Computational Construction of a Single-Chain Bi-Paratopic Antibody Allosterically Inhibiting TCR-Staphylococcal Enterotoxin B Binding

Abstract

Staphylococcal enterotoxin B (SEB) simultaneously crosslinks MHC class II antigen and TCR, promoting proliferation of T cells and releasing a large number of toxic cytokines. In this report, we computationally examined the possibility of using a single-chain biparatopic bispecific antibody to target SEB and prevent TCR binding. The design was inspired by the observation that mixing two anti-SEB antibodies 14G8 and 6D3 can block SEB-TCR activation, and we used 14G8-6D3-SEB tertiary crystal structure as a template. Twelve simulation systems were constructed to systematically examine the effects of the designed bispecific scFV MB102a, including isolated SEB, MB102a with different linkers, MB102a-SEB complex, MB102a-SEB-TCRβ complex, MB102a-SEB-TCR-MHC II complex, and MB102a-SEB-MHC II. Our all atom molecular dynamics simulations (total 18,900 ns) confirmed that the designed single-chain bispecific antibody may allosterically prevent SEB-TCRβ chain binding and inhibit SEB-TCR-MHC II formation. Subsequent analysis indicated that the binding of scFV to SEB correlates with SEB-TCR binding site motion and weakens SEB-TCR interactions.

Evaluation of Molecular Simulations and Deep Learning Prediction of Antibodies’ Recognition of TRBC1 and TRBC2

“…Our previous work [ 14 ] indicated that the communication between antibody and antigen could be reflected in the amino acid residue covariance matrix, which measures the motion correlations between any two residues in a protein complex. Figure 5 compares the covariance matrixes for the antibody–TRBC system with higher affinities (upper panel) and lower affinities (lower panel).…”

“…This model is trained on SKEMPI [27] Antibody-Bind (AB-Bind) [28] datasets, both curated antibody-antigen complexes with single-site and multi-site mutations and corresponding free energy change values (∆∆G). The training dataset comprises Computational antibody designs have been developed to help antibody designs [10][11][12][13][14][15][16], including molecular mechanical energy-based de novo design [11], molecular dynamics simulations [14,[17][18][19], structure-based antibody prediction and similarity measure of antibody-antigen interfaces [20,21]. Molecular docking and subsequent MD simulation have also been used to predict the binding mode of JOVI-1 with TRBC1 [19].…”

“…Computational antibody designs have been developed to help antibody designs [ 10 , 11 , 12 , 13 , 14 , 15 , 16 ], including molecular mechanical energy-based de novo design [ 11 ], molecular dynamics simulations [ 14 , 17 , 18 , 19 ], structure-based antibody prediction and similarity measure of antibody–antigen interfaces [ 20 , 21 ]. Molecular docking and subsequent MD simulation have also been used to predict the binding mode of JOVI-1 with TRBC1 [ 19 ].…”

“…Interestingly, based on computational structure-guided specificity redirection of JOVI-1, three mutations of the JOVI-1 VH chain (T28K, Y32F, A96N) successfully switched JOVI-1 to bind the highly homologous target TRBC2-TCR (TCRαβ2) [9], opening another opportunity for the T-cell malignancy treatments. Computational antibody designs have been developed to help antibody designs [10][11][12][13][14][15][16], including molecular mechanical energy-based de novo design [11], molecular dynamics simulations [14,[17][18][19], structure-based antibody prediction and similarity measure of antibody-antigen interfaces [20,21]. Molecular docking and subsequent MD simulation have also been used to predict the binding mode of JOVI-1 with TRBC1 [19].…”

Oral exposure to Staphylococcus aureus enterotoxin B could promote the Ovalbumin-induced food allergy by enhancing the activation of DCs and T cells

“…Heat-labile toxins expressed by E. coli and Vibrio cholerae lead to apoptosis or elimination in T cells ( 36 ). Superantigens, represented by staphylococcal enterotoxins, could induce a non-antigen-specific activation of T cells by cross-linking MHC and TCR with the presence of APCs, leading to rapid proliferation and release of cytokines ( 37 , 38 ). Our results suggested a potential risk raised by co-exposure of enterotoxins and food allergens.…”