<i>In silico</i> design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection

Badhe, Yogesh; Gupta, Rakesh; Rai, Beena

doi:10.1039/d0ra09123e

Cited by 21 publications

(23 citation statements)

References 41 publications

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“…Based on the in silico computed interaction between the substrate, peptide, and spike protein, it was possible to evaluate the potential for the screened peptides for the detection of the spike protein of the virus. Recently [47], a biosensing platform based on an in silico modeling pipeline (Figure 2a) was developed to test the effectiveness of graphene sheets and carbon nanotubes (CNT), to act as a sensor-support structure for the detection of SARS-CoV-2. The authors screened twelve different peptides based on their potential binding affinity toward the receptorbinding domain (RBD) of the spike protein of the virus, using a series of atomistic molecular dynamic simulations performed with CHARMM36 FF [41].…”

Section: Graphene-based Biosensorsmentioning

confidence: 99%

Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications

Dutta

Corni

Brancolini

2022

IJMS

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Nanoscale biosensors, a highly promising technique in clinical analysis, can provide sensitive yet label-free detection of biomolecules. The spatial and chemical specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to experimental limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with experimental measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, associated with the collective contribution from “substrate–receptor–analyte” conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomolecules are usually unable to correctly describe the biomolecule/surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomolecules onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomolecule–surface complex formation as a whole.

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Section: Graphene-based Biosensorsmentioning

confidence: 99%

Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications

Dutta

Corni

Brancolini

2022

IJMS

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“…Two of the designed peptides exhibited both good RBD affinity as well as aqueous stability. However, for all the above studies, the peptides that have been designed by the in silico approach need to be synthesized and evaluated in in vitro and in vivo studies, before their use in COVID-19 therapy is proposed [ 32 ].…”

Section: Peptides As Drugs Against Covid-19mentioning

confidence: 99%

Antimicrobial peptides: A plausible approach for COVID-19 treatment

Rani

Kapoor

Gulati

et al. 2022

Expert Opinion on Drug Discovery

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Introduction Coronavirus disease 2019 (COVID-19), which emerged as a major public health threat, has affected >400 million people globally leading to >5 million mortalities to date. Treatments of COVID-19 are still to be developed as the available therapeutic approaches are not able to combat the virus causing the disease (severe acute respiratory syndrome coronavirus-2; SARS-CoV-2) satisfactorily. However, antiviral peptides (AVPs) have demonstrated prophylactic and therapeutic effects against many coronaviruses (CoVs). Areas covered This review critically discusses various types of AVPs evaluated for the treatment of COVID-19 along with their mechanisms of action. Furthermore, the peptides inhibiting the entry of the virus by targeting its binding to angiotensin-converting enzyme 2 (ACE2) or integrins, fusion mechanism as well as activation of proteolytic enzymes (cathepsin L, transmembrane serine protease 2 (TMPRSS2), or furin) are also discussed. Expert opinion Although extensively investigated, successful treatment of COVID-19 is still a challenge due to emergence of virus mutants. Antiviral peptides are anticipated to be blockbuster drugs for the management of this serious infection because of their formulation and therapeutic advantages. Although they may act on different pathways, AVPs having a multi-targeted approach are considered to have the upper hand in the management of this infection.

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“…MD simulations are frequently used to investigate macromolecules and their surrounding environment to assess fundamental properties that might be useful in proposing new sensing devices. A recent work on the SARS-CoV-2 virus by Badhe et al [160] using MD presented an investigation of twelve peptides that could be used to both propose therapeutics and detect the virus. The authors studied the functionalization of graphene and CNT using the proposed peptides, evidencing the possibility of detecting the SARS-CoV-2 virus based on the binding of its spike protein into the peptides.…”

Section: Theory and Simulation Of Biosensingmentioning

confidence: 99%

Addressing the Theoretical and Experimental Aspects of Low-Dimensional-Materials-Based FET Immunosensors: A Review

et al. 2021

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Electrochemical immunosensors (EI) have been widely investigated in the last several years. Among them, immunosensors based on low-dimensional materials (LDM) stand out, as they could provide a substantial gain in fabricating point-of-care devices, paving the way for fast, precise, and sensitive diagnosis of numerous severe illnesses. The high surface area available in LDMs makes it possible to immobilize a high density of bioreceptors, improving the sensitivity in biorecognition events between antibodies and antigens. If on the one hand, many works present promising results in using LDMs as a sensing material in EIs, on the other hand, very few of them discuss the fundamental interactions involved at the interfaces. Understanding the fundamental Chemistry and Physics of the interactions between the surface of LDMs and the bioreceptors, and how the operating conditions and biorecognition events affect those interactions, is vital when proposing new devices. Here, we present a review of recent works on EIs, focusing on devices that use LDMs (1D and 2D) as the sensing substrate. To do so, we highlight both experimental and theoretical aspects, bringing to light the fundamental aspects of the main interactions occurring at the interfaces and the operating mechanisms in which the detections are based.

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In silico design of peptides with binding to the receptor binding domain (RBD) of the SARS-CoV-2 and their utility in bio-sensor development for SARS-CoV-2 detection

Abstract: The protocol for peptide design and testing for its usage as a sensor.

Cited by 21 publications

References 41 publications

Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications

Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications

Antimicrobial peptides: A plausible approach for COVID-19 treatment

Addressing the Theoretical and Experimental Aspects of Low-Dimensional-Materials-Based FET Immunosensors: A Review

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