GhanaNPDB: a database of Ghana-derived natural products

Natural products (NPs) have long provided a foundation for drug discovery, offering structurally diverse and biologically active molecules not readily accessible through purely synthetic approaches. More than half of all approved small-molecule drugs originate from, are inspired by, or are structurally related to NPs, reflecting their importance in medicinal chemistry and therapeutic innovation [1][2][3][4] . NPs have yielded numerous anti-infective [5][6][7] , anticancer 8,9 , anti-inflammatory 10 , and neuroactive agents 11 .Ghana is endowed with rich biodiversity spanning tropical rainforests, savannah ecosystems, coastal habitats, freshwater systems, and marine environments 12 , all of which support numerous plant species, microorganisms, and aquatic invertebrates that represent promising sources of bioactive NPs. Despite decades of phytochemical, microbiological, and ethnobotanical research, information on Ghana's chemical diversity remains fragmented across journal articles, academic theses, institutional repositories, and laboratory records, limiting its accessibility and effective utilization. Furthermore, although databases such as PubChem, NPAtlas 13 , KNApSAcK 14 , COCONUT 15 , NANPDB 16 and ANPDB 17 have significantly enhanced access to NP data, they primarily aggregate compounds across multiple geographic regions and taxonomic sources Our analysis revealed that many Ghana-derived NPs products remain underrepresented in these repositories.To address this gap, we developed the Ghana Natural Product Database (GhanaNPDB), a centralized and curated knowledge base that consolidates NP discoveries from Ghana into a single accessible platform. The current version is available at https://np.lib-gh.net GhanaNPDB was developed as a curated, open-access repository of NPs isolated from plants, microbes, and aquatic invertebrates occurring in Ghana. The database integrates chemical, biological, and biodiversity metadata to support the discovery of NPs, cheminformatics applications, and translational research. The initial public release (v1.0) comprises 256 unique compounds curated from peer-reviewed journal articles, theses, and other institutional scholarly outputs identified through searches completed on December 31, 2024. Therefore, GhanaNPDB v1.0 includes literature available up to 2024.A systematic search was conducted to identify NPs isolated from Ghanaian biodiversity. Bibliographic databases including PubMed, Scopus, Google Scholar, ScienceDirect, ResearchGate, and SciFinder, as well as institutional repositories, were queried for publications and theses published between 1966 and 2024. Search terms included combinations of keywords such as Ghana, natural products, phytochemistry, microbial metabolites, marine/aquatic invertebrates, isolation, structure elucidation, bioactivity.Records were included if they described structurally characterized NPs isolated from organisms collected in Ghana and provided clear taxonomic and collection information. Synthetic or semisynthetic compounds were excluded. Duplicate entries were identified through name searches and verified against the original sources. Where duplicates were confirmed, the most complete record was retained as the primary entry, while related publications and any unique findings were cross-referenced to the retained record.Extracted data were organized into six categories: (i) compound names and unique identifiers;( 1a). These compounds span diverse natural product classes, including terpenoids, alkaloids, flavonoids, phenolics, polyketides, stilbenes, and siderophores. Terpenoids are the most abundant class (53, 24%), followed closely by alkaloids (45, 21%), while flavonoids and phenolics each account for 10% (22). The remaining compounds belong to several less represented classes (Figure 1b). This diversity reflects the breadth of Ghana's biodiversity and its potential as a source of novel bioactive natural products.Descriptor analyses reveal substantial variation in molecular properties, reflecting the chemical diversity of the NPs represented in GhanaNPDB. Molecular weights range from 62.02 g/mol for fluoroacetylaldehyde 18 to 3600.86 g/mol for the macrocyclic compound legonaridin 1 19 , while log P values range from -4.90 to 18.62, indicating the presence of both highly polar and highly lipophilic compounds. Similarly, hydrogen bond donor and acceptor counts range from 0 to 20, indicating a wide spectrum of molecular functionalities. Together, these features enable the database to cover an extensive chemical space relevant to multiple biological targets and ADME-related investigations.The database also contains compounds with diverse biological activities, including antibacterial, antifungal, antiparasitic, anti-inflammatory, and antiproliferative effects (Figure 1c). Quantitative measures such as IC₅₀, MIC, and EC₅₀ values are linked to detailed assay information, including the target, cell line, or test organism used (Table 1). Collectively, these data reveal strong representation in antimicrobial and cytotoxic screening while identifying underexplored targets and pathways that may warrant further investigation. Natural Product from Ghanaian Marine Biodiversity Dakaramine 28 Axinella sp. Cytotoxic IC50 = 35.0 μg/mL against Jurkat; 26.5 μg/mL against HL60Our comparative analysis revealed limited overlap between GhanaNPDB and the existing databases. Only 19 NPs were common to GhanaNPDB, COCONUT and ANPDB, while 82 and 73 NPs were shared between GhanaNPDB and COCONUT and between GhanaNPDB and ANPDB, respectively (Figure 1d). These findings indicate the substantial number of Ghanaderived compounds that remain absent from widely used NP repositories.GhanaNPDB is a web-based platform accessible through any standard internet browser and designed for ease of use across devices. The portal comprises three main sections-Search, Browse, and Contact-that support efficient exploration of the database.The Search section offers two query options: a general keyword search that retrieves records across all data fields and an advanced search that enables targeted retrieval using structured parameters such as species name, compound name, or chemical class. The Browse section provides organized access to curated datasets, allowing users to explore compound records without constructing complex queries. To facilitate navigation and data interpretation, the platform includes a user guide and a Frequently Asked Questions (FAQ) section. The Contact section enables users to submit feedback, report corrections, and contribute additional data, supporting community engagement and the continuous improvement of the database.Figure 1e shows GhanaNPDB user interface and an example of the query result for heudelotol B 25 .The current version of GhanaNPDB is derived from published reports of NPs isolated from Ghanaian biodiversity and may not capture unpublished studies or compounds reported in difficult-to-access sources. Future updates will incorporate similarity-and substructure-based search options, machine-learning approaches for literature mining and compound recognition to support the continuous identification and integration of new records. Expanded data pipelines, enhanced annotations, and community contributions will further strengthen GhanaNPDB as a resource for NP research and drug discovery.To promote collaboration and support database expansion, data may be contributed through the Contact Us section of the GhanaNPDB website. Users wishing to submit data will be required to provide their name, email address, institutional affiliation, and a brief description of the proposed data. Upon receipt, submissions will undergo initial screening by the database administrator for relevance and adherence to database standards. Where necessary, contributors may be contacted for clarification or additional information. Once a submission satisfies the review requirements, the contributor will be granted access or provided with instructions to upload their data for integration into the database.GhanaNPDB is the first curated database dedicated to NPs isolated from Ghanaian biodiversity.It integrates chemical, biological, taxonomic, geographic, and methodological information, together with links to source publications, into a searchable resource that supports NP research and drug discovery. Access is provided through a dedicated web platform. To ensure its continued relevance and accuracy, GhanaNPDB will be maintained through quarterly reviews and ongoing curation to enable timely incorporation of newly reported compounds and emerging scientific data.Future developments will focus on enhancing functionality and interoperability, including integration with major NP repositories such as COCONUT and ANPDB. These efforts are expected to improve data accessibility, visibility, and reuse, thereby increasing the value of GhanaNPDB.