Applications of integrated data mining methods to exploring natural product space for acetylcholinesterase inhibitors

Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities

As coronavirus disease 2019 (COVID-19) threatens human health globally, infectious disorders have become one of the most challenging problem for the medical community. Natural products (NP) have been a prolific source of antimicrobial agents with widely divergent structures and a range vast biological activities. A dataset comprising 618 articles, including 646 NP-based compounds from 672 species of natural sources with biological activities against 21 infectious pathogens from five categories, was assembled through manual selection of published articles. These data were used to identify 268 NP-based compounds classified into ten groups, which were used for network pharmacology analysis to capture the most promising lead-compounds such as agelasine D, dicumarol, dihydroartemisinin and pyridomycin. The distribution of maximum Tanimoto scores indicated that compounds which inhibited parasites exhibited low diversity, whereas the chemistries inhibiting bacteria, fungi, and viruses showed more structural diversity. A total of 331 species of medicinal plants with compounds exhibiting antimicrobial activities were selected to classify the family sources. The family Asteraceae possesses various compounds against C. neoformans, the family Anacardiaceae has compounds against Salmonella typhi, the family Cucurbitacea against the human immunodeficiency virus (HIV), and the family Ancistrocladaceae against Plasmodium. This review summarizes currently available data on NP-based antimicrobials against refractory infections to provide information for further discovery of drugs and synthetic strategies for anti-infectious agents.

Future Directions for the Discovery of Natural Product-Derived Immunomodulating Drugs

Drug discovery from natural sources is going through a renaissance, having spent many decades in the shadow of synthetic molecule drug discovery, despite the fact that natural product-derived compounds occupy a much greater chemical space than those created through synthetic chemistry methods. With this new era comes new possibilities, not least the novel targets that have emerged in recent times and the development of state-of-the-art technologies that can be applied to drug discovery from natural sources. Although progress has been made with some immunomodulating drugs, there remains a pressing need for new agents that can be used to treat the wide variety of conditions that arise from disruption, or over-activation, of the immune system; natural products may therefore be key in filling this gap. Recognising that, at present, there is no authoritative article that details the current state-of-the-art of the immunomodulatory activity of natural products, this in-depth review has arisen from a joint effort between the International Union of Basic and Clinical Pharmacology (IUPHAR) Natural Products and Immunopharmacology, with contributions from a Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation number of world-leading researchers in the field of natural product drug discovery, to provide a "position statement" on what natural products has to offer in the search for new immunomodulatory argents. To this end, we provide a historical look at previous discoveries of naturally occurring immunomodulators, present a picture of the current status of the field and provide insight into the future opportunities and challenges for the discovery of new drugs to treat immune-related diseases.

A review of pharmacological and pharmacokinetic properties of Forsythiaside A

Traditional Chinese medicine plays a significant role in the treatment of various diseases and has attracted increasing attention for clinical applications. Forsythiae Fructus, the dried fruit of Forsythia suspensa (Thunb.) Vahl, is a widely used Chinese medicinal herb in clinic for its extensive pharmacological activities. Forsythiaside A is the main active index component isolated from Forsythiae Fructus and possesses prominent bioactivities. Modern pharmacological studies have confirmed that Forsythiaside A exhibits significant activities in treating various diseases, including inflammation, virus infection, neurodegeneration, oxidative stress, liver injury, and bacterial infection. In this review, the pharmacological activities of Forsythiaside A have been comprehensively reviewed and summarized. According to the data, Forsythiaside A shows remarkable anti-inflammation, antivirus, neuroprotection, antioxidant, hepatoprotection, and antibacterial activities through regulating multiple signaling transduction pathways such as NF-κB, MAPK, JAK/STAT, Nrf2, RLRs, TRAF, TLR7, and ER stress. In addition, the toxicity and pharmacokinetic properties of Forsythiaside A are also discussed in this review, thus providing a solid foundation and evidence for further studies to explore novel effective drugs from Chinese medicine monomers.

Isolation and Characterization of Acetylcholinesterase Inhibitors from Piper longum and Binding Mode Predictions

Restoration of cholinergic function is considered a rational approach to enhance cognitive performance. Acetylcholinesterase inhibitors are still the best therapeutic option for Alzheimer's disease. The fruits of Piper longum have been used in traditional medicines for the treatment of memory loss. It was demonstrated that the dichloromethane extract of these fruits is able to inhibit acetylcholinesterase. Thus, the aim of this study was to identify the contained acetylcholinesterase inhibitors. The active zones were presented via TLC-bioautography, and five compounds were isolated in the process of a bioassay-guided phytochemical investigation. Their structures were characterized as piperine, methyl piperate, guineenisine, pipercide, and pellitorine using spectroscopy and spectrometry methods (UV, IR, MS, ¹H-, and ¹³C-NMR). In vitro acetylcholinesterase inhibitory activities of the isolates and their IC₅₀ values were determined via a colorimetric assay. Three of them exhibited enzyme inhibitory activities, with piperine being the most potent compound (IC₅₀ of 0.3 mM). In order to investigate the binding mode of the tested compounds, docking studies were performed using the X-ray crystal structure of acetylcholinesterase from Tetronarce californica with the Protein Data Bank code 1EVE. The content of the active compounds in the extract was determined by a developed HPLC method. Piperine was present in the maximum quantity in the fruits (0.57%), whereas methyl piperate contained the minimum content (0.10%).

A Strength-Weaknesses-Opportunities-Threats (SWOT) Analysis of Cheminformatics in Natural Product Research

Cheminformatics-based techniques, such as molecular modeling, docking, virtual screening, and machine learning, are well accepted for their usefulness in drug discovery and development of therapeutically relevant small molecules. Although delayed by several decades, their application in natural product research has led to outstanding findings. Combining information obtained from different sources, i.e., virtual predictions, traditional medicine, structural, biochemical, and biological data, and handling big data effectively will open up new possibilities, but also challenges in the future. Strategies and examples will be presented on how to integrate cheminformatics in pharmacognostic workflows to benefit from these two highly complementary disciplines toward streamlining experimental efforts. While considering their limits and pitfalls and by exploiting their potential, computer-aided strategies should successfully guide future studies and thereby augment our knowledge of bioactive natural lead structures.

Antiviral effect of forsythoside A from Forsythia suspensa (Thunb.) Vahl fruit against influenza A virus through reduction of viral M1 protein

ETHNOPHARMACOLOGICAL RELEVANCE

Yinqiaosan is a classical traditional Chinese medicine formula, which has been used to treat respiratory diseases since ancient China. It consists of nine herbs and among them, Forsythia suspensa (Thunb.) Vahl fruit is one of the major herbal components. Despite the long history of Yinqiaosan, the active compounds and the mechanisms of action of this formula remain elusive.

AIM OF THE STUDY

The present study aimed to examine the suppressive effect of Yinqiaosan on influenza virus and to identify the active components in the formula targeting influenza.

MATERIALS AND METHODS

Anti-influenza virus effect of Yinqiaosan was assessed by tissue culture infective dose assay, and was also tested in an in vivo mouse model. Active compound from the formula was identified with a bioactivity-guided fractionation scheme. The potential mode of action of the compound was further investigated by identifying the host cell signaling pathways and viral protein production using in vitro cell culture models.

RESULTS

Our results showed that forsythoside A from Forsythia suspensa (Thunb.) Vahl fruit, a major herbal component in Yinqiaosan, reduced the viral titers of different influenza virus subtypes in cell cultures and increased the survival rate of the mice in an in vivo influenza virus infection model. Further experiments on the mode of action of forsythoside A showed that it reduced the influenza M1 protein, which in turn intervened the budding process of the newly formed virions and eventually limited the virus spread.

CONCLUSION

Results of our present study provides scientific evidence to support to the application of a traditional herbal formula. We also identify novel candidate compound for future drug development against influenza virus.

The re-emergence of natural products for drug discovery in the genomics era

Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.

Catechol alkenyls from Semecarpus anacardium: acetylcholinesterase inhibition and binding mode predictions

ETHNOPHARMACOLOGICAL RELEVANCE

The fruits of Semecarpus anacardium L. f. (Anacardiaceae) are used in Ayurvedic medicine and also in Iranian Traditional Medicine for various indications, among those for retarding and treatment of dementia.

AIM OF THE STUDY

The severity of Alzheimer's disease obviously correlates with a cholinergic deficit. In a screening for acetylcholinesterase (AChE) inhibitory activity, an extract from the fruit resin of Semecarpus anacardium was among the most active ones. Thus, the aim of this study was to isolate the active compounds and to investigate them in detail. Their binding mode to the active site of AChE was investigated by in silico docking experiments.

MATERIALS AND METHODS

From a dichloromethane extract in an activity-guided fractionation the active compounds were isolated under use of different chromatographic techniques. Their structures were unambiguously identified by one and two-dimensional (1)H and (13)C NMR spectroscopy and mass spectrometry and their cholinesterase inhibitory activities were determined by a microplate assay. In order to compare the 3D active sites of AChE from Torpedo californica (TcAChE) and from Electrophorus electricus (EeAChE), three files from the Protein Data Bank (PDB) were used and for docking experiments, GOLD 3.1 software was employed. The concentrations of active compounds in the extract and the fruits were determined by HPLC analysis.

RESULTS

The active compounds were determined as 1',2'-dihydroxy-3'-pentadec-8-enylbenzene (A) and 1',2'-dihydroxy-3'-pentadeca-8,11-dienylbenzene (B). Their IC(50) values in an in vitro assay on AChE inhibition were determined as 12 and 34 μg/mL, respectively, while they were not active in the inhibition of butyrylcholinesterase (BChE). In silico docking experiments showed a similar bioactivity for compounds A and B. The concentration of compounds A and B in the fruits was 1.85% and 1.88%, respectively.

CONCLUSION

In the search for the active principle of the fruit resin of Semecarpus anacardium, compounds A and B were identified as two selective inhibitors for AChE versus BChE.

Morphinans and isoquinolines: acetylcholinesterase inhibition, pharmacophore modeling, and interaction with opioid receptors

Following indications from pharmacophore-based virtual screening of natural product databases, morphinan and isoquinoline compounds were tested in vitro for acetylcholinesterase (AChE) inhibition. After the first screen, active and inactive compounds were used to build a ligand-based pharmacophore model in order to prioritize compounds for biological testing. Among the virtual hits tested, the enrichment of actives was significantly higher than in a random selection of test compounds. The most active compounds were biochemically tested for their activity on mu, delta, and kappa opioid receptors.