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Xu Z, Zhang R, Chen H, Zhang L, Yan X, Qin Z, Cong S, Tan Z, Li T, Du M. Characterization and preparation of food-derived peptides on improving osteoporosis: A review. Food Chem X 2024; 23:101530. [PMID: 38933991 PMCID: PMC11200288 DOI: 10.1016/j.fochx.2024.101530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/18/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
Osteoporosis is a systemic bone disease characterized by reduced bone mass and deterioration of the microstructure of bone tissue, leading to an increased risk of fragility fractures and affecting human health worldwide. Food-derived peptides are widely used in functional foods due to their low toxicity, ease of digestion and absorption, and potential to improve osteoporosis. This review summarized and discussed methods of diagnosing osteoporosis, treatment approaches, specific peptides as alternatives to conventional drugs, and the laboratory preparation and identification methods of peptides. It was found that peptides interacting with RGD (arginine-glycine-aspartic acid)-binding active sites in integrin could alleviate osteoporosis, analyzed the interaction sites between these osteogenic peptides and integrin, and further discussed their effects on improving osteoporosis. These may provide new insights for rapid screening of osteogenic peptides, and provide a theoretical basis for their application in bone materials and functional foods.
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Affiliation(s)
- Zhe Xu
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, China
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
- Institute of Bast Fiber Crops & Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Rui Zhang
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, China
| | - Hongrui Chen
- School of Food and Bioengineering, Food Microbiology Key Laboratory of Sichuan Province, Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Xihua University, Chengdu, Sichuan 611130, China
| | - Lijuan Zhang
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Xu Yan
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Zijin Qin
- Department of Food Science and Technology, University of Georgia, Clarke, Athens, GA 30602, USA
| | - Shuang Cong
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China
| | - Zhijian Tan
- Institute of Bast Fiber Crops & Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Tingting Li
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Ming Du
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, China
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2
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Jain S, Gupta S, Patiyal S, Raghava GPS. THPdb2: compilation of FDA approved therapeutic peptides and proteins. Drug Discov Today 2024; 29:104047. [PMID: 38830503 DOI: 10.1016/j.drudis.2024.104047] [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: 02/01/2024] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
During the past 20 years, there has been a significant increase in the number of protein-based drugs approved by the US Food and Drug Administration (FDA). This paper presents THPdb2, an updated version of the THPdb database, which holds information about all types of protein-based drugs, including peptides, antibodies, and biosimilar proteins. THPdb2 contains a total of 6,385 entries, providing comprehensive information about 894 FDA-approved therapeutic proteins, including 354 monoclonal antibodies and 85 peptides or polypeptides. Each entry includes the name of therapeutic molecule, the amino acid sequence, physical and chemical properties, and route of drug administration. The therapeutic molecules that are included in the database target a wide range of biological molecules, such as receptors, factors, and proteins, and have been approved for the treatment of various diseases, including cancers, infectious diseases, and immune disorders.
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Affiliation(s)
- Shipra Jain
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi 110020, India
| | - Srijanee Gupta
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi 110020, India
| | - Sumeet Patiyal
- Cancer and Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi 110020, India.
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3
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Kozak F, Brandis D, Pötzl C, Epasto LM, Reichinger D, Obrist D, Peterlik H, Polyansky A, Zagrovic B, Daus F, Geyer A, Becker CF, Kurzbach D. An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401239. [PMID: 38874418 DOI: 10.1002/advs.202401239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/23/2024] [Indexed: 06/15/2024]
Abstract
Deciphering nature's remarkable way of encoding functions in its biominerals holds the potential to enable the rational development of nature-inspired materials with tailored properties. However, the complex processes that convert solution-state precursors into solid biomaterials remain largely unknown. In this study, an unconventional approach is presented to characterize these precursors for the diatom-derived peptides R5 and synthetic Silaffin-1A1 (synSil-1A1). These molecules can form defined supramolecular assemblies in solution, which act as templates for solid silica structures. Using a tailored structural biology toolbox, the structure-function relationships of these self-assemblies are unveiled. NMR-derived constraints are employed to enable a recently developed fractal-cluster formalism and then reveal the architecture of the peptide assemblies in atomistic detail. Finally, by monitoring the self-assembly activities during silica formation at simultaneous high temporal and residue resolution using real-time spectroscopy, the mechanism is elucidated underlying template-driven silica formation. Thus, it is demonstrated how to exercise morphology control over bioinorganic solids by manipulating the template architectures. It is found that the morphology of the templates is translated into the shape of bioinorganic particles via a mechanism that includes silica nucleation on the solution-state complexes' surfaces followed by complete surface coating and particle precipitation.
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Affiliation(s)
- Fanny Kozak
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Dörte Brandis
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Christopher Pötzl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Ludovica M Epasto
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Daniela Reichinger
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Dominik Obrist
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Herwig Peterlik
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Vienna, 1090, Austria
| | - Anton Polyansky
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, Vienna, A-1030, Austria
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, Vienna, A-1030, Austria
| | - Fabian Daus
- Faculty of Chemistry, Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Armin Geyer
- Faculty of Chemistry, Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Christian Fw Becker
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Dennis Kurzbach
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
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4
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Seixas Feio JA, de Oliveira ECL, de Sales CDS, da Costa KS, e Lima AHL. Investigating molecular descriptors in cell-penetrating peptides prediction with deep learning: Employing N, O, and hydrophobicity according to the Eisenberg scale. PLoS One 2024; 19:e0305253. [PMID: 38870192 PMCID: PMC11175476 DOI: 10.1371/journal.pone.0305253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/27/2024] [Indexed: 06/15/2024] Open
Abstract
Cell-penetrating peptides comprise a group of molecules that can naturally cross the lipid bilayer membrane that protects cells, sharing physicochemical and structural properties, and having several pharmaceutical applications, particularly in drug delivery. Investigations of molecular descriptors have provided not only an improvement in the performance of classifiers but also less computational complexity and an enhanced understanding of membrane permeability. Furthermore, the employment of new technologies, such as the construction of deep learning models using overfitting treatment, promotes advantages in tackling this problem. In this study, the descriptors nitrogen, oxygen, and hydrophobicity on the Eisenberg scale were investigated, using the proposed ConvBoost-CPP composed of an improved convolutional neural network with overfitting treatment and an XGBoost model with adjusted hyperparameters. The results revealed favorable to the use of ConvBoost-CPP, having as input nitrogen, oxygen, and hydrophobicity together with ten other descriptors previously investigated in this research line, showing an increase in accuracy from 88% to 91.2% in cross-validation and 82.6% to 91.3% in independent test.
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Affiliation(s)
- Juliana Auzier Seixas Feio
- Laboratório de Inteligência Computacional e Pesquisa Operacional, Campus Belém, Instituto de Tecnologia, Universidade Federal do Pará, Pará, Brazil
| | - Ewerton Cristhian Lima de Oliveira
- Laboratório de Inteligência Computacional e Pesquisa Operacional, Campus Belém, Instituto de Tecnologia, Universidade Federal do Pará, Pará, Brazil
- Instituto Tecnológico Vale, Belém, Pará, Brazil
| | - Claudomiro de Souza de Sales
- Laboratório de Inteligência Computacional e Pesquisa Operacional, Campus Belém, Instituto de Tecnologia, Universidade Federal do Pará, Pará, Brazil
| | - Kauê Santana da Costa
- Laboratório de Simulação Computacional, Campus Marechal Rondom, Instituto de Biodiversidade, Universidade Federal do Oeste do Pará, Santarém, Pará, Brazil
| | - Anderson Henrique Lima e Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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5
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Chourasia R, Dabrha G, Abedin MM, Phukon LC, Singh AK, Sahoo D, Singh SP, Rai AK. Exploring peptidomes of by-products generated during chhurpi production using Lactobacillus delbrueckii WS4 for identification of novel bioactive peptides. Food Funct 2024; 15:5987-5999. [PMID: 38742436 DOI: 10.1039/d4fo00405a] [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: 05/16/2024]
Abstract
The considerable value of whey is evident from its significant potential applications and contributions to the functional food and nutraceutical market. The by-products were individually obtained during functional chhurpi and novel soy chhurpi cheese production using defined lactic acid bacterial strains of Sikkim Himalaya's traditional chhurpi. Hydrolysis of substrate proteins by starter proteinases resulted in a comparable peptide content in whey and soy whey which was associated with antioxidant and ACE inhibition potential. Peptidome analysis of Lactobacillus delbrueckii WS4 whey and soy whey revealed the presence of several bioactive peptides including the multifunctional peptides PVVVPPFLQPE and YQEPVLGPVRGPFPIIV. In silico analyses predicted the antihypertensive potential of whey and soy whey peptides with strong binding affinity for ACE active sites. QSAR models predicted the highest ACE inhibition potential (IC50) for the β-casein-derived decapeptide PVRGPFPIIV (0.95 μM) and the Kunitz trypsin inhibitor protein-derived nonapeptide KNKPLVVQF (16.64 μM). Chhurpi whey and soy whey can be explored as a valuable source of diverse and novel bioactive peptides for applications in designer functional foods development.
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Affiliation(s)
- Rounak Chourasia
- National Agri-food Biotechnology Institute, SAS Nagar, Mohali, India.
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Gayatri Dabrha
- National Agri-food Biotechnology Institute, SAS Nagar, Mohali, India.
| | | | | | - Ashish Kumar Singh
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India.
| | - Dinabandhu Sahoo
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
- Department of Botany, University of Delhi, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India.
- Gujarat Biotechnology University, Shahpur, Gandhinagar, Gujarat, India
| | - Amit Kumar Rai
- National Agri-food Biotechnology Institute, SAS Nagar, Mohali, India.
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
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6
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R K, Kumar A, Vinod Kumar K, Sengupta A, Kundal K, Sharma S, Pawar A, Krishna PS, Alfatah M, Ray S, Tiwari B, Kumar R. AagingBase: a comprehensive database of anti-aging peptides. Database (Oxford) 2024; 2024:baae016. [PMID: 38470883 PMCID: PMC10930205 DOI: 10.1093/database/baae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/07/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
The process of aging is an intrinsic and inevitable aspect of life that impacts every living organism. As biotechnological advancements continue to shape our understanding of medicine, peptide therapeutics have emerged as a promising strategy for anti-aging interventions. This is primarily due to their favorable attributes, such as low immunogenicity and cost-effective production. Peptide-based treatments have garnered widespread acceptance and interest in aging research, particularly in the context of age-related therapies. To effectively develop anti-aging treatments, a comprehensive understanding of the physicochemical characteristics of anti-aging peptides is essential. Factors such as amino acid composition, instability index, hydrophobic areas and other relevant properties significantly determine their efficacy as potential therapeutic agents. Consequently, the creation of 'AagingBase', a comprehensive database for anti-aging peptides, aims to facilitate research on aging by leveraging the potential of peptide therapies. AagingBase houses experimentally validated 282 anti-aging peptides collected from 54 research articles and 236 patents. Employing state-of-the-art computational techniques, the acquired sequences have undergone rigorous physicochemical calculations. Furthermore, AagingBase presents users with various informative analyses highlighting atomic compositions, secondary structure fractions, tertiary structure, amino acid compositions and frequencies. The database also offers advanced search and filtering options and similarity search, thereby aiding researchers in understanding their biological functions. Hence, the database enables efficient identification and prioritization of potential peptide candidates in geriatric medicine and holds immense potential for advancing geriatric medicine research and innovations. AagingBase can be accessed without any restriction. Database URL: https://project.iith.ac.in/cgntlab/aagingbase/.
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Affiliation(s)
- Kunjulakshmi R
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Odisha 760010, India
| | - Ambuj Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Keerthana Vinod Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Avik Sengupta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Kavita Kundal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Simran Sharma
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Ankita Pawar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O., Kollam, Kerala 690525, India
| | - Pithani Sai Krishna
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O., Kollam, Kerala 690525, India
| | - Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore 138671, Republic of Singapore
| | - Sandipan Ray
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Bhavana Tiwari
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Odisha 760010, India
| | - Rahul Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
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7
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Iwaniak A, Minkiewicz P, Darewicz M. Bioinformatics and bioactive peptides from foods: Do they work together? ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 108:35-111. [PMID: 38461003 DOI: 10.1016/bs.afnr.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.
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Affiliation(s)
- Anna Iwaniak
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland.
| | - Piotr Minkiewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
| | - Małgorzata Darewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
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8
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Alpízar-Pedraza D, Roque-Diaz Y, Garay-Pérez H, Rosenau F, Ständker L, Montero-Alejo V. Insights into the Adsorption Mechanisms of the Antimicrobial Peptide CIDEM-501 on Membrane Models. Antibiotics (Basel) 2024; 13:167. [PMID: 38391553 PMCID: PMC10886324 DOI: 10.3390/antibiotics13020167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
CIDEM-501 is a hybrid antimicrobial peptide rationally designed based on the structure of panusin and panulirin template peptides. The new peptide exhibits significant antibacterial activity against multidrug-resistant pathogens (MIC = 2-4 μM) while conserving no toxicity in human cell lines. We conducted molecular dynamics (MD) simulations using the CHARMM-36 force field to explore the CIDEM-501 adsorption mechanism with different membrane compositions. Several parameters that characterize these interactions were analyzed to elucidate individual residues' structural and thermodynamic contributions. The membrane models were constructed using CHARMM-GUI, mimicking the bacterial and eukaryotic phospholipid compositions. Molecular dynamics simulations were conducted over 500 ns, showing rapid and highly stable peptide adsorption to bacterial lipids components rather than the zwitterionic eucaryotic model membrane. A predominant peptide orientation was observed in all models dominated by an electric dipole. The peptide remained parallel to the membrane surface with the center loop oriented to the lipids. Our findings shed light on the antibacterial activity of CIDEM-501 on bacterial membranes and yield insights valuable for designing potent antimicrobial peptides targeting multi- and extreme drug-resistant bacteria.
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Affiliation(s)
- Daniel Alpízar-Pedraza
- Biochemistry and Molecular Biology Department, Center for Pharmaceutical Research and Development, Ave. 26 # 1605, Nuevo Vedado, Ciudad de La Habana 10400, Cuba
| | - Yessica Roque-Diaz
- Biochemistry and Molecular Biology Department, Center for Pharmaceutical Research and Development, Ave. 26 # 1605, Nuevo Vedado, Ciudad de La Habana 10400, Cuba
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Hilda Garay-Pérez
- Peptide Synthesis Group, Center for Genetic Engineering and Biotechnology, Ave. 31 e/158 y 190, Playa, Habana 11600, Cuba
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Ludger Ständker
- Core Facility for Functional Peptidomics, Ulm Peptide Pharmaceuticals (U-PEP), Faculty of Medicine, Ulm University, 89081 Ulm, Germany
| | - Vivian Montero-Alejo
- Biochemistry and Molecular Biology Department, Center for Pharmaceutical Research and Development, Ave. 26 # 1605, Nuevo Vedado, Ciudad de La Habana 10400, Cuba
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9
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Villamar-Cruz O, Loza-Mejía MA, Vivar-Sierra A, Saldivar-Cerón HI, Patiño-López G, Olguín JE, Terrazas LI, Armas-López L, Ávila-Moreno F, Saha S, Chernoff J, Camacho-Arroyo I, Arias-Romero LE. A PTP1B-Cdk3 Signaling Axis Promotes Cell Cycle Progression of Human Glioblastoma Cells through an Rb-E2F Dependent Pathway. Mol Cell Biol 2023; 43:631-649. [PMID: 38014992 PMCID: PMC10761042 DOI: 10.1080/10985549.2023.2273193] [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: 06/17/2023] [Accepted: 09/11/2023] [Indexed: 11/29/2023] Open
Abstract
PTP1B plays a key role in developing different types of cancer. However, the molecular mechanism underlying this effect is unclear. To identify molecular targets of PTP1B that mediate its role in tumorigenesis, we undertook a SILAC-based phosphoproteomic approach, which allowed us to identify Cdk3 as a novel PTP1B substrate. Substrate trapping experiments and docking studies revealed stable interactions between the PTP1B catalytic domain and Cdk3. In addition, we observed that PTP1B dephosphorylates Cdk3 at tyrosine residue 15 in vitro and interacts with it in human glioblastoma cells. Next, we found that pharmacological inhibition of PTP1B or its depletion with siRNA leads to cell cycle arrest with diminished activity of Cdk3, hypophosphorylation of Rb, and the downregulation of E2F target genes Cdk1, Cyclin A, and Cyclin E1. Finally, we observed that the expression of a constitutively active Cdk3 mutant bypasses the requirement of PTP1B for cell cycle progression and expression of E2F target genes. These data delineate a novel signaling pathway from PTP1B to Cdk3 required for efficient cell cycle progression in an Rb-E2F dependent manner in human GB cells.
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Affiliation(s)
- Olga Villamar-Cruz
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Marco Antonio Loza-Mejía
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Mexico City, Mexico
| | - Alonso Vivar-Sierra
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Mexico City, Mexico
| | | | - Genaro Patiño-López
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de Mexico Federico Gómez, Mexico City, Mexico
| | - Jonadab Efraín Olguín
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
- Laboratorio Nacional en Salud FES-Iztacala, Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
| | - Luis Ignacio Terrazas
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
- Laboratorio Nacional en Salud FES-Iztacala, Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
| | - Leonel Armas-López
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
| | - Federico Ávila-Moreno
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
- Unidad de Investigación, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Sayanti Saha
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Jonathan Chernoff
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Ignacio Camacho-Arroyo
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Luis Enrique Arias-Romero
- Unidad de Investigación en Biomedicina (UBIMED), Facultad de Estudios Superiores-Iztacala, UNAM Tlalnepantla, Estado de México, Mexico
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10
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Ochoa R, Fox T. Assessing the fast prediction of peptide conformers and the impact of non-natural modifications. J Mol Graph Model 2023; 125:108608. [PMID: 37659134 DOI: 10.1016/j.jmgm.2023.108608] [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: 06/29/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/04/2023]
Abstract
We present an assessment of different approaches to predict peptide structures using modeling tools. Several small molecule, protein, and peptide-focused methodologies were used for the fast prediction of conformers for peptides shorter than 30 amino acids. We assessed the effect of including restraints based on annotated or predicted secondary structure motifs. A number of peptides in bound conformations and in solution were collected to compare the tools. In addition, we studied the impact of changing single amino acids to non-natural residues using molecular dynamics simulations. Deep learning methods such as AlphaFold2, or the combination of physics-based approaches with secondary structure information, produce the most accurate results for natural sequences. In the case of peptides with non-natural modifications, modeling the peptide containing natural amino acids first and then modifying and simulating the peptide using benchmarked force fields is a recommended pipeline. The results can guide the modeling of oligopeptides for drug discovery projects.
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Affiliation(s)
- Rodrigo Ochoa
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach/Riss, Germany.
| | - Thomas Fox
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach/Riss, Germany
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11
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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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12
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Shukla P, Sakure A, Basaiawmoit B, Khakhariya R, Maurya R, Bishnoi M, Kondepudi KK, Liu Z, Padhi S, Rai AK, Hati S. Molecular binding mechanism and novel antidiabetic and anti-hypertensive bioactive peptides from fermented camel milk with anti-inflammatory activity in raw macrophages cell lines. Amino Acids 2023; 55:1621-1640. [PMID: 37749439 DOI: 10.1007/s00726-023-03335-9] [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: 10/18/2022] [Accepted: 09/12/2023] [Indexed: 09/27/2023]
Abstract
The investigation was to determine the effect of camel milk fermented with Limosilactobacillus fermentum KGL4 (MTCC 25515) on ACE-inhibiting, anti-inflammatory, and diabetes-preventing properties and also to release the novel peptides with antidiabetic and anti-hypertensive attributes with molecular interaction studies. Growth conditions were optimised on the basis of total peptide production by inoculating the culture in camel milk at different rates (1.5, 2.0, and 2.5%) along with different incubation periods (12, 24, 36, and 48 h). However, after 48 h of fermentation with a 2.5% rate of inoculum, the highest proteolytic activity was obtained. Reverse phase high-pressure liquid chromatography (RP-HPLC) was used to calculate the % Rpa from permeates of 3 kDa and 10 kDa fractions. Molecular weight distributions of fermented and unfermented camel milk protein fractions were compared using SDS-PAGE. Spots obtained from 2D gel electrophoresis were separated on the basis of pH and molecular weight. Spots obtained from 2D gel were digested with trypsin, and the digested samples were subjected to RP-LC/MS for the generation of peptide sequences. The inhibition of tumour necrosis factor alpha, interleukin-6, and interleukin-1 during fermentation was studied using RAW 264.7 macrophages. In the study, fermented camel milk with KGL4 (CMKGL4) inhibited LPS-induced nitric oxide (NO) production and pro-inflammatory cytokine production (TNF-α, IL-6, and IL-1β) by the murine macrophages. The results showed that the peptide structures (YLEELHRLNK and YLQELYPHSSLKVRPILK) exhibited considerable binding affinity against hPAM and hMGA during molecular interaction studies.
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Affiliation(s)
- Pratik Shukla
- Dairy Microbiology Department, SMC College of Dairy Science, Kamdhenu University, Anand, 388110, Gujarat, India
| | - Amar Sakure
- Department of Plant Biotechnology, B.A College of Agriculture, Anand Agricultural University, Anand, 388110, Gujarat, India
| | - Bethsheba Basaiawmoit
- Dept. of Rural Development and Agricultural Production, North-Eastern Hill University, Tura Campus, Chasingre, 794002, Meghalaya, India
| | - Ruchita Khakhariya
- Dairy Microbiology Department, SMC College of Dairy Science, Kamdhenu University, Anand, 388110, Gujarat, India
| | - Ruchika Maurya
- Healthy Gut Research Group, Food and Nutritional Biotechnology Division, Centre of Excellence in Functional Foods, National Agri-Food Biotechnology Institute (NABI), Knowledge City, Sector 81, SAS Nagar, 140306, Punjab, India
- Regional Center for Biotechnology, Faridabad, 121001, Haryana, India
| | - Mahendra Bishnoi
- Healthy Gut Research Group, Food and Nutritional Biotechnology Division, Centre of Excellence in Functional Foods, National Agri-Food Biotechnology Institute (NABI), Knowledge City, Sector 81, SAS Nagar, 140306, Punjab, India
| | - Kanthi Kiran Kondepudi
- Healthy Gut Research Group, Food and Nutritional Biotechnology Division, Centre of Excellence in Functional Foods, National Agri-Food Biotechnology Institute (NABI), Knowledge City, Sector 81, SAS Nagar, 140306, Punjab, India
| | - Zhenbin Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, 18, Xi'an, 710021, China
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, 737102, Sikkim, India
| | - Amit Kumar Rai
- Healthy Gut Research Group, Food and Nutritional Biotechnology Division, Centre of Excellence in Functional Foods, National Agri-Food Biotechnology Institute (NABI), Knowledge City, Sector 81, SAS Nagar, 140306, Punjab, India
| | - Subrota Hati
- Dairy Microbiology Department, SMC College of Dairy Science, Kamdhenu University, Anand, 388110, Gujarat, India.
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13
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Karami Y, Murail S, Giribaldi J, Lefranc B, Defontaine F, Lesouhaitier O, Leprince J, de Vries S, Tufféry P. Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. J Chem Inf Model 2023; 63:6436-6450. [PMID: 37827517 PMCID: PMC10599322 DOI: 10.1021/acs.jcim.3c00865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 10/14/2023]
Abstract
Peptides have recently regained interest as therapeutic candidates, but their development remains confronted with several limitations including low bioavailability. Backbone head-to-tail cyclization, i.e., setting a covalent peptide bond linking the last amino acid with the first one, is one effective strategy of peptide-based drug design to stabilize the conformation of bioactive peptides while preserving peptide properties in terms of low toxicity, binding affinity, target selectivity, and preventing enzymatic degradation. Starting from an active peptide, it usually requires the design of a linker of a few amino acids to make it possible to cyclize the peptide, possibly preserving the conformation of the initial peptide and not affecting its activity. However, very little is known about the sequence-structure relationship requirements of designing linkers for peptide cyclization in a rational manner. Recently, we have shown that large-scale data-mining of available protein structures can lead to the precise identification of protein loop conformations, even from remote structural classes. Here, we transpose this approach to linkers, allowing head-to-tail peptide cyclization. First we show that given a linker sequence and the conformation of the linear peptide, it is possible to accurately predict the cyclized peptide conformation. Second, and more importantly, we show that it seems possible to elaborate on the information inferred from protein structures to propose effective candidate linker sequences constrained by length and amino acid composition, providing the first framework for the rational design of head-to-tail cyclization linkers. Finally, we illustrate this for two peptides using a limited set of amino-acids likely not to interfere with peptide function. For a linear peptide derived from Nrf2, the peptide cyclized starting from the experimental structure showed a 26-fold increase in the binding affinity. For urotensin II, a peptide already cyclized by a disulfide bond that exerts a broad array of biological activities, we were able, starting from models of the structure, to design a head-to-tail cyclized peptide, the first synthesized bicyclic 14-residue long urotensin II analogue, showing a retention of in vitro activity. Although preliminary, our results strongly suggest that such an approach has strong potential for cyclic peptide-based drug design.
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Affiliation(s)
- Yasaman Karami
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Samuel Murail
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Julien Giribaldi
- Institut
des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier-CNRS, 34293 Montpellier, France
| | - Benjamin Lefranc
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Florian Defontaine
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Jérôme Leprince
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Sjoerd de Vries
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Pierre Tufféry
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
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14
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Ochoa R, Brown JB, Fox T. pyPept: a python library to generate atomistic 2D and 3D representations of peptides. J Cheminform 2023; 15:79. [PMID: 37700347 PMCID: PMC10498622 DOI: 10.1186/s13321-023-00748-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023] Open
Abstract
We present pyPept, a set of executables and underlying python-language classes to easily create, manipulate, and analyze peptide molecules using the FASTA, HELM, or recently-developed BILN notations. The framework enables the analysis of both pure proteinogenic peptides as well as those with non-natural amino acids, including support to assemble a customizable monomer library, without requiring programming. From line notations, a peptide is transformed into a molecular graph for 2D depiction tasks, the calculation of physicochemical properties, and other systematic analyses or processing pipelines. The package includes a module to rapidly generate approximate peptide conformers by incorporating secondary structure restraints either given by the user or predicted via pyPept, and a wrapper tool is also provided to automate the generation and output of 2D and 3D representations of a peptide directly from the line notation. HELM and BILN notations that include circular, branched, or stapled peptides are fully supported, eliminating errors in structure creation that are prone during manual drawing and connecting. The framework and common workflows followed in pyPept are described together with illustrative examples. pyPept has been released at: https://github.com/Boehringer-Ingelheim/pyPept .
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Affiliation(s)
- Rodrigo Ochoa
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany
| | - J B Brown
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany
| | - Thomas Fox
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany.
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15
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Thamarai Kannan H, Issac PK, Dey N, Guru A, Arockiaraj J. A Review on Mitochondrial Derived Peptide Humanin and Small Humanin-Like Peptides and Their Therapeutic Strategies. Int J Pept Res Ther 2023; 29:86. [DOI: 10.1007/s10989-023-10558-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2023] [Indexed: 10/16/2023]
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16
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Zeng P, Zhang P, Yi L, Wong KY, Chen S, Chan KF, Leung SSY. A novel ESKAPE-sensitive peptide with enhanced stability and its application in controlling multiple bacterial contaminations in chilled fresh pork. Food Chem 2023; 413:135647. [PMID: 36796263 DOI: 10.1016/j.foodchem.2023.135647] [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: 12/02/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
The co-existence of various pathogenic bacteria on the surface of pork products exacerbates difficulties in food safety control. Developing broad-spectrum and stable antibacterial agents that are not antibiotics is an unmet need. To address this issue, all l-arginine residues of a reported peptide (IIRR)4-NH2 (zp80) were substituted with the corresponding D enantiomers. This novel peptide (IIrr)4-NH2 (zp80r) was expected to maintain favourable bioactivity against ESKAPE strains and have enhanced proteolytic stability compared with zp80. In a series of experiments, zp80r maintained favourable bioactivities against starvation-induced persisters. Electron microscopy and fluorescent dye assays were used to verify the antibacterial mechanism of zp80r. Importantly, zp80r reduced bacterial colonies in chilled fresh pork contaminated with multiple bacterial species. This newly designed peptide is a potential antibacterial candidate to combat problematic foodborne pathogens during storage of pork.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong; State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Lanhua Yi
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong; College of Food Science, Southwest University, Chongqing, PR China
| | - Kwok-Yin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kin-Fai Chan
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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17
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Choi JM, Vuppala S, Park MJ, Kim J, Jegal ME, Han YS, Kim YJ, Jang J, Jeong MH, Joo BS. Computer simulation approach to the identification of visfatin-derived angiogenic peptides. PLoS One 2023; 18:e0287577. [PMID: 37384629 PMCID: PMC10309634 DOI: 10.1371/journal.pone.0287577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023] Open
Abstract
Angiogenesis plays an essential role in various normal physiological processes, such as embryogenesis, tissue repair, and skin regeneration. Visfatin is a 52 kDa adipokine secreted by various tissues including adipocytes. It stimulates the expression of vascular endothelial growth factor (VEGF) and promotes angiogenesis. However, there are several issues in developing full-length visfatin as a therapeutic drug due to its high molecular weight. Therefore, the purpose of this study was to develop peptides, based on the active site of visfatin, with similar or superior angiogenic activity using computer simulation techniques.Initially, the active site domain (residues 181∼390) of visfatin was first truncated into small peptides using the overlapping technique. Subsequently, the 114 truncated small peptides were then subjected to molecular docking analysis using two docking programs (HADDOCK and GalaxyPepDock) to generate small peptides with the highest affinity for visfatin. Furthermore, molecular dynamics simulations (MD) were conducted to investigate the stability of the protein-ligand complexes by computing root mean square deviation (RSMD) and root mean square fluctuation(RMSF) plots for the visfatin-peptide complexes. Finally, peptides with the highest affinity were examined for angiogenic activities, such as cell migration, invasion, and tubule formation in human umbilical vein endothelial cells (HUVECs). Through the docking analysis of the 114 truncated peptides, we screened nine peptides with a high affinity for visfatin. Of these, we discovered two peptides (peptide-1: LEYKLHDFGY and peptide-2: EYKLHDFGYRGV) with the highest affinity for visfatin. In an in vitrostudy, these two peptides showed superior angiogenic activity compared to visfatin itself and stimulated mRNA expressions of visfatin and VEGF-A. These results show that the peptides generated by the protein-peptide docking simulation have a more efficient angiogenic activity than the original visfatin.
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Affiliation(s)
- Ji Myung Choi
- Lab-to-Medi CRO Inc., Seoul, Republic of Korea
- Department of Microbiology, Dong-A University College of Medicine, Busan, Republic of Korea
| | - Srimai Vuppala
- Department of Nanoenergy Engineering, Pusan National University, Busan, Republic of Korea
| | - Min Jung Park
- Lab-to-Medi CRO Inc., Seoul, Republic of Korea
- The Korea Institute for Public Sperm Bank, Busan, Republic of Korea
| | - Jaeyoung Kim
- Department of Nanoenergy Engineering, Pusan National University, Busan, Republic of Korea
| | - Myeong-Eun Jegal
- Korea Nanobiotechnology Center, Pusan National University, Busan, Republic of Korea
| | - Yu-Seon Han
- Korea Nanobiotechnology Center, Pusan National University, Busan, Republic of Korea
| | - Yung-Jin Kim
- Korea Nanobiotechnology Center, Pusan National University, Busan, Republic of Korea
- Department of Molecular Biology, Pusan National University, Busan, Republic of Korea
| | - Joonkyung Jang
- Department of Nanoenergy Engineering, Pusan National University, Busan, Republic of Korea
| | - Min-Ho Jeong
- Department of Microbiology, Dong-A University College of Medicine, Busan, Republic of Korea
| | - Bo Sun Joo
- Lab-to-Medi CRO Inc., Seoul, Republic of Korea
- The Korea Institute for Public Sperm Bank, Busan, Republic of Korea
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18
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Castro TG, Melle-Franco M, Sousa CEA, Cavaco-Paulo A, Marcos JC. Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications. Biomolecules 2023; 13:981. [PMID: 37371561 DOI: 10.3390/biom13060981] [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: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
This review provides a fresh overview of non-canonical amino acids and their applications in the design of peptidomimetics. Non-canonical amino acids appear widely distributed in nature and are known to enhance the stability of specific secondary structures and/or biological function. Contrary to the ubiquitous DNA-encoded amino acids, the structure and function of these residues are not fully understood. Here, results from experimental and molecular modelling approaches are gathered to classify several classes of non-canonical amino acids according to their ability to induce specific secondary structures yielding different biological functions and improved stability. Regarding side-chain modifications, symmetrical and asymmetrical α,α-dialkyl glycines, Cα to Cα cyclized amino acids, proline analogues, β-substituted amino acids, and α,β-dehydro amino acids are some of the non-canonical representatives addressed. Backbone modifications were also examined, especially those that result in retro-inverso peptidomimetics and depsipeptides. All this knowledge has an important application in the field of peptidomimetics, which is in continuous progress and promises to deliver new biologically active molecules and new materials in the near future.
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Affiliation(s)
- Tarsila G Castro
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Cristina E A Sousa
- BioMark Sensor Research-School of Engineering of the Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Artur Cavaco-Paulo
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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19
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Renzi F, Seamann A, Ganguly K, Pandey K, Byrareddy SN, Batra S, Kumar S, Ghersi D. Engineering an ACE2-Derived Fragment as a Decoy for Novel SARS-CoV-2 Virus. ACS Pharmacol Transl Sci 2023; 6:857-867. [PMID: 37325447 PMCID: PMC10262318 DOI: 10.1021/acsptsci.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 06/17/2023]
Abstract
Entry inhibitors are an important resource in the response against emerging pathogens like the novel SARS-CoV-2, which enters human cells via interaction between the surface spike glycoprotein and the cellular membrane receptor angiotensin-converting enzyme 2 (ACE2). Using a combination of comparative structural analyses of the binding surface of the spike to ACE2, docking experiments, and molecular dynamics simulations, we identified a stable fragment of ACE2 that binds to the spike, is soluble, and is not predicted to bind to its physiological ligand angiotensin II. From this fragment we computationally designed and experimentally validated a smaller, stable peptide that disrupts ACE2-spike interaction at nanomolar concentrations, suggesting its potential use as a decoy that could interfere with viral binding by competition.
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Affiliation(s)
- Fabiana Renzi
- Department
of Physics, Università di Roma ”La
Sapienza”, 00185 Rome, Italy
| | - Austin Seamann
- School
of Interdisciplinary Informatics, University
of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Koelina Ganguly
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Kabita Pandey
- Department
of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Siddappa N. Byrareddy
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
- Department
of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Surinder Batra
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Sushil Kumar
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Dario Ghersi
- School
of Interdisciplinary Informatics, University
of Nebraska at Omaha, Omaha, Nebraska 68182, USA
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20
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Barman P, Joshi S, Sharma S, Preet S, Sharma S, Saini A. Strategic Approaches to Improvise Peptide Drugs as Next Generation Therapeutics. Int J Pept Res Ther 2023; 29:61. [PMID: 37251528 PMCID: PMC10206374 DOI: 10.1007/s10989-023-10524-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2023] [Indexed: 05/31/2023]
Abstract
In recent years, the occurrence of a wide variety of drug-resistant diseases has led to an increase in interest in alternate therapies. Peptide-based drugs as an alternate therapy hold researchers' attention in various therapeutic fields such as neurology, dermatology, oncology, metabolic diseases, etc. Previously, they had been overlooked by pharmaceutical companies due to certain limitations such as proteolytic degradation, poor membrane permeability, low oral bioavailability, shorter half-life, and poor target specificity. Over the last two decades, these limitations have been countered by introducing various modification strategies such as backbone and side-chain modifications, amino acid substitution, etc. which improve their functionality. This has led to a substantial interest of researchers and pharmaceutical companies, moving the next generation of these therapeutics from fundamental research to the market. Various chemical and computational approaches are aiding the production of more stable and long-lasting peptides guiding the formulation of novel and advanced therapeutic agents. However, there is not a single article that talks about various peptide design approaches i.e., in-silico and in-vitro along with their applications and strategies to improve their efficacy. In this review, we try to bring different aspects of peptide-based therapeutics under one article with a clear focus to cover the missing links in the literature. This review draws emphasis on various in-silico approaches and modification-based peptide design strategies. It also highlights the recent progress made in peptide delivery methods important for their enhanced clinical efficacy. The article would provide a bird's-eye view to researchers aiming to develop peptides with therapeutic applications. Graphical Abstract
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Affiliation(s)
- Panchali Barman
- Institute of Forensic Science and Criminology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014 India
| | - Shubhi Joshi
- Energy Research Centre, Panjab University, Sector 14, Chandigarh, 160014 India
| | - Sheetal Sharma
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, U.T 160014 India
| | - Simran Preet
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, U.T 160014 India
| | - Shweta Sharma
- Institute of Forensic Science and Criminology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014 India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, U.T 160014 India
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21
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Khakhariya R, Basaiawmoit B, Sakure AA, Maurya R, Bishnoi M, Kondepudi KK, Padhi S, Rai AK, Liu Z, Hati S. Production and Characterization of ACE Inhibitory and Anti-Diabetic Peptides from Buffalo and Camel Milk Fermented with Lactobacillus and Yeast: A Comparative Analysis with In Vitro, In Silico, and Molecular Interaction Study. Foods 2023; 12:foods12102006. [PMID: 37238823 DOI: 10.3390/foods12102006] [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: 02/20/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
The investigation aimed at assessing a comparative study on the production and characterization of ACE inhibitory, anti-diabetic, and anti-inflammatory activities, along with the production of ACE inhibitory and anti-diabetic peptides through the fermentation of buffalo and camel milk by Limosilactobacillus fermentum (KGL4) and Saccharomyces cerevisiae (WBS2A). The angiotensin-converting enzyme (ACE) inhibitory and anti-diabetic properties were evaluated at particular time intervals (12, 24, 36, and 48 h) at 37 °C, and we discovered maximum activity at 37 °C after 48 h of incubation. The maximum ACE inhibitory, lipase inhibitory activities, alpha-glucosidase inhibitory, and alpha-amylase inhibitory activities were found in the fermented camel milk (77.96 ± 2.61, 73.85 ± 1.19, 85.37 ± 2.15, and 70.86 ± 1.02), as compared to the fermented buffalo milk (FBM) (75.25 ± 1.72, 61.79 ± 2.14, 80.09 ± 0.51, and 67.29 ± 1.75). Proteolytic activity was measured with different inoculation rates (1.5%, 2.0%, and 2.5%) and incubation times (12, 24, 36, and 48 h) to optimize the growth conditions. Maximum proteolysis was found at a 2.5% inoculation rate and at a 48 h incubation period in both fermented buffalo (9.14 ± 0.06) and camel milk (9.10 ± 0.17). SDS-PAGE and 2D gel electrophoresis were conducted for protein purification. The camel and buffalo milk that had not been fermented revealed protein bands ranging from 10 to 100 kDa and 10 to 75 kDa, respectively, whereas all the fermented samples showed bands ranging from 10 to 75 kDa. There were no visible protein bands in the permeates on SDS-PAGE. When fermented buffalo and camel milk were electrophoresed in 2D gel, 15 and 20 protein spots were detected, respectively. The protein spots in the 2D gel electrophoresis ranged in size from 20 to 75 kDa. To distinguish between different peptide fractions, water-soluble extract (WSE) fractions of ultrafiltration (3 and 10 kDa retentate and permeate) of fermented camel and buffalo milk were employed in RP-HPLC (reversed-phase high-performance liquid chromatography). The impact of fermented buffalo and camel milk on inflammation induced by LPS (lipopolysaccharide) was also investigated in the RAW 264.7 cell line. Novel peptide sequences with ACE inhibitory and anti-diabetic properties were also analyzed on the anti-hypertensive database (AHTDB) and bioactive peptide (BIOPEP) database. We found the sequences SCQAQPTTMTR, EMPFPK, TTMPLW, HPHPHLSFMAIPPK, FFNDKIAK, ALPMHIR, IPAVFK, LDQWLCEK, and AVPYPQR from the fermented buffalo milk and the sequences TDVMPQWW, EKTFLLYSCPHR, SSHPYLEQLY, IDSGLYLGSNYITAIR, and FDEFLSQSCAPGSDPR from the fermented camel milk.
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Affiliation(s)
- Ruchita Khakhariya
- Department of Dairy Microbiology, SMC College of Dairy Science, Kamdhenu University, Anand 388110, Gujarat, India
| | - Bethsheba Basaiawmoit
- Department of Rural Development and Agricultural Production, Tura Campus, North-Eastern Hill University, Chasingre 794002, Meghalaya, India
| | - Amar A Sakure
- Department of Agriculture Biotechnology, Anand Agricultural University, Anand 388110, Gujarat, India
| | - Ruchika Maurya
- Regional Center for Biotechnology, Faridabad 121001, Haryana, India
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, SAS Nagar 140306, Punjab, India
| | - Mahendra Bishnoi
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, SAS Nagar 140306, Punjab, India
| | - Kanthi Kiran Kondepudi
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, Knowledge City, Sector 81, SAS Nagar 140306, Punjab, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong 737102, Sikkim, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong 737102, Sikkim, India
| | - Zhenbin Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Subrota Hati
- Department of Dairy Microbiology, SMC College of Dairy Science, Kamdhenu University, Anand 388110, Gujarat, India
- Department of Dairy Microbiology, Kamdhenu University, Anand 388110, Gujarat, India
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22
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Makarov M, Sanchez Rocha AC, Krystufek R, Cherepashuk I, Dzmitruk V, Charnavets T, Faustino AM, Lebl M, Fujishima K, Fried SD, Hlouchova K. Early Selection of the Amino Acid Alphabet Was Adaptively Shaped by Biophysical Constraints of Foldability. J Am Chem Soc 2023; 145:5320-5329. [PMID: 36826345 PMCID: PMC10017022 DOI: 10.1021/jacs.2c12987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Whereas modern proteins rely on a quasi-universal repertoire of 20 canonical amino acids (AAs), numerous lines of evidence suggest that ancient proteins relied on a limited alphabet of 10 "early" AAs and that the 10 "late" AAs were products of biosynthetic pathways. However, many nonproteinogenic AAs were also prebiotically available, which begs two fundamental questions: Why do we have the current modern amino acid alphabet and would proteins be able to fold into globular structures as well if different amino acids comprised the genetic code? Here, we experimentally evaluate the solubility and secondary structure propensities of several prebiotically relevant amino acids in the context of synthetic combinatorial 25-mer peptide libraries. The most prebiotically abundant linear aliphatic and basic residues were incorporated along with or in place of other early amino acids to explore these alternative sequence spaces. The results show that foldability was likely a critical factor in the selection of the canonical alphabet. Unbranched aliphatic amino acids were purged from the proteinogenic alphabet despite their high prebiotic abundance because they generate polypeptides that are oversolubilized and have low packing efficiency. Surprisingly, we find that the inclusion of a short-chain basic amino acid also decreases polypeptides' secondary structure potential, for which we suggest a biophysical model. Our results support the view that, despite lacking basic residues, the early canonical alphabet was remarkably adaptive at supporting protein folding and explain why basic residues were only incorporated at a later stage of protein evolution.
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Affiliation(s)
- Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12843, Czech Republic
| | - Alma C Sanchez Rocha
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12843, Czech Republic
| | - Robin Krystufek
- Department of Physical Chemistry, Faculty of Science, Charles University, Prague 12843, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12843, Czech Republic
| | - Volha Dzmitruk
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec 25250, Czech Republic
| | - Tatsiana Charnavets
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec 25250, Czech Republic
| | - Anneliese M Faustino
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Michal Lebl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12843, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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23
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Biological Activity of Cyclic Peptide Extracted from Sphaeranthus amaranthoides Using De Novo Sequencing Strategy by Mass Spectrometry for Cancer. BIOLOGY 2023; 12:biology12030412. [PMID: 36979104 PMCID: PMC10045366 DOI: 10.3390/biology12030412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 03/10/2023]
Abstract
Though there are several advancements and developments in cancer therapy, the treatment remains challenging. In recent years, the antimicrobial peptides (AMPs) from traditional herbs are focused for identifying and developing potential anticancer molecules. In this study, AMPs are identified from Sphaeranthus amaranthoides, a natural medicinal herb widely used as a crucial immune stimulant in Indian medicine. A total of 86 peptide traces were identified using liquid-chromatography–electrospray-ionisation mass spectrometry (LC-ESI-MS). Among them, three peptides were sequenced using the manual de novo sequencing technique. The in-silico prediction revealed that SA923 is a cyclic peptide with C-N terminal interaction of the carbon atom of ASP7 with the nitrogen atom of GLU1 (1ELVFYRD7). Thus, SA923 is presented under the orbitides class of peptides, which lack the disulfide bonds for cyclization. In addition, SA923, steered with the physicochemical properties and support vector machine (SVM) algorithm mentioned for the segment, has the highest in silico anticancer potential. Further, the in vitro cytotoxicity assay revealed the peptide has anti-proliferative activity, and toxicity studies were demonstrated in Danio rerio (zebrafish) embryos.
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24
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Strobl J, Kozak F, Kamalov M, Reichinger D, Kurzbach D, Becker CF. Understanding Self-Assembly of Silica-Precipitating Peptides to Control Silica Particle Morphology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207586. [PMID: 36509953 DOI: 10.1002/adma.202207586] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The most advanced materials are those found in nature. These evolutionary optimized substances provide highest efficiencies, e.g., in harvesting solar energy or providing extreme stability, and are intrinsically biocompatible. However, the mimicry of biological materials is limited to a few successful applications since there is still a lack of the tools to recreate natural materials. Herein, such means are provided based on a peptide library derived from the silaffin protein R5 that enables rational biomimetic materials design. It is now evident that biomaterials do not form via mechanisms observed in vitro. Instead, the material's function and morphology are predetermined by precursors that self-assemble in solution, often from a combination of protein and salts. These assemblies act as templates for biomaterials. The RRIL peptides used here are a small part of the silica-precipitation machinery in diatoms. By connecting RRIL motifs via varying central bi- or trifunctional residues, a library of stereoisomers is generated, which allows characterization of different template structures in the presence of phosphate ions by combining residue-resolved real-time NMR spectroscopy and molecular dynamics (MD) simulations. Understanding these templates in atomistic detail, the morphology of silica particles is controlled via manipulation of the template precursors.
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Affiliation(s)
- Johannes Strobl
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Fanny Kozak
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Meder Kamalov
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Daniela Reichinger
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Dennis Kurzbach
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
| | - Christian Fw Becker
- Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 38, Vienna, 109, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna, 1090, Austria
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25
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Ma J, Ma B, Wang Z, Chen Y, Ma R, Dong Y. Effect of splenic transfer factor on the development of intestinal mucosal barrier in laying hens. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1342-1354. [PMID: 36151767 DOI: 10.1002/jsfa.12228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/28/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The aim of this study was to investigate the effects of different doses of chicken spleen transfer factor (TF) on the structure of intestinal epithelial cells in different age groups. One-day-old White Leghorns laying hens were randomly divided into four groups: three groups were administered TF at different dosages (0.10, 0.25 or 1.00 mL) and a fourth group was set as control (administered saline, 1.00 mL). Using hematoxylin and eosin staining, high-throughput sequencing, microbiota analysis, quantitative polymerase reaction and western blotting. RESULTS We measured the effects of different doses of TF on the following: intestinal mucosal epithelial tissue morphology, intestinal mucosal epithelial barrier-related gene expression profiles, and intestinal epithelial tight junction gene protein levels. The collected data show that TF can improve the absorption of nutrients by increasing villus height and crypt depth, and regulate intestinal flora disorders. Furthermore, we verified that the expression of the claudin and occludin tight junctions between intestinal epithelial cells was increased with TF. this research is very important for focusing on the structure and gene expression of intestinal tissues. CONCLUSION The results provide a scientific rationale for feeding and nutrition programs for green and healthy farming, as well as technical support to improve the production efficiency of the livestock and poultry breeding industry. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Junxing Ma
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Baochen Ma
- China Animal Husbandry Group, Beijing, China
| | - Zixu Wang
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yaoxing Chen
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruiqin Ma
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yulan Dong
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, College of Veterinary Medicine, China Agricultural University, Beijing, China
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26
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Pande A, Patiyal S, Lathwal A, Arora C, Kaur D, Dhall A, Mishra G, Kaur H, Sharma N, Jain S, Usmani SS, Agrawal P, Kumar R, Kumar V, Raghava GPS. Pfeature: A Tool for Computing Wide Range of Protein Features and Building Prediction Models. J Comput Biol 2023; 30:204-222. [PMID: 36251780 DOI: 10.1089/cmb.2022.0241] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In the last three decades, a wide range of protein features have been discovered to annotate a protein. Numerous attempts have been made to integrate these features in a software package/platform so that the user may compute a wide range of features from a single source. To complement the existing methods, we developed a method, Pfeature, for computing a wide range of protein features. Pfeature allows to compute more than 200,000 features required for predicting the overall function of a protein, residue-level annotation of a protein, and function of chemically modified peptides. It has six major modules, namely, composition, binary profiles, evolutionary information, structural features, patterns, and model building. Composition module facilitates to compute most of the existing compositional features, plus novel features. The binary profile of amino acid sequences allows to compute the fraction of each type of residue as well as its position. The evolutionary information module allows to compute evolutionary information of a protein in the form of a position-specific scoring matrix profile generated using Position-Specific Iterative Basic Local Alignment Search Tool (PSI-BLAST); fit for annotation of a protein and its residues. A structural module was developed for computing of structural features/descriptors from a tertiary structure of a protein. These features are suitable to predict the therapeutic potential of a protein containing non-natural or chemically modified residues. The model-building module allows to implement various machine learning techniques for developing classification and regression models as well as feature selection. Pfeature also allows the generation of overlapping patterns and features from a protein. A user-friendly Pfeature is available as a web server python library and stand-alone package.
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Affiliation(s)
- Akshara Pande
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Anjali Lathwal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Chakit Arora
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Dilraj Kaur
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Gaurav Mishra
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.,Department of Electrical Engineering, Shiv Nadar University, Greater Noida, India
| | - Harpreet Kaur
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Neelam Sharma
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Shipra Jain
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Salman Sadullah Usmani
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Piyush Agrawal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Rajesh Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Vinod Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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27
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Tufféry P, Derreumaux P. A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution. FRONTIERS IN BIOINFORMATICS 2023; 3:1113928. [PMID: 36727106 PMCID: PMC9885153 DOI: 10.3389/fbinf.2023.1113928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/06/2023] [Indexed: 01/17/2023] Open
Abstract
Introduction: Peptides carry out diverse biological functions and the knowledge of the conformational ensemble of polypeptides in various experimental conditions is important for biological applications. All fast dedicated softwares perform well in aqueous solution at neutral pH. Methods: In this study, we go one step beyond by combining the Debye-Hückel formalism for charged-charged amino acid interactions and a coarse-grained potential of the amino acids to treat pH and salt variations. Results: Using the PEP-FOLD framework, we show that our approach performs as well as the machine-leaning AlphaFold2 and TrRosetta methods for 15 well-structured sequences, but shows significant improvement in structure prediction of six poly-charged amino acids and two sequences that have no homologous in the Protein Data Bank, expanding the range of possibilities for the understanding of peptide biological roles and the design of candidate therapeutic peptides.
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Affiliation(s)
- Pierre Tufféry
- Université Paris Cité, CNRS UMR 8251, INSERM U1133, Paris, France,*Correspondence: Pierre Tufféry,
| | - Philippe Derreumaux
- Université Paris Cité, CNRSUPR9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France,Institut Universitaire de France (IUF), Paris, France
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28
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A comparative study of fermented buffalo and camel milk with anti-inflammatory, ACE-inhibitory and anti-diabetic properties and release of bio active peptides with molecular interactions: In vitro, in silico and molecular study. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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29
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Srivastava S, Verma S, Kamthania M, Saxena AK, Pandey KC, Pande V, Kolbe M. Exploring the structural basis to develop efficient multi-epitope vaccines displaying interaction with HLA and TAP and TLR3 molecules to prevent NIPAH infection, a global threat to human health. PLoS One 2023; 18:e0282580. [PMID: 36920996 PMCID: PMC10016716 DOI: 10.1371/journal.pone.0282580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
Nipah virus (NiV) is an emerging zoonotic virus that caused several serious outbreaks in the south asian region with high mortality rates ranging from 40 to 90% since 2001. NiV infection causes lethal encephalitis and respiratory disease with the symptom of endothelial cell-cell fusion. No specific and effective vaccine has yet been reported against NiV. To address the urgent need for a specific and effective vaccine against NiV infection, in the present study, we have designed two Multi-Epitope Vaccines (MEVs) composed of 33 Cytotoxic T lymphocyte (CTL) epitopes and 38 Helper T lymphocyte (HTL) epitopes. Out of those CTL and HTL combined 71 epitopes, 61 novel epitopes targeting nine different NiV proteins were not used before for vaccine design. Codon optimization for the cDNA of both the designed MEVs might ensure high expression potential in the human cell line as stable proteins. Both MEVs carry potential B cell linear epitope overlapping regions, B cell discontinuous epitopes as well as IFN-γ inducing epitopes. Additional criteria such as sequence consensus amongst CTL, HTL and B Cell epitopes was implemented for the design of final constructs constituting MEVs. Hence, the designed MEVs carry the potential to elicit cell-mediated as well as humoral immune response. Selected overlapping CTL and HTL epitopes were validated for their stable molecular interactions with HLA class I and II alleles and in case of CTL epitopes with human Transporter Associated with antigen Processing (TAP) cavity. The structure based epitope cross validation for interaction with TAP cavity was used as another criteria choosing final epitopes for NiV MEVs. Finally, human Beta-defensin 2 and Beta-defensin 3 were used as adjuvants to enhance the immune response of both the MEVs. Molecular dynamics simulation studies of MEVs-TLR3 ectodomain (Human Toll-Like Receptor 3) complex indicated the stable molecular interaction. We conclude that the MEVs designed and in silico validated here could be highly potential vaccine candidates to combat NiV infections, with great effectiveness, high specificity and large human population coverage worldwide.
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Affiliation(s)
- Sukrit Srivastava
- Infection Biology Group, Indian Foundation for Fundamental Research Trust, RaeBareli, India
- Department for Structural Infection Biology, Centre for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection Research, Hamburg, Germany
- * E-mail: (SS); (MK)
| | - Sonia Verma
- Protein Biochemistry & Engineering Lab, Parasite-Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Mohit Kamthania
- Infection Biology Group, Indian Foundation for Fundamental Research Trust, RaeBareli, India
| | - Ajay Kumar Saxena
- Molecular Medicine Lab., School of Life Science, Jawaharlal Nehru University, New Delhi, India
| | - Kailash C. Pandey
- Protein Biochemistry & Engineering Lab, Parasite-Host Biology Group, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Veena Pande
- Kumaun University, Bheemtal, Nainital, Uttarakhand, India
| | - Michael Kolbe
- Department for Structural Infection Biology, Centre for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection Research, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
- * E-mail: (SS); (MK)
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30
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Mahapatra SR, Dey J, Kushwaha GS, Puhan P, Mohakud NK, Panda SK, Lata S, Misra N, Suar M. Immunoinformatic approach employing modeling and simulation to design a novel vaccine construct targeting MDR efflux pumps to confer wide protection against typhoidal Salmonella serovars. J Biomol Struct Dyn 2022; 40:11809-11821. [PMID: 34463211 DOI: 10.1080/07391102.2021.1964600] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Overcoming multi drug resistance is one of the crucial challenges to control enteric typhoid fever caused by Salmonella typhi and Salmonella paratyphi. Overexpression of efflux pumps predominantly causes drug resistance in microorganisms. Therefore, immunotherapy targeting the various efflux pumps antigens could be a promising strategy to increase the success of vaccines. An immunoinformatic approach was employed to design a Salmonellosis multi-epitope subunit vaccine peptide consisting of linear B-cell and T-cell epitopes of multidrug resistance protein families including ATP Binding Cassette (ABC), major facilitator superfamily (MFS), resistance nodulation cell division (RND), small multidrug resistance (SMR), and multidrug and toxin extrusion (MATE). The selected epitopes exhibited conservation in both S. typhi and S. paratyphi and thus could be helpful for cross-protection. Further, the final vaccine construct encompassing the peptides, adjuvants and specific linker sequences showed high immunogenicity, solubility, non-allergenic, nontoxic, and wide population coverage due to strong binding affinity to maximum HLA alleles. The three-dimensional structure was predicted, and validated using various structure validation tools. Additionally, protein-protein docking of the chimeric vaccine construct with the TLR-2 protein and molecular dynamics demonstrated stable and efficient binding. Conclusively, the immunoinformatic study showed that the novel multi epitopic vaccine construct can simulate the both T-cell and B-cell immune responses in typhoidal Salmonella serovars and could potentially be used for prophylactic or therapeutic applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumya Ranjan Mahapatra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Jyotirmayee Dey
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Gajraj Singh Kushwaha
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.,Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Puspasree Puhan
- Science and Technology Department, Government of Odisha, Bhubaneswar, India
| | - Nirmal Kumar Mohakud
- Kalinga Institute of Medical Sciences, KIIT, Deemed to Be University, Bhubaneswar, India
| | - Santosh Kumar Panda
- Kalinga Institute of Medical Sciences, KIIT, Deemed to Be University, Bhubaneswar, India
| | - S Lata
- Kalinga Institute of Dental Sciences, KIIT Deemed to Be University, Bhubaneswar, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.,KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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Ali MC, Khatun MS, Jahan SI, Das R, Munni YA, Rahman MM, Dash R. In silico design of epitope-based peptide vaccine against non-typhoidal Salmonella through immunoinformatic approaches. J Biomol Struct Dyn 2022; 40:10696-10714. [PMID: 36529187 DOI: 10.1080/07391102.2021.1947381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Non-typhoidal Salmonella (NTS) is one of the leading bacterial causes of many invasive human infections with a high antibiotic resistance profile. With this concern, the current study aimed to design an effective epitope-based peptide vaccine against NTS species as a successive and substitutive protective measure of invasive NTS disease. To design rationally, the current study considered a comprehensive in silico workflow combination of both immunoinformatics and molecular modeling approaches, including molecular docking and molecular dynamics (MD) simulation. We identified the two most promising T cell epitopes KVLYGIFAI and YGIFAITAL, and three B cell epitopes AAPVQVGEAAGS, TGGGDGSNT, and TGGGDGSNTGTTTT, in the outer membrane of NTS. Using these epitopes, a multiepitope vaccine was subsequently constructed along with appropriate adjuvant and linkers, which showed a good binding affinity and stability with toll-like receptor 2 (TLR2) in both molecular docking and MD simulation. Furthermore, in silico immune simulation described a strong immune response with a high number of antibodies, interferon-γ, and activated B and T cells. This study collectively suggests that predicted vaccine constructs could be considered potential vaccine candidates against common NTS species.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Chayan Ali
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Mst Shanzeda Khatun
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Sultana Israt Jahan
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Raju Das
- Department of Physiology, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Yeasmin Akter Munni
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Md Mafizur Rahman
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Republic of Korea
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Chopada K, Basaiawmoit B, Sakure AA, Maurya R, Bishnoi M, Kondepudi KK, Solanki D, Singh BP, Padhi S, Rai AK, Liu Z, Mishra BK, Hati S. Purification and Characterization of Novel Antihypertensive and Antioxidative Peptides From Whey Protein Fermentate: In Vitro, In Silico, and Molecular Interactions Studies. JOURNAL OF THE AMERICAN NUTRITION ASSOCIATION 2022:1-20. [PMID: 36416542 DOI: 10.1080/27697061.2022.2110966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
OBJECTIVE The goal of this research was to purify and characterize the novel angiotensin-converting enzyme (ACE)-inhibitory and antioxidant peptides from fermented whey protein concentrate produced by Lactobacillus paracasei and Saccharomyces cerevisiae in a co-fermentation system. METHOD Whey protein fermented with lactic acid bacteria and yeast culture was analyzed for antioxidative, ACE inhibition, as well as anti-inflammatory activity followed by SDS-PAGE, isoelectric focusing, and 2-dimensional (2D) analysis. Anti-inflammatory activity of whey protein fermentate was also studied on the RAW 264.7 cell line. The bioactive peptides were separated from the whey protein fermentate using reverse-phase high-performance liquid chromatography (RP-HPLC) and reverse-phase liquid chromatography mass spectrometry (RPLC/MS), and thus identification and characterization of purified bioactive peptide was performed. RESULTS Whey protein fermentate samples' bioactivity was analyzed at specific time intervals at 12, 24, 36, and 48 hours at 37 °C for M11 and at 25 °C for WBS2A. The development settings (incubation time [12, 24, 36, and 48 hours) and inoculation rates [1.5%, 2.0%, and 2.5%]) were optimized for peptide synthesis via the o-phthaldialdehyde (OPA) method (proteolytic activity). Maximum proteolytic activity was observed at 37 °C for M11 (6.50 mg/mL) and at 25 °C for WBS2A (8.59 mg/mL) for 48 hours of incubation. Protein profiling was carried out using SDS-PAGE and 2D gel electrophoresis, in which Sodium dodecyl-sulfate (SDS) exhibited protein bands in the 10- to 55-kDa range, while 2D showed protein bands varying from 10 to 70 kDa. Every spot from 2D was digested by trypsin and identified by RPLC/MS. Protein fractionations (3- and 10-kDa permeates) were carried out employing RP-HPLC. Whey protein fermentate has anti-inflammatory action in RAW 264.7 macrophages that have been exposed to lipopolysaccharide. A molecular docking system was also used to investigate the interactions of peptides (AFLDSRTR, ILGAFIQIITFR) with human myeloperoxidase enzyme. CONCLUSIONS The antihypertensive and antioxidative peptides discovered from whey protein fermentate may be helpful in the design of pharmacologically active healthy ingredients in the upcoming years.
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Affiliation(s)
- Keval Chopada
- Department of Dairy Microbiology, SMC College of Dairy Science, Kamdhenu University, Gandhinagar, Gujarat, India
| | - Bethsheba Basaiawmoit
- Department of Rural Development and Agricultural Production, North-Eastern Hill University, Tura, Meghalaya, India
| | - Amar A Sakure
- Department of Agriculture Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Ruchika Maurya
- Regional Center for Biotechnology, Faridabad, Haryana, India
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, Knowledge City, Punjab, India
| | - Mahendra Bishnoi
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, Knowledge City, Punjab, India
| | - Kanthi Kiran Kondepudi
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, Knowledge City, Punjab, India
| | - Divyang Solanki
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - B P Singh
- Department of Microbiology, Central University of Haryana, Mahendragarh, Haryana, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Zhenbin Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - B K Mishra
- Department of Rural Development and Agricultural Production, North-Eastern Hill University, Tura, Meghalaya, India
| | - Subrota Hati
- Department of Dairy Microbiology, SMC College of Dairy Science, Kamdhenu University, Gandhinagar, Gujarat, India
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Shukla P, Sakure A, Maurya R, Bishnoi M, Kondepudi KK, Das S, Liu Z, Padhi S, Rai AK, Hati S. Antidiabetic, angiotensin‐converting enzyme inhibitory and anti‐inflammatory activities of fermented camel milk and characterisation of novel bioactive peptides from lactic‐fermented camel milk with molecular interaction study. INT J DAIRY TECHNOL 2022. [DOI: 10.1111/1471-0307.12910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pratik Shukla
- Dairy Microbiology Department, SMC College of Dairy Science Anand Agricultural University Anand 388110 Gujarat India
| | - Amar Sakure
- Department of Plant Biotechnology B.A College of Agriculture Anand 388110 Gujarat India
| | - Ruchika Maurya
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, Centre of Excellence in Functional Foods National Agri‐Food Biotechnology Institute (NABI) Knowledge City, Sector 81, SAS Nagar Mohali Punjab 140306 India
| | - Mahendra Bishnoi
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, Centre of Excellence in Functional Foods National Agri‐Food Biotechnology Institute (NABI) Knowledge City, Sector 81, SAS Nagar Mohali Punjab 140306 India
| | - Kanthi Kiran Kondepudi
- Healthy Gut Research Group, Food & Nutritional Biotechnology Division, Centre of Excellence in Functional Foods National Agri‐Food Biotechnology Institute (NABI) Knowledge City, Sector 81, SAS Nagar Mohali Punjab 140306 India
| | - Sujit Das
- Department of Rural Development and Agricultural Production North‐Eastern Hill University Tura Campus Chasingre 794002 Meghalaya India
| | - Zhenbin Liu
- School of Food and Biological Engineering Shaanxi University of Science and Technology 18 Xi'an 710021, China
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre Tadong 737102 Sikkim India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre Tadong 737102 Sikkim India
| | - Subrota Hati
- Dairy Microbiology Department, SMC College of Dairy Science Kamdhenu University Anand ‐388110 Gujarat India
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Cyclic peptides as an inhibitor of metastasis in breast cancer targeting MMP-1: Computational approach. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Proteomics Characterization of Food-Derived Bioactive Peptides with Anti-Allergic and Anti-Inflammatory Properties. Nutrients 2022; 14:nu14204400. [PMID: 36297084 PMCID: PMC9609859 DOI: 10.3390/nu14204400] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/30/2022] Open
Abstract
Bioactive peptides are found in foods and dietary supplements and are responsible for health benefits with applications in human and animal medicine. The health benefits include antihypertensive, antimicrobial, antithrombotic, immunomodulatory, opioid, antioxidant, anti-allergic and anti-inflammatory functions. Bioactive peptides can be obtained by microbial action, mainly by the gastrointestinal microbiota from proteins present in food, originating from either vegetable or animal matter or by the action of different gastrointestinal proteases. Proteomics can play an important role in the identification of bioactive peptides. High-resolution mass spectrometry is the principal technique used to detect and identify different types of analytes present in complex mixtures, even when available at low concentrations. Moreover, proteomics may provide the characterization of epitopes to develop new food allergy vaccines and the use of immunomodulating peptides to induce oral tolerance toward offending food allergens or even to prevent allergic sensitization. In addition, food-derived bioactive peptides have been investigated for their anti-inflammatory properties to provide safer alternatives to nonsteroidal anti-inflammatory drugs (NSAIDs). All these bioactive peptides can be a potential source of novel drugs and ingredients in food and pharmaceuticals. The following review is focused on food-derived bioactive peptides with antiallergic and anti-inflammatory properties and summarizes the new insights into the use of proteomics for their identification and quantification.
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36
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Shahraki PZ, Farrokh P. PL‐101‐WK
, a novel tryptophan‐ and lysine‐rich peptide with antimicrobial activity against
Staphylococcus aureus. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Parisa Farrokh
- School of Biology Damghan University Damghan Iran
- Institute of Biological Sciences Damghan University Damghan Iran
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Chourasia R, Chiring Phukon L, Minhajul Abedin M, Sahoo D, Kumar Rai A. Production and characterization of bioactive peptides in novel functional soybean chhurpi produced using Lactobacillus delbrueckii WS4. Food Chem 2022; 387:132889. [PMID: 35430540 DOI: 10.1016/j.foodchem.2022.132889] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 02/14/2022] [Accepted: 04/02/2022] [Indexed: 12/24/2022]
Abstract
A novel soy chhurpi product was developed by fermentation of soymilk using proteolytic Lactobacillus delbrueckii strains isolated from traditional chhurpi production of Sikkim Himalaya. Soymilk fermentation by L. delbrueckii WS4 was associated with the hydrolysis of globulin proteins, with observed antioxidant, and ACE-inhibitory activity which further increased upon simulated in vitro gastrointestinal digestion. Peptidomics analysis of soy chhurpi and its gastrointestinal digest resulted in the identification of bioactive peptides with ACE-inhibitory and antioxidant properties. In silico antihypertensive property prediction followed by molecular docking study demonstrated strong binding affinity of selected peptides with ACE. The glycinin-derived peptide, SVIKPPTDE escaped gastrointestinal digestion and demonstrated strong non-bond interactions with ACE catalytic residues. QSAR models predicted an ACE-inhibitory IC50 of 21.29 µM for SVIKPPTDE. This is the first report on the production of novel functional soy chhurpi cheese using defined starter strains and the identification of bioactive peptides in undigested and gastrointestinal digested soy chhurpi.
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Affiliation(s)
- Rounak Chourasia
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India; School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Md Minhajul Abedin
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Dinabandhu Sahoo
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India; Department of Botany, University of Delhi, Delhi, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India.
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Furman O, Zaporozhets A, Tobi D, Bazylevich A, Firer MA, Patsenker L, Gellerman G, Lubin BCR. Novel Cyclic Peptides for Targeting EGFR and EGRvIII Mutation for Drug Delivery. Pharmaceutics 2022; 14:pharmaceutics14071505. [PMID: 35890400 PMCID: PMC9318536 DOI: 10.3390/pharmaceutics14071505] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 02/05/2023] Open
Abstract
The epidermal growth factor–epidermal growth factor receptor (EGF-EGFR) pathway has become the main focus of selective chemotherapeutic intervention. As a result, two classes of EGFR inhibitors have been clinically approved, namely monoclonal antibodies and small molecule kinase inhibitors. Despite an initial good response rate to these drugs, most patients develop drug resistance. Therefore, new treatment approaches are needed. In this work, we aimed to find a new EGFR-specific, short cyclic peptide, which could be used for targeted drug delivery. Phage display peptide technology and biopanning were applied to three EGFR expressing cells, including cells expressing the EGFRvIII mutation. DNA from the internalized phage was extracted and the peptide inserts were sequenced using next-generation sequencing (NGS). Eleven peptides were selected for further investigation using binding, internalization, and competition assays, and the results were confirmed by confocal microscopy and peptide docking. Among these eleven peptides, seven showed specific and selective binding and internalization into EGFR positive (EGFR+ve) cells, with two of them—P6 and P9—also demonstrating high specificity for non-small cell lung cancer (NSCLC) and glioblastoma cells, respectively. These peptides were chemically conjugated to camptothecin (CPT). The conjugates were more cytotoxic to EGFR+ve cells than free CPT. Our results describe a novel cyclic peptide, which can be used for targeted drug delivery to cells overexpressing the EGFR and EGFRvIII mutation.
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Affiliation(s)
- Olga Furman
- Department of Chemical Engineering, Biotechnology and Materials, Ariel University, Ariel 40700, Israel; (O.F.); (M.A.F.)
- Agriculture and Oenology Department, Eastern Regional R&D Center, Ariel 40700, Israel
| | - Alisa Zaporozhets
- Department of Chemical Sciences, Ariel University, Ariel 40700, Israel; (A.Z.); (A.B.); (L.P.); (G.G.)
| | - Dror Tobi
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel;
- Department of Molecular Biology, Ariel University, Ariel 40700, Israel
| | - Andrii Bazylevich
- Department of Chemical Sciences, Ariel University, Ariel 40700, Israel; (A.Z.); (A.B.); (L.P.); (G.G.)
| | - Michael A. Firer
- Department of Chemical Engineering, Biotechnology and Materials, Ariel University, Ariel 40700, Israel; (O.F.); (M.A.F.)
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel;
- Ariel Center for Applied Cancer Research, Ariel 40700, Israel
| | - Leonid Patsenker
- Department of Chemical Sciences, Ariel University, Ariel 40700, Israel; (A.Z.); (A.B.); (L.P.); (G.G.)
| | - Gary Gellerman
- Department of Chemical Sciences, Ariel University, Ariel 40700, Israel; (A.Z.); (A.B.); (L.P.); (G.G.)
- Ariel Center for Applied Cancer Research, Ariel 40700, Israel
| | - Bat Chen R. Lubin
- Department of Chemical Engineering, Biotechnology and Materials, Ariel University, Ariel 40700, Israel; (O.F.); (M.A.F.)
- Agriculture and Oenology Department, Eastern Regional R&D Center, Ariel 40700, Israel
- Correspondence: ; Tel.: +972-50-6554655
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Albutti A. Proteome-Wide and Protein-Specific Multi-Epitope Vaccine Constructs Against the Rift Valley Fever Virus Outbreak Using Integrated Omics Approaches. Front Microbiol 2022; 13:921683. [PMID: 35711778 PMCID: PMC9195176 DOI: 10.3389/fmicb.2022.921683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Rift Valley fever (RVF) is a viral disease caused by a member of the Bunyavirales family causing severe infections in humans. The RVF virus is an enveloped, negative-sense, single-stranded RNA virus that can infect both animals and humans. The symptoms associated with these infections span from minor (fever and headaches) to severe (meningoencephalitis and hemorrhagic fever syndrome) symptoms. Despite the outbreaks of the RVF virus being reported in different parts of the world, no effective therapy is available. Herein, the development of an efficient vaccine is critical for the control of infections associated with the RVF virus. Moreover, computational vaccine approaches are helpful in the design of specific, safe, and stable peptide-based designs when compared to the conventional methods of vaccine development. In this study, the whole proteome of the virus, comprising four proteins (NP, L, GP, and NSP), was screened to find putative vaccine epitope sequences (T cell, B cell, and HTL) specific for each protein. These shortlisted epitopes were then combined with flexible linkers to design protein-specific and proteome-wide immunogenic multi-epitope-based vaccine constructs. The results revealed that these multi-epitope vaccine constructs (MEVCs) are strongly antigenic and non-allergenic in nature. The efficacy of these constructs was further validated by docking with immune receptors, which revealed strong binding interactions with human TLR8. Using the MD simulation approach, the binding stability and residual flexibility of the best vaccine construct (proteome-wide) were confirmed, which revealed stable dynamic and favorable features. Furthermore, in-silico cloning and immune simulation analysis confirmed the expression and production of immune factors, that is, IgM, IgG, and IL-6, against the proposed vaccine designs. Additionally, 3D models of all the MEVC constructs have been developed and evaluated for potential immunization against the RVF virus. Finally, the proteome-wide vaccine candidate (MEVC-PW-RVFV) with the highest immune reinforcement potential provides new insights into the development of future vaccines against the emerging RVF virus.
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Affiliation(s)
- Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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40
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Ashokbhai JK, Basaiawmoit B, Das S, Sakure A, Maurya R, Bishnoi M, Kondepudi KK, Padhi S, Rai AK, Liu Z, Hatia S. Antioxidative, antimicrobial and anti-inflammatory activities and release of ultra-filtered antioxidative and antimicrobial peptides during fermentation of sheep milk: In-vitro, in-silico and molecular interaction studies. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Repositioning of experimentally validated anti-breast cancer peptides to target FAK-PAX complex to halt the breast cancer progression: a biomolecular simulation approach. Mol Divers 2022; 27:603-618. [PMID: 35635599 DOI: 10.1007/s11030-022-10438-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 04/07/2022] [Indexed: 12/11/2022]
Abstract
FAK (focal adhesin kinase), a tyrosine kinase, plays an imperative role in cell-cell communication, particularly in cell signaling systems. It is a multi-functional signaling protein, which integrates and transduces signals into cancer cells through growth factor receptors or integrin and its interaction with Paxillin (PAX). The molecular processes by which FAK promotes the development and progression of cancer have progressively established the possible relationship between FAK-PAX complex in many types of cancer. The interaction of FAX and PAX is very important in breast cancer and thus acts as an essential biomarker for drugs, vaccines or peptide inhibitor designing. In this regard, computational approaches, particularly peptide designing to target the binding interface of the interacting partners, would greatly assist the design of peptide inhibitors against various cancer. Accordingly, in this present study, we screened 236 experimentally validated anti-breast cancer peptides using computational drugs repositioning approach to design peptides targeting the FAK-PAX complex. Using protein-peptide docking the binding site for the HP1 was confirmed and a total of 236 anti-breast cancer peptides were screened. Among the 236, only 12 peptides reported a docking score better than the control. From these 12, Magainin with the docking score - 103.8 ± 10.3 kcal/mol, NRC-07 with the docking score - 100.8 ± 16.5 kcal/mol, and Indolicidin with the docking score - 101.7 ± 3.9 kcal/mol, peptides potentially inhibit the FAX-PAX binding. Calculation of protein's motion and FEL revealed the binding and inhibitory behavior. Moreover, binding free energy (MM/GBSA) confirmed that Magainin exhibited the total binding energy - 53.28 kcal/mol, NRC-07 possessed the TBE - 44.16 kcal/mol, and Indolicidin reported the TBE of - 40.48 kcal/mol, thus explaining the inhibitory potential of these peptides. In conclusion, these peptides exhibit strong inhibitory potential and could abrogate the FAK-PAX complex in in vitro models and thus may relieve the burden of breast cancer.
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Toldrá F, Mora L. Peptidomics as a useful tool in the follow-up of food bioactive peptides. ADVANCES IN FOOD AND NUTRITION RESEARCH 2022; 100:1-47. [PMID: 35659349 DOI: 10.1016/bs.afnr.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
There is an intense research activity on bioactive peptides derived from food proteins in view of their health benefits for consumers. However, their identification is quite challenging as a consequence of their small size and low abundance in complex matrices such as foods or hydrolyzates. Recent advances in peptidomics and bioinformatics are getting improved sensitivity and accuracy and therefore such tools are contributing to the development of sophisticated methodologies for the identification and quantification of peptides. These developments are very useful for the follow-up of peptides released through proteolysis either in the food itself through the action of endogenous peptidases during processing stages like fermentation, drying or ripening, or from food proteins hydrolyzed by commercial peptidases or microorganisms with proteolytic activity. This chapter is presenting the latest advances in peptidomics and its use for the identification and quantification of peptides, and as a useful tool for controlling the proteolysis phenomena in foods and protein hydrolyzates.
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Affiliation(s)
- Fidel Toldrá
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Paterna, Spain.
| | - Leticia Mora
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Paterna, Spain
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Knight A, Piskacek M. Cryptic inhibitory regions nearby activation domains. Biochimie 2022; 200:19-26. [PMID: 35561946 DOI: 10.1016/j.biochi.2022.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 11/27/2022]
Abstract
Previously, the Nine amino acid TransActivation Domain (9aaTAD) was identified in the Gal4 region 862-870 (DDVYNYLFD). Here, we identified 9aaTADs in the distal Gal4 orthologs by our prediction algorithm and found their conservation in the family. The 9aaTAD function as strong activators was demonstrated. We identified adjacent Gal4 region 871-811 (DEDTPPNPKKE) as a natural 9aaTAD inhibitory domain located at the extreme Gal4 terminus. Moreover, we identified conserved Gal4 region 172-185 (FDWSEEDDMSDGLP), which was capable to reverse the 9aaTAD inhibition. In conclusion, our results uncover the existence of the cryptic inhibitory domains, which need to be carefully implemented in all functional studies with transcription factors to avoid incorrect conclusions.
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Affiliation(s)
- Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic.
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Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond. J Cheminform 2022; 14:26. [PMID: 35505401 PMCID: PMC9066754 DOI: 10.1186/s13321-022-00605-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/03/2022] [Indexed: 02/07/2023] Open
Abstract
Cyclic peptides formed by disulfide bonds have been one large group of common drug candidates in drug development. Structural information of a peptide is essential to understand its interaction with its target. However, due to the high flexibility of peptides, it is difficult to sample the near-native conformations of a peptide. Here, we have developed an extended version of our MODPEP approach, named MODPEP2.0, to fast generate the conformations of cyclic peptides formed by a disulfide bond. MODPEP2.0 builds the three-dimensional (3D) structures of a cyclic peptide from scratch by assembling amino acids one by one onto the cyclic fragment based on the constructed rotamer and cyclic backbone libraries. Being tested on a data set of 193 diverse cyclic peptides, MODPEP2.0 obtained a considerable advantage in both accuracy and computational efficiency, compared with other sampling algorithms including PEP-FOLD, ETKDG, and modified ETKDG (mETKDG). MODPEP2.0 achieved a high sampling accuracy with an average C\documentclass[12pt]{minimal}
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\begin{document}$$\alpha$$\end{document}α RMSD of 2.20 Å and 1.66 Å when 10 and 100 conformations were considered, respectively, compared with 3.41 Å and 2.62 Å for PEP-FOLD, 3.44 Å and 3.16 Å for ETKDG, 3.09 Å and 2.72 Å for mETKDG. MODPEP2.0 also reproduced experimental peptide structures for 81.35% of the test cases when an ensemble of 100 conformations were considered, compared with 54.95%, 37.50% and 50.00% for PEP-FOLD, ETKDG, and mETKDG. MODPEP2.0 is computationally efficient and can generate 100 peptide conformations in one second. MODPEP2.0 will be useful in sampling cyclic peptide structures and modeling related protein-peptide interactions, facilitating the development of cyclic peptide drugs.
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Padhi S, Chourasia R, Kumari M, Singh SP, Rai AK. Production and characterization of bioactive peptides from rice beans using Bacillus subtilis. BIORESOURCE TECHNOLOGY 2022; 351:126932. [PMID: 35248709 DOI: 10.1016/j.biortech.2022.126932] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
A bioprocess was developed for production of bioactive peptides on microbial fermentation of rice beans using proteolytic Bacillus subtilis strains. The peptides produced were identified by LC-MS/MS analysis, revealing the presence of many unique peptide sequences to individual hydrolysates. On functional properties prediction, antihypertensive peptides (3.90%) were found to be higher in comparison to other bioactive peptides. Among different strains, B. subtilis KN2B fermented hydrolysate exhibited highest angiotensin converting enzyme (ACE)-inhibitory activity (45.73%). Furthermore, 19 selected peptides, including the common and unique peptides were examined for their affinity towards the binding cavity of ACE using molecular docking. The results showed a common peptide PFPIPFPIPIPLP, and another IPFPPIPFLPPI unique to B. subtilis KN2B fermented hydrolysate exhibited promising binding at the ACE binding site with substantial free binding energy. The process developed can be used for the production of bioactive peptides from rice bean for application in nutraceutical industries.
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Affiliation(s)
- Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | - Rounak Chourasia
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | - Megha Kumari
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | - Sudhir P Singh
- Centre of Innovative and Applied Bioprocessing, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India; Institute of Bioresources and Sustainable Development, Mizoram Node, Aizawl, India.
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46
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Krebs SK, Rakotoarinoro N, Stech M, Zemella A, Kubick S. A CHO-Based Cell-Free Dual Fluorescence Reporter System for the Straightforward Assessment of Amber Suppression and scFv Functionality. Front Bioeng Biotechnol 2022; 10:873906. [PMID: 35573244 PMCID: PMC9098822 DOI: 10.3389/fbioe.2022.873906] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022] Open
Abstract
Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein’s coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyrCUA were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs).
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Affiliation(s)
- Simon K. Krebs
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute for Biotechnology, Technical University of Berlin, Berlin, Germany
| | - Nathanaël Rakotoarinoro
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
- *Correspondence: Stefan Kubick,
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Gupta S, Kumar A. Design of an Epitope-Based Peptide Vaccine Against Dengue Virus Isolate from Eastern Uttar Pradesh, India. Int J Pept Res Ther 2022; 28:91. [PMID: 35463186 PMCID: PMC9014403 DOI: 10.1007/s10989-022-10402-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Siddharth Gupta
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, G.T. Road, Kanpur, 209217 India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, G.T. Road, Kanpur, 209217 India
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48
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Abedin MM, Chourasia R, Chiring Phukon L, Singh SP, Kumar Rai A. Characterization of ACE inhibitory and antioxidant peptides in yak and cow milk hard chhurpi cheese of the Sikkim Himalayan region. Food Chem X 2022; 13:100231. [PMID: 35499015 PMCID: PMC9039942 DOI: 10.1016/j.fochx.2022.100231] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 01/08/2022] [Accepted: 01/24/2022] [Indexed: 01/15/2023] Open
Abstract
Yak and cow hard chhurpi cheese of Sikkim Himalaya. ACE-inhibitory activities of undigested and GI digested yak and cow hard chhurpi. Bioactive peptides identified by LC-MS/MS peptidomics of yak and cow hard chhurpi. In silico prediction and molecular docking of potential ACE-inhibitory peptides.
In this study, simulated in vitro GI digestion of the Himalayan hard chhurpi cheese resulted in the increase of hydrolyzed protein content, antioxidant and ACE-inhibitory activities. LC-MS/MS-based peptidomics revealed a total of 1473 peptides in the samples originating from different milk proteins, including α-S1-casein, α-S2-casein, β-casein, κ-casein, α-lactalbumin, and β-lactoglobulin, out of which 60 peptides have been reported for different functional properties. A total of 101 peptides were predicted to be antihypertensive using the bioactivity prediction web servers, AHTpin and mAHTPred. In silico molecular docking studies predicted 20 antihypertensive peptides, exhibiting non-bond interactions between hard chhurpi peptides and ACE catalytic residues. A peptide, SLVYPFPGPI, identified in GI digested cow hard chhurpi and undigested, and GI digested samples of yak hard chhurpi, showed a stronger binding affinity towards ACE. Identifying antioxidant and ACE inhibitory peptides in hard cheese products adds value to them as functional foods of the Himalayan region.
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Affiliation(s)
- Md Minhajul Abedin
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Rounak Chourasia
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, SAS Nagar, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Tadong, Sikkim, India.,Institute of Bioresources and Sustainable Development, Mizoram Node, Aizawl, Mizoram, India
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49
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Binette V, Mousseau N, Tuffery P. A Generalized Attraction-Repulsion Potential and Revisited Fragment Library Improves PEP-FOLD Peptide Structure Prediction. J Chem Theory Comput 2022; 18:2720-2736. [PMID: 35298162 DOI: 10.1021/acs.jctc.1c01293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fast and accurate structure prediction is essential to the study of peptide function, molecular targets, and interactions and has been the subject of considerable efforts in the past decade. In this work, we present improvements to the popular simplified PEP-FOLD technique for small peptide structure prediction. PEP-FOLD originality is threefold: (i) it uses a predetermined structural alphabet, (ii) it uses a sequential algorithm to reconstruct the tridimensional structures of these peptides in a discrete space using a fragment library, and (iii) it assesses the energy of these structures using a coarse-grained representation in which all of the backbone atoms but the α-hydrogen are present, and the side chain corresponds to a unique bead. In former versions of PEP-FOLD, a van der Waals formulation was used for non-bonded interactions, with each side chain being associated with a fixed radius. Here, we explore the relevance of using instead a generalized formulation in which not only the optimal distance of interaction and the energy at this distance are parameters but also the distance at which the potential is zero. This allows each side chain to be associated with a different radius and potential energy shape, depending on its interaction partner, and in principle to make more effective the coarse-grained representation. In addition, the new PEP-FOLD version is associated with an updated library of fragments. We show that these modifications lead to important improvements for many of the problematic targets identified with the former PEP-FOLD version while maintaining already correct predictions. The improvement is in terms of both model ranking and model accuracy. We also compare the PEP-FOLD enhanced version to state-of-the-art techniques for both peptide and structure predictions: APPTest, RaptorX, and AlphaFold2. We find that the new predictions are superior, in particular with respect to the prediction of small β-targets, to those of APPTest and RaptorX and bring, with its original approach, additional understanding on folded structures, even when less precise than AlphaFold2. With their strong physical influence, the revised structural library and coarse-grained potential offer, however, the means for a deeper understanding of the nature of folding and open a solid basis for studying flexibility and other dynamical properties not accessible to IA structure prediction approaches.
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Affiliation(s)
- Vincent Binette
- Départment de Physique, Université de Montréal, Case postale 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Normand Mousseau
- Départment de Physique, Université de Montréal, Case postale 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Pierre Tuffery
- Université de Paris, INSERM U1133, CNRS UMR 8251, F-75205 Paris, France
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50
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Nguyen L, Nguyen Vo TH, Trinh QH, Nguyen BH, Nguyen-Hoang PU, Le L, Nguyen BP. iANP-EC: Identifying Anticancer Natural Products Using Ensemble Learning Incorporated with Evolutionary Computation. J Chem Inf Model 2022; 62:5080-5089. [PMID: 35157472 DOI: 10.1021/acs.jcim.1c00920] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer is one of the most deadly diseases that annually kills millions of people worldwide. The investigation on anticancer medicines has never ceased to seek better and more adaptive agents with fewer side effects. Besides chemically synthetic anticancer compounds, natural products are scientifically proved as a highly potential alternative source for anticancer drug discovery. Along with experimental approaches being used to find anticancer drug candidates, computational approaches have been developed to virtually screen for potential anticancer compounds. In this study, we construct an ensemble computational framework, called iANP-EC, using machine learning approaches incorporated with evolutionary computation. Four learning algorithms (k-NN, SVM, RF, and XGB) and four molecular representation schemes are used to build a set of classifiers, among which the top-four best-performing classifiers are selected to form an ensemble classifier. Particle swarm optimization (PSO) is used to optimise the weights used to combined the four top classifiers. The models are developed by a set of curated 997 compounds which are collected from the NPACT and CancerHSP databases. The results show that iANP-EC is a stable, robust, and effective framework that achieves an AUC-ROC value of 0.9193 and an AUC-PR value of 0.8366. The comparative analysis of molecular substructures between natural anticarcinogens and nonanticarcinogens partially unveils several key substructures that drive anticancerous activities. We also deploy the proposed ensemble model as an online web server with a user-friendly interface to support the research community in identifying natural products with anticancer activities.
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Affiliation(s)
- Loc Nguyen
- Computational Biology Center, International University - VNU HCMC, Ho Chi Minh City 700000, Vietnam
| | - Thanh-Hoang Nguyen Vo
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Quang H Trinh
- Computational Biology Center, International University - VNU HCMC, Ho Chi Minh City 700000, Vietnam.,School of Information and Communication Technology, Hanoi University of Science and Technology, Hanoi 100000, Vietnam
| | - Bach Hoai Nguyen
- School of Engineering and Computer Science, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Phuong-Uyen Nguyen-Hoang
- Computational Biology Center, International University - VNU HCMC, Ho Chi Minh City 700000, Vietnam
| | - Ly Le
- Computational Biology Center, International University - VNU HCMC, Ho Chi Minh City 700000, Vietnam.,Vingroup Big Data Institute, Ha Noi 100000, Vietnam
| | - Binh P Nguyen
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington 6140, New Zealand
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