Studies on computational grafting of malarial epitopes in serum albumin

BACKGROUND Antigens (or their epitopes)-carrier protein combinations are extensively utilized for vaccine development strategies. Chemical conjugation methods are cumbersome with limited conjugation sites. Computational protein modelling methods can evaluate every position of a carrier protein for conjugation via epitope grafting in a reasonable time frame as compared to wet experimental techniques. Graftibility of positions can be estimated by the presence of native atomic contacts in resulting chimeric antigen. METHODOLOGY Five epitopes were selected, and computational grafting at each position was performed in three templates of serum albumin. Protein modelling algorithms such as segment matching and satisfaction of spatial restraints were employed for computational grafting. Contact-based protein discriminatory function was used to evaluate the chimeric proteins having native atomic contacts. RESULTS On the evaluation of approximately 1 million distinct protein modelling simulations, region around the 450th position of serum albumin was observed to be suitable for epitope grafting. CONCLUSION Computational protein modelling tools may be used to design a chimeric antigen. The approach may overcome the limitations associated with chemical conjugation and furthermore harness the potential of custom gene synthesis/recombinant protein production.

[1]  D. Baker,et al.  Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold , 2011, Science.

[2]  V. Nussenzweig,et al.  A bicomponent Plasmodium falciparum investigational vaccine composed of protein-peptide conjugates , 2009, Proceedings of the National Academy of Sciences.

[3]  J M Thornton,et al.  Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis. , 1998, Protein engineering.

[4]  A. Thomas,et al.  Antibodies to Malaria Peptide Mimics Inhibit Plasmodium falciparum Invasion of Erythrocytes , 2004, Infection and Immunity.

[5]  Ram Samudrala,et al.  The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection. , 2006, Protein engineering, design & selection : PEDS.

[6]  Pratyoosh Shukla,et al.  Computational tools for modern vaccine development , 2019, Human vaccines & immunotherapeutics.

[7]  Guido Tiana,et al.  SAGE: A Fast Computational Tool for Linear Epitope Grafting onto a Foreign Protein Scaffold , 2017, J. Chem. Inf. Model..

[8]  K. Marsh,et al.  Antibodies to Polymorphic Invasion-Inhibitory and Non-Inhibitory Epitopes of Plasmodium falciparum Apical Membrane Antigen 1 in Human Malaria , 2013, PloS one.

[9]  D. Peabody,et al.  Identification of an Immunogenic Mimic of a Conserved Epitope on the Plasmodium falciparum Blood Stage Antigen AMA1 Using Virus-Like Particle (VLP) Peptide Display , 2015, PloS one.

[10]  A. Thomas,et al.  Fine Mapping of an Epitope Recognized by an Invasion-inhibitory Monoclonal Antibody on the Malaria Vaccine Candidate Apical Membrane Antigen 1* , 2007, Journal of Biological Chemistry.

[11]  T. Horii,et al.  Recent advances in recombinant protein-based malaria vaccines , 2015, Vaccine.

[12]  David Baker,et al.  Proof of principle for epitope-focused vaccine design , 2014, Nature.

[13]  D. Burton.  Scaffolding to build a rational vaccine design strategy , 2010, Proceedings of the National Academy of Sciences.

[14]  W. Minor,et al.  Structural and immunologic characterization of bovine, horse, and rabbit serum albumins. , 2012, Molecular immunology.

[15]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[16]  B. Krantz,et al.  Domain flexibility modulates the heterogeneous assembly mechanism of anthrax toxin protective antigen. , 2012, Journal of molecular biology.

[17]  Alessandro Sette,et al.  The Immune Epitope Database 2.0 , 2009, Nucleic Acids Res..

[18]  Yolanda Gil,et al.  Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome , 2013, PloS one.

[19]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[20]  D. Peabody,et al.  Immunogenic display of diverse peptides on virus-like particles of RNA phage MS2. , 2008, Journal of molecular biology.

[21]  I. Wilson,et al.  Approaching rational epitope vaccine design for hepatitis C virus with meta-server and multivalent scaffolding , 2015, Scientific Reports.

[22]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[23]  M. J. Rosovitz,et al.  Alanine-scanning Mutations in Domain 4 of Anthrax Toxin Protective Antigen Reveal Residues Important for Binding to the Cellular Receptor and to a Neutralizing Monoclonal Antibody* , 2003, Journal of Biological Chemistry.

[24]  D. Kaslow,et al.  RTS,S: Toward a first landmark on the Malaria Vaccine Technology Roadmap. , 2015, Vaccine.

[25]  G. Georgiou,et al.  Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen. , 2009, Journal of molecular biology.

[26]  Markus S. Mueller,et al.  A Role for Apical Membrane Antigen 1 during Invasion of Hepatocytes by Plasmodium falciparum Sporozoites* , 2004, Journal of Biological Chemistry.

[27]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using Modeller , 2006, Current protocols in bioinformatics.

[28]  R. Samudrala,et al.  An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. , 1998, Journal of molecular biology.

[29]  A. Jin,et al.  Development of a Pfs25-EPA malaria transmission blocking vaccine as a chemically conjugated nanoparticle. , 2013, Vaccine.

[30]  Patrice Koehl,et al.  The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..

[31]  A. Tramontano,et al.  Critical assessment of methods of protein structure prediction: Progress and new directions in round XI , 2016, Proteins.

[32]  Roland L. Dunbrack,et al.  proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 , 2022 .

[33]  D. Baker,et al.  Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope , 2011, Journal of Molecular Biology.

[34]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[35]  Srinivasan Ramachandran,et al.  MalVac: Database of malarial vaccine candidates , 2008, Malaria Journal.

[36]  J. Thornton,et al.  Stereochemical quality of protein structure coordinates , 1992, Proteins.

[37]  Myron M. Levine,et al.  Safety and immunogenicity in man of a synthetic peptide malaria vaccine against Plasmodium falciparum sporozoites , 1987, Nature.

[38]  Aditi Gupta,et al.  Structure of the Malaria Antigen AMA1 in Complex with a Growth-Inhibitory Antibody , 2007, PLoS pathogens.

[39]  Yang Zhang,et al.  Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. , 2011, Biophysical journal.

[40]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[41]  D. Baker,et al.  Elicitation of structure-specific antibodies by epitope scaffolds , 2010, Proceedings of the National Academy of Sciences.

[42]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[43]  L. Stamatatos,et al.  Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. , 2010, Structure.

[44]  Meenakshi Sharma,et al.  Identification and characterization of immunodominant B-cell epitope of the C-terminus of protective antigen of Bacillus anthracis. , 2009, Molecular immunology.