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Bizzotto E, Zampieri G, Treu L, Filannino P, Di Cagno R, Campanaro S. Classification of bioactive peptides: A systematic benchmark of models and encodings. Comput Struct Biotechnol J 2024; 23:2442-2452. [PMID: 38867723 PMCID: PMC11168199 DOI: 10.1016/j.csbj.2024.05.040] [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: 03/19/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
Bioactive peptides are short amino acid chains possessing biological activity and exerting physiological effects relevant to human health. Despite their therapeutic value, their identification remains a major problem, as it mainly relies on time-consuming in vitro tests. While bioinformatic tools for the identification of bioactive peptides are available, they are focused on specific functional classes and have not been systematically tested on realistic settings. To tackle this problem, bioactive peptide sequences and functions were here gathered from a variety of databases to generate a unified collection of bioactive peptides from microbial fermentation. This collection was organized into nine functional classes including some previously studied and some unexplored such as immunomodulatory, opioid and cardiovascular peptides. Upon assessing their sequence properties, four alternative encoding methods were tested in combination with a multitude of machine learning algorithms, from basic classifiers like logistic regression to advanced algorithms like BERT. Tests on a total of 171 models showed that, while some functions are intrinsically easier to detect, no single combination of classifiers and encoders worked universally well for all classes. For this reason, we unified all the best individual models for each class and generated CICERON (Classification of bIoaCtive pEptides fRom micrObial fermeNtation), a classification tool for the functional classification of peptides. State-of-the-art classifiers were found to underperform on our realistic benchmark dataset compared to the models included in CICERON. Altogether, our work provides a tool for real-world peptide classification and can serve as a benchmark for future model development.
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Affiliation(s)
- Edoardo Bizzotto
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35131, Italy
| | - Guido Zampieri
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35131, Italy
| | - Laura Treu
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35131, Italy
| | - Pasquale Filannino
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via G. Amendola 165/a, Bari 70126, Italy
| | - Raffaella Di Cagno
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Piazza Universita, 5, Bolzano 39100, Italy
| | - Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35131, Italy
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Stany B, Mishra S, Tharani PV, Sarkar A, Mandal AKA, Rao KVB. Investigation of anticancer potential of a novel bioactive molecule from Trichosporon asahii VITSTB1 in breast cancer cell lines: an in vitro study. Med Oncol 2024; 42:19. [PMID: 39609299 DOI: 10.1007/s12032-024-02569-1] [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: 10/07/2024] [Accepted: 11/12/2024] [Indexed: 11/30/2024]
Abstract
The current study investigates the anticancer activity of protein derived from yeast against breast cancer. Yeast-derived proteins illustrate potential as an anticancer agent through mechanisms, such as immune system stimulation via beta-glucans, cytotoxic effects, and modulation of gut microbiota by probiotic strains. The antioxidant activity of yeast-derived proteins can aid in anticancer activity by neutralizing free radicals, thereby reducing oxidative stress and preventing damage to cellular DNA. Employing a comprehensive methodology encompassing yeast isolation, antioxidant screening, molecular characterization, bioactive protein purification, and MTT assay, the research provides crucial insights into the anticancer attributes of the protein extracted from the yeast. The findings reveal significant antioxidant activity that reduces reactive oxygen species (ROS) levels, which are implicated in cancer development. The MTT assay on MCF-7 breast cancer cell lines, characterized by estrogen receptor and progesterone receptor positivity and HER-2 negativity, determined an IC50 value of 54.89 µg/ml, indicating a dose-dependent decrease in cytotoxic effects. These results suggest that the protein derived from Trichosporon asahii VITSTB1 exhibits promising anti-breast cancer properties. Further research is necessary to elucidate the underlying mechanisms, assess efficacy and safety profiles, explore synergies with existing therapies, and conduct animal model studies. Advancing this line of inquiry will significantly contribute to biomedical research and industrial innovation.
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Affiliation(s)
- B Stany
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Shatakshi Mishra
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - P V Tharani
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Anwesha Sarkar
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Abul Kalam Azad Mandal
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - K V Bhaskara Rao
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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Sánchez-Elvira A, Hernández-Corroto E, García MC, Castro-Puyana M, Marina ML. Sustainable extraction of proteins from lime peels using ultrasound, deep eutectic solvents, and pressurized liquids, as a source of bioactive peptides. Food Chem 2024; 458:140139. [PMID: 38943952 DOI: 10.1016/j.foodchem.2024.140139] [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: 02/29/2024] [Revised: 05/19/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
The aim of this work was to develop, for the first time, sustainable strategies, based on the use of Ultrasound-Assisted Extraction, Natural Deep Eutectic Solvents, and Pressurized Liquid Extraction, to extract proteins from lime (Citrus x latifolia) peels and to evaluate their potential to release bioactive peptides. PLE showed the largest extraction of proteins (66-69%), which were hydrolysed using three different enzymes (Alcalase 2.4 L FG, Alcalase®PURE 2.4 L, and Thermolysin). The in vitro antioxidant and antihypertensive activities of released peptides were evaluated. Although all hydrolysates showed antioxidant and antihypertensive activity, the hydrolysate obtained with Thermolysin showed the most significant values. Since the Total Phenolic Content in all hydrolysates was low, peptides were likely the main contributors to these bioactivities. Hydrolysates were analyzed by UHPLC-QTOF-MS and a total of 98 different peptides were identified. Most of these peptides were rich in amino acids associated with antioxidant activity.
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Affiliation(s)
- A Sánchez-Elvira
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain
| | - E Hernández-Corroto
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain
| | - M C García
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain; Universidad de Alcalá, Instituto de Investigación Química "Andrés M. del Río" (IQAR), Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain
| | - M Castro-Puyana
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain; Universidad de Alcalá, Instituto de Investigación Química "Andrés M. del Río" (IQAR), Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain
| | - M L Marina
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain; Universidad de Alcalá, Instituto de Investigación Química "Andrés M. del Río" (IQAR), Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain.
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Hou J, Wei W, Geng Z, Zhang Z, Yang H, Zhang X, Li L, Gao Q. Developing Plant Exosomes as an Advanced Delivery System for Cosmetic Peptide. ACS APPLIED BIO MATERIALS 2024; 7:3050-3060. [PMID: 38598772 DOI: 10.1021/acsabm.4c00096] [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] [Indexed: 04/12/2024]
Abstract
Peptides are a promising skincare ingredient, but due to their inherent instability and the barrier function of the skin's surface, they often have limited skin absorption and penetration, which can significantly hinder their skincare benefits. To address this, a novel technique called NanoGlow has been introduced for encapsulating peptide-based cosmetic raw materials into engineered nanosized plant-derived exosomes (pExo) to achieve the goal of a healthier and more radiant skin state. In this approach, pExo served as carriers for cosmetic peptides across the intact skin barrier, enhancing their biological effectiveness in skin beauty. The NanoGlow strategy combines chemical activation and physical proencapsulation, boasting a high success rate and straightforward and stable operation, making it suitable for large-scale production. Comprehensive analysis using in vitro cellular absorption and skin penetration models has demonstrated that the nanosized pExo carriers significantly improve peptide penetration into the skin compared to free peptides. Furthermore, in vivo tissue slice studies have shown that pExo carriers efficiently deliver acetyl hexapeptide-8 to the skin's dermis, surpassing the performance of free peptides. Cosmetic skincare effect analysis has also indicated that pExo-loaded cosmetic peptides deliver superior results. Therefore, the NanoGlow technique harnesses the natural size and properties of pExo to maximize the bioavailability of cosmetic peptides, holding great promise for developing advanced peptide delivery systems in both the cosmetic and medical drug industries.
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Affiliation(s)
- Jiali Hou
- Beijing Youngen Biotechnology Co. Ltd., Beijing 102600, China
| | - Wei Wei
- Beijing Youngen Biotechnology Co. Ltd., Beijing 102600, China
| | - Zaijun Geng
- Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Zhenxing Zhang
- Beijing Youngen Biotechnology Co. Ltd., Beijing 102600, China
| | - Hui Yang
- Beijing Youngen Biotechnology Co. Ltd., Beijing 102600, China
| | - Xuhui Zhang
- Beijing Youngen Biotechnology Co. Ltd., Beijing 102600, China
| | - Li Li
- Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Qi Gao
- Beijing Youngen Biotechnology Co. Ltd., Beijing 102600, China
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Chattaraj S, Mitra D, Ganguly A, Thatoi H, Das Mohapatra PK. A critical review on the biotechnological potential of Brewers' waste: Challenges and future alternatives. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100228. [PMID: 38450031 PMCID: PMC10915524 DOI: 10.1016/j.crmicr.2024.100228] [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] [Indexed: 03/08/2024] Open
Abstract
In order to comply with the stringent discharge guidelines issued by governmental organizations to protect the ecosystem, the substantial amounts of effluent and sturdy wastes produced by the beer brewing process need to be discarded or handled in the most affordable and secure manner. Huge quantities of waste material released with each brew bestow a significant opportunity for the brewing sector to move towards sustainability. The concept of circular economy and the development of technological advancements in brewery waste processing have spurred interest to valorize brewery waste for implementation in various sectors of medical and food science, industrial science, and many more intriguing fields. Biotechnological methods for valorizing brewery wastes are showing a path towards green chemistry and are feasible and advantageous to environment. The study unfolds most recent prospectus for brewery waste usage and discusses major challenges with brewery waste treatment and valorization and offers suggestions for further work.
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Affiliation(s)
- Sourav Chattaraj
- Department of Microbiology, Raiganj University, Uttar Dinajpur, Raiganj, West Bengal PIN - 733134, India
- Centre for Industrial Biotechnology Research, School of Pharmaceutical Science, Siksha ‘O’ Anusandhan University, Kalinga Nagar, Bhubaneswar, Odisha 751 003, India
| | - Debasis Mitra
- Department of Microbiology, Raiganj University, Uttar Dinajpur, Raiganj, West Bengal PIN - 733134, India
- Department of Microbiology, Graphic Era (Deemed to be University), 566/6, Bell Road, Clement Town, Dehradun, 248002 Uttarakhand, India
| | - Arindam Ganguly
- Department of Microbiology, Bankura Sammilani College, Bankura, West Bengal PIN - 722102, India
| | - Hrudayanath Thatoi
- Centre for Industrial Biotechnology Research, School of Pharmaceutical Science, Siksha ‘O’ Anusandhan University, Kalinga Nagar, Bhubaneswar, Odisha 751 003, India
| | - Pradeep K. Das Mohapatra
- Department of Microbiology, Raiganj University, Uttar Dinajpur, Raiganj, West Bengal PIN - 733134, India
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