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Lee B, Shin D. Contrastive learning for enhancing feature extraction in anticancer peptides. Brief Bioinform 2024; 25:bbae220. [PMID: 38725157 PMCID: PMC11082072 DOI: 10.1093/bib/bbae220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/28/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
Cancer, recognized as a primary cause of death worldwide, has profound health implications and incurs a substantial social burden. Numerous efforts have been made to develop cancer treatments, among which anticancer peptides (ACPs) are garnering recognition for their potential applications. While ACP screening is time-consuming and costly, in silico prediction tools provide a way to overcome these challenges. Herein, we present a deep learning model designed to screen ACPs using peptide sequences only. A contrastive learning technique was applied to enhance model performance, yielding better results than a model trained solely on binary classification loss. Furthermore, two independent encoders were employed as a replacement for data augmentation, a technique commonly used in contrastive learning. Our model achieved superior performance on five of six benchmark datasets against previous state-of-the-art models. As prediction tools advance, the potential in peptide-based cancer therapeutics increases, promising a brighter future for oncology research and patient care.
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Affiliation(s)
- Byungjo Lee
- Research Institute, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang, 10408, Republic of Korea
| | - Dongkwan Shin
- Research Institute, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang, 10408, Republic of Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, 323, Ilsan-ro, Ilsandong-gu, Goyang, 10408, Republic of Korea
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Origone AL, Hissi EGV, Liggieri CS, Camí GE, Illanes A, Barberis SE. Effect of Organic Solvents on the Activity, Stability and Secondary Structure of asclepain cI, Using FTIR and Molecular Dynamics Simulations. Protein J 2024:10.1007/s10930-024-10182-4. [PMID: 38453735 DOI: 10.1007/s10930-024-10182-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2024] [Indexed: 03/09/2024]
Abstract
The present study aims at understanding the effect of organic solvents on the specific proteolytic activity and operational stability of asclepain cI in aqueous-organic media, using correlations between geometrical and structural parameters of asclepain cI. These correlations were determined by molecular dynamics (MD) simulations and the secondary structure of the enzyme validated by Fourier-transform Infrared (FTIR) spectroscopy. Asclepain cI exhibited significantly higher catalytic potential in 29 of the 42 aqueous-organic media tested, composed by 0.1 mM TRIS hydrochloride buffer pH 8 (TCB) and an organic solvent, than in buffer alone. Asclepain cI in water-organic miscible systems showed high FTIR spectral similarity with that obtained in TCB, while in immiscible systems the enzyme acquired different secondary structures than in buffer. Among the conditions studied, asclepain cI showed the highest catalytic potential in 50% v/v ethyl acetate in TCB. According to MD simulations, that medium elicited solvation and flexibility changes around the active center of asclepain cI and conducted to a new secondary structure with the active center preserved. These results provide valuable insights into the elucidation of the molecular mechanism of asclepain cI tolerance to organic solvents and pave the way for its future application for the synthesis of peptides in aqueous-organic media.
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Affiliation(s)
- Anabella L Origone
- Laboratory of Bromatology, Faculty of Chemistry, Biochemistry and Pharmacy (FQByF), National University of San Luis, Chacabuco N° 917, San Luis, Argentina
- Institute of Applied Physics (INFAP) - Technological Scientific Center of San Luis - National Council of Scientific and Technique Research (CONICET), Ejército de los Andes N° 950, Block II, 2nd Floor, 5700, San Luis, Argentina
| | - Esteban G Vega Hissi
- Physical-Chemistry Area, FQByF, National University of San Luis, Ejército de los Andes 950, 5700, San Luis, Argentina.
- Multidisciplinary Institute of Biological Research (IMIBIO) - CONICET, Ejército de los Andes N° 950, 5700, San Luis, Argentina.
| | - Constanza S Liggieri
- Plant Protein Research Center (CIProVe), National University of La Plata, Calle 47 y 115, La Plata, Argentina
| | - Gerardo E Camí
- Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Suipacha N° 531, Rosario, Santa Fe, Argentina
- Faculty of Engineering and Chemistry, Av. Pellegrini N° 3314, Rosario, Santa Fe, Argentina
| | - Andrés Illanes
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Avenida Brasil N° 2085, Valparaiso, Chile
| | - Sonia E Barberis
- Laboratory of Bromatology, Faculty of Chemistry, Biochemistry and Pharmacy (FQByF), National University of San Luis, Chacabuco N° 917, San Luis, Argentina.
- Institute of Applied Physics (INFAP) - Technological Scientific Center of San Luis - National Council of Scientific and Technique Research (CONICET), Ejército de los Andes N° 950, Block II, 2nd Floor, 5700, San Luis, Argentina.
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Hiago Bellaver E, Eliza Redin E, Militão da Costa I, Schittler Moroni L, Pinto Kempka A. Food peptidomic analysis of bovine milk fermented by Lacticaseibacillus casei LBC 237: In silico prediction of bioactive peptides and anticancer potential. Food Res Int 2024; 180:114060. [PMID: 38395580 DOI: 10.1016/j.foodres.2024.114060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Bioactive peptides, which exhibited diverse biological activities such as anti-cancer, anti-inflammatory, bactericidal, antiviral, and quorum sensing properties, were considered promising alternative therapeutic agents. Sourced from various raw materials, particularly foods, these peptides garnered significant interest. In this context, the study focused on exploring bioactive peptides derived from bovine whole milk fermentation by Lacticaseibacillus casei LBC 237. Comprehensive peptidomic analysis and in silico predictions, with a specific emphasis on anti-cancer properties, were conducted. The study categorized peptides into BP-LBC, originating from the metabolism of L. casei LBC 237 and not matching any sequence in the Bos taurus database, and BP-MILK, matching a sequence in the Bos taurus database. Among the 143 identified peptides with potential biological activity, 33.56% were attributed to BP-LBC, while 66.43% originated from BP-MILK, demonstrating the important contribution of proteins in bovine milk in the generation of bioactive peptides. Hydrophobic peptides, enriched in Leucine, Lysine, and Proline, dominated both fractions, significantly influencing their functional properties. Pearson correlation analysis revealed inverse relationships between bioactive peptides, molecular weight, and anti-tumor activity in BP-MILK. The DGKVWEESLK peptide exhibited in silico activity against 10 different cancer cell lines. Studying the bioactive properties of peptides from familiar sources enhances the connection between food science and human health. In addition, in silico studies have been crucial in deepening our understanding of the bioactive potential of these peptides and their mode of action.
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Affiliation(s)
- Emyr Hiago Bellaver
- Santa Catarina State University. Department of Animal Production and Food Science, Multicentric Graduate Program in Biochemistry and Molecular Biology. Lages, SC, Brazil
| | - Eduarda Eliza Redin
- Santa Catarina State University. Department of Food Engineering and Chemical Engineering, Pinhalzinho, SC, Brazil.
| | - Ingrid Militão da Costa
- Santa Catarina State University. Department of Food Engineering and Chemical Engineering, Pinhalzinho, SC, Brazil.
| | - Liziane Schittler Moroni
- Santa Catarina State University. Department of Food Engineering and Chemical Engineering, Pinhalzinho, SC, Brazil.
| | - Aniela Pinto Kempka
- Santa Catarina State University. Department of Animal Production and Food Science, Multicentric Graduate Program in Biochemistry and Molecular Biology. Lages, SC, Brazil; Santa Catarina State University. Department of Food Engineering and Chemical Engineering, Pinhalzinho, SC, Brazil.
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Arini APK, Namangkalakul W, Limraksasin P, Osathanon T. Effects of lactalbumin enzymatic hydrolysate on human squamous cell carcinoma cells-an in vitro study. J Oral Biol Craniofac Res 2024; 14:222-229. [PMID: 38495954 PMCID: PMC10940804 DOI: 10.1016/j.jobcr.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 01/08/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024] Open
Abstract
Objectives Alpha-lactalbumin, the protein from human and bovine milk has been found to be promising as an alternative of anticancer agent. This study was aimed to investigate the effects of lactalbumin enzymatic hydrolysate (LAH) on cell proliferation, migration, and mRNA expression of matrix metalloproteinase (MMP) on human squamous cell carcinoma (hSCC) cell lines, in vitro. Methods Tongue (HSC-4 and 7) and pharyngeal (HN-30 and 31) hSCC cell lines were treated with a two-fold dilution of LAH (0.39-100 mg/ml). Cell viability and cell proliferation were examined by MTT assay. Colony forming unit (CFU) was assessed by crystal violet blue staining. Cell migration was investigated by scratch wound healing assay. Gene expression of metastasis-associated MMPs was assessed by RT-qPCR. Statistical analyses were evaluated at p value = 0.05. Results LAH at concentration of 50 and 100 mg/ml exhibited cytotoxicity on hSCC cells. The proliferation and CFU ability of hSCC cells were significantly attenuated after LAH treatment. The mRNA expression of MMP2, MMP9, and MMP14 was reduced in HN-30 and HN-31 cells while expression of MMP2 and MMP14 was downregulated in HSC-7 cells. Only MMP1 mRNA level was reduced in HSC-4 cells. However, cell migration of all hSCC cell lines did not alter after LAH treatment. Conclusion LAH treatment exhibits inhibitory effects on hSCC cell growth, proliferation and MMPs gene expression. Thus, LAH should be the promising alternative agent to develop the prospective anti-cancer drug.
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Affiliation(s)
| | - Worachat Namangkalakul
- Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence for Dental Stem Cell Biology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Phoonsuk Limraksasin
- Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence for Dental Stem Cell Biology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanaphum Osathanon
- Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence for Dental Stem Cell Biology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand
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Librizzi M, Martino C, Mauro M, Abruscato G, Arizza V, Vazzana M, Luparello C. Natural Anticancer Peptides from Marine Animal Species: Evidence from In Vitro Cell Model Systems. Cancers (Basel) 2023; 16:36. [PMID: 38201464 PMCID: PMC10777987 DOI: 10.3390/cancers16010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Anticancer peptides are short and structurally heterogeneous aminoacidic chains, which display selective cytotoxicity mostly against tumor cells, but not healthy cells, based on their different cell surface properties. Their anti-tumoral activity is carried out through interference with intracellular homeostasis, such as plasmalemma integrity, cell cycle control, enzymatic activities and mitochondrial functions, ultimately acting as angiogenesis-, drug resistance- and metastasis-inhibiting agents, immune stimulators, differentiation inducers and necrosis or extrinsic/intrinsic apoptosis promoters. The marine environment features an ever-growing level of biodiversity, and seas and oceans are poorly exploited mines in terms of natural products of biomedical interest. Adaptation processes to extreme and competitive environmental conditions led marine species to produce unique metabolites as a chemical strategy to allow inter-individual signalization and ensure survival against predators, infectious agents or UV radiation. These natural metabolites have found broad use in various applications in healthcare management, due to their anticancer, anti-angiogenic, anti-inflammatory and regeneration abilities. The aim of this review is to pick selected studies that report on the isolation of marine animal-derived peptides and the identification of their anticancer activity in in vitro cultures of cancer cells, and list them with respect to the taxonomical hierarchy of the source organism.
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Affiliation(s)
- Mariangela Librizzi
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, 90128 Palermo, Italy; (M.L.); (C.M.); (M.M.); (V.A.); (M.V.)
| | - Chiara Martino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, 90128 Palermo, Italy; (M.L.); (C.M.); (M.M.); (V.A.); (M.V.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Manuela Mauro
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, 90128 Palermo, Italy; (M.L.); (C.M.); (M.M.); (V.A.); (M.V.)
| | - Giulia Abruscato
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, 90128 Palermo, Italy; (M.L.); (C.M.); (M.M.); (V.A.); (M.V.)
| | - Vincenzo Arizza
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, 90128 Palermo, Italy; (M.L.); (C.M.); (M.M.); (V.A.); (M.V.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Mirella Vazzana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, 90128 Palermo, Italy; (M.L.); (C.M.); (M.M.); (V.A.); (M.V.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
| | - Claudio Luparello
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, 90128 Palermo, Italy; (M.L.); (C.M.); (M.M.); (V.A.); (M.V.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
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Zhang Y, Xue W, Xu C, Nan Y, Mei S, Ju D, Wang S, Zhang X. Innate Immunity in Cancer Biology and Therapy. Int J Mol Sci 2023; 24:11233. [PMID: 37510993 PMCID: PMC10379825 DOI: 10.3390/ijms241411233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Immunotherapies including adaptive immune checkpoint inhibitors (ICIs) and chimeric antigen receptor (CAR) T cells, have developed the treatment of cancer in clinic, and most of them focus on activating T cell immunity. Although these strategies have obtained unprecedented clinical responses, only limited subsets of cancer patients could receive long-term benefits, highlighting the demand for identifying novel targets for the new era of tumor immunotherapy. Innate immunity has been demonstrated to play a determinative role in the tumor microenvironment (TME) and influence the clinical outcomes of tumor patients. A thorough comprehension of the innate immune cells that infiltrate tumors would allow for the development of new therapeutics. In this review, we outline the role and mechanism of innate immunity in TME. Moreover, we discuss innate immunity-based cancer immunotherapy in basic and clinical studies. Finally, we summarize the challenges in sufficiently motivating innate immune responses and the corresponding strategies and measures to improve anti-tumor efficacy. This review could aid the comprehension of innate immunity and inspire the creation of brand-new immunotherapies for the treatment of cancer.
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Affiliation(s)
- Yuxia Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Wenjing Xue
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Caili Xu
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yanyang Nan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shuang Mei
- Shanghai Tinova Immune Therapeutics Co., Ltd., Shanghai 201413, China
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shaofei Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xuyao Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, China
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