Novel Angiotensin‐Converting Enzyme Inhibitory Peptides Derived from <i>Oncorhynchus mykiss</i> Nebulin: Virtual Screening and <i>In Silico</i> Molecular Docking Study

Yu, Zhipeng; Yang, Fan; Zhao, Wenzhu; Ding, Long; Lǐ, Jiànróng; Liu, Jingbo

doi:10.1111/1750-3841.14299

Cited by 30 publications

(17 citation statements)

References 43 publications

(48 reference statements)

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“…This code may be converted into more than one hundred formats used in chemical informatics, for instance, by OpenBabel software [32]. Examples of using programs which require chemical codes as input data for in silico analysis and prediction of properties of food peptides have been recently presented by Ortiz-Martinez et al [33], Mojica et al [34], and Yu et al [35]. Amino acid sequences are converted into SMILES code using applications available in the BIOPEP-UWM database via the “analysis” tab.…”

Section: Peptide Informationmentioning

confidence: 99%

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Minkiewicz

Iwaniak

Darewicz

2019

IJMS

482

340

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The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress. New opportunities include the possibility of annotating peptides containing D-enantiomers of amino acids, batch processing option, converting amino acid sequences into SMILES code, new quantitative parameters characterizing the presence of bioactive fragments in protein sequences, and finding proteinases that release particular peptides.

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Section: Peptide Informationmentioning

confidence: 99%

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Minkiewicz

Iwaniak

Darewicz

2019

IJMS

482

340

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“…They used docking to study the orientation and chemical interactions of these peptides forming complexes with ACE. In other recent report, Yu et al [30] identified three novel ACE inhibitory peptides EGF, HGR, and VDF derived from Oncorhynchus mykiss nebulin by in silico methods and tested their activities in vitro. Authors simulated the hydrolysis of nebulin and predicted online activity, solubility, absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of generated peptides.…”

Section: Molecular Modeling Applied To the Study Of Ace Inhibitors Inmentioning

confidence: 99%

Considerations for Docking of Selective Angiotensin-Converting Enzyme Inhibitors

Caballero

2020

Molecules

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The angiotensin-converting enzyme (ACE) is a two-domain dipeptidylcarboxypeptidase, which has a direct involvement in the control of blood pressure by performing the hydrolysis of angiotensin I to produce angiotensin II. At the same time, ACE hydrolyzes other substrates such as the vasodilator peptide bradykinin and the anti-inflammatory peptide N-acetyl-SDKP. In this sense, ACE inhibitors are bioactive substances with potential use as medicinal products for treatment or prevention of hypertension, heart failures, myocardial infarction, and other important diseases. This review examined the most recent literature reporting ACE inhibitors with the help of molecular modeling. The examples exposed here demonstrate that molecular modeling methods, including docking, molecular dynamics (MD) simulations, quantitative structure-activity relationship (QSAR), etc, are essential for a complete structural picture of the mode of action of ACE inhibitors, where molecular docking has a key role. Examples show that too many works identified ACE inhibitory activities of natural peptides and peptides obtained from hydrolysates. In addition, other works report non-peptide compounds extracted from natural sources and synthetic compounds. In all these cases, molecular docking was used to provide explanation of the chemical interactions between inhibitors and the ACE binding sites. For docking applications, most of the examples exposed here do not consider that: (i) ACE has two domains (nACE and cACE) with available X-ray structures, which are relevant for the design of selective inhibitors, and (ii) nACE and cACE binding sites have large dimensions, which leads to non-reliable solutions during docking calculations. In support of the solution of these problems, the structural information found in Protein Data Bank (PDB) was used to perform an interaction fingerprints (IFPs) analysis applied on both nACE and cACE domains. This analysis provides plots that identify the chemical interactions between ligands and both ACE binding sites, which can be used to guide docking experiments in the search of selective natural components or novel drugs. In addition, the use of hydrogen bond constraints in the S2 and S2′ subsites of nACE and cACE are suggested to guarantee that docking solutions are reliable.

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“…ADMET calculation would significantly aid the in silico evaluation of the potential bioactivity of peptides. To date, there were only few publications including the calculation of ADMET properties of bioactive peptides from food [85][86][87][88].…”

Section: Pglmentioning

confidence: 99%

Characteristics of Biopeptides Released In Silico from Collagens Using Quantitative Parameters

Iwaniak

Minkiewicz

Pliszka

et al. 2020

Foods

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The potential of collagens to release biopeptides was evaluated using the BIOPEP-UWM-implemented quantitative criteria including the frequency of the release of fragments with a given activity by selected enzyme(s) (AE), relative frequency of release of fragments with a given activity by selected enzyme(s) (W), and the theoretical degree of hydrolysis (DHt). Cow, pig, sheep, chicken, duck, horse, salmon, rainbow trout, goat, rabbit, and turkey collagens were theoretically hydrolyzed using: stem bromelain, ficin, papain, pepsin, trypsin, chymotrypsin, pepsin+trypsin, and pepsin+trypsin+chymotrypsin. Peptides released from the collagens having comparable AE and W were estimated for their likelihood to be bioactive using PeptideRanker Score. The collagens tested were the best sources of angiotensin I-converting enzyme (ACE) and dipeptidyl peptidase IV (DPP-IV) inhibitors. AE and W values revealed that pepsin and/or trypsin were effective producers of such peptides from the majority of the collagens examined. Then, the SwissTargetPrediction program was used to estimate the possible interactions of such peptides with enzymes and proteins, whereas ADMETlab was applied to evaluate their safety and drug-likeness properties. Target prediction revealed that the collagen-derived peptides might interact with several human proteins, especially proteinases, but with relatively low probability. In turn, their bioactivity may be limited by their short half-life in the body.

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Novel Angiotensin‐Converting Enzyme Inhibitory Peptides Derived from Oncorhynchus mykiss Nebulin: Virtual Screening and In Silico Molecular Docking Study

Cited by 30 publications

References 43 publications

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

Considerations for Docking of Selective Angiotensin-Converting Enzyme Inhibitors

Characteristics of Biopeptides Released In Silico from Collagens Using Quantitative Parameters

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