Improved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method

Abstract As anticancer peptides (ACPs) have attracted great interest for cancer treatment, several approaches based on machine learning have been proposed for ACP identification. Although existing methods have afforded high prediction accuracies, however such models are using a large number of descr...

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Autores principales:	Phasit Charoenkwan, Wararat Chiangjong, Vannajan Sanghiran Lee, Chanin Nantasenamat, Md. Mehedi Hasan, Watshara Shoombuatong
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4da6028b3ec44c70afc3d6b6a8e19110
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spelling	oai:doaj.org-article:4da6028b3ec44c70afc3d6b6a8e191102021-12-02T10:44:21ZImproved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method10.1038/s41598-021-82513-92045-2322https://doaj.org/article/4da6028b3ec44c70afc3d6b6a8e191102021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82513-9https://doaj.org/toc/2045-2322Abstract As anticancer peptides (ACPs) have attracted great interest for cancer treatment, several approaches based on machine learning have been proposed for ACP identification. Although existing methods have afforded high prediction accuracies, however such models are using a large number of descriptors together with complex ensemble approaches that consequently leads to low interpretability and thus poses a challenge for biologists and biochemists. Therefore, it is desirable to develop a simple, interpretable and efficient predictor for accurate ACP identification as well as providing the means for the rational design of new anticancer peptides with promising potential for clinical application. Herein, we propose a novel flexible scoring card method (FSCM) making use of propensity scores of local and global sequential information for the development of a sequence-based ACP predictor (named iACP-FSCM) for improving the prediction accuracy and model interpretability. To the best of our knowledge, iACP-FSCM represents the first sequence-based ACP predictor for rationalizing an in-depth understanding into the molecular basis for the enhancement of anticancer activities of peptides via the use of FSCM-derived propensity scores. The independent testing results showed that the iACP-FSCM provided accuracies of 0.825 and 0.910 as evaluated on the main and alternative datasets, respectively. Results from comparative benchmarking demonstrated that iACP-FSCM could outperform seven other existing ACP predictors with marked improvements of 7% and 17% for accuracy and MCC, respectively, on the main dataset. Furthermore, the iACP-FSCM (0.910) achieved very comparable results to that of the state-of-the-art ensemble model AntiCP2.0 (0.920) as evaluated on the alternative dataset. Comparative results demonstrated that iACP-FSCM was the most suitable choice for ACP identification and characterization considering its simplicity, interpretability and generalizability. It is highly anticipated that the iACP-FSCM may be a robust tool for the rapid screening and identification of promising ACPs for clinical use.Phasit CharoenkwanWararat ChiangjongVannajan Sanghiran LeeChanin NantasenamatMd. Mehedi HasanWatshara ShoombuatongNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Phasit Charoenkwan Wararat Chiangjong Vannajan Sanghiran Lee Chanin Nantasenamat Md. Mehedi Hasan Watshara Shoombuatong Improved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method
description	Abstract As anticancer peptides (ACPs) have attracted great interest for cancer treatment, several approaches based on machine learning have been proposed for ACP identification. Although existing methods have afforded high prediction accuracies, however such models are using a large number of descriptors together with complex ensemble approaches that consequently leads to low interpretability and thus poses a challenge for biologists and biochemists. Therefore, it is desirable to develop a simple, interpretable and efficient predictor for accurate ACP identification as well as providing the means for the rational design of new anticancer peptides with promising potential for clinical application. Herein, we propose a novel flexible scoring card method (FSCM) making use of propensity scores of local and global sequential information for the development of a sequence-based ACP predictor (named iACP-FSCM) for improving the prediction accuracy and model interpretability. To the best of our knowledge, iACP-FSCM represents the first sequence-based ACP predictor for rationalizing an in-depth understanding into the molecular basis for the enhancement of anticancer activities of peptides via the use of FSCM-derived propensity scores. The independent testing results showed that the iACP-FSCM provided accuracies of 0.825 and 0.910 as evaluated on the main and alternative datasets, respectively. Results from comparative benchmarking demonstrated that iACP-FSCM could outperform seven other existing ACP predictors with marked improvements of 7% and 17% for accuracy and MCC, respectively, on the main dataset. Furthermore, the iACP-FSCM (0.910) achieved very comparable results to that of the state-of-the-art ensemble model AntiCP2.0 (0.920) as evaluated on the alternative dataset. Comparative results demonstrated that iACP-FSCM was the most suitable choice for ACP identification and characterization considering its simplicity, interpretability and generalizability. It is highly anticipated that the iACP-FSCM may be a robust tool for the rapid screening and identification of promising ACPs for clinical use.
format	article
author	Phasit Charoenkwan Wararat Chiangjong Vannajan Sanghiran Lee Chanin Nantasenamat Md. Mehedi Hasan Watshara Shoombuatong
author_facet	Phasit Charoenkwan Wararat Chiangjong Vannajan Sanghiran Lee Chanin Nantasenamat Md. Mehedi Hasan Watshara Shoombuatong
author_sort	Phasit Charoenkwan
title	Improved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method
title_short	Improved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method
title_full	Improved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method
title_fullStr	Improved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method
title_full_unstemmed	Improved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method
title_sort	improved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/4da6028b3ec44c70afc3d6b6a8e19110
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Improved prediction and characterization of anticancer activities of peptides using a novel flexible scoring card method

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