In Silico Engineering Towards Enhancement of Bap–VHH Monoclonal Antibody Binding Affinity

  • Fateme Sefid
  • Zahra Payandeh
  • Ghasem Azamirad
  • Razieh Abdolhamidi
  • Iraj RasooliEmail author


Antibodies play major role in immunotherapy, basic researches, and industrial processes. Interactions between antibody–antigen complexes are important to know how they function that help improve their properties in designing new antibodies through rational engineering for therapeutic or biotechnological applications, including the production of biosensors. Nowadays, antibody engineering is widely used in many fields such as medicine, criminal sciences, military, defense industries, etc. Designing antibodies with desired properties is a challenging task. Computational docking is the method of predicting the conformation of a complex structure such as antibody–antigen from its separated elements. The validation of designed antibodies is carried out by docking tools. In the previous study we produced VHH against Bap antigen in Acinetobacter baumannii using phage display technique. In this study, the VHH selected using phage display technique was modeled and docked with its antigen. We made an attempt to find the important amino acids of this antibody, then replaced these amino acids with others to improve their binding affinity of antibody variants to antigens. In this regard, the VHH was mutated. Docking structural prediction of Bap–VHH complex was used for designing and validation of VHHs with higher affinity for binding to Bap receptor. By analysis of the model, several mutants of VHH were designed, and their properties improved in a predictable manner especially for their binding ability to Bap. In conclusion, the designed nanobodies, considering their binding site on Bap, were found to be potential candidates for the treatment of Acinetobacter baumannii infections.


Acinetobacter baumannii Antibody engineering Antigen binding Bap VHH Bioinformatic tools 



The authors wish to thank Molecular Microbiology Research Center, Shahed University, Tehran- Iran for their support by an unrestricted free access to web site for data collection.

Author Contributions

Prof. IR laid out the main idea and participated in the design of the study, conducted coordination, and revised the manuscript. FS, ZP, GA and RA participated in the data collection, data analysis, software trouble shooting, and drafting the manuscript respectively. All authors read and approved the final manuscript.


The authors appreciate National Institute for Medical Research Development, Grant Number 958302.

Compliance with Ethical Standards

Conflict of interest

All authors declare no potential conflicts of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Fateme Sefid
    • 1
    • 2
  • Zahra Payandeh
    • 3
  • Ghasem Azamirad
    • 4
  • Razieh Abdolhamidi
    • 5
  • Iraj Rasooli
    • 5
    • 6
    Email author
  1. 1.Departeman of Medical GeneticsShahid Sadoughi University of Medical ScienceYazdIran
  2. 2.Departeman of BiologyScience and Art UniversityYazdIran
  3. 3.Department of Medical Biotechnology and Nanotechnology, Faculty of MedicineZanjan University of Medical ScienceZanjanIran
  4. 4.School of Mechanical EngineeringYazd UniversityYazdIran
  5. 5.Molecular Microbiology Research CenterShahed UniversityTehranIran
  6. 6.Department of BiologyShahed UniversityTehranIran

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