Special Issue "Computational Antibody and Antigen Design"

A special issue of Antibodies (ISSN 2073-4468).

Deadline for manuscript submissions: closed (31 May 2018)

Special Issue Editor

Guest Editor
Dr. Buyong Ma

Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, NIH, Frederick, MD 21702, USA
E-Mail
Interests: Computational chemistry and biology; Computational Immunology; Protein-Protein Interaction; Protein aggregation diseases; Neurodegenerative disease; Alzheimer's Disease; Cancer and Inflammation; Antigen receptors and signaling; Antibody design

Special Issue Information

Dear Colleagues,

Using computational modeling to help antibody engineering is complementary to traditional animal models and phage display methodologies, hopefully speeding up and providing additional variations into antibody design. Starting from antibody/antigen sequences, one can model the structures of antibody and antigen, predict antibody–antigen interactions through docking and/or molecular dynamics simulations, and provide computationally designed/optimized systems for experimental verification. Computational antibody design can lead to high affinity, high stability, and high specificity. In vaccine design, computational modeling can generate small and stable protein scaffolds, mimicking antigen epitopes to induce potent neutralizing antibodies. Even with this promising power, widely-integrated application of computational modeling in antibody engineering is still yet to arrive. This Special Issue will showcase various aspects of computational antibody and antigen design.

This Special Issue of Antibodies focuses on: (1) computational/structural characterization of antibody structures; (2) bioinformatics study of antibody and antigens; (3) computational algorithms in antibody and antigen design; and (4) applications of computational methods in antibody/antigen development. 

Dr. Buyong Ma
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibodies is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 350 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • antibody design
  • antibody engineering
  • vaccine design
  • protein-protein interaction
  • computational biology

Published Papers (2 papers)

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Research

Open AccessArticle Thinking outside the Laboratory: Analyses of Antibody Structure and Dynamics within Different Solvent Environments in Molecular Dynamics (MD) Simulations
Antibodies 2018, 7(3), 21; https://doi.org/10.3390/antib7030021 (registering DOI)
Received: 2 May 2018 / Revised: 11 June 2018 / Accepted: 20 June 2018 / Published: 24 June 2018
PDF Full-text (4451 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Monoclonal antibodies (mAbs) have revolutionized the biomedical field, directly influencing therapeutics and diagnostics in the biopharmaceutical industry, while continuing advances in computational efficiency have enabled molecular dynamics (MD) simulations to provide atomistic insight into the structure and function of mAbs. Despite the success
[...] Read more.
Monoclonal antibodies (mAbs) have revolutionized the biomedical field, directly influencing therapeutics and diagnostics in the biopharmaceutical industry, while continuing advances in computational efficiency have enabled molecular dynamics (MD) simulations to provide atomistic insight into the structure and function of mAbs. Despite the success of MD tools, further optimizations are still required to enhance the computational efficiency of complex mAb simulations. This issue can be tackled by changing the way the solvent system is modelled to reduce the number of atoms to be tracked but must be done without compromising the accuracy of the simulations. In this work, the structure of the IgG2a antibody was analyzed in three solvent systems: explicit water and ions, implicit water and ions, and implicit water and explicit ions. Root-mean-square distance (RMSD), root-mean-square fluctuations (RMSF), and interchain angles were used to quantify structural changes. The explicit system provides the most atomistic detail but is ~6 times slower in its exploration of configurational space and required ~4 times more computational time on our supercomputer than the implicit simulations. Overall, the behavior of the implicit and explicit simulations is quantifiably similar, with the inclusion of explicit ions in the implicit simulation stabilizing the antibody to reproduce well the statistical fluctuations of the fully explicit system. Therefore, this approach holds promise to maximize the use of computational resources to explore antibody behavior. Full article
(This article belongs to the Special Issue Computational Antibody and Antigen Design)
Figures

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Open AccessArticle Allosteric Effects between the Antibody Constant and Variable Regions: A Study of IgA Fc Mutations on Antigen Binding
Antibodies 2018, 7(2), 20; https://doi.org/10.3390/antib7020020
Received: 14 May 2018 / Revised: 2 June 2018 / Accepted: 5 June 2018 / Published: 7 June 2018
PDF Full-text (1852 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Therapeutic antibodies have shifted the paradigm of disease treatments from small molecules to biologics, especially in cancer therapy. Despite the increasing number of antibody candidates, much remains unknown about the antibody and how its various regions interact. Recent findings showed that the antibody
[...] Read more.
Therapeutic antibodies have shifted the paradigm of disease treatments from small molecules to biologics, especially in cancer therapy. Despite the increasing number of antibody candidates, much remains unknown about the antibody and how its various regions interact. Recent findings showed that the antibody constant region can govern localization effects that are useful in reducing side effects due to systemic circulation by the commonly used IgG isotypes. Given their localized mucosal effects, IgA antibodies are increasingly promising therapeutic biologics. While the antibody Fc effector cell activity has been a focus point, recent research showed that the Fc could also influence antigen binding, challenging the conventional idea of region-specific antibody functions. To investigate this, we analysed the IgA antibody constant region and its distal effects on the antigen binding regions using recombinant Pertuzumab IgA1 and IgA2 variants. We found that mutations in the C-region reduced Her2 binding experimentally, and computational structural analysis showed that allosteric communications were highly dependent on the antibody hinge, providing strong evidence that we should consider antibodies as whole proteins rather than a sum of functional regions. Full article
(This article belongs to the Special Issue Computational Antibody and Antigen Design)
Figures

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