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Molecular Design of Artificial Receptors Using Virtual Approaches
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Molecular Design of Artificial Receptors Using Virtual Approaches

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 20 November 2025 | Viewed by 1630

Special Issue Editor

Prof. Dr. Houjin Zhang

E-Mail Website
Guest Editor
School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
Interests: synthetic biology; biosensing; protein design; bioinformatics; metagenomics; protein structure; structural biology; enzyme engineering

Special Issue Information

Dear Colleagues,

In 2024, the Nobel Prize in Chemistry was awarded to biochemist David Baker for his pioneering work on the "computational design of proteins", while Demis Hassabis and John Jumper received the prize for their contributions using artificial intelligence (AI) to "predict protein structures". This recognition signifies the development of research in virtual protein design, with artificial receptors emerging as a significant application area.

This Special Issue invites original and review articles that explore recent advancements in artificial receptor research, particularly focusing on their design and application in disease treatment, biomedical engineering, and synthetic biology. Topics of interest include the mechanisms of receptor-related diseases, enhancing drug targeting specificity, regulating immune systems or metabolic pathways, biosensors, tissue engineering, artificial cells, and transmembrane proteins.

We also welcome submissions on related aspects of the virtual design and application of artificial receptors.

Prof. Dr. Houjin Zhang
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 submissions that pass pre-check are 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • artificial receptors
  • protein design
  • computational biology
  • drug targeting
  • biosensors
  • tissue engineering
  • synthetic biology

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Published Papers (2 papers)

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Research

25 pages, 3601 KiB  
Article
Efficient Design of Affilin® Protein Binders for HER3
by Anna M. Diaz-Rovira, Jonathan Lotze, Gregor Hoffmann, Chiara Pallara, Alexis Molina, Ina Coburger, Manja Gloser-Bräunig, Maren Meysing, Madlen Zwarg, Lucía Díaz, Victor Guallar, Eva Bosse-Doenecke and Sergi Roda
Int. J. Mol. Sci. 2025, 26(10), 4683; https://doi.org/10.3390/ijms26104683 - 14 May 2025
Viewed by 284
Abstract
Engineered scaffold-based proteins that bind to concrete targets with high affinity offer significant advantages over traditional antibodies in theranostic applications. Their development often relies on display methods, where large libraries of variants are physically contacted with the desired target protein and pools of [...] Read more.
Engineered scaffold-based proteins that bind to concrete targets with high affinity offer significant advantages over traditional antibodies in theranostic applications. Their development often relies on display methods, where large libraries of variants are physically contacted with the desired target protein and pools of binding variants can be selected. Herein, we use a novel combined artificial intelligence/physics-based computational framework and phage display approach to obtain ubiquitin based Affilin® proteins targeting the human epidermal growth factor receptor 3 (HER3) extracellular domain, a relevant tumor target. As traditional antibodies against the receptor have failed so far, we sought to provide molecules in a smaller more versatile format to cover the medical need in HER3 related diseases. We demonstrate that the developed in silico pipeline can generate de novo Affilin® proteins binding the biochemical HER3 target using a small training set of <1000 sequences. The classical phage display yielded primary candidates with low nanomolar affinities to the biochemical target and HER3-expressing cells. The latter could be further optimized by phage display and computational maturation alike. These combined efforts resulted in four HER3 ligands with high affinity, cell binding, and serum stability with theranostic potential. Full article
(This article belongs to the Special Issue Molecular Design of Artificial Receptors Using Virtual Approaches)
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35 pages, 10583 KiB  
Article
Leveraging Artificial Intelligence and Gene Expression Analysis to Identify Some Potential Bovine Coronavirus (BCoV) Receptors and Host Cell Enzymes Potentially Involved in the Viral Replication and Tissue Tropism
by Mohd Yasir Khan, Abid Ullah Shah, Nithyadevi Duraisamy, Reda Nacif ElAlaoui, Mohammed Cherkaoui and Maged Gomaa Hemida
Int. J. Mol. Sci. 2025, 26(3), 1328; https://doi.org/10.3390/ijms26031328 - 4 Feb 2025
Viewed by 1045
Abstract
Bovine coronavirus (BCoV) exhibits dual tissue tropism, infecting both the respiratory and enteric tracts of cattle. Viral entry into host cells requires a coordinated interaction between viral and host proteins. However, the specific cellular receptors and co-receptors facilitating BCoV entry remain poorly understood. [...] Read more.
Bovine coronavirus (BCoV) exhibits dual tissue tropism, infecting both the respiratory and enteric tracts of cattle. Viral entry into host cells requires a coordinated interaction between viral and host proteins. However, the specific cellular receptors and co-receptors facilitating BCoV entry remain poorly understood. Similarly, the roles of host proteases such as Furin, TMPRSS2, and Cathepsin-L (CTS-L), known to assist in the replication of other coronaviruses, have not been extensively explored for BCoV. This study aims to identify novel BCoV receptors and host proteases that modulate viral replication and tissue tropism. Bovine cell lines were infected with BCoV isolates from enteric and respiratory origins, and the host cell gene expression profiles post-infection were analyzed using next-generation sequencing (NGS). Differentially expressed genes encoding potential receptors and proteases were further assessed using in-silico prediction and molecular docking analysis. These analyses focused on known coronavirus receptors, including ACE2, NRP1, DPP4, APN, AXL, and CEACAM1, to identify their potential roles in BCoV infection. Validation of these findings was performed using the qRT-PCR assays targeting individual genes. We confirmed the gene expression profiles of these receptors and enzymes in some BCoV (+/−) lung tissues. Results revealed high binding affinities of 9-O-acetylated sialic acid and NRP1 to BCoV spike (S) and hemagglutinin-esterase (HE) proteins compared to ACE2, DPP4, and CEACAM1. Additionally, Furin and TMPRSS2 were predicted to interact with the BCoV-S polybasic cleavage site (RRSRR|A), suggesting their roles in S glycoprotein activation. This is the first study to explore the interactions of BCoV with multiple host receptors and proteases. Functional studies are recommended to confirm their roles in BCoV infection and replication. Full article
(This article belongs to the Special Issue Molecular Design of Artificial Receptors Using Virtual Approaches)
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