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PubMed Central
Article . 2025
License: CC BY NC
Data sources: PubMed Central
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Open Veterinary Journal
Article . 2025
Data sources: DOAJ
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Computational insights in CD58 binding to ASFV CD2v and in silico optimization of nanobody designs against the interface.

Authors: Albert Neil Gura Dulay; Richelle Mae Evasco Padilla; Nyzar Mabeth Obenio Odchimar; Fredmoore Legaspi Orosco;

Computational insights in CD58 binding to ASFV CD2v and in silico optimization of nanobody designs against the interface.

Abstract

African swine fever (ASF) continues to hamper pork production worldwide. In addition to vaccines, there is a need to develop curative therapeutics, such as highly-specific antibodies or nanobodies (NB), against immunogenic proteins with important functions such as the viral CD2 (CD2v)-like protein. However, further characterization of CD2v, such as its binding with cellular partners, is needed for the rational development of such biologics.We aimed to analyze the binding interaction of CD2v from pandemic genotypes I and II and swine CD58 using molecular simulations and optimize the NB to target the conserved epitope around the identified binding site using a computational pipeline.CD2v-CD58 complexes and equivalents from swine and humans were generated and simulated to characterize their binding. Mapping of residue contributions to the binding, variability, epitope propensity, and epitope multiplicity allowed us to select a conserved region near the site. Optimized NB were developed from sequences deposited in the NanoLAS repository, following screening for physicochemical and reactogenic parameters, docking, iterative optimization, and molecular dynamics simulations compared to controls.Simulations report poor affinity of CD2v to CD58 in the "canonical" pose and present a novel pose backed by docking, simulation data, and recent observations. The new site might have developed due to immunological considerations and may reproduce observed lymphocyte non-proliferation by hijacking CD58-CD2 ruler functions in immunological synapse formation. Two NB were also developed targeting genotype I and II CD2vs with stable binding and better affinity, solubility, allergenicity, and antigenicity than the controls NB22 and 18a3.Herein, we showcase the power of computational biology techniques to elucidate ASF virus (ASFV)-host interactions and simultaneously design therapeutics to target the identified novel binding site. Further validation is needed to confirm these findings; however, future work on other relevant ASFV proteins may lead to potent cocktails with therapeutic potential.

Keywords

Swine, Single-Domain Antibodies, Molecular Dynamics Simulation, CD58 Antigens, antiviral, African Swine Fever Virus, cd2v, Molecular Docking Simulation, Viral Proteins, computational biology, QL1-991, asfv, Animals, Humans, Computer Simulation, site-directed mutagenesis, African Swine Fever, Zoology, Research Article, Protein Binding

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
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gold