Computational electrostatic engineering of nanobodies for enhanced SARS−CoV−2 receptor binding domain recognition

Computational electrostatic engineering of nanobodies for enhanced SARS−CoV−2 receptor binding domain recognition

This study presents a novel computational approach for engineering nanobodies (Nbs) for improved interaction with receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Using Protein Structure Reliability reports, RBD (7VYR_R) was selected and refined for subsequent Nb-RBD interactions. By l...

Full description

Saved in:

Bibliographic Details
Main Authors:	Zafar Iqbal, Muhammad Asim, Umair Ahmad Khan, Neelam Sultan, Irfan Ali
Format:	Article
Language:	English
Published:	Frontiers Media S.A. 2025-03-01
Series:	Frontiers in Molecular Biosciences
Subjects:	electrostatic potential nanobodies ACE-2 receptor SARS-CoV-2 spike protein receptor binding domain
Online Access:	https://www.frontiersin.org/articles/10.3389/fmolb.2025.1512788/full
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Neutralisation resistance of SARS-CoV-2 spike-variants is primarily mediated by synergistic receptor binding domain substitutions
by: Long V. Pham, et al.
Published: (2024-12-01)

Lopinavir and Ritonavir have High Affinity Toward the SARS-CoV-2 S-protein Receptor-binding Domain Sequenced in Brazil
by: Aline Diogo Marinho, et al.
Published: (2025-01-01)

Recombinant receptor-binding motif of spike COVID-19 vaccine candidate induces SARS-CoV-2 neutralizing antibody response
by: Hossein Samiei-Abianeh, et al.
Published: (2024-11-01)

Fixation and reversion of mutations in the receptor-binding domain of the SARS-CoV-2 spike protein: A 2020–2024 analysis
by: Daniele Focosi, et al.
Published: (2024-12-01)

SARS-CoV-2 Receptor Binding Domain (RBD) Protein–Protein Conjugate Induces Similar or Better Antibody Responses as Spike mRNA in Rhesus Macaques
by: Puthupparampil V. Scaria, et al.
Published: (2025-06-01)

Antibodies to the receptor-binding domain of the SARS-Cov-2 spike protein: association with age, pneumonia, duration of the period after COVID-19
by: E. A. Kolosova, et al.
Published: (2022-04-01)

NANOBODIES: STRUCTURE, MANUFACTURING, APPLICATION (REVIEW)
by: A. V. Shatalova, et al.
Published: (2019-02-01)

Discovery and preclinical development of a therapeutically active nanobody-based chimeric antigen receptor targeting human CD22
by: Scott McComb, et al.
Published: (2024-03-01)

Characterization of Nanobody Binding to Distinct Regions of the SARS-CoV-2 Spike Protein by Flow Virometry
by: Mariam Maltseva, et al.
Published: (2025-04-01)

Glycosylated Receptor-Binding-Domain-Targeting Mucosal Vaccines Protect Against SARS-CoV-2 Omicron and MERS-CoV
by: Xiaoqing Guan, et al.
Published: (2025-03-01)

Revisiting phage tail spike architecture: evidence for undetected receptor-binding proteins in Caudoviricetes with non-contractile tails
by: Rafał Matusiak, et al.
Published: (2025-07-01)

Disrupting SARS-CoV-2 Spike–ACE2 Interactions via Glycosaminoglycans in a Pseudoviral Study of Heparan Sulfate and Enoxaparin
by: Virginia Fuochi, et al.
Published: (2025-06-01)

The Use of Heterologous Antigens for Biopanning Enables the Selection of Broadly Neutralizing Nanobodies Against SARS-CoV-2
by: Vazirbek S. Aripov, et al.
Published: (2025-03-01)

Uncovering a conserved vulnerability site in SARS‐CoV‐2 by a human antibody
by: Tingting Li, et al.
Published: (2021-11-01)

Nanobodies: From Discovery to AI-Driven Design
by: Haoran Zhu, et al.
Published: (2025-05-01)

Broad‐Spectrum Engineered Multivalent Nanobodies Against SARS‐CoV‐1/2
by: Zhihong Wang, et al.
Published: (2024-12-01)

From immune evasion to broad in silico binding: computational optimization of SARS-CoV-2 RBD-targeting nanobody
by: Shuyuan Cao, et al.
Published: (2025-08-01)

The inactivation of the Niemann Pick C1 cholesterol transporter restricts SARS-CoV-2 entry into host cells by decreasing ACE2 abundance at the plasma membrane
by: Piergiorgio La Rosa, et al.
Published: (2024-12-01)

Natural compounds from ethno-medicinal plants exhibit multiple binding activities on SARS-CoV-2 spike protein receptor-binding domains
by: Trizah K. Milugo, et al.
Published: (2025-05-01)

Computational Design and Evaluation of Peptides to Target SARS-CoV-2 Spike–ACE2 Interaction
by: Saja Almabhouh, et al.
Published: (2025-04-01)

Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 Receptor
by: Majed S. Aljohani, et al.
Published: (2025-02-01)

Chimeric receptor-binding domain vaccine design and sequential immunization enhanced broadly neutralizing antibody responses against COVID-19
by: Xiao Yang, et al.
Published: (2025-03-01)

Nanobody-as versatile tool emerging in autoimmune diseases
by: Ling Wang, et al.
Published: (2024-12-01)

Potential Beneficial Role of Nitric Oxide in SARS-CoV-2 Infection: Beyond Spike-Binding Inhibition
by: Sergio Sánchez-García, et al.
Published: (2024-10-01)

Development of potent humanized TNFα inhibitory nanobodies for therapeutic applications in TNFα-mediated diseases
by: Tao Yin, et al.
Published: (2025-12-01)

Production and characterisation of a SARS-CoV-2 S-protein RBD homodimer with increased avidity for specific antibodies
by: A. A. Derkaev, et al.
Published: (2023-04-01)

Critical amino acid residues in human ACE2 for SARS-CoV-2 spike protein binding and virus entry
by: Weiyi Chen, et al.
Published: (2025-08-01)

The Omicron variant BA.2.86.1 of SARS- CoV-2 demonstrates an altered interaction network and dynamic features to enhance the interaction with the hACE2
by: Taimur Khan, et al.
Published: (2025-02-01)

Escherichia coli Nissle 1917 efficiently expresses the RBD domain of SARS-CoV-2 spike protein without codon optimization
by: Shanmugaraja Meenakshi, et al.
Published: (2025-05-01)

A competitive ELISA based on nanobodies for the detection of serum neutralizing antibodies against porcine epidemic diarrhea virus
by: Jiakai Zhao, et al.
Published: (2025-03-01)

Characterization of key spike RBD residues influencing SARS-CoV-2 variant adaptation to avian ACE2
by: Weitong Yao, et al.
Published: (2025-07-01)

Basic implications on three pathways associated with SARS-CoV-2
by: Jong hoon Lee, et al.
Published: (2025-04-01)

The ACE2 decoy receptor can overcome immune escape by rapid mutating SARS-CoV-2 variants and reduce cytokine induction and clot formation
by: Ming-Shiu Lin, et al.
Published: (2025-06-01)

Receptor Binding Domain-Specific B Cell Memory Responses Among Individuals Vaccinated Against SARS-CoV-2
by: Atharv Athavale, et al.
Published: (2024-12-01)

Computational nanobody design through deep generative modeling and epitope landscape profiling
by: Liyun Huo, et al.
Published: (2025-01-01)

Comparative Analysis of Host Cell Entry Efficiency and Neutralization Sensitivity of Emerging SARS-CoV-2 Lineages KP.2, KP.2.3, KP.3, and LB.1
by: Nianzhen Chen, et al.
Published: (2024-10-01)

Polyethyleneimine-polyethylene glycol copolymer targeted by anti-HER2 nanobody for specific delivery of transcriptionally targeted tBid containing construct
by: Batoul Saqafi, et al.
Published: (2019-12-01)

In Vitro Inhibitory Effect of Nigella sativa L. Extracts on SARS-COV-2 Spike Protein-ACE2 Interaction
by: Najma Ali, et al.
Published: (2024-01-01)

Recombinant expression of receptor binding domains of all eight subtypes of botulinum neurotoxin type A for generation of antitoxins with broad reactivity [version 1; peer review: 1 approved, 2 approved with reservations]
by: Anh Thi Phuong Tran, et al.
Published: (2025-02-01)

Enhanced variant neutralization through glycan masking of SARS-CoV-2 XBB1.5 RBD
by: Joey Olivier, et al.
Published: (2025-12-01)