2021
DOI: 10.3389/fmolb.2021.669431
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In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein–Protein Interactions

Abstract: Large contact surfaces of protein–protein interactions (PPIs) remain to be an ongoing issue in the discovery and design of small molecule modulators. Peptides are intrinsically capable of exploring larger surfaces, stable, and bioavailable, and therefore bear a high therapeutic value in the treatment of various diseases, including cancer, infectious diseases, and neurodegenerative diseases. Given these promising properties, a long way has been covered in the field of targeting PPIs via peptide design strategie… Show more

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Cited by 51 publications
(45 citation statements)
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References 249 publications
(272 reference statements)
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“…Protein/peptide docking remains a challenging task due to the high flexibility of peptides, which undermines the prediction of accurate bound conformations (Rentzsch and Renard, 2015;Ciemny et al, 2018;Hashemi et al, 2021). To address this issue, existing protein/peptide docking methodologies have relied on different strategies.…”
Section: Discussionmentioning
confidence: 99%
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“…Protein/peptide docking remains a challenging task due to the high flexibility of peptides, which undermines the prediction of accurate bound conformations (Rentzsch and Renard, 2015;Ciemny et al, 2018;Hashemi et al, 2021). To address this issue, existing protein/peptide docking methodologies have relied on different strategies.…”
Section: Discussionmentioning
confidence: 99%
“…2001; Staneva and Wallin, 2009;Hashemi et al, 2021). However, this approach, coined as de novo docking, is not suitable for larger peptides, as exhaustive conformational sampling becomes prohibitive due to the presence of many freely-rotatable covalent bonds (Yan et al, 2017;Ansar and Vetrivel, 2019).…”
Section: Discussionmentioning
confidence: 99%
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“…These amino acids could be determined in vitro or silico (using bioinformatics tools). Bioinformatics is an expanding field applied in rapid and accurate diagnosis of diseases using protein biomarkers (Hashemi et al 2019 ; Jamadi et al 2020 ; Khalili et al 2017 ; Khodashenas et al 2019 ; Mard-Soltani et al 2018 ; Rahbar et al 2019 ; Ramezani et al 2019 ), cost-effective production of vaccines (Asadi-Ghalehni et al 2018 ; Asadi-Ghalehni et al 2017 ), design of newer and more effective drugs (Hashemi et al 2021 ; Pourzardosht et al 2020 ), improving the quality and quantity of agricultural products, and a better understanding of the biological mechanisms (Noori et al 2020 ). Recently, an engineered ACE2 was designed and evaluated as a novel therapeutics against COVID-19 (Payandeh et al 2020 ).…”
Section: Introductionmentioning
confidence: 99%