1
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Chen Q, Ge Y, He X, Li S, Fang Z, Li C, Chen H. Virtual-screening of xanthine oxidase inhibitory peptides: Inhibition mechanisms and prediction of activity using machine-learning. Food Chem 2024; 460:140741. [PMID: 39128372 DOI: 10.1016/j.foodchem.2024.140741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
Xanthine oxidase (XO) inhibitory peptides can prevent XO-mediated hyperuricemia. Currently, QSAR about XO inhibitory peptides with different lengths remains to be enriched. Here, XO inhibitory peptides were obtained from porcine visceral proteins through virtual-screening. A prediction model was established by machine-learning. Virtual-screening retained four lengths of peptides, including 3-6. Molecular-docking recognized their binding sites with XO and showed residues W, F, and G were the key amino acids. Datasets of XO inhibitory peptides therewith were established. The optimal model was used to generalize the peptides reported. Results showed that the R2 of the tripeptide, tetrapeptide, pentapeptide and hexapeptide in the generalisation test were R2 = 0.81, R2 = 0.82, R2 = 0.83 and R2 = 0.83, respectively. Overall, this work can serve as a reference for explaining the activity mechanism of XO inhibitory peptides and predicting the activity of XO inhibitory peptides.
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Affiliation(s)
- Qian Chen
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Yuxi Ge
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Xiaoyu He
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Shanshan Li
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Zhengfeng Fang
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Cheng Li
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Hong Chen
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China.
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2
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Ozden B, Şamiloğlu E, Özsan A, Erguven M, Yükrük C, Koşaca M, Oktayoğlu M, Menteş M, Arslan N, Karakülah G, Barlas AB, Savaş B, Karaca E. Benchmarking the accuracy of structure-based binding affinity predictors on Spike-ACE2 deep mutational interaction set. Proteins 2024; 92:529-539. [PMID: 37991066 DOI: 10.1002/prot.26645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 11/23/2023]
Abstract
Since the start of COVID-19 pandemic, a huge effort has been devoted to understanding the Spike (SARS-CoV-2)-ACE2 recognition mechanism. To this end, two deep mutational scanning studies traced the impact of all possible mutations across receptor binding domain (RBD) of Spike and catalytic domain of human ACE2. By concentrating on the interface mutations of these experimental data, we benchmarked six commonly used structure-based binding affinity predictors (FoldX, EvoEF1, MutaBind2, SSIPe, HADDOCK, and UEP). These predictors were selected based on their user-friendliness, accessibility, and speed. As a result of our benchmarking efforts, we observed that none of the methods could generate a meaningful correlation with the experimental binding data. The best correlation is achieved by FoldX (R = -0.51). When we simplified the prediction problem to a binary classification, that is, whether a mutation is enriching or depleting the binding, we showed that the highest accuracy is achieved by FoldX with a 64% success rate. Surprisingly, on this set, simple energetic scoring functions performed significantly better than the ones using extra evolutionary-based terms, as in Mutabind and SSIPe. Furthermore, we demonstrated that recent AI approaches, mmCSM-PPI and TopNetTree, yielded comparable performances to the force field-based techniques. These observations suggest plenty of room to improve the binding affinity predictors in guessing the variant-induced binding profile changes of a host-pathogen system, such as Spike-ACE2. To aid such improvements we provide our benchmarking data at https://github.com/CSB-KaracaLab/RBD-ACE2-MutBench with the option to visualize our mutant models at https://rbd-ace2-mutbench.github.io/.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Eda Şamiloğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Atakan Özsan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehmet Erguven
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Can Yükrük
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehdi Koşaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Melis Oktayoğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Muratcan Menteş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Nazmiye Arslan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ayşe Berçin Barlas
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Büşra Savaş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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3
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Meng L, Song Y, Zheng B, Zhao Y, Hong B, Ma M, Wen Z, Miao W, Xu Y. Preparation, identification, activity prediction, and protective effects on IR-HepG2 cells of five novel DPP-IV inhibitory peptides from protein hydrolysate of skipjack tuna dark muscles. Food Funct 2023; 14:10991-11004. [PMID: 38019161 DOI: 10.1039/d3fo02948d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
To produce peptides with high dipeptidyl peptidase IV (DPP-IV) inhibitory activity, neutrase was selected from five proteases (trypsin, neutrase, pepsin, alcalase and flavor protease) with the highest degree of hydrolysis (DH) (18.23 ± 1.08%) and DPP-IV inhibitory rate (53.35 ± 4.02%) to produce protein hydrolysate (NPH) from the dark muscles of skipjack tuna (Katsuwonus pelamis). Then, NPH-1 was isolated from NPH by gel permeation chromatography and found to possess the highest DPP-IV inhibitory rate (65.12 ± 7.94% at 0.5 mg ml-1) in the separated components (including NPH-1, NPH-2, NPH-3 and NPH-4). Subsequently, the available prediction models of tripeptides and tetrapeptides with the DPP-IV inhibitory rate were established using an artificial neural network (ANN). The RMSE (0.56 and 0.33 for the model established through collected tripeptides and tetrapeptides, respectively) and R2 (0.95 and 0.99 for the model established through collected tripeptides and tetrapeptides, respectively) of the ANN model's parameters were within acceptable limits, indicating that this model is available. Next, the ANN model was applied to predict tripeptides and tetrapeptides from the hydrolysate of skipjack tuna dark muscles, and five peptides (Ala-Pro-Pro (APP), Pro-Pro-Pro (PPP), Asp-Pro-Leu-Leu (DPLL), Glu-Ala-Val-Pro (EAVP) and Glu-Ala-Iie-Pro (EAIP)) possessing a noticeable DPP-IV inhibitory rate (with DPP-IV IC50 values of 42.46 ± 5.02, 37.71 ± 9.17, 58.85 ± 14.42, 49.94 ± 6.69 and 57.15 ± 6.13 μM, respectively) were screened from the protein hydrolysate. The above five peptides were proved to effectively promote glucose consumption in the insulin resistant-HepG2 (IR-HepG2) cell model considering that the glucose consumption rates of APP, PPP, DPLL, EAVP and EAIP treatment groups are all more than twice that of the dexamethasone group. Accordingly, mechanistic studies showed that these peptides interacted with PI3K/AKT and AMPK signaling pathways and promoted the phosphorylation of PI3K p110, AKT and AMPK (the protein expressions of PI3K p110, p-AKT and p-AMPK in APP, PPP, DPLL, EAVP and EAIP treatment groups are 1.64-2.22 fold compared with that in the dexamethasone group), thereby enhancing glucose uptake and further alleviating insulin resistance. These findings demonstrated that skipjack tuna dark muscle is a potential DPP-IV inhibitory peptide source, and five DPP-IV inhibitory peptides from its hydrolysate may exert potent anti-diabetic activity. In comparison, PPP may be the most potential active ingredient for healthy food against type 2 diabetes mellitus in the five screened peptides considering synthetically the DPP-IV inhibitory rate, bioavailability and synthesis cost.
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Affiliation(s)
- Lingting Meng
- School of Food and Pharmacy, Zhejiang Ocean University, Zhejiang 316022, China.
| | - Yan Song
- School of Food and Pharmacy, Zhejiang Ocean University, Zhejiang 316022, China.
| | - Bin Zheng
- School of Food and Pharmacy, Zhejiang Ocean University, Zhejiang 316022, China.
| | - Yadong Zhao
- School of Food and Pharmacy, Zhejiang Ocean University, Zhejiang 316022, China.
| | - Bingyuan Hong
- School of Petrochemical Engineering & Environment, Zhejiang Ocean University, Zhejiang 316022, China
| | - Mingzhu Ma
- Zhejiang Marine Development Research Institute, Zhejiang 316000, China
| | - Zhengshun Wen
- School of Food and Pharmacy, Zhejiang Ocean University, Zhejiang 316022, China.
| | - Wenhua Miao
- School of Food and Pharmacy, Zhejiang Ocean University, Zhejiang 316022, China.
| | - Yan Xu
- School of Food and Pharmacy, Zhejiang Ocean University, Zhejiang 316022, China.
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4
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Fleury L, Deracinois B, Dugardin C, Nongonierma AB, FitzGerald RJ, Flahaut C, Cudennec B, Ravallec R. In Vivo and In Vitro Comparison of the DPP-IV Inhibitory Potential of Food Proteins from Different Origins after Gastrointestinal Digestion. Int J Mol Sci 2022; 23:8365. [PMID: 35955493 PMCID: PMC9369239 DOI: 10.3390/ijms23158365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Dipeptidyl-peptidase IV (DPP-IV) plays an essential role in glucose metabolism by inactivating incretins. In this context, food-protein-derived DPP-IV inhibitors are promising glycemic regulators which may act by preventing the onset of type 2 diabetes in personalized nutrition. In this study, the DPP-IV-inhibitory potential of seven proteins from diverse origins was compared for the first time in vitro and in vivo in rat plasma after the intestinal barrier (IB) passage of the indigested proteins. The DPP-IV-inhibitory potentials of bovine hemoglobin, caseins, chicken ovalbumin, fish gelatin, and pea proteins were determined in rat plasma thirty minutes after oral administration. In parallel, these proteins, together with bovine whey and gluten proteins, were digested using the harmonized INFOGEST protocol adapted for proteins. The DPP-IV half-maximal inhibitory concentration (IC50) was determined in situ using Caco-2 cells. The DPP-IV-inhibitory activity was also measured after IB passage using a Caco2/HT29-MTX mixed-cell model. The peptide profiles were analyzed using reversed-phase high-performance liquid chromatography tandem mass spectrometry (RP-HPLC-MS/MS) with MS data bioinformatics management, and the IC50 of the identified peptides was predicted in silico. The in vitro and in vivo DPP-IV-inhibitory activity of the proteins differed according to their origin. Vegetable proteins and hemoglobin yielded the highest DPP-IV-inhibitory activity in vivo. However, no correlation was found between the in vivo and in vitro results. This may be partially explained by the differences between the peptidome analysis and the in silico predictions, as well as the study complexity.
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Affiliation(s)
- Léa Fleury
- UMR-T 1158, BioEcoAgro, University of Lille, 59650 Lille, France; (L.F.); (B.D.); (C.D.); (C.F.)
| | - Barbara Deracinois
- UMR-T 1158, BioEcoAgro, University of Lille, 59650 Lille, France; (L.F.); (B.D.); (C.D.); (C.F.)
| | - Camille Dugardin
- UMR-T 1158, BioEcoAgro, University of Lille, 59650 Lille, France; (L.F.); (B.D.); (C.D.); (C.F.)
| | - Alice B. Nongonierma
- Department of Biological Sciences, University of Limerick, V94 T9PX Limerick, Ireland; (A.B.N.); (R.J.F.)
| | - Richard J. FitzGerald
- Department of Biological Sciences, University of Limerick, V94 T9PX Limerick, Ireland; (A.B.N.); (R.J.F.)
| | - Christophe Flahaut
- UMR-T 1158, BioEcoAgro, University of Lille, 59650 Lille, France; (L.F.); (B.D.); (C.D.); (C.F.)
| | - Benoit Cudennec
- UMR-T 1158, BioEcoAgro, University of Lille, 59650 Lille, France; (L.F.); (B.D.); (C.D.); (C.F.)
| | - Rozenn Ravallec
- UMR-T 1158, BioEcoAgro, University of Lille, 59650 Lille, France; (L.F.); (B.D.); (C.D.); (C.F.)
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5
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Identify Bitter Peptides by Using Deep Representation Learning Features. Int J Mol Sci 2022; 23:ijms23147877. [PMID: 35887225 PMCID: PMC9315524 DOI: 10.3390/ijms23147877] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/01/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023] Open
Abstract
A bitter taste often identifies hazardous compounds and it is generally avoided by most animals and humans. Bitterness of hydrolyzed proteins is caused by the presence of bitter peptides. To improve palatability, bitter peptides need to be identified experimentally in a time-consuming and expensive process, before they can be removed or degraded. Here, we report the development of a machine learning prediction method, iBitter-DRLF, which is based on a deep learning pre-trained neural network feature extraction method. It uses three sequence embedding techniques, soft symmetric alignment (SSA), unified representation (UniRep), and bidirectional long short-term memory (BiLSTM). These were initially combined into various machine learning algorithms to build several models. After optimization, the combined features of UniRep and BiLSTM were finally selected, and the model was built in combination with a light gradient boosting machine (LGBM). The results showed that the use of deep representation learning greatly improves the ability of the model to identify bitter peptides, achieving accurate prediction based on peptide sequence data alone. By helping to identify bitter peptides, iBitter-DRLF can help research into improving the palatability of peptide therapeutics and dietary supplements in the future. A webserver is available, too.
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6
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Yin JY, Han YN, Liu MQ, Piao ZH, Zhang X, Xue YT, Zhang YH. Structure-guided discovery of antioxidant peptides bounded to the Keap1 receptor as hunter for potential dietary antioxidants. Food Chem 2022; 373:130999. [PMID: 34710694 DOI: 10.1016/j.foodchem.2021.130999] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 07/17/2021] [Accepted: 08/29/2021] [Indexed: 01/27/2023]
Abstract
Human health can be damaged by free radicals, and antioxidant peptides are excellent radical scavengers. Antioxidant tripeptides data set based on 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulofnic acid) (ABTS) assay was created, 9 types of descriptors were integrated and 4 quantitative structure-activity relationship (QSAR) models were constructed in this study. Several structural factors influencing the activity of antioxidant tripeptides and the dominant amino acids at each position of tripeptides were revealed by the optimal model. Ten food-derived tripeptides with higher activity were selected for synthesis and activity determination. Molecular docking results demonstrated that these tripeptides were stably bound to the Keap1 receptor, further elucidating the antioxidant mechanism. It was known from the simulation of gastrointestinal digestion experiments that the model results possessed a guiding effect on the selection of proteins with high antioxidant activity. The performance of the model was proved to be robust after validation.
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Affiliation(s)
- Jia-Yi Yin
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Ya-Ning Han
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Meng-Qi Liu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Zan-Hao Piao
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Xu Zhang
- Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Yu-Ting Xue
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Ying-Hua Zhang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China; Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China.
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7
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Samukhina YV, Matyushin DD, Grinevich OI, Buryak AK. A Deep Convolutional Neural Network for Prediction of Peptide Collision Cross Sections in Ion Mobility Spectrometry. Biomolecules 2021; 11:1904. [PMID: 34944547 PMCID: PMC8699202 DOI: 10.3390/biom11121904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 11/26/2022] Open
Abstract
Most frequently, the identification of peptides in mass spectrometry-based proteomics is carried out using high-resolution tandem mass spectrometry. In order to increase the accuracy of analysis, additional information on the peptides such as chromatographic retention time and collision cross section in ion mobility spectrometry can be used. An accurate prediction of the collision cross section values allows erroneous candidates to be rejected using a comparison of the observed values and the predictions based on the amino acids sequence. Recently, a massive high-quality data set of peptide collision cross sections was released. This opens up an opportunity to apply the most sophisticated deep learning techniques for this task. Previously, it was shown that a recurrent neural network allows for predicting these values accurately. In this work, we present a deep convolutional neural network that enables us to predict these values more accurately compared with previous studies. We use a neural network with complex architecture that contains both convolutional and fully connected layers and comprehensive methods of converting a peptide to multi-channel 1D spatial data and vector. The source code and pre-trained model are available online.
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Affiliation(s)
| | - Dmitriy D. Matyushin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31 Leninsky Prospect, GSP-1, 119071 Moscow, Russia; (Y.V.S.); (O.I.G.); (A.K.B.)
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8
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Picarazzi F, Manetti F, Marigo V, Mori M. Conformational insights into the C-terminal mutations of human rhodopsin in retinitispigmentosa. J Mol Graph Model 2021; 110:108076. [PMID: 34798368 DOI: 10.1016/j.jmgm.2021.108076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 10/19/2022]
Abstract
Rhodopsin is a light-sensitive transmembrane receptor involved in the visual transduction cascade. Among the several rhodopsin mutations related to retinitis pigmentosa (RP), those affecting the C-terminal VAPA-COOH motif that is implicated in rhodopsin trafficking from the Golgi to the rod outer segment are notably associated with more aggressive RP forms. However, molecular reasons for defective rhodopsin signaling due to VAPA-COOH mutations, which might include steric hindrance, physicochemical features and structural determinants, are yet unknown, thus limiting further drug design approaches. In this work, clinically relevant rhodopsin mutations at the P347 site within the VAPA-COOH motif were investigated by molecular dynamics (MD) simulations and compared to the wild-type (WT) system. In agreement with experimental evidence, conformational fluctuations of the intrinsically disordered C-terminal tail of WT and mutant rhodopsin were found not to affect the overall structure of the transmembrane domain, including binding to the retinal cofactor. The WT VAPA-COOH motif adopts a unique conformation that is not found in pathological mutants, suggesting that structural features could better explain the pathogenicity of P347 rhodopsin mutants than physicochemical or steric determinants. These results were confirmed by MD simulations in both membrane-embedded full-length opsin and membrane-free C-terminal deca-peptides, these latter becoming very useful and small-size model systems for further investigations of rhodopsin C-terminal mutations. Structural details elucidated in this work might facilitate the understanding of the pathological mechanisms of this class of rhodopsin mutants, which will be instrumental to the development of new therapeutic strategies.
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Affiliation(s)
- Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, "Department of Excellence 2018-2022", University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, "Department of Excellence 2018-2022", University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi, 287, 41125 Modena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, "Department of Excellence 2018-2022", University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
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9
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Yang ZR. In silico prediction of Severe Acute Respiratory Syndrome Coronavirus 2 main protease cleavage sites. Proteins 2021; 90:791-801. [PMID: 34739145 PMCID: PMC8661936 DOI: 10.1002/prot.26274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 11/07/2022]
Abstract
One of the emerging subjects to combat the SARS-CoV-2 virus is to design accurate and efficient drug such as inhibitors against the viral protease to stop the viral spread. In addition to laboratory investigation of the viral protease, which is fundamental, the in silico research of viral protease such as the protease cleavage site prediction is critically important and urgent. However, this problem has yet to be addressed. This article has, for the first time, investigated this problem using the pattern recognition approaches. The article has shown that the pattern recognition approaches incorporating a specially tailored kernel function for dealing with amino acids has the outstanding performance in the accuracy of cleavage site prediction and the discovery of the prototype cleavage peptides.
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10
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iBitter-Fuse: A Novel Sequence-Based Bitter Peptide Predictor by Fusing Multi-View Features. Int J Mol Sci 2021; 22:ijms22168958. [PMID: 34445663 PMCID: PMC8396555 DOI: 10.3390/ijms22168958] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/08/2021] [Accepted: 08/17/2021] [Indexed: 12/19/2022] Open
Abstract
Accurate identification of bitter peptides is of great importance for better understanding their biochemical and biophysical properties. To date, machine learning-based methods have become effective approaches for providing a good avenue for identifying potential bitter peptides from large-scale protein datasets. Although few machine learning-based predictors have been developed for identifying the bitterness of peptides, their prediction performances could be improved. In this study, we developed a new predictor (named iBitter-Fuse) for achieving more accurate identification of bitter peptides. In the proposed iBitter-Fuse, we have integrated a variety of feature encoding schemes for providing sufficient information from different aspects, namely consisting of compositional information and physicochemical properties. To enhance the predictive performance, the customized genetic algorithm utilizing self-assessment-report (GA-SAR) was employed for identifying informative features followed by inputting optimal ones into a support vector machine (SVM)-based classifier for developing the final model (iBitter-Fuse). Benchmarking experiments based on both 10-fold cross-validation and independent tests indicated that the iBitter-Fuse was able to achieve more accurate performance as compared to state-of-the-art methods. To facilitate the high-throughput identification of bitter peptides, the iBitter-Fuse web server was established and made freely available online. It is anticipated that the iBitter-Fuse will be a useful tool for aiding the discovery and de novo design of bitter peptides.
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11
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Bo W, Chen L, Qin D, Geng S, Li J, Mei H, Li B, Liang G. Application of quantitative structure-activity relationship to food-derived peptides: Methods, situations, challenges and prospects. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.05.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Pant S, Singh M, Ravichandiran V, Murty USN, Srivastava HK. Peptide-like and small-molecule inhibitors against Covid-19. J Biomol Struct Dyn 2021; 39:2904-2913. [PMID: 32306822 PMCID: PMC7212534 DOI: 10.1080/07391102.2020.1757510] [Citation(s) in RCA: 204] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
Coronavirus disease strain (SARS-CoV-2) was discovered in 2019, and it is spreading very fast around the world causing the disease Covid-19. Currently, more than 1.6 million individuals are infected, and several thousand are dead across the globe because of Covid-19. Here, we utilized the in-silico approaches to identify possible protease inhibitors against SARS-CoV-2. Potential compounds were screened from the CHEMBL database, ZINC database, FDA approved drugs and molecules under clinical trials. Our study is based on 6Y2F and 6W63 co-crystallized structures available in the protein data bank (PDB). Seven hundred compounds from ZINC/CHEMBL databases and fourteen hundred compounds from drug-bank were selected based on positive interactions with the reported binding site. All the selected compounds were subjected to standard-precision (SP) and extra-precision (XP) mode of docking. Generated docked poses were carefully visualized for known interactions within the binding site. Molecular mechanics-generalized born surface area (MM-GBSA) calculations were performed to screen the best compounds based on docking scores and binding energy values. Molecular dynamics (MD) simulations were carried out on four selected compounds from the CHEMBL database to validate the stability and interactions. MD simulations were also performed on the PDB structure 6YF2F to understand the differences between screened molecules and co-crystallized ligand. We screened 300 potential compounds from various databases, and 66 potential compounds from FDA approved drugs. Cobicistat, ritonavir, lopinavir, and darunavir are in the top screened molecules from FDA approved drugs. The screened drugs and molecules may be helpful in fighting with SARS-CoV-2 after further studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suyash Pant
- Department of Pharmacoinformatics, National
Institute of Pharmaceutical Education and Research Kolkata, Kolkata, West
Bengal, India
| | - Meenakshi Singh
- Department of Natural Products, National
Institute of Pharmaceutical Education and Research Kolkata, Kolkata, West
Bengal, India
| | - V. Ravichandiran
- Department of Natural Products, National
Institute of Pharmaceutical Education and Research Kolkata, Kolkata, West
Bengal, India
| | - U. S. N. Murty
- Department of Medicinal Chemistry, National
Institute of Pharmaceutical Education and Research Guwahati, Guwahati,
Assam, India
| | - Hemant Kumar Srivastava
- Department of Medicinal Chemistry, National
Institute of Pharmaceutical Education and Research Guwahati, Guwahati,
Assam, India
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13
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Amengual-Rigo P, Fernández-Recio J, Guallar V. UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes. Bioinformatics 2021; 37:334-341. [PMID: 32761082 DOI: 10.1093/bioinformatics/btaa708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 07/23/2020] [Accepted: 07/31/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Single protein residue mutations may reshape the binding affinity of protein-protein interactions. Therefore, predicting its effects is of great interest in biotechnology and biomedicine. Unfortunately, the availability of experimental data on binding affinity changes upon mutation is limited, which hampers the development of new and more precise algorithms. Here, we propose UEP, a classifier for predicting beneficial and detrimental mutations in protein-protein complexes trained on interactome data. RESULTS Regardless of the simplicity of the UEP algorithm, which is based on a simple three-body contact potential derived from interactome data, we report competitive results with the gold standard methods in this field with the advantage of being faster in terms of computational time. Moreover, we propose a consensus selection procedure by involving the combination of three predictors that showed higher classification accuracy in our benchmark: UEP, pyDock and EvoEF1/FoldX. Overall, we demonstrate that the analysis of interactome data allows predicting the impact of protein-protein mutations using UEP, a fast and reliable open-source code. AVAILABILITY AND IMPLEMENTATION UEP algorithm can be found at: https://github.com/pepamengual/UEP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pep Amengual-Rigo
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Juan Fernández-Recio
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de la Rioja-Gobierno de la Rioja, 26007 Logroño, Spain
| | - Victor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain.,ICREA: Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
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14
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Wang YT, Russo DP, Liu C, Zhou Q, Zhu H, Zhang YH. Predictive Modeling of Angiotensin I-Converting Enzyme Inhibitory Peptides Using Various Machine Learning Approaches. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:12132-12140. [PMID: 32915574 DOI: 10.1021/acs.jafc.0c04624] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Food-derived angiotensin I-converting enzyme (ACE) inhibitory peptides could potentially be used as safe supportive therapeutic products for high blood pressure. Theoretical approaches are promising methods with the advantage through exploring the relationships between peptide structures and their bioactivities. In this study, peptides with ACE inhibitory activity were collected and curated. Quantitative structure-activity relationship (QSAR) models were developed by using the combination of various machine learning approaches and chemical descriptors. The resultant models have revealed several structure features accounting for the ACE inhibitions. 14 new dipeptides predicted to lower blood pressure by inhibiting ACE were selected. Molecular docking indicated that these dipeptides formed hydrogen bonds with ACE. Five of these dipeptides were synthesized for experimental testing. The QSAR models developed were proofed to design and propose novel ACE inhibitory peptides. Machine learning algorithms and properly selected chemical descriptors can be promising modeling approaches for rational design of natural functional food components.
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Affiliation(s)
- Yu-Tang Wang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
- Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Daniel P Russo
- The Rutgers Center for Computational and Integrative Biology, Camden, New Jersey 08102, United States
| | - Chang Liu
- Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Qian Zhou
- Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Hao Zhu
- The Rutgers Center for Computational and Integrative Biology, Camden, New Jersey 08102, United States
- Department of Chemistry, Rutgers University, Camden, New Jersey 08102, United States
| | - Ying-Hua Zhang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, PR China
- Department of Food Science, Northeast Agricultural University, Harbin 150030, PR China
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15
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iBitter-SCM: Identification and characterization of bitter peptides using a scoring card method with propensity scores of dipeptides. Genomics 2020; 112:2813-2822. [DOI: 10.1016/j.ygeno.2020.03.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/19/2020] [Accepted: 03/22/2020] [Indexed: 12/21/2022]
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16
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Mahmoodi-Reihani M, Abbasitabar F, Zare-Shahabadi V. In Silico Rational Design and Virtual Screening of Bioactive Peptides Based on QSAR Modeling. ACS OMEGA 2020; 5:5951-5958. [PMID: 32226875 PMCID: PMC7097998 DOI: 10.1021/acsomega.9b04302] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/27/2020] [Indexed: 05/15/2023]
Abstract
Predicting the bioactivity of peptides is an important challenge in drug development and peptide research. In this study, numerical descriptive vectors (NDVs) for peptide sequences were calculated based on the physicochemical properties of amino acids (AAs) and principal component analysis (PCA). The resulted NDV had the same length as the peptide sequence, so that each entry of NDV corresponded to one AA in the sequence. They were then applied to quantitative structure-activity relationship (QSAR) analysis of angiotensin-converting enzyme (ACE) inhibitor dipeptides, bitter-tasting dipeptides, and nonameric binding peptides of the human leukocyte antigens (HLA-A*0201). Multiple linear regression was used to construct the QSAR models. For each peptide set, a proper subset of physicochemical properties was chosen by the ant colony optimization algorithm. The leave-one-out cross-validation (q loo 2) values were 0.855, 0.936, and 0.642 and the root-mean-square errors (RMSEs) were 0.450, 0.149, and 0.461. Our results revealed that the new numerical descriptive vector can afford extensive characterization of peptide sequence so that it can be easily employed in peptide QSAR studies. Moreover, the proposed numerical descriptive vectors were able to determine hot spot residues in the peptides under study.
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Affiliation(s)
| | - Fatemeh Abbasitabar
- Department
of Chemistry, Marvdasht Branch, Islamic
Azad University, Marvdasht, Iran
| | - Vahid Zare-Shahabadi
- Department
of Chemistry, Mahshahr Branch, Islamic Azad
University, Mahshahr Iran
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17
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Suzuki A, Aikawa Y, Ito R, Hoshino T. Oryza sativa
Parkeol Cyclase: Changes in the Substrate‐Folding Conformation and the Deprotonation Sites on Mutation at Tyr257: Importance of the Hydroxy Group and Steric Bulk. Chembiochem 2019; 20:2862-2875. [DOI: 10.1002/cbic.201900314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Asuka Suzuki
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| | - Yuko Aikawa
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| | - Ryousuke Ito
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2-8050 Nishi-ku Niigata 950–2181 Japan
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18
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Xu B, Chung HY. Quantitative Structure-Activity Relationship Study of Bitter Di-, Tri- and Tetrapeptides Using Integrated Descriptors. Molecules 2019; 24:molecules24152846. [PMID: 31387305 PMCID: PMC6696392 DOI: 10.3390/molecules24152846] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/23/2019] [Accepted: 08/05/2019] [Indexed: 11/16/2022] Open
Abstract
New quantitative structure–activity relationship (QSAR) models for bitter peptides were built with integrated amino acid descriptors. Datasets contained 48 dipeptides, 52 tripeptides and 23 tetrapeptides with their reported bitter taste thresholds. Independent variables consisted of 14 amino acid descriptor sets. A bootstrapping soft shrinkage approach was utilized for variable selection. The importance of a variable was evaluated by both variable selecting frequency and standardized regression coefficient. Results indicated model qualities for di-, tri- and tetrapeptides with R2 and Q2 at 0.950 ± 0.002, 0.941 ± 0.001; 0.770 ± 0.006, 0.742 ± 0.004; and 0.972 ± 0.002, 0.956 ± 0.002, respectively. The hydrophobic C-terminal amino acid was the key determinant for bitterness in dipeptides, followed by the contribution of bulky hydrophobic N-terminal amino acids. For tripeptides, hydrophobicity of C-terminal amino acids and the electronic properties of the amino acids at the second position were important. For tetrapeptides, bulky hydrophobic amino acids at N-terminus, hydrophobicity and partial specific volume of amino acids at the second position, and the electronic properties of amino acids of the remaining two positions were critical. In summary, this study not only constructs reliable models for predicting the bitterness in different groups of peptides, but also facilitates better understanding of their structure-bitterness relationships and provides insights for their future studies.
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Affiliation(s)
- Biyang Xu
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hau Yin Chung
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.
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19
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Fukuda Y, Watanabe T, Hoshino T. Mutated variants of squalene-hopene cyclase: enzymatic syntheses of triterpenes bearing oxygen-bridged monocycles and a new 6,6,6,6,6-fusded pentacyclic scaffold, named neogammacerane, from 2,3-oxidosqualene. Org Biomol Chem 2019; 16:8365-8378. [PMID: 30209480 DOI: 10.1039/c8ob02009d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Squalene-hopene cyclase (SHC) catalyzes the conversion of acyclic squalene molecule into a 6,6,6,6,5-fused pentacyclic hopene and hopanol. SHC is also able to convert (3S)-2,3-oxidosqualene into 3β-hydroxyhopene and 3β-hydroxyhopanol and can generate 3α-hydroxyhopene and 3α-hydroxyhopanol from (3R)-2,3-oxidosqualene. Functional analyses of active site residues toward the squalene cyclization reaction have been extensively reported, but investigations of the cyclization reactions of (3R,S)-oxidosqualene by SHC have rarely been reported. The cyclization reactions of oxidosqualene with W169X, G600F/F601G and F601G/P602F were examined. The variants of the W169L generated new triterpene skeletons possessing a 7-oxabicyclo[2.2.1]heptane moiety (oxygen-bridged monocycle) with (1S,2S,4R)- and (1R,2S,4S)-stereochemistry, which were produced from (3R)- and (3S)-oxidosqualenes, respectively. The F601G/P602F double mutant also furnished a novel triterpene, named neogammacer-21(22)-en-3β-ol, consisting of a 6,6,6,6,6-fused pentacyclic system, in which Me-29 at C-22 of the gammacerane skeleton migrated to C-21. We propose to name this novel scaffold neogammacerane. The formation mechanisms of the enzymatic products from 2,3-oxidosqualene are discussed.
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Affiliation(s)
- Yoriyuki Fukuda
- Graduate School of Science and Technology and Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.
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20
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Deng B, Long H, Tang T, Ni X, Chen J, Yang G, Zhang F, Cao R, Cao D, Zeng M, Yi L. Quantitative Structure-Activity Relationship Study of Antioxidant Tripeptides Based on Model Population Analysis. Int J Mol Sci 2019; 20:ijms20040995. [PMID: 30823542 PMCID: PMC6413046 DOI: 10.3390/ijms20040995] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 11/16/2022] Open
Abstract
Due to their beneficial effects on human health, antioxidant peptides have attracted much attention from researchers. However, the structure-activity relationships of antioxidant peptides have not been fully understood. In this paper, quantitative structure-activity relationships (QSAR) models were built on two datasets, i.e., the ferric thiocyanate (FTC) dataset and ferric-reducing antioxidant power (FRAP) dataset, containing 214 and 172 unique antioxidant tripeptides, respectively. Sixteen amino acid descriptors were used and model population analysis (MPA) was then applied to improve the QSAR models for better prediction performance. The results showed that, by applying MPA, the cross-validated coefficient of determination (Q²) was increased from 0.6170 to 0.7471 for the FTC dataset and from 0.4878 to 0.6088 for the FRAP dataset, respectively. These findings indicate that the integration of different amino acid descriptors provide additional information for model building and MPA can efficiently extract the information for better prediction performance.
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Affiliation(s)
- Baichuan Deng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Hongrong Long
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Tianyue Tang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaojun Ni
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Jialuo Chen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Guangming Yang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Fan Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Ruihua Cao
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410083, China.
| | - Maomao Zeng
- State Key Laboratory of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.
| | - Lunzhao Yi
- Yunnan Food Safety Research Institute, Kunming University of Science and Technology, Kunming 650500, China.
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21
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Feron G. Unstimulated saliva: Background noise in taste molecules. J Texture Stud 2018; 50:6-18. [PMID: 30246386 DOI: 10.1111/jtxs.12369] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/16/2022]
Abstract
Saliva is a highly complex bodily fluid composed of many proteins, peptides, small organic molecules, and ions. Saliva is produced and secreted by the major and minor salivary glands to protect the mouth and to participate in digestion. Generally, a distinction is made between unstimulated saliva that is a result of autonomic stimulation and stimulated saliva that is produced during chewing and taste stimulation. The link between saliva and sensory perception can thus be regarded in two ways: the role of unstimulated saliva as a background taste and the mechanistic role of stimulated saliva during eating. Indeed, unstimulated saliva (and its components) is continuously bathing our oral cavity and as such stimulates our taste receptors, thus playing a role in taste sensitivity. However, the role of unstimulated salivary components in mediating taste has been studied only in very few substances. To explore this question, this review attempts to compare data from the literature on unstimulated salivary composition with those on taste sensitivity. The main conclusion centres around the concept that the gustatory self-adaptation phenomenon may be relevant for only a few salivary compounds. Further studies at the level of the salivary Von Ebner glands and salivary pellicle are necessary before arriving at definitive conclusions on this subject. PRACTICAL APPLICATION: Unstimulated saliva contains taste substances that can influence sensory perception through taste adaptation. However, large inter-individual variability exists in unstimulated salivary composition both qualitatively and quantitatively. These differences may explain the variability in taste perception and thus the food choices and behaviors of an individual. Thus, in the context of providing personalized food and nutrition to the consumer, variability of unstimulated saliva should be considered for specific formulation of food products.
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Affiliation(s)
- Gilles Feron
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
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22
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Ideno N, Umeyama S, Watanabe T, Nakajima M, Sato T, Hoshino T. Alicyclobacillus acidocaldarius
Squalene‐Hopene Cyclase: The Critical Role of Steric Bulk at Ala306 and the First Enzymatic Synthesis of Epoxydammarane from 2,3‐Oxidosqualene. Chembiochem 2018; 19:1873-1886. [DOI: 10.1002/cbic.201800281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Natsumi Ideno
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Shikou Umeyama
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Takashi Watanabe
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Mami Nakajima
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Tsutomu Sato
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
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23
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Nongonierma AB, Dellafiora L, Paolella S, Galaverna G, Cozzini P, FitzGerald RJ. In Silico Approaches Applied to the Study of Peptide Analogs of Ile-Pro-Ile in Relation to Their Dipeptidyl Peptidase IV Inhibitory Properties. Front Endocrinol (Lausanne) 2018; 9:329. [PMID: 29963014 PMCID: PMC6010526 DOI: 10.3389/fendo.2018.00329] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/31/2018] [Indexed: 12/17/2022] Open
Abstract
Inhibition of dipeptidyl peptidase IV (DPP-IV) may be exploited to maintain the incretin effect during the postprandial phase. As a result, glycemic regulation and energy homeostasis may be improved. Food protein-derived peptides have been identified as natural agents capable of inhibiting DPP-IV. Ile-Pro-Ile is the most potent DPP-IV inhibitory peptide identified to date. A minimum analog peptide set approach was used to study peptide analogs of Ile-Pro-Ile. The DPP-IV half maximal inhibitory concentration (IC50) values of the 25 peptides evaluated ranged from 3.9 ± 1.0 µM (Ile-Pro-Ile) to 247.0 ± 32.7 µM (Phe-Pro-Phe). The presence of Pro at position 2 of tripeptides was required to achieve high DPP-IV inhibition. Most peptides behaved as competitive inhibitors of DPP-IV with the exception of peptides with a N-terminal Trp, which were mixed-type inhibitors. While possessing the structure of preferred DPP-IV substrates, most peptides studied were particularly stable during 30 min incubation with DPP-IV. Molecular docking revealed that Ile-Pro-Ile and its peptide analogs interacted in a very similar manner with the active site of DPP-IV. In addition, no correlation was found between the Hydropathic INTeraction score and the DPP-IV IC50 values of the peptides studied. This outcome suggests that free energy may not be directly responsible for enzyme inhibition by the peptides. Finally, novel DPP-IV inhibitory peptides were identified using the strategy employed herein. These results may be relevant for the development of food protein-derived peptides with serum glucose lowering and food intake regulatory properties in humans.
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Affiliation(s)
- Alice B. Nongonierma
- Department of Biological Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
| | | | - Sara Paolella
- Department of Biological Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
| | | | - Pietro Cozzini
- Food and Drug Department, University of Parma, Parma, Italy
| | - Richard J. FitzGerald
- Department of Biological Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
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24
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Kapusta K, Sizochenko N, Karabulut S, Okovytyy S, Voronkov E, Leszczynski J. QSPR modeling of optical rotation of amino acids using specific quantum chemical descriptors. J Mol Model 2018; 24:59. [DOI: 10.1007/s00894-018-3593-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/24/2018] [Indexed: 11/28/2022]
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25
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Aiba Y, Watanabe T, Terasawa Y, Nakano C, Hoshino T. Strictly Conserved Residues in Euphorbia tirucalli
β-Amyrin Cyclase: Trp612 Stabilizes Transient Cation through Cation-π Interaction and CH-π Interaction of Tyr736 with Leu734 Confers Robust Local Protein Architecture. Chembiochem 2018; 19:486-495. [DOI: 10.1002/cbic.201700572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Yukari Aiba
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Takumi Watanabe
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Yuri Terasawa
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Chiaki Nakano
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology and Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan
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26
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Deng B, Ni X, Zhai Z, Tang T, Tan C, Yan Y, Deng J, Yin Y. New Quantitative Structure-Activity Relationship Model for Angiotensin-Converting Enzyme Inhibitory Dipeptides Based on Integrated Descriptors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:9774-9781. [PMID: 28984136 DOI: 10.1021/acs.jafc.7b03367] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Angiotensin-converting enzyme (ACE) inhibitory peptides derived from food proteins have been widely reported for hypertension treatment. In this paper, a benchmark data set containing 141 unique ACE inhibitory dipeptides was constructed through database mining, and a quantitative structure-activity relationships (QSAR) study was carried out to predict half-inhibitory concentration (IC50) of ACE activity. Sixteen descriptors were tested and the model generated by G-scale descriptor showed the best predictive performance with the coefficient of determination (R2) and cross-validated R2 (Q2) of 0.6692 and 0.6220, respectively. For most other descriptors, R2 were ranging from 0.52 to 0.68 and Q2 were ranging from 0.48 to 0.61. A complex model combining all 16 descriptors was carried out and variable selection was performed in order to further improve the prediction performance. The quality of model using integrated descriptors (R2 0.7340 ± 0.0038, Q2 0.7151 ± 0.0019) was better than that of G-scale. An in-depth study of variable importance showed that the most correlated properties to ACE inhibitory activity were hydrophobicity, steric, and electronic properties and C-terminal amino acids contribute more than N-terminal amino acids. Five novel predicted ACE-inhibitory peptides were synthesized, and their IC50 values were validated through in vitro experiments. The results indicated that the constructed model could give a reliable prediction of ACE-inhibitory activity of peptides, and it may be useful in the design of novel ACE-inhibitory peptides.
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Affiliation(s)
- Baichuan Deng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Xiaojun Ni
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Zhenya Zhai
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Tianyue Tang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Chengquan Tan
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Yijing Yan
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Jinping Deng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Yulong Yin
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, Subtropical Institute of Animal Nutrition and Feed, College of Animal Science, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences , Changsha 410125, Hunan, P.R. China
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Nongonierma AB, Paolella S, Mudgil P, Maqsood S, FitzGerald RJ. Identification of novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides in camel milk protein hydrolysates. Food Chem 2017; 244:340-348. [PMID: 29120791 DOI: 10.1016/j.foodchem.2017.10.033] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/13/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]
Abstract
Nine novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides (FLQY, FQLGASPY, ILDKEGIDY, ILELA, LLQLEAIR, LPVP, LQALHQGQIV, MPVQA and SPVVPF) were identified in camel milk proteins hydrolysed with trypsin. This was achieved using a sequential approach combining liquid chromatography tandem mass spectrometry (LC-MS/MS), qualitative/quantitative structure activity relationship (QSAR) and confirmatory studies with synthetic peptides. The most potent camel milk protein-derived DPP-IV inhibitory peptides, LPVP and MPVQA, had DPP-IV half maximal inhibitory concentrations (IC50) of 87.0 ± 3.2 and 93.3 ± 8.0 µM, respectively. DPP-IV inhibitory peptide sequences identified within camel and bovine milk protein hydrolysates generated under the same hydrolysis conditions differ. This was linked to differences in enzyme selectivity for peptide bond cleavage of camel and bovine milk proteins as well as dissimilarities in their amino acid sequences. Camel milk proteins contain novel DPP-IV inhibitory peptides which may play a role in the regulation of glycaemia in humans.
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Affiliation(s)
- Alice B Nongonierma
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
| | - Sara Paolella
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
| | - Priti Mudgil
- Department of Food Science, College of Food and Agriculture, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Sajid Maqsood
- Department of Food Science, College of Food and Agriculture, United Arab Emirates University, Al Ain 15551, United Arab Emirates.
| | - Richard J FitzGerald
- Department of Biological Sciences, University of Limerick, Limerick, Ireland; Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland.
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28
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Hoshino T, Nakagawa K, Aiba Y, Itoh D, Nakada C, Masukawa Y. Euphorbia tirucalli
β-Amyrin Synthase: Critical Roles of Steric Sizes at Val483 and Met729 and the CH-π Interaction between Val483 and Trp534 for Catalytic Action. Chembiochem 2017; 18:2145-2155. [DOI: 10.1002/cbic.201700368] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Tsutomu Hoshino
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Kazuya Nakagawa
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Yukari Aiba
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Daichi Itoh
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Chika Nakada
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
| | - Yukari Masukawa
- Graduate School of Science and Technology and; Department of Applied Biological Chemistry; Faculty of Agriculture; Niigata University; Ikarashi 2-8050 Nishi-ku Niigata 950-2181 Japan), E-mail: address
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29
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Yadav R, Kumar V, Baweja M, Shukla P. Gene editing and genetic engineering approaches for advanced probiotics: A review. Crit Rev Food Sci Nutr 2017; 58:1735-1746. [PMID: 28071925 DOI: 10.1080/10408398.2016.1274877] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The applications of probiotics are significant and thus resulted in need of genome analysis of probiotic strains. Various omics methods and systems biology approaches enables us to understand and optimize the metabolic processes. These techniques have increased the researcher's attention towards gut microbiome and provided a new source for the revelation of uncharacterized biosynthetic pathways which enables novel metabolic engineering approaches. In recent years, the broad and quantitative analysis of modified strains relies on systems biology tools such as in silico design which are commonly used methods for improving strain performance. The genetic manipulation of probiotic microorganisms is crucial for defining their role in intestinal microbiota and exploring their beneficial properties. This review describes an overview of gene editing and systems biology approaches, highlighting the advent of omics methods which allows the study of new routes for studying probiotic bacteria. We have also summarized gene editing tools like TALEN, ZFNs and CRISPR-Cas that edits or cleave the specific target DNA. Furthermore, in this review an overview of proposed design of advanced customized probiotic is also hypothesized to improvise the probiotics.
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Affiliation(s)
- Ruby Yadav
- a Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Vishal Kumar
- a Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Mehak Baweja
- a Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , Haryana , India
| | - Pratyoosh Shukla
- a Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology , Maharshi Dayanand University , Rohtak , Haryana , India
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30
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Sun MA, Wang Y, Zhang Q, Xia Y, Ge W, Guo D. Prediction of reversible disulfide based on features from local structural signatures. BMC Genomics 2017; 18:279. [PMID: 28376774 PMCID: PMC5379614 DOI: 10.1186/s12864-017-3668-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 03/28/2017] [Indexed: 11/12/2022] Open
Abstract
Background Disulfide bonds are traditionally considered to play only structural roles. In recent years, increasing evidence suggests that the disulfide proteome is made up of structural disulfides and reversible disulfides. Unlike structural disulfides, reversible disulfides are usually of important functional roles and may serve as redox switches. Interestingly, only specific disulfide bonds are reversible while others are not. However, whether reversible disulfides can be predicted based on structural information remains largely unknown. Methods In this study, two datasets with both types of disulfides were compiled using independent approaches. By comparison of various features extracted from the local structural signatures, we identified several features that differ significantly between reversible and structural disulfides, including disulfide bond length, along with the number, amino acid composition, secondary structure and physical-chemical properties of surrounding amino acids. A SVM-based classifier was developed for predicting reversible disulfides. Results By 10-fold cross-validation, the model achieved accuracy of 0.750, sensitivity of 0.352, specificity of 0.953, MCC of 0.405 and AUC of 0.751 using the RevSS_PDB dataset. The robustness was further validated by using RevSS_RedoxDB as independent testing dataset. This model was applied to proteins with known structures in the PDB database. The results show that one third of the predicted reversible disulfide containing proteins are well-known redox enzymes, while the remaining are non-enzyme proteins. Given that reversible disulfides are frequently reported from functionally important non-enzyme proteins such as transcription factors, the predictions may provide valuable candidates of novel reversible disulfides for further experimental investigation. Conclusions This study provides the first comparative analysis between the reversible and the structural disulfides. Distinct features remarkably different between these two groups of disulfides were identified, and a SVM-based classifier for predicting reversible disulfides was developed accordingly. A web server named RevssPred can be accessed freely from: http://biocomputer.bio.cuhk.edu.hk/RevssPred. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3668-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming-An Sun
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, SAR, China
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Nanhai Ave 3688, Shenzhen, 518060, China
| | - Qing Zhang
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, SAR, China
| | - Yiji Xia
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong, SAR, China
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Dianjing Guo
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, SAR, China.
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Comprehensive comparison of twenty structural characterization scales applied as QSAM of antimicrobial dodecapeptides derived from Bac2A against P. aeruginosa. J Mol Graph Model 2017; 71:88-95. [DOI: 10.1016/j.jmgm.2016.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 11/02/2016] [Accepted: 11/06/2016] [Indexed: 02/04/2023]
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Ito R, Nakada C, Hoshino T. β-Amyrin synthase from Euphorbia tirucalli L. functional analyses of the highly conserved aromatic residues Phe413, Tyr259 and Trp257 disclose the importance of the appropriate steric bulk, and cation-π and CH-π interactions for the efficient catalytic action of the polyolefin cyclization cascade. Org Biomol Chem 2016; 15:177-188. [PMID: 27942657 DOI: 10.1039/c6ob02539k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Many of the functions of the active site residues in β-amyrin synthase and its catalytic mechanism remain unclear. Herein, we examined the functions of the highly conserved Phe413, Tyr259, and Trp257 residues in the β-amyrin synthase of Euphorbia tirucalli. The site-specific mutants F413V and F413M [corrected] showed nearly the same enzymatic activities as the wild type, indicating that π-electrons are not needed for the catalytic reaction. However, the F413A [corrected] mutant yielded a large amount of the tetracyclic dammarane skeleton, with decreased production of β-amyrin. This indicates that the Phe413 [corrected] residue is located near the D-ring formation site and works to position the oxidosqualene substrate correctly within the reaction cavity. On the other hand, the major catalysis-related function of the Tyr259 and Trp257 residues is to yield their π-electrons to the cationic intermediates. The Y259F variant showed nearly equivalent activity to that of the wild type, but aliphatic mutants such as the Ala, Val, and Leu variants showed significantly decreased the activity and yielded the tetracyclic dammarane scaffold, strongly demonstrating that the Tyr259 residue stabilizes the baccharenyl secondary cation via cation-π interaction. The aliphatic variants of Trp257 exhibited remarkably decreased enzymatic activity, and lupeol was produced in a high production ratio, indicating that Trp257 stabilizes the oleanyl cation via cation-π interaction. The aromatic Phe and Tyr mutants exhibited high activities owing to their more increased π-electron density relative to that of the aliphatic mutants, but lupeol was produced in a significantly high yield besides β-amyrin. The Trp residue is likely to be responsible for the robust binding of Me-30 through CH-π interaction. The decreased π-electron density of the Phe and Tyr mutants compared to that of Trp would have resulted in the high production of lupeol.
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Affiliation(s)
- Ryousuke Ito
- Graduate School of Science and Technology and Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.
| | - Chika Nakada
- Graduate School of Science and Technology and Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.
| | - Tsutomu Hoshino
- Graduate School of Science and Technology and Department of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.
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Sun MA, Zhang Q, Wang Y, Ge W, Guo D. Prediction of redox-sensitive cysteines using sequential distance and other sequence-based features. BMC Bioinformatics 2016; 17:316. [PMID: 27553667 PMCID: PMC4995733 DOI: 10.1186/s12859-016-1185-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 08/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Reactive oxygen species can modify the structure and function of proteins and may also act as important signaling molecules in various cellular processes. Cysteine thiol groups of proteins are particularly susceptible to oxidation. Meanwhile, their reversible oxidation is of critical roles for redox regulation and signaling. Recently, several computational tools have been developed for predicting redox-sensitive cysteines; however, those methods either only focus on catalytic redox-sensitive cysteines in thiol oxidoreductases, or heavily depend on protein structural data, thus cannot be widely used. Results In this study, we analyzed various sequence-based features potentially related to cysteine redox-sensitivity, and identified three types of features for efficient computational prediction of redox-sensitive cysteines. These features are: sequential distance to the nearby cysteines, PSSM profile and predicted secondary structure of flanking residues. After further feature selection using SVM-RFE, we developed Redox-Sensitive Cysteine Predictor (RSCP), a SVM based classifier for redox-sensitive cysteine prediction using primary sequence only. Using 10-fold cross-validation on RSC758 dataset, the accuracy, sensitivity, specificity, MCC and AUC were estimated as 0.679, 0.602, 0.756, 0.362 and 0.727, respectively. When evaluated using 10-fold cross-validation with BALOSCTdb dataset which has structure information, the model achieved performance comparable to current structure-based method. Further validation using an independent dataset indicates it is robust and of relatively better accuracy for predicting redox-sensitive cysteines from non-enzyme proteins. Conclusions In this study, we developed a sequence-based classifier for predicting redox-sensitive cysteines. The major advantage of this method is that it does not rely on protein structure data, which ensures more extensive application compared to other current implementations. Accurate prediction of redox-sensitive cysteines not only enhances our understanding about the redox sensitivity of cysteine, it may also complement the proteomics approach and facilitate further experimental investigation of important redox-sensitive cysteines. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1185-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming-An Sun
- State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Qing Zhang
- State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Nanhai Ave 3688, Shenzhen, 518060, People's Republic of China
| | - Wei Ge
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau, People's Republic of China
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, People's Republic of China.
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Nongonierma AB, FitzGerald RJ. Structure activity relationship modelling of milk protein-derived peptides with dipeptidyl peptidase IV (DPP-IV) inhibitory activity. Peptides 2016; 79:1-7. [PMID: 26988873 DOI: 10.1016/j.peptides.2016.03.005] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 02/07/2023]
Abstract
Quantitative structure activity type models were developed in an attempt to predict the key features of peptide sequences having dipeptidyl peptidase IV (DPP-IV) inhibitory activity. The models were then employed to help predict the potential of peptides, which are currently reported in the literature to be present in the intestinal tract of humans following milk/dairy product ingestion, to act as inhibitors of DPP-IV. Two models (z- and v-scale) for short (2-5 amino acid residues) bovine milk peptides, behaving as competitive inhibitors of DPP-IV, were developed. The z- and the v-scale models (p<0.05, R(2) of 0.829 and 0.815, respectively) were then applied to 56 milk protein-derived peptides previously reported in the literature to be found in the intestinal tract of humans which possessed a structural feature of DPP-IV inhibitory peptides (P at the N2 position). Ten of these peptides were synthetized and tested for their in vitro DPP-IV inhibitory properties. There was no agreement between the predicted and experimentally determined DPP-IV half maximal inhibitory concentrations (IC50) for the competitive peptide inhibitors. However, the ranking for DPP-IV inhibitory potency of the competitive peptide inhibitors was conserved. Furthermore, potent in vitro DPP-IV inhibitory activity was observed with two peptides, LPVPQ (IC50=43.8±8.8μM) and IPM (IC50=69.5±8.7μM). Peptides present within the gastrointestinal tract of human may have promise for the development of natural DPP-IV inhibitors for the management of serum glucose.
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Affiliation(s)
- Alice B Nongonierma
- Department of Life Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
| | - Richard J FitzGerald
- Department of Life Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland.
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35
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Nongonierma AB, FitzGerald RJ. Learnings from quantitative structure–activity relationship (QSAR) studies with respect to food protein-derived bioactive peptides: a review. RSC Adv 2016. [DOI: 10.1039/c6ra12738j] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
QSAR studies may help to better understand structural requirements for peptide bioactivity and therefore to develop potent BAPs.
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Affiliation(s)
- Alice B. Nongonierma
- Department of Life Sciences and Food for Health Ireland (FHI)
- University of Limerick
- Limerick
- Ireland
| | - Richard J. FitzGerald
- Department of Life Sciences and Food for Health Ireland (FHI)
- University of Limerick
- Limerick
- Ireland
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36
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Tan PL, Liong MT. In silico approaches for probiotic-derived bioactives. Trends Biotechnol 2014; 32:599-601. [DOI: 10.1016/j.tibtech.2014.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 09/25/2014] [Accepted: 09/30/2014] [Indexed: 12/24/2022]
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Quantitative sequence–activity modeling of antimicrobial hexapeptides using a segmented principal component strategy: an approach to describe and predict activities of peptide drugs containing l/d and unnatural residues. Amino Acids 2014; 47:125-34. [DOI: 10.1007/s00726-014-1850-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 10/03/2014] [Indexed: 12/20/2022]
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38
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Jing P, Qian B, He Y, Zhao X, Zhang J, Zhao D, Lv Y, Deng Y. Screening milk-derived antihypertensive peptides using quantitative structure activity relationship (QSAR) modelling and in vitro/in vivo studies on their bioactivity. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2013.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Wang L, Dai Z, Zhang H, Bai L, Yuan Z. Quantitative Sequence-Activity Model Analysis of Oligopeptides Coupling an Improved High-Dimension Feature Selection Method with Support Vector Regression. Chem Biol Drug Des 2014; 83:379-91. [DOI: 10.1111/cbdd.12242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 08/31/2013] [Accepted: 09/27/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Lifeng Wang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha 410128 China
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
| | - Zhijun Dai
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha 410128 China
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
| | - Hongyan Zhang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha 410128 China
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
| | - Lianyang Bai
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
- Hunan Academy of Agricultural Sciences; Changsha 410125 China
| | - Zheming Yuan
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization; Hunan Agricultural University; Changsha 410128 China
- College of Plant Protection; Hunan Agricultural University; Changsha 410128 China
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Dai Z, Wang L, Chen Y, Wang H, Bai L, Yuan Z. A pipeline for improved QSAR analysis of peptides: physiochemical property parameter selection via BMSF, near-neighbor sample selection via semivariogram, and weighted SVR regression and prediction. Amino Acids 2014; 46:1105-19. [PMID: 24468929 DOI: 10.1007/s00726-014-1667-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/03/2014] [Indexed: 12/21/2022]
Abstract
In this paper, we present a pipeline to perform improved QSAR analysis of peptides. The modeling involves a double selection procedure that first performs feature selection and then conducts sample selection before the final regression analysis. Five hundred and thirty-one physicochemical property parameters of amino acids were used as descriptors to characterize the structure of peptides. These high-dimensional descriptors then go through a feature selection process given by the binary matrix shuffling filter (BMSF) to obtain a set of important low-dimensional features. Each descriptor that passes the BMSF filtering also receives a weight defined through its contribution to reduce the estimation error. These selected features served as the predictors for subsequent sample selection and modeling. Based on the weighted Euclidean distances between samples, a common range was determined with high-dimensional semivariogram and then used as a threshold to select the near-neighbor samples from the training set. For each sample to be predicted, the QSAR model was established using SVR with the weighted, selected features based on the exclusive set of near-neighbor training samples. Prediction was conducted for each test sample accordingly. The performances of this pipeline are tested with the QSAR analysis of angiotensin-converting enzyme inhibitors and HLA-A*0201 data sets. Improved prediction accuracy was obtained in both applications. This pipeline can optimize the QSAR modeling from both the feature selection and sample selection perspectives. This leads to improved accuracy over single selection methods. We expect this pipeline to have extensive application prospect in the field of regression prediction.
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Affiliation(s)
- Zhijun Dai
- Hunan Provincial Key Laboratory for Germplasm Innovation and Utilization of Crop, Hunan Agricultural University, Changsha, China,
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Ito R, Masukawa Y, Nakada C, Amari K, Nakano C, Hoshino T. β-Amyrin synthase from Euphorbia tirucalli. Steric bulk, not the π-electrons of Phe, at position 474 has a key role in affording the correct folding of the substrate to complete the normal polycyclization cascade. Org Biomol Chem 2014; 12:3836-46. [DOI: 10.1039/c4ob00064a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The importance of the steric bulk at 474 residue is described for completion of the cyclization cascade, but not the π-electrons of the Phe residue.
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Affiliation(s)
- Ryousuke Ito
- Graduate School of Science and Technology
- and Department of Applied Biological Chemistry
- Faculty of Agriculture
- Niigata University
- Niigata 950-2181, Japan
| | - Yukari Masukawa
- Graduate School of Science and Technology
- and Department of Applied Biological Chemistry
- Faculty of Agriculture
- Niigata University
- Niigata 950-2181, Japan
| | - Chika Nakada
- Graduate School of Science and Technology
- and Department of Applied Biological Chemistry
- Faculty of Agriculture
- Niigata University
- Niigata 950-2181, Japan
| | - Kanako Amari
- Graduate School of Science and Technology
- and Department of Applied Biological Chemistry
- Faculty of Agriculture
- Niigata University
- Niigata 950-2181, Japan
| | - Chiaki Nakano
- Graduate School of Science and Technology
- and Department of Applied Biological Chemistry
- Faculty of Agriculture
- Niigata University
- Niigata 950-2181, Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology
- and Department of Applied Biological Chemistry
- Faculty of Agriculture
- Niigata University
- Niigata 950-2181, Japan
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QSBR study of bitter taste of peptides: application of GA-PLS in combination with MLR, SVM, and ANN approaches. BIOMED RESEARCH INTERNATIONAL 2013; 2013:501310. [PMID: 24371826 PMCID: PMC3859174 DOI: 10.1155/2013/501310] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 09/16/2013] [Accepted: 09/25/2013] [Indexed: 11/17/2022]
Abstract
Detailed information about the relationships between structures and properties/activities of peptides as drugs and nutrients is useful in the development of drugs and functional foods containing peptides as active compounds. The bitterness of the peptides is an undesirable property which should be reduced during drug/nutrient production, and quantitative structure bitter taste relationship (QSBR) studies can help researchers to design less bitter peptides with higher target efficiency. Calculated structural parameters were used to develop three different QSBR models (i.e., multiple linear regression, support vector machine, and artificial neural network) to predict the bitterness of 229 peptides (containing 2–12 amino acids, obtained from the literature). The developed models were validated using internal and external validation methods, and the prediction errors were checked using mean percentage deviation and absolute average error values. All developed models predicted the activities successfully (with prediction errors less than experimental error values), whereas the prediction errors for nonlinear methods were less than those for linear methods. The selected structural descriptors successfully differentiated between bitter and nonbitter peptides.
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Long HX, Wang YQ, Lin Y, Lin ZH. QSAR Study on ACE Inhibitors by Using OSC-PLS Algorithm. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201000062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Borkar MR, Pissurlenkar RRS, Coutinho EC. HomoSAR: Bridging comparative protein modeling with quantitative structural activity relationship to design new peptides. J Comput Chem 2013; 34:2635-46. [DOI: 10.1002/jcc.23436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/17/2013] [Accepted: 08/21/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Mahesh R. Borkar
- Department of Pharmaceutical Chemistry; Bombay College of Pharmacy; Kalina, Santacruz (East) Mumbai 400098 India
| | - Raghuvir R. S. Pissurlenkar
- Department of Pharmaceutical Chemistry; Bombay College of Pharmacy; Kalina, Santacruz (East) Mumbai 400098 India
| | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry; Bombay College of Pharmacy; Kalina, Santacruz (East) Mumbai 400098 India
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Wang JH, Liu YL, Ning JH, Yu J, Li XH, Wang FX. Is the structural diversity of tripeptides sufficient for developing functional food additives with satisfactory multiple bioactivities? J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Characterization of structure–antioxidant activity relationship of peptides in free radical systems using QSAR models: Key sequence positions and their amino acid properties. J Theor Biol 2013; 318:29-43. [DOI: 10.1016/j.jtbi.2012.10.029] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 10/21/2012] [Accepted: 10/22/2012] [Indexed: 11/22/2022]
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A segmented principal component analysis—regression approach to QSAR study of peptides. J Theor Biol 2012; 305:37-44. [DOI: 10.1016/j.jtbi.2012.03.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 03/08/2012] [Accepted: 03/26/2012] [Indexed: 12/22/2022]
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Toropova AP, Toropov AA, Rasulev BF, Benfenati E, Gini G, Leszczynska D, Leszczynski J. QSAR models for ACE-inhibitor activity of tri-peptides based on representation of the molecular structure by graph of atomic orbitals and SMILES. Struct Chem 2012. [DOI: 10.1007/s11224-012-9996-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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49
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New autocorrelation QTMS-based descriptors for use in QSAM of peptides. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2012. [DOI: 10.1007/s13738-012-0070-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wang XY, Wang J, Hu Y, Lin Y, Shu M, Wang L, Cheng XM, Lin ZH. Predicting the Activity of Peptides Based on Amino Acid Information. J CHIN CHEM SOC-TAIP 2011. [DOI: 10.1002/jccs.201190139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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