, but also show effective preventive and therapeutic effects in CVA16 mouse infection models (Figures a, b).

Biochemical studies have shown that the two antibodies have different neutralization mechanisms: 9B5 inhibits viral adsorption to the cell surface by blocking the binding of CVA16 to the adsorption receptor heparin sulfate; 8C4, on the other hand, acts in the post-viral adsorption phase, impeding the binding of the virus to the decoating shell receptor SCARB2 (Figure C).

Cong Yao's team analyzed the cryo-EM structure
of the complex formed by CVA16 virus particles bound to antibodies 9B5 and 8C4, respectively.
Both systems obtained three different conformations, named C1, C2, C3 (Figure d-o), with CVA16-9B5-C1 and CVA16-8C4-C2 both reaching a resolution of 2.
9 angstroms
。 CVA16 in C1 showed mature viral conformation (Figures d, g, j, m); CVA16 in C2 is compact empty shell conformation, virus-free RNA (Figure e, h, k, n); CVA16 in C3 is an expanded hollow shell conformation, showing significant conformational differences, including capsid expansion, opening of secondary axis holes, and viral RNA deletion (Fig.
f, i, l, o).

Structural analysis showed that 9B5 binds to the quintuple axis of CVA16, with each monomer binding to a 9B5 Fab (Figure d).

9B5 binds to the north side of the canyon area of CVA16, and the binding footprint of 9B5 on the viral capsid can mask the binding site of the adsorption receptor heparin sulfate (Figure p), thereby inhibiting the binding of CVA16 virus to the heparin sulfate receptor
.
8C4 is combined on the triple axis of CVA16 (Figure j).

Interestingly, 8C4 combines only the C1 and C2 states of compact conformation, but not the expansion conformation C3 (Figure j-o).

In addition, the researchers found that 8C4 and SCARB2 clashed both at the binding site and space on the capsid (Figure q), revealing the structural basis
of 8C4 antibody inhibition of CVA16's binding to SCARB2.
The cryo-EM structure superimposed on CVA16-9B5-C1 and CVA16-8C4-C1 shows that 8C4 and 9B5 recognize different, non-overlapping epitopes (panel r), so that the two antibodies can simultaneously bind to the same CVA16 viral capsid to form a non-competitive antibody pair
.
Further analysis showed that the pair showed a stronger neutralizing ability than a single antibody and demonstrated the ability to stop the
virus from escaping.
In contrast, viral escape is prone to occur
when a single antibody is used.

In summary, the study developed a unique pair of CVA16 neutralizing monoclonal antibodies, revealing their different binding epitopes and neutralizing mechanisms
.
The combination of these antibodies can be further developed as a broad-spectrum therapeutic agent against human CVA16 infection, which has important theoretical significance and potential clinical transformation value
.

Zhang Chao, associate researcher of Shanghai Pasteur Institute, Liu Caixuan, doctoral student of the Center of Excellence of Molecular Cells, and Shi Jinping, a doctoral student graduated from Shanghai Pasteur Institute, are the joint first authors
of this paper.
Prof.
Zhong Huang of the Instint Pasteur Institute in Shanghai and Yao Cong from the Center of Excellence of Molecular Cells are co-corresponding authors
of this paper.
The research was supported by the Chinese Academy of Sciences, the Ministry of Science and Technology of the People's Republic of China, the National Natural Science Foundation of China, and the Shanghai Municipal Science and Technology Commission.
It has also received great assistance
from the cryo-EM system of the National Protein Science Research (Shanghai) Facility.

Article link:

a-b, CVA16 monoclonal antibodies 8C4 and 9B5 neutralizing activity against CVA16 live virus (a) and therapeutic effect in vivo (b).

c, Pretreatment with 9B5 instead of 8C4 can dose-dependently inhibit adsorption
of CVA16 live virus to host cells.
Cryo-EM structure
of d-f, j-l CVA16-9B5(d-f) and CVA16-8C4(j-l) complexes.
CVA16 is compact conformation in C1 and C2, and CVA16 is expansion conformation in C3
.
Central slices of three state EMM densitograms
of g-i, m-o, CVA16-9B5(g-i) and CVA16-8C4(m-o).
The C2 and C3 states were shown to contain no viral RNA
in the CVA16 lumen.
p, 9B5 binding footprint
on viral capsids.
q, 8C4 binding footprint
on viral capsids.
r, superimposed cryo-EM structures of CVA16-9B5-C1 and CVA16-8C4-C1, showing that 8C4 and 9B5 identify different, non-overlapping epitopes
.