ANPDB - African Natural Products Database

The African Natural Products Database (ANPDB) is a collection of natural product databases from various regions of Africa, it is a repository of natural products (NPs) isolated from native African organisms. It consists of the Northern African Natural Products Database (NANPDB) and the Eastern African Natural Products Database (EANPDB), covering data from 1962 to 2019. The information is derived from mainstream natural product journals as well as MSc and PhD theses from African universities. The database contains data compounds isolated from source organisms, primarily plants, but also microorganisms, animals, and marine sources. In addition to the names and molecular structures of compounds, ANPDB provides details about source organisms, biological activities (such as antimalarial, anticancer, and cytotoxic effects), modes of action (when available), and references.

APD3 - Antimicrobial Peptide Database

Antimicrobial Peptide Database (APD) is a database system dedicated to discovery timeline, glossary, nomenclature, classification, structure, function, information search, prediction, design, statistics and tools of AMPs. The peptide data stored in this original database were gleaned from the literature. Among the natural AMPs with know antimicrobial activity, there are human host defense peptides, from mammals annotated, active peptides from amphibians ( from frogs and toads), fish peptides, reptile peptides, birds, arthropods, insects, crustaceans, myriapods, chelicerata, spiders, scorpions, molluscs, AMPs from protozoa.

MMDBD - Medicinal Materials DNA Barcode Database

Medicinal Materials DNA Barcode Database is a database to retrieve and analyze DNA sequences of medicinal materials. It is includes DNA sequences and information and key references of the medicinal materials recorded in the Pharmacopoeia of the People’s Republic of China, American Herbal Pharmacopoeia and other related references. Relevant information of common adulterants and substitutes are also listed. This database provides a web-based platform for storage, retrieval, comparison and analysis of DNA sequences, for distinguishing medicinal materials from their common substitutes and adulterants.

NAPROC-13- Natural Products 13C

The Natural Products 13C NMR Database, NAPROC-13, is a database provides various search tools to identify the structure of natural product compounds. Developed through a collaborative effort at the University of Salamanca and global research institutions, this resource offers a specialized database of natural product structures identified using 13C NMR spectroscopy. Acess by login.

NP-MRD Natural Products Magnetic Resonance Database

The Natural Products Magnetic Resonance Database (NP-MRD) is an open-access, web-enabled, FAIR-compliant database containing NMR spectra and structure data for all known natural products. The database accepts raw (time domain data, processed spectra, assigned chemical shifts, J-couplings, RDCs, etc.) and meta-data (structures, sources, methods, taxonomy, geospatial data, etc) from natural products. The NP-MRD includes NPs such as vitamins, minerals, and probiotics as well as small molecules derived from plants, fungi, bacteria, marine organisms, or animals.

NPASS - Natural Product Activity and Species Source Database

The Natural Product Activity and Species Source Database (NPASS) is a database provides access to unique natural products derived from organisms, alongside activity records against biological targets. It includes data on co-culture systems, engineered organisms, and comprehensive biological activity information. Users can query based on compound names, structures, or species. The database supports natural product research by offering detailed profiles of compounds, biological activities, and source organisms.

NuBBE - Núcleo de Bioensaios Biossíntese e Ecofisiologia de Produtos Naturais

NuBBEDB - Núcleo de Bioensaios Biossíntese e Ecofisiologia de Produtos Naturais is a database source of information for the scientific community of natural products and medicinal chemistry. It is an tool for studies on naturally occurring bioactive compounds, molecular and physicochemical properties, database generation, virtual screening, dereplication, metabolomics, and for the design and synthesis of bioactive compounds. NuBBE database contains a variety of natural products isolated from Braziian Biodiversity and provides information on Chemical (metabolic class, chemical structure, physicochemical properties, common and IUPAC name and molecular mass), biological (species, geographic location, biological activities), pharmacological and spectroscopic data (molar mass and nuclear magnetic resonance). This is also an effort to make natural products accessible for virtual screening in the academic community, with the 3D structure format compatible with the most widely used docking programs.

SANCDB - South African Natural Compounds Database

South African Natural Compounds Database (SANCDB) is a free database containing compounds isolated from the plant and marine life in and around South Africa. These plant extracts have been shown to display antimicrobial, anticancer and antidiabetic activity, as well as activity against various neurological disorders. Compounds isolated from marine organisms found off the coast of South Africa have similarly shown promising pharmaceutical potential. Compound information has been extracted manually from literature.

SuperNatural 3.0

SuperNatural 3.0 is a database of natural products and natural product-based derivatives. The database contains different structures including isomers and unique natural compounds along with their structural and physicochemical information. Additionally, information on pathways, mechanism of action, toxicity, vendor information (if available), drug-like chemical space prediction for several diseases as antiviral, antibacterial, antimalarial, anticancer, and target specific cells like the central nervous system (CNS) are also provided for the natural compounds.

SUPP. Al - Discover Supplement-Drug Interactions

SUPP. Al - Discover Supplement-Drug Interactions is an application for browsing evidence of supplement-drug interactions (SDIs) extracted from the biomedical literature. It is a model to automatically extract supplement information and identify such interactions from the scientific literature. To address the lack of labeled data for SDI identification, it is use labels of the closely related task of identifying drug-drug interactions (DDIs) for supervision. It is fine-tune the contextualized word representations of the RoBERTa language model using labeled DDI data, and apply the fine-tuned model to identify supplement interactions. It is extract 195k evidence sentences from 22M articles (P=0.82, R=0.58, F1=0.68) for 60k interactions.

SWMD - Seaweed Metabolite Database

Seaweed Metabolite Database (SWMD) is an open access database of secondary metabolites from seaweeds, providing text and structure search access of chemical structures. The database comprises seaweed compounds mostly from the Red algae Laurencia spp. with comprehensive information of geographical origin, extraction and biological activity. In addition to structure and property information, it links compound information across web in PubChem and ChemSpider. The search works using Accession Number, Compound type, Seaweed Binomial name, IUPAC name, SMILES notation or InChI. Marine algae have been historically an exceptionally rich source of pharmacologically active metabolites.

Evaluation of adverse clinical outcomes in patients with inflammatory bowel disease receiving different sequences of first- and second-line biologic treatments: findings from ROTARY.

BACKGROUND: Patients with inflammatory bowel disease (IBD) are at risk of developing dysplasia and, subsequently, colorectal cancer (CRC) owing to chronic inflammation. Patients may also experience other severe disease complications, such as hospitalization and surgery. Several biologics are available for the treatment of patients with IBD and some patients require multiple lines of treatment owing to loss of response or tolerability to their prescribed biologic. Previous studies suggest that the choice of initial biologic treatment may impact the outcomes of later treatment lines. In this study, we assessed adverse clinical outcomes in patients with Crohn's disease (CD) or ulcerative colitis (UC) who received different biologic treatment sequences. METHODS: ROTARY part B was a retrospective cohort study using the Optum® Clinical Database that evaluated the incidences of IBD-related hospitalization, IBD-related surgery, dysplasia, CRC, and infections in patients with CD or UC who received two biologics successively. First-line biologics included adalimumab, infliximab, ustekinumab (CD only), and vedolizumab; second-line biologics included infliximab and adalimumab. RESULTS: In patients with CD, the treatment sequence of ustekinumab to infliximab was associated with the highest overall incidences of hospitalization (51.9%), surgery (40.7%), CRC (3.7%), and infection (37.0%). Vedolizumab followed by an anti-tumor necrosis factor alpha (anti-TNFα) treatment was associated with a significantly lower risk of experiencing an adverse medical event (hospitalization, surgery, or infection) than two successive anti-TNFα treatments (odds ratio, 1.526; 95% confidence interval, 1.004-2.320; P < 0.05). In patients with UC, the treatment sequence of vedolizumab to adalimumab resulted in the lowest overall incidence of adverse outcomes (20.3%, 6.3%, 0.0%, 6.3%, and 4.7% for hospitalization, surgery, CRC, dysplasia, and infection, respectively). CONCLUSIONS: We describe differences in adverse clinical outcomes associated with sequencing of biologics in patients with CD or UC and demonstrate favorable results in patients who received vedolizumab as a first-line biologic. These results provide potential guidance to clinicians choosing sequences of biologic treatments in patients with IBD.

New insight into oxidative stress and inflammatory responses to kidney stones: Potential therapeutic strategies with natural active ingredients.

Kidney stones, a prevalent urological disorder, are closely associated with oxidative stress (OS) and the inflammatory response. Recent research in the field of kidney stone treatment has indicated the potential of natural active ingredients to modulate OS targets and the inflammatory response in kidney stones. Oxidative stress can occur through various pathways, increasing the risk of stone formation, while the inflammatory response generated during kidney stone formation further exacerbates OS, forming a detrimental cycle. Both antioxidant systems related to OS and inflammatory mediators associated with inflammation play roles in the pathogenesis of kidney stones. Natural active ingredients, abundant in resources and possessing antioxidative and anti-inflammatory properties, have the ability to decrease the risk of stone formation and improve prognosis by reducing OS and suppressing pro-inflammatory cytokine expression or pathways. Currently, numerous developed natural active ingredients have been clinically applied and demonstrated satisfactory therapeutic efficacy. This review aims to provide novel insights into OS and inflammation targets in kidney stones as well as summarize research progress on potential therapeutic strategies involving natural active ingredients. Future studies should delve deeper into exploring efficacy and mechanisms of action of diverse natural active ingredients, proposing innovative treatment strategies for kidney stones, and continuously uncovering their potential applications.

Jintiange capsule may have a positive effect on pain relief and functional activity in OVCF patients with PVA: A meta-analysis of randomized control trials.

BACKGROUND: This study aims to systematically evaluate the clinical efficacy and adverse reactions associated with Jintiange capsule (JTG capsule)-assisted percutaneous vertebral augmentation (PVA) in the treatment of osteoporotic vertebral compression fracture (OVCF). METHODS: A comprehensive search was conducted across multiple databases including PubMed, Cochrane Library, EMBASE, Web of Science Database, China Biomedical Database, China VIP Network, China National Knowledge Infrastructure, Wanfang, and VIP Chinese Journal databases until June 1, 2022. Manual searches were also performed in relevant journals. Randomized controlled trials investigating the efficacy of JTG capsule-assisted PVA in the treatment of OVCF were identified and selected for inclusion. The quality of the included studies was assessed using the Cochrane risk bias assessment tool and Jadad scale. Meta-analysis was conducted using Stata MP18 software. RESULTS: A total of 138 literatures were retrieved, and 12 RCTS were finally included after screening, involving 1099 patients. Overall, the quality of the included literature was low, and all the included literatures were randomized controlled experiments, among which 9 were grouped by random number table, and 3 did not specify the random assignment plan. The total effective rate of the experimental group was higher than that of the control group (relative ratio: 1.19, 95% confidence interval: 1.11, 1.26, P = .868, I2 = 0%). The heterogeneity of visual analog score, Oswestry disability index, bone mineral density (BMD) of lumbar vertebrae, BMD of femoral neck and bone-γ-carboxyglutamic acid-containing protein was high. The reasons for the high heterogeneity were the age of patients, the follow-up time and the small sample size. There is publication bias in visual analog score, Oswestry disability index scores, and lumbar spine bone mineral density, and we believe that publication bias may be related to selective reporting of positive results by the authors and selective publication of positive results by the publishers. CONCLUSION: JTG capsule has demonstrated promising outcomes in alleviating the pain experienced by OVCF patients following PVP. Additionally, it has shown efficacy in enhancing postoperative lumbar and back function. Furthermore, JTG capsule has been associated with improvements in postoperative vertebral BMD and serum bone-γ-carboxyglutamic acid-containing protein levels. These findings suggest that JTG capsule could potentially serve as a viable adjunctive treatment option for managing osteoporosis following PVA.

Chemoenzymatic Oxidation of Labdane and Formal Synthesis of Nimbolide.

In nature, basic terpene skeletons are produced and subsequently undergo enzymatic or nonenzymatic oxidative transformations, leading to diverse structural variations. To date, thousands of natural products featuring a variety of oxidation patterns have been isolated solely from the labdane family. This work describes a strategy for the comprehensive introduction of oxidation states into the labdane core by employing a combination of enzyme library screening, directed evolution, and sequential chemical oxidation processes. Furthermore, we showcase the functional viability of our chemoenzymatic approach by accomplishing a formal synthesis of nimbolide, highlighting its potential for streamlining the synthesis of complex natural products.

Targeting neutrophils extracellular traps, a promising anti-thrombotic therapy for natural products from traditional Chinese herbal medicine.

Thrombi are the main cause of vascular occlusion and contribute significantly to cardiovascular events and death. Neutrophils extracellular traps (NETs)-induced thrombosis plays a vital role in thrombotic complications and it takes the main responsibility for the resistance of fibrinolysis. However, the conventional anti-thrombotic therapies are inadequate to treat NETs-induced thrombotic complications but carry a high risk of bleeding. Consequently, increased attention has shifted towards exploring novel anti-thrombotic treatments targeting NETs. Interestingly, accumulating evidences prove that natural products from traditional Chinese herbal medicines have a great potential to mitigate thrombosis through inhibiting generous NETs formation and degrading excessive NETs. In this review, we elaborated the formation and degradation of NETs and highlighted its pivotal role in immunothrombosis through interactions with platelets and coagulation factors. Since available anti-thrombotic drugs targeting NETs are deficient, we further summarized the natural products and compounds from traditional Chinese herbal medicines which exert effective actions on regulating NETs formation and also have anti-thrombotic effects. Our findings underscore the diverse effects of natural products in targeting NETs, including relieving inflammation and oxidative stress of neutrophils, inhibiting neutrophils activation and DNA efflux, suppressing granule proteins release, reducing histones and promoting DNA degradation. This review aims to highlight the significance of natural medicines in anti-thrombotic therapies through targeting NETs and to lay a groundwork for developing novel anti-thrombotic agents from traditional Chinese herbal medicines.

AChE inhibitory activity of N-substituted natural galanthamine derivatives.

Galanthamine derivatives are known for their AChE inhibitory activity. Among them, galanthamine has been approved for treatment of Alzheimer's disease. N-Acetylnorgalanthamine (narcisine) and N-(2'-methyl)allylnorgalanthamine (the most potent natural AChE inhibitor of galanthamine type) were synthetized using N-norgalanthamine as a precursor. The NMR data described previously for narcisine were revised by two-dimensional 1H-1H and 1H-13C chemical shift correlation experiments. AChE inhibitory assays showed that N-acetylnorgalanthamine and N-formylnorgalanthamine (with previously unknown activity) are 4- and 43-times, respectively, less potent than galanthamine. In vitro (AChE inhibitory) and in silico (docking, ADME) assays and comparison of N-(2'-methyl)allylnorgalanthamine with galanthamine prove that this molecule is a very promising natural AChE inhibitor (33-times more potent than galanthamine) which further in vivo studies would provide better estimation about its applicability as a drug.

Real-world multidisciplinary outcomes of onasemnogene abeparvovec monotherapy in patients with spinal muscular atrophy type 1: experience of the French cohort in the first three years of treatment.

BACKGROUND: Spinal muscular atrophy type 1 (SMA1) is the most severe and early form of SMA, a genetic disease with motor neuron degeneration. Onasemnogene abeparvovec gene transfer therapy (GT) has changed the natural history of SMA1, but real-world data are scarce. METHODS: A French national expert committee identified 95 newly diagnosed treatment-naive SMA1 patients between June 2019 and June 2022. We prospectively report on children treated with GT as the first and only therapy who had more than one-year of follow-up. RESULTS: Forty-six SMA1 patients received GT. Twelve patients received other treatments. Patients with respiratory insufficiency were oriented toward palliative care after discussion with families. Twenty-nine of the treated patients with more than 12 months of follow-up were included in the follow-up analysis. Among them, 17 had 24 months of follow-up. The mean age at treatment was 7.5 (2.1-12.5) months. Twenty-two patients had two SMN2 copies, and seven had three copies. One infant died in the month following GT due to severe thrombotic microangiopathy, and another died due to respiratory distress. Among the 17 patients with 24 months of follow-up, 90% required spinal bracing (15/17), three patients required nocturnal noninvasive ventilation, and two needed gastrostomy. Concerning motor milestones at the 24-month follow-up, all patients held their head, 15/17 sat for 30 s unassisted, and 12/17 stood with aid. Motor scores (CHOPINTEND and HINE-2) and thoracic circumference significantly improved in all patients. CONCLUSIONS: Our study shows favorable motor outcomes and preserved respiratory and feeding functions in treatment-naive SMA1 infants treated by GT as the first and only therapy before respiratory and bulbar dysfunctions occurred. Nevertheless, almost all patients developed spinal deformities.

Natural Products and Altered Metabolism in Cancer: Therapeutic Targets and Mechanisms of Action.

Cancer is characterized by uncontrolled cell proliferation and the dysregulation of numerous biological functions, including metabolism. Because of the potential implications of targeted therapies, the metabolic alterations seen in cancer cells, such as the Warburg effect and disruptions in lipid and amino acid metabolism, have gained attention in cancer research. In this review, we delve into recent research examining the influence of natural products on altered cancer metabolism. Natural products were selected based on their ability to target cancer's altered metabolism. We identified the targets and explored the mechanisms of action of these natural products in influencing cellular energetics. Studies discussed in this review provide a solid ground for researchers to consider natural products in cancer treatment alone and in combination with conventional anticancer therapies.