Comparative analysis of retrosynthesis applications for predicting of pathways for plant Secondary metabolite production

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dc.authorid0000-0002-8827-4887
dc.contributor.authorYonet, Nilay
dc.contributor.authorYuka, Selcen Ari
dc.contributor.authorTurker, Musa
dc.contributor.authorYilmaz, Alper
dc.date.accessioned2026-01-24T12:31:27Z
dc.date.available2026-01-24T12:31:27Z
dc.date.issued2024
dc.departmentAlanya Alaaddin Keykubat Üniversitesi
dc.description.abstractSecondary metabolites (SMs), organic compounds synthesized by plants, play crucial roles in their own physiology and within their ecological niches, and have extensive usages in industries like pharmaceuticals, cosmetics, and food. Due to the complex nature of these metabolites, utilizing microorganisms has been proposed for their efficient and cost-effective production. In addressing challenges in SM synthesis, retrosynthesis has become essential. Applications such as RetroPath2.0, BioNavi-NP, and RetroBioCat have been developed to predict and design biosynthetic pathways, supporting synthetic biology and metabolic engineering efforts. These applications employ different methodologies to enhance the synthesis of target compounds, yet often face limitations in user-friendliness, functionality, and adaptability. This study evaluates the potential of RetroPath2.0, RetroBioCat, and BioNavi-NP in predicting the production pathways of 11 alkaloids, a class of plant secondary metabolites (PSMs). Through comparative analysis, the efficacy of these applications in proposing alternative production strategies was assessed. Findings highlighted RetroPath2.0's capability in outlining precise production pathways in host organisms, despite some restrictions in its broader practicability. The study also demonstrated the production pathways of dimethyltryptamine, nicotine, and higenamine in non-plant hosts, illustrating the practical uses of these applications.
dc.description.sponsorshipYildiz Technical University Scientific Research Projects Coordination Unit [FBA-2021-4698]
dc.description.sponsorshipThis work has been supported by Yildiz Technical University Scientific Research Projects Coordination Unit under project number FBA-2021-4698.
dc.identifier.doi10.1080/13102818.2024.2431041
dc.identifier.issn1310-2818
dc.identifier.issn1314-3530
dc.identifier.issue1
dc.identifier.scopus2-s2.0-85211961705
dc.identifier.scopusqualityQ3
dc.identifier.urihttps://doi.org/10.1080/13102818.2024.2431041
dc.identifier.urihttps://hdl.handle.net/20.500.12868/5896
dc.identifier.volume38
dc.identifier.wosWOS:001374133700001
dc.identifier.wosqualityQ4
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.language.isoen
dc.publisherTaylor & Francis Ltd
dc.relation.ispartofBiotechnology & Biotechnological Equipment
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_WoS_20260121
dc.subjectSecondary metabolites
dc.subjectretrosynthesis applications
dc.subjectsynthetic biology
dc.subjectmetabolic engineering
dc.subjectalkaloid biosynthesis
dc.titleComparative analysis of retrosynthesis applications for predicting of pathways for plant Secondary metabolite production
dc.typeArticle

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