Challenges in natural product-based drug discovery assisted with in silico-based methods

Epigallocatechin gallate with nobiletin as a novel combination therapy to induce autophagy and apoptosis in oral cancer

Oral cancer (OC) represents a serious health and economic problem and the global prevalence of OC is still increasing. Epigallocatechin gallate (EGCG) is the most abundant polyphenol in green tea, and nobiletin (NOB) is a bioactive polyethoxylated flavone isolated from the peels of citrus fruits. Both have been proven to exert an anti-cancer effect in OC. Integrated stress response (ISR) is a key translation signaling network activated by oncogenic stress, modulating ISR activity is an innovative drug target in cancer therapy. Herein, we investigated combined EGCG and NOB in a ratio at 125 μM:25 μM additively decreased cell viability of OC cells most. Combination treatment with 125 μM EGCG and 25 μM NOB increased LC3 expression and autophagosome formation, and induced autophagic cell death. In addition, this combination increased cleaved caspase-3, cleaved caspase-9, and cleaved PARP levels, induced apoptotic cell death. Furthermore, we explored the effect of the EGCG and NOB combination in regulating ISR activity. Our results showed that this combination inhibited the GCN2/eIF2α axis and activated the PERK/ATF4/CHOP pathway. Results further demonstrated that silencing either GCN2 or PERK reversed EGCG+NOB-induced cell proliferation inhibition, autophagy and apoptosis. In this combined system, GCN2 and PERK are targets of EGCG-induced autophagy and NOB-induced apoptosis, EGCG and NOB produce additive effects to induce OC cell death. In summary, our study identified that EGCG combined with NOB, as a potent ISR mediator, cooperates to induce autophagy and apoptosis, further supporting the combination of EGCG and NOB as a promising strategy for OC treatment.

Nutraceuticals Targeting Cannabinoid Receptor 1 and Transient Receptor Potential Vanilloid 1 for Pain Relief: A Computational Screening Approach

OBJECTIVE

This study examined the binding affinities and therapeutic potential of natural products targeting pain-related receptors using molecular docking and molecular dynamics (MD) simulations. Drug-like properties and absorption, distribution, metabolism, excretion, and toxicity (ADMET) analyses were also conducted.

METHODS

AutoDock Vina (The Scripps Research Institute, La Jolla, CA, USA) was used for docking against pain-related receptors, including transient receptor potential vanilloid 1 (TRPV1), cyclooxygenase-2 (COX-2), cannabinoid receptor 1 (CB1), mu-opioid receptor, and nicotinic acetylcholine receptors. Celecoxib was included as a reference drug for docking score comparison. Protein-ligand complex stability was assessed via 100-nanosecond (ns) MD simulations using GROMACS (GROningen MAchine for Chemical Simulations; the University of Groningen, Netherlands), analyzing root mean square deviation (RMSD) and radius of gyration (Rg). Drug-likeness was evaluated by Lipinski's rule of five, and ADMET analysis was performed for pharmacokinetics and toxicity profiling.

RESULTS

Ginsenoside Rb1 exhibited a strong affinity for TRPV1 (-9.5 kcal/mol) and mu-opioid (-9.0 kcal/mol) receptors, suggesting its potential as a non-opioid analgesic candidate. Cyanidin 3-O-rutinoside demonstrated high binding to TRPV1 (-9.35 kcal/mol), COX-2 (-9.65 kcal/mol), and CB1 (-9.18 kcal/mol), surpassing the reference drug celecoxib (-7.22 kcal/mol) in COX-2 binding. MD simulations confirmed complex stability, with RMSD (~3.0 Å) and Rg (~3.0 nm) values lower than unbound proteins. Most compounds met Lipinski's criteria, indicating good oral bioavailability. ADMET analysis revealed favorable absorption and distribution with low toxicity.

CONCLUSION

Ginsenoside Rb1 and cyanidin 3-O-rutinoside exhibit high binding affinity, stability, and favorable pharmacokinetic properties, supporting their potential as non-opioid analgesic candidates. Their ability to modulate pain pathways in vitro and in vivo warrants further investigation.

NaturAr: A Collaborative, Open-Source Database of Natural Products from Argentinian Biodiversity for Drug Discovery and Bioprospecting

Since the early stages of modern medicine, natural products have been a source of inspiration for the development of bioactive compounds. Around half of the approved small-molecule drugs trace their origins to natural products or their derivatives, highlighting the importance of their correct classification and identification. The information generated by the experimental groups is not usually unified and is available only in publications or general databases, where the compounds are not linked to their natural sources. To address this need, numerous natural product databases specific to distinct geographic regions have emerged. In this work, we introduce NaturAr, a natural products database dedicated to the cataloging of the rich biodiversity of Argentina. At the time of submission, 243 papers were reviewed, leading to a database of more than 1200 compounds from all across the country. A distinctive quality of this database is its collaborative and open-source framework, which promotes contributions from the research community. NaturAr is freely available online at https://naturar.quimica.unlp.edu.ar.

StreptomeDB 4.0: a comprehensive database of streptomycetes natural products enriched with protein interactions and interactive spectral visualization

Streptomycetes remain an important bacterial source of natural products (NPs) with significant therapeutic promise, particularly in the fight against antimicrobial resistance. Herein, we present StreptomeDB 4.0, a substantial update of the database that includes expanded content and several new features. Currently, StreptomeDB 4.0 contains over 8500 NPs originating from ∼3900 streptomycetes, manually annotated from ∼7600 PubMed-indexed peer-reviewed articles. The database was enhanced by two in-house developments: (i) automated literature-mined NP-protein relationships (hyperlinked to the CPRiL web server) and (ii) pharmacophore-based NP-protein interactions (predicted with the ePharmaLib dataset). Moreover, genome mining was supplemented through hyperlinks to the widely used antiSMASH database. To facilitate NP structural dereplication, interactive visualization tools were implemented, namely the JSpecView applet and plotly.js charting library for predicted nuclear magnetic resonance and mass spectrometry spectral data, respectively. Furthermore, both the backend database and the frontend web interface were redesigned, and several software packages, including PostgreSQL and Django, were updated to the latest versions. Overall, this comprehensive database serves as a vital resource for researchers seeking to delve into the metabolic intricacies of streptomycetes and discover novel therapeutics, notably antimicrobial agents. StreptomeDB is publicly accessible at https://www.pharmbioinf.uni-freiburg.de/streptomedb.

In Vitro and In Silico Studies of the Biological Activities of Some Secondary Metabolites Belonging to Ficus sur Forssk (Moraceae): Towards Optimization of Wighteone Metabolite

Based on ethnomedicinal and chemotaxonomic records of Ficus plants, Ficus sur Forssk was studied in the search for bioactive compounds. Eleven known compounds including mixture α -amyrin acetate and β -amyrin acetate (1 and 2), lupeol (3), 3β-acetoxy-olean-12-en-11-one (4), lupenyl acetate (5), taraxastan-3,20-diol (6), 3'- (3-methylbut-2-enyl) biochanin A (7), derrone (8), quercetin (9), stigmasterol (10), and stigmasterol glycoside (11) were isolated from stem barks of Ficus sur Forssk. Their structures were obtained through analysis of spectroscopic data 1D and 2D NMR), mass spectrometry, and by comparison of these data with the literature. Nine isolated compounds (1-7, 10, 11) were tested as the active wighteone metabolite previously isolated from the roots of this plant against the human HepG2 hepatocellular carcinoma cells and a small panel of sensitive microbial strains for structure- activity relationship purpose. The compounds didn't show any activity. With the aim of understanding the impact of the structural difference between wighteone metabolite and its analogs, the former were cross-docked to evaluate their anticancer properties via the apoptosis pathway. Wighteone metabolite proved to be the best ligand confirming its previous bioassay result. Thus, the current study lays the framework for the further optimization of wighteone metabolite regarding its anticancer activity.

Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products

Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.

Targeting Hypoglycemic Natural Products from the Cloud Forest Plants Using Chemotaxonomic Computer-Assisted Selection

The cloud forest (CF), a hugely biodiverse ecosystem, is a hotspot of unexplored plants with potential for discovering pharmacologically active compounds. Without sufficient ethnopharmacological information, developing strategies for rationally selecting plants for experimental studies is crucial. With this goal, a CF metabolites library was created, and a ligand-based virtual screening was conducted to identify molecules with potential hypoglycemic activity. From the most promising botanical families, plants were collected, methanolic extracts were prepared, and hypoglycemic activity was evaluated through in vitro enzyme inhibition assays on α-amylase, α-glucosidase, and dipeptidyl peptidase IV (DPP-IV). Metabolomic analyses were performed to identify the dominant metabolites in the species with the best inhibitory activity profile, and their affinity for the molecular targets was evaluated using ensemble molecular docking. This strategy led to the identification of twelve plants (in four botanical families) with hypoglycemic activity. Sida rhombifolia (Malvaceae) stood out for its DPP-IV selective inhibition versus S. glabra. A comparison of chemical profiles led to the annotation of twenty-seven metabolites over-accumulated in S. rhombifolia compared to S. glabra, among which acanthoside D and cis-tiliroside were noteworthy for their potential selective inhibition due to their specific intermolecular interactions with relevant amino acids of DPP-IV. The workflow used in this study presents a novel targeting strategy for identifying novel bioactive natural sources, which can complement the conventional selection criteria used in Natural Product Chemistry.

Assessment of the conceivable inhibitory activity of pathogenic microorganisms extracted from seaweed using phytochemicals, antioxidants, and in-silico molecular dynamic simulation

Turbinaria ornata, Polycladia myrica, and Padina pavonica is a perennial Mediterranean-native seaweed that is commonly used for mass display. The principal aims of this reconnaissance were the isolation of various compounds from methanolic seaweeds extraction and screening the potential effect as antibacterial, and antioxidant. The micro-dilution method was used to measure antibacterial activity. Gas chromatography-mass spectrophotometry (GC. Mass) abused to analyze the chemical components of the methanolic seaweed extract. The existence of 19 secondary metabolites was discovered using GC-MS analysis: 8 different compounds for each seaweed's species. Among these bioactive compounds, 4 compounds from P. pavonica extract showed the binding affinity and ability to react with Beta-ketoacyl synthase (PDB ID 1EK4) of Escherichia coli. The phytocompounds' drug-like and poisonous characteristics were predicted. Auto Dock was used to examine the ligand receptor complexes' binding strength. T. ornate and P. pavonica had the highest activity against K. pneumonia, with 22.50 mm (0.78 µg/ml) and 22.23 mm (5.10 µg/ml) obtained, respectively. In a concentration-dependent manner, the extract components demonstrated substantial antioxidant activity. P. pavonica had the highest scavenging activity (78.00%, IC50 = 6.35 µg/ml), while ascorbic acid had a 96.45% scavenging impact. Because the chemicals bind to the Lipinski Ro5, they have drug-like characteristics. The compounds had no hepatotoxic effects. P. pavonica extract has the prospect of being used as a source of medicinal drug-like chemicals. The docking investigation found a strong correlation between the experimental results and the docking results. Finally, brown seaweed extract, particularly P. pavonica extract, demonstrated strong antibacterial, antioxidant, and free radical scavenging properties.

Chemoinformatic Characterization of NAPROC-13: A Database for Natural Product 13C NMR Dereplication

Natural products (NPs) are secondary metabolites of natural origin with broad applications across various human activities, particularly the discovery of bioactive compounds. Structural elucidation of new NPs entails significant cost and effort. On the other hand, the dereplication of known compounds is crucial for the early exclusion of irrelevant compounds in contemporary pharmaceutical research. NAPROC-13 stands out as a publicly accessible database, providing structural and 13C NMR spectroscopic information for over 25 000 compounds, rendering it a pivotal resource in natural product (NP) research, favoring open science. This study seeks to quantitatively analyze the chemical content, structural diversity, and chemical space coverage of NPs within NAPROC-13, compared to FDA-approved drugs and a very diverse subset of NPs, UNPD-A. Findings indicated that NPs in NAPROC-13 exhibit properties comparable to those in UNPD-A, albeit showcasing a notably diverse array of structural content, scaffolds, ring systems of pharmaceutical interest, and molecular fragments. NAPROC-13 covers a specific region of the chemical multiverse (a generalization of the chemical space from different chemical representations) regarding physicochemical properties and a region as broad as UNPD-A in terms of the structural features represented by fingerprints.

Current Treatments, Emerging Therapeutics, and Natural Remedies for Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a chronic, lifelong disorder characterized by inflammation of the gastrointestinal (GI) tract. The exact etiology of IBD remains incompletely understood due to its multifaceted nature, which includes genetic predisposition, environmental factors, and host immune response dysfunction. Currently, there is no cure for IBD. This review discusses the available treatment options and the challenges they present. Importantly, we examine emerging therapeutics, such as biologics and immunomodulators, that offer targeted treatment strategies for IBD. While many IBD patients do not respond adequately to most biologics, recent clinical trials combining biologics with small-molecule drugs (SMDs) have provided new insights into improving the IBD treatment landscape. Furthermore, numerous novel and specific therapeutic targets have been identified. The high cost of IBD drugs poses a significant barrier to treatment, but this challenge may be alleviated with the development of more affordable biosimilars. Additionally, emerging point-of-care protein biomarkers from serum and plasma are showing potential for enhancing the precision of IBD diagnosis and prognosis. Several natural products (NPs), including crude extracts, small molecules, and peptides, have demonstrated promising anti-inflammatory activity in high-throughput screening (HTS) systems and advanced artificial intelligence (AI)-assisted platforms, such as molecular docking and ADMET prediction. These platforms are advancing the search for alternative IBD therapies derived from natural sources, potentially leading to more affordable and safer treatment options with fewer side effects.

Natural Products in the Treatment of Retinopathy of Prematurity: Exploring Therapeutic Potentials

Retinopathy of prematurity (ROP) is a vascular disorder affecting the retinas of preterm infants. This condition arises when preterm infants in incubators are exposed to high oxygen levels, leading to oxidative stress, inflammatory responses, and a downregulation of vascular endothelial growth factors, which causes the loss of retinal microvascular capillaries. Upon returning to room air, the upregulation of vascular growth factors results in abnormal vascular growth of retinal endothelial cells. Without appropriate intervention, ROP can progress to blindness. The prevalence of ROP has risen, making it a significant cause of childhood blindness. Current treatments, such as laser therapy and various pharmacologic approaches, are limited by their potential for severe adverse effects. Therefore, a deeper understanding of ROP's pathophysiology and the development of innovative treatments are imperative. Natural products from plants, fungi, bacteria, and marine organisms have shown promise in treating various diseases and have gained attention in ROP research due to their minimal side effects and wide-ranging beneficial properties. This review discusses the roles and mechanisms of natural products that hold potential as therapeutic agents in ROP management.

Computational discovery of dual potential inhibitors of SARS-CoV-2 spike/ACE2 and Mpro: 3D-pharmacophore, docking-based virtual screening, quantum mechanics and molecular dynamics

To find drugs against COVID-19, caused by the SARS-CoV-2, promising targets include the fusion of the viral spike with the human angiotensin-converting enzyme 2 (ACE2) as well as the main protease (Mpro). These proteins are responsible for viral entry and replication, respectively. We combined several state-of-the-art computational methods, including, protein-ligand interaction fingerprint, 3D-pharmacophores, molecular-docking, MM-GBSA, DFT, and MD simulations to explore two databases: ChEMBL and NANPDB to identify molecules that could both block spike/ACE2 fusion and inhibit Mpro. A total of 1,690,649 compounds from the two databases were screened using the pharmacophore model obtained from PLIF analysis. Five recent complexes of Mpro co-crystallized with different ligands were used to generate the pharmacophore model, allowing 4,829 compounds that passed this prefilter. These were then submitted to molecular docking against Mpro. The 5% top-ranked docking hits from docking result having scores < -8.32 kcal mol-1 were selected and then docked against spike/ACE2. Only four compounds: ChEMBL244958, ChEMBL266531, ChEMBL3680003, and 1-methoxy-3-indolymethyl glucosinolate (4) displayed binding energies < - 8.21 kcal mol-1 (for the native ligand) were considered as putative dual-target inhibitors. Furthermore, predictive ADMET, MM-GBSA and DFT/6-311G(d,p) were performed on these compounds and compared with those of well-known antivirals. DFT calculations showed that ChEMBL244958 and compound 4 had significant predicted reactivity values. Molecular dynamics simulations of the docked complexes were run for 100 ns and used to validate the stability docked poses and to confirm that these hits are putative dual binders of the spike/ACE2 and the Mpro.

The interplay of p38 MAPK signaling and mitochondrial metabolism, a dynamic target in cancer and pathological contexts

Mitochondria play a crucial role in cellular metabolism and bioenergetics, orchestrating various cellular processes, including energy production, metabolism, adaptation to stress, and redox balance. Besides, mitochondria regulate cellular metabolic homeostasis through coordination with multiple signaling pathways. Importantly, the p38 mitogen-activated protein kinase (MAPK) signaling pathway is a key player in the intricate communication with mitochondria, influencing various functions. This review explores the multifaced interaction between the mitochondria and p38 MAPK signaling and the consequent impact on metabolic alterations. Overall, the p38 MAPK pathway governs the activities of key mitochondrial proteins, which are involved in mitochondrial biogenesis, oxidative phosphorylation, thermogenesis, and iron homeostasis. Additionally, p38 MAPK contributes to the regulation of mitochondrial responses to oxidative stress and apoptosis induced by cancer therapies or natural substances by coordinating with other pathways responsible for energy homeostasis. Therefore, dysregulation of these interconnected pathways can lead to various pathologies characterized by aberrant metabolism. Consequently, gaining a deeper understanding of the interaction between mitochondria and the p38 MAPK pathway and their implications presents exciting forecasts for novel therapeutic interventions in cancer and other disorders characterized by metabolic dysregulation.

Aptamers for the Delivery of Plant-Based Compounds: A Review

Natural compounds have a high potential for the treatment of various conditions, including infections, inflammatory diseases, and cancer. However, they usually present poor pharmacokinetics, low specificity, and even toxicity, which limits their use. Therefore, targeted drug delivery systems, typically composed of a carrier and a targeting ligand, can enhance natural product selectivity and effectiveness. Notably, aptamers-short RNA or single-stranded DNA molecules-have gained attention as promising ligands in targeted drug delivery since they are simple to synthesize and modify, and they present high tissue permeability, stability, and a wide array of available targets. The combination of natural products, namely plant-based compounds, with a drug delivery system utilizing aptamers as targeting agents represents an emerging strategy that has the potential to broaden its applications. This review discusses the potential of aptamers as targeting agents in the delivery of natural compounds, as well as new trends and developments in their utilization in the field of medicine.