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Optimisation of human VH domain antibodies specific to Mycobacterium tuberculosis heat shock protein (HSP16.3)

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Abstract

Mycobacterium tuberculosis (Mtb) 16.3 kDa heat shock protein 16.3 (HSP16.3) is a latency-associated antigen that can be targeted for latent tuberculosis (TB) diagnostic and therapeutic development. We have previously developed human VH domain antibodies (dAbs; clone E3 and F1) specific against HSP16.3. In this work, we applied computational methods to optimise and design the antibodies in order to improve the binding affinity with HSP16.3. The VH domain antibodies were first docked to the dimer form of HSP16.3 and further sampled using molecular dynamics simulation. The calculated binding free energy of the HSP16.3-dAb complexes showed non-polar interactions were responsible for the antigen–antibody association. Per-residue free energy decomposition and computational alanine scanning have identified one hotspot residue for E3 (Y391) and 4 hotspot residues for F1 (M394, Y396, R397 and M398). These hotspot residues were then mutated and evaluated by binding free energy calculations. Phage ELISA assay was carried out on the potential mutants (E3Y391W, F1M394E, F1R397N and F1M398Y). The experimental assay showed improved binding affinities of E3Y391W and F1M394E against HSP16.3 compared with the wild type E3 and F1. This case study has thus showed in silico methods are able to assist in optimisation or improvement of antibody-antigen binding.

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Funding

This work was supported by Bridging Grant (Grant No. 304/CIPPM/6316018) and Research University Grant (Grant No. RUi; 1001/CIPPM/811051) from Universiti Sains Malaysia. The computational resources were supported by Fundamental Research Grant Scheme (Grant No. FRGS; FRGS/1/2018/STG05/USM/02/01). T.S. Lim would like to acknowledge Higher Institution Centre of Excellence Grant (Grant No. HICoE; 311/CIPPM/44001005) from Malaysia Ministry of Education. Appreciation also extended to MyBrain15 from Ministry of Education Malaysia for the scholarship for J.X. Soong.

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Authors and Affiliations

  1. Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia

    Jia Xin Soong, Soo Khim Chan, Theam Soon Lim & Yee Siew Choong

  2. Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia

    Theam Soon Lim

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  1. Jia Xin Soong
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Computational work was carried out by JX Soong. Experimental work was performed by SK Chan. TS Lim and YS Choong planned the workflow. All authors contributed to the writing of the paper.

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Correspondence to Yee Siew Choong.

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Soong, J.X., Chan, S.K., Lim, T.S. et al. Optimisation of human VH domain antibodies specific to Mycobacterium tuberculosis heat shock protein (HSP16.3). J Comput Aided Mol Des 33, 375–385 (2019). https://doi.org/10.1007/s10822-019-00186-z

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