Identification of tuna protein-derived peptides as potent SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation

Yu, Zhipeng; Kan, Ruotong; Ji, Huizhuo; Wu, Sijia; Zhao, Wenzhu; Shuian, David; Liu, Jingbo; Lǐ, Jiànróng

doi:10.1016/j.foodchem.2020.128366

Cited by 62 publications

(59 citation statements)

References 45 publications

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“…As discussed, the entry process of SARS-CoV-2 in human cells is mediated by interactions between S proteins at the surface of the viral membrane and the ACE2 receptor on human cells. Consequently, most computational protocols aimed at preventing the protein – protein interaction between the ACE2 receptor and the RBD domain of the SARS-CoV-2 S proteins [ 53 , [155] , [156] , [157] , [158] , [159] , [160] , [163] , [164] , [165] , [166] ]. The structure of this complex was elucidated early in this year, 2020, and the first coordinates were reported in the Protein Data Bank under the ID codes: 6VW1 [ 167 ], 6 M17 [ 168 ], 6lZG [ 169 ], and 6M0J [ 33 ].…”

Section: Computational Strategies For the Design Of New Peptide Inhibmentioning

confidence: 99%

“…Specifically, peptide design strategies mainly focused on extracting candidates based on the ligand binding motif of the ACE2 receptor, and optimizing the sequences of these peptides to obtain potent inhibitors targeting the RBD [ 53 , [155] , [156] , [157] , [158] , [159] , [160] , 163 , 164 , 166 ]. Similarly, efforts have been devoted to the in-silico design of peptide inhibitors targeting the ACE2 receptor [ 165 ] and the HR1 domain of the S protein [ 154 ]. The computational workflow used in these designs usually comprised well-established techniques such as homology modeling, computational mutagenesis, docking protocols, re-scoring methods and molecular dynamics simulations ( Table 4 ).…”

Section: Computational Strategies For the Design Of New Peptide Inhibmentioning

confidence: 99%

“…The computational workflow used in these designs usually comprised well-established techniques such as homology modeling, computational mutagenesis, docking protocols, re-scoring methods and molecular dynamics simulations ( Table 4 ). The applications of these techniques allowed the exploration of peptide libraries [ 158 , [163] , [164] , [165] ] and to build models of new peptides [ 53 , [154] , [155] , [156] , [157] , [158] , [159] , 166 ], as well as the structural and dynamical characterization of the interactions of ACE2 and the peptides with the interface of the viral S protein [ 156 , 160 , 164 , 166 ]. In addition, computational protocols have been used to predict the antiviral activity and the toxicity of peptides with potential inhibitory effect [ 154 , 158 ] ( Table 4 ).…”

Section: Computational Strategies For the Design Of New Peptide Inhibmentioning

confidence: 99%

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Peptide and peptide-based inhibitors of SARS-CoV-2 entry

Schütz

Ruiz‐Blanco

Münch

et al. 2020

Advanced Drug Delivery Reviews

157

138

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To date, no effective vaccines or therapies are available against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pandemic agent of coronavirus disease 2019 (COVID-19). Due to their safety, efficacy and specificity, peptide inhibitors hold great promise for the treatment of newly emerging viral pathogens. Based on the known structures of viral proteins and their cellular targets, antiviral peptides can be rationally designed and optimized. The resulting peptides may be highly specific for their respective targets and particular viral pathogens or exert broad antiviral activity. Here, we summarize the current status of peptides inhibiting SARS-CoV-2 entry and outline the strategies used to design peptides targeting the ACE2 receptor or the viral Spike protein and its activating proteases furin, transmembrane serine protease 2 (TMPRSS2), or cathepsin L. In addition, we present approaches used against related viruses such as SARS-CoV-1 that might be implemented for inhibition of SARS-CoV-2 infection.

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Section: Computational Strategies For the Design Of New Peptide Inhibmentioning

confidence: 99%

Section: Computational Strategies For the Design Of New Peptide Inhibmentioning

confidence: 99%

Section: Computational Strategies For the Design Of New Peptide Inhibmentioning

confidence: 99%

See 1 more Smart Citation

Peptide and peptide-based inhibitors of SARS-CoV-2 entry

Schütz

Ruiz‐Blanco

Münch

et al. 2020

Advanced Drug Delivery Reviews

157

138

View full text Add to dashboard Cite

show abstract

“…In view of this, scores of studies have investigated the possible antiviral effects of several natural metabolites, including organic compounds and peptides, and drugs against SARS-CoV-2 protein targets (Luo et al, 2020;Vincent et al, 2020;Padhi et al, 2021;Yu et al, 2021). Fermented soy products have been recommended as a possible therapy for SARS-CoV-2 infected patients in Japan.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, researchers worldwide are racing to find a possible intervention using functional foods and natural compounds as pharmaceuticals. In view of this, scores of studies have investigated the possible antiviral effects of several natural metabolites, including organic compounds and peptides, and drugs against SARS-CoV-2 protein targets ( Luo et al, 2020 ; Vincent et al, 2020 ; Padhi et al, 2021 ; Yu et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

A Multifunctional Peptide From Bacillus Fermented Soybean for Effective Inhibition of SARS-CoV-2 S1 Receptor Binding Domain and Modulation of Toll Like Receptor 4: A Molecular Docking Study

Padhi

Sanjukta

Chourasia

et al. 2021

Front. Mol. Biosci.

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Fermented soybean products are traditionally consumed and popular in many Asian countries and the northeastern part of India. To search for potential agents for the interruption of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike glycoprotein 1 (S1) and human angiotensin-converting enzyme 2 (ACE2) receptor interactions, the in silico antiviral prospective of peptides identified from the proteome of kinema was investigated. Soybean was fermented using Bacillus licheniformis KN1G, Bacillus amyloliquefaciens KN2G and two different strains of Bacillus subtilis (KN2B and KN2M). The peptides were screened in silico for possible antiviral activity using two different web servers (AVPpred and meta-iAVP), and binding interactions of selected 44 peptides were further explored against the receptor-binding domain (RBD) of the S1 protein (PDB ID: 6M0J) by molecular docking using ZDOCK. The results showed that a peptide ALPEEVIQHTFNLKSQ (P13) belonging to B. licheniformis KN1G fermented kinema was able to make contacts with the binding motif of RBD by blocking specific residues designated as critical (GLN493, ASN501) in the binding of human angiotensin-converting enzyme 2 (ACE2) cell receptor. The selected peptide was also observed to have a significant affinity towards human toll like receptor 4 (TLR4)/Myeloid Differentiation factor 2 (MD2) (PDB ID: 3FXI) complex known for its essential role in cytokine storm. The energy properties of the docked complexes were analyzed through the Generalized Born model and Solvent Accessibility method (MM/GBSA) using HawkDock server. The results showed peptidyl amino acids GLU5, GLN8, PHE11, and LEU13 contributed most to P13-RBD binding. Similarly, ARG90, PHE121, LEU61, PHE126, and ILE94 were appeared to be significant in P13-TLR4/MD2 complex. The findings of the study suggest that the peptides from fermented soy prepared using B. licheniformis KN1G have better potential to be used as antiviral agents. The specific peptide ALPEEVIQHTFNLKSQ could be synthesized and used in combination with experimental studies to validate its effect on SARS-CoV-2-hACE2 interaction and modulation of TLR4 activity. Subsequently, the protein hydrolysate comprising these peptides could be used as prophylaxis against viral diseases, including COVID-19.

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Effects of preheating temperatures on β‐lactoglobulin structure and binding interaction with dihydromyricetin

Zhang

Guan

Huang

et al. 2022

eFood

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Low aqueous solubility limits the bioactivity and bioaccessibility of dihydromyricetin (DHM). Preheating treatment affects the loading efficiency of β-lactoglobulin (β-Lg) to polyphenols, but the mechanism remained unclear. In this study, a serial of temperatures (298 K, 318 K, 338 K, 358 K, and 373 K) were set to analyze the preheating effects on the loading efficiency of β-Lg to DHM, and secondary structure change, binding interactions, and particle size distribution were measured and compared with discover the effects. β-Lg preheated at 358 K possessed the highest binding percentage of 0.45, higher than 0.27, 0.30, 0.36, and 0.40 at 298 K, 318 K, 338 K, and 373 K, the exposure of inside hydrophobic residues contribute the hydrophobic interaction with DHM. Fluorescence quenching and molecular docking analysis showed that DHM tend to bind to β-Lg preheated at 358 K with a binding constant of 1.76 × 10 5 L mol −1 and a binding score of −5.84 kcal mol −1 , higher than that of other temperatures. Particle size distribution showed that Z-average size at 358 K was 16.34 nm, significantly higher than others of 7.64, 8.06, 6.84, and 13.4 nm. Preheating unfolded the structure of β-Lg, exposing the internal residues and enhancing the interaction with DHM.

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Identification of tuna protein-derived peptides as potent SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation

Cited by 62 publications

References 45 publications

Peptide and peptide-based inhibitors of SARS-CoV-2 entry

Peptide and peptide-based inhibitors of SARS-CoV-2 entry

A Multifunctional Peptide From Bacillus Fermented Soybean for Effective Inhibition of SARS-CoV-2 S1 Receptor Binding Domain and Modulation of Toll Like Receptor 4: A Molecular Docking Study

Effects of preheating temperatures on β‐lactoglobulin structure and binding interaction with dihydromyricetin

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