Cheminformatic comparison of approved drugs from natural product versus synthetic origins

Occurrence of "Natural Selection" in Successful Small Molecule Drug Discovery

Published compounds from ChEMBL version 32 are used to seek evidence for the occurrence of "natural selection" in drug discovery. Three measures of natural product (NP) character were applied, to compare time- and target-matched compounds reaching the clinic (clinical compounds in phase 1-3 development and approved drugs) with background compounds (reference compounds). Pseudo-NPs (PNPs), containing NP fragments combined in ways inaccessible by nature, are increasing over time, reaching 67% of clinical compounds first disclosed since 2010. PNPs are 54% more likely to be found in post-2008 clinical versus reference compounds. The majority of target classes show increased clinical compound NP character versus their reference compounds. Only 176 NP fragments appear in >1000 clinical compounds published since 2008, yet these make up on average 63% of the clinical compound's core scaffolds. There is untapped potential awaiting exploitation, by applying nature's building blocks─"natural intelligence"─to drug design.

Natural Products Have Increased Rates of Clinical Trial Success throughout the Drug Development Process

Natural products (NPs) or their derivatives represent a large proportion of drugs that successfully progress through clinical trials to approval. This study explores the presence of NPs in both early- and late-stage drug discovery to determine their success rate, and the factors or features of natural products that contribute to such success. As a proxy for early drug development stages, we analyzed patent applications over several decades, finding a consistent proportion of NP, NP-derived, and synthetic-compound-based patent documents, with the latter group outnumbering NP and NP-derived ones (approximately 77% vs 23%). We next assessed clinical trial data, where we observed a steady increase in NP and NP-derived compounds from clinical trial phases I to III (from approximately 35% in phase I to 45% in phase III), with an inverse trend observed in synthetics (from approximately 65% in phase I to 55% in phase III). Finally, in vitro and in silico toxicity studies revealed that NPs and their derivatives were less toxic alternatives to their synthetic counterparts. These discoveries offer valuable insights for successful NP-based drug development, highlighting the potential benefits of prioritizing NPs and their derivatives as starting points.

Hybrid non-animal modeling: A mechanistic approach to predict chemical hepatotoxicity

Developing mechanistic non-animal testing methods based on the adverse outcome pathway (AOP) framework must incorporate molecular and cellular key events associated with target toxicity. Using data from an in vitro assay and chemical structures, we aimed to create a hybrid model to predict hepatotoxicants. We first curated a reference dataset of 869 compounds for hepatotoxicity modeling. Then, we profiled them against PubChem for existing in vitro toxicity data. Of the 2560 resulting assays, we selected the mitochondrial membrane potential (MMP) assay, a high-throughput screening (HTS) tool that can test chemical disruptors for mitochondrial function. Machine learning was applied to develop quantitative structure-activity relationship (QSAR) models with 2536 compounds tested in the MMP assay for screening new compounds. The MMP assay results, including QSAR model outputs, yielded hepatotoxicity predictions for reference set compounds with a Correct Classification Ratio (CCR) of 0.59. The predictivity improved by including 37 structural alerts (CCR = 0.8). We validated our model by testing 37 reference set compounds in human HepG2 hepatoma cells, and reliably predicting them for hepatotoxicity (CCR = 0.79). This study introduces a novel AOP modeling strategy that combines public HTS data, computational modeling, and experimental testing to predict chemical hepatotoxicity.

A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery

The ENPKG framework organizes large heterogeneous metabolomics data sets as a knowledge graph, offering exciting opportunities for drug discovery and chemodiversity characterization.

Preparation and characterization of new salts of tioconazole. Comparison of their dissolution performance

Tioconazole is an effective antifungal agent with very low solubility in aqueous media, which limits its bioavailability and efficacy. Aiming to overcome the drug limitations by improving the solubility of this active pharmaceutical ingredient, solution precipitation techniques were employed to prepare four new crystalline salts, namely the mesylate, tosylate, maleate (1:1), and fumarate (1:1) hemihydrate. The thermal stabilities, dissolution properties, and structural characteristics of the solids were determined, and the study was extended to compare their properties with the already-known oxalate salt. The structural characterization of the new phases was carried out using a multi-method approach, which included thermal (differential scanning calorimetry and thermogravimetry), diffractometric (powder X-ray diffraction), and spectroscopic (near-infrared and mid-infrared) methodologies. The determination of the melting point of the salts confirmed the findings made by thermal methods. Functional characteristics of the salts, involving their intrinsic dissolution rates were also determined. It was found that the salts exhibited improved thermal stability and that the nature of the counterion modulated their dissolution characteristics. The salts displayed better intrinsic dissolution rates than the free base, to the point of being "highly soluble" according to the Biopharmaceutical Classification System. At pH 4.3, the sulfonic acid derivatives exhibited better dissolution rates than their carboxylic acid-derived counterparts, greatly improved regarding bare tioconazole. The results suggest that the salts have great potential to be used as replacements for the free base; in principle, careful salt selection may help to fulfill each solubility need for the different scenarios where the drug may be used.

Plants in Menstrual Diseases: A Systematic Study from Italian Folk Medicine on Current Approaches

Background: Plant-based remedies have been used since antiquity to treat menstrual-related diseases (MD). From the late nineteenth to the early to mid-twentieth century, Italian folk remedies to treat "women's diseases" were documented in a vast corpus of literature sources. Aim: The purpose of this paper is to bring to light the plant-based treatments utilized by Italian folk medicine to heal clinical manifestations of premenstrual syndrome (PMS), dysmenorrhea, amenorrhea and menstrual disorders in an attempt to discuss these remedies from a modern pharmacological point of view. Moreover, we compare the medical applications described by Hippocrates with those utilized by Italian folk medicine to check if they result from a sort of continuity of use by over two thousand years. Results: Out of the 54 plants employed in Italian folk medicine, 25 (46.3%) were already documented in the pharmacopoeia of the Corpus Hippocraticum for treating MD. Subsequently, a detailed search of scientific data banks such as Medline and Scopus was undertaken to uncover recent results concerning bioactivities of the plant extracts to treat MD. About 26% of the plants used by Italian folk medicine, nowadays, have undergone human trials to assess their actual efficacy. At the same time, about 41% of these herbal remedies come back to in different countries. Conclusions: Active principles extracted from plants used by Italian folk healers could be a promising source of knowledge and represent strength candidates for future drug discovery for the management of MD.

Micromonosporaceae biosynthetic gene cluster diversity highlights the need for broad-spectrum investigations

Investigations of the bacterial family Micromonosporaceae have enabled the development of secondary metabolites critical to human health. Historical investigation of bacterial families for natural product discovery has focused on terrestrial strains, where time-consuming isolation processes often lead to the rediscovery of known compounds. To investigate the secondary metabolite potential of marine-derived Micromonosporaceae , 38 strains were sequenced, assembled and analysed using antiSMASH and BiG-SLiCE. BiG-SLiCE contains a near-comprehensive dataset of approximately 1.2 million publicly available biosynthetic gene clusters from primarily terrestrial strains. Our marine-derived Micromonosporaceae were directly compared to BiG-SLiCE’s preprocessed database using BiG-SLiCE’s query mode; genetic diversity within our strains was uncovered using BiG-SCAPE and metric multidimensional scaling analysis. Our analysis of marine-derived Micromonosporaceae emphasizes the clear need for broader genomic investigations of marine strains to fully realize their potential as sources of new natural products.

Learning from Safe-by-Design for Safe-and-Sustainable-by-Design: Mapping the current landscape of Safe-by-Design reviews, case studies, and frameworks

With the introduction of the European Commission's "Safe and Sustainable-by-Design" (SSbD) framework, the interest in understanding the implications of safety and sustainability assessments of chemicals, materials, and processes at early-innovation stages has skyrocketed. Our study focuses on the "Safe-by-Design" (SbD) approach from the nanomaterials sector, which predates the SSbD framework. In this assessment, SbD studies have been compiled and categorized into reviews, case studies, and frameworks. Reviews of SbD tools have been further classified as quantitative, qualitative, or toolboxes and repositories. We assessed the SbD case studies and classified them into three categories: safe(r)-by-modeling, safe(r)-by-selection, or safe(r)-by-redesign. This classification enabled us to understand past SbD work and subsequently use it to define future SSbD work so as to avoid confusion and possibilities of "SSbD-washing" (similar to greenwashing). Finally, the preexisting SbD frameworks have been studied and contextualized against the SSbD framework. Several key recommendations for SSbD based on our analysis can be made. Knowledge gained from existing approaches such as SbD, green and sustainable chemistry, and benign-by-design approaches needs to be preserved and effectively transferred to SSbD. Better incorporation of chemical and material functionality into the SSbD framework is required. The concept of lifecycle thinking and the stage-gate innovation model need to be reconciled for SSbD. The development of high-throughput screening models is critical for the operationalization of SSbD. We conclude that the rapid pace of both SbD and SSbD development necessitates a regular mapping of the newly published literature that is relevant to this field.

Synthetic Matching of Complex Monoterpene Indole Alkaloid Chemical Space

Monoterpene indole alkaloids (MIAs) are endowed with high structural and spatial complexity and characterized by diverse biological activities. Given this complexity-activity combination in MIAs, rapid and efficient access to chemical matter related to and with complexity similar to these alkaloids would be highly desirable, since such compound classes might display novel bioactivity. We describe the design and synthesis of a pseudo-natural product (pseudo-NP) collection obtained by the unprecedented combination of MIA fragments through complexity-generating transformations, resulting in arrangements not currently accessible by biosynthetic pathways. Cheminformatic analyses revealed that both the pseudo-NPs and the MIAs reside in a unique and common area of chemical space with high spatial complexity-density that is only sparsely populated by other natural products and drugs. Investigation of bioactivity guided by morphological profiling identified pseudo-NPs that inhibit DNA synthesis and modulate tubulin. These results demonstrate that the pseudo-NP collection occupies similar biologically relevant chemical space that Nature has endowed MIAs with.

Clinical development and informatics analysis of natural and semi-synthetic flavonoid drugs: A critical review

BACKGROUND

Flavonoids are one of the most important metabolites with vast structural diversity and a plethora of potential pharmacological applications, which have drawn considerable attention in the laboratory. Nevertheless, it remains uncertain how many candidates were progressed to clinical application.

AIM OF REVIEW

We carried out a critical review of natural and semi-synthetic flavonoid drugs and candidates undergoing different clinical phases worldwide by applying an adequate search method and conducted a brief cheminformatic and bioinformatic analysis. It was expected that the obtained results might narrow the screening scope and reduce the cost of drug research and development.

KEY SCIENTIFIC CONCEPTS OF REVIEW

To our knowledge, this is the most systematic summarization of flavonoid-based drugs and clinical candidates to date. It was found that a total of 19 flavonoid-based drugs have been approved for the market, and of these, natural flavonoids accounted for 52.6%. Besides, a total of 36 flavonoid-based clinical candidates are undergoing or suspended in different phases, and of these, natural flavonoids account for 44.4%. Thus, natural flavonoids remain the best option for finding novel agents/active templates, and when investigated in conjunction with synthetic chemicals and biologicals, they offer the potential to discover novel structures that can lead to effective agents against a variety of human diseases. Additionally, flavonoid-based marketed drugs have been successful in cardiovascular treatment, and the related drugs account for more than 30% of marketed drugs. However, the use of flavonoids as antineoplastic and immunomodulating agents is not likely for approximately 50% of the candidates suspended in the clinical stage. Interestingly, the marketed drugs covered a broader range of chemical spaces based on size, polarity, and three-dimensional structure compared to the clinical candidates. In addition, flavonoid glycosides with poor oral bioavailability account for 36.8% of the marketed drugs, and thus, they could be thoroughly investigated.

In-silico investigations on the anticancer activity of selected 2-aryloxazoline derivatives against breast cancer

As the in-silico study has become an important tool to search for new drugs in the concurrent era with towering acceptance and accuracy, it has been employed in our research to unearth effective cancer drugs. Breast cancer has accounted for the most serious diseases for both men and women. Although few research outputs have been obtained on breast cancer, these are not an adequate amount to ascertain new drugs. Due to this gap, virtual screening, in-silico study, and computational techniques have been used to provide the ability to design and select anticancer compounds with desirable drug-like properties of breast cancer protein, which is commonly known as fatty acid synthase. A total of nine derivatives of 2-aryloxazoline compounds were chosen, and In-silico was studied to evaluate as a potential anticancer agent with the comparison of seven Food and Drug Administration(FDA) approved breast cancer drugs. These compounds were subjected to computational studies for quantum calculations, ADME and Lipinski analysis, as well as molecular docking and MD simulations against a variety of therapeutic targets involved in cell proliferation of fatty acid synthase (PDB ID:3TJM, 3ERT, 4OAR, 2J6M). An in-silico docking study reveals that ligands Hit-4, Hit-6, and Hit-8 had the highest docking scores at -10.3 kcal/mol, -10.3 kcal/mol, and -10.2 kcal/mol towards the protein of fatty acid synthase. The ligands had docking scores better than the standard anti-breast cancer drug gefitinib (-5.3 kcal/mole). Our findings demonstrate how crucial it is for pharmaceutical researchers to develop novel drugs for the treatment of breast cancer.Communicated by Ramaswamy H. Sarma.

Spacial Score─A Comprehensive Topological Indicator for Small-Molecule Complexity

The fraction of sp3-hybridized carbons (Fsp3) and the fraction of stereogenic carbons (FCstereo) are two widely employed scores of molecular complexity with strong links to biologically relevant features. However, they do not comprehensively express molecular topology, and they often do not match the chemical intuition of complexity. We propose the spacial score (SPS) as an empirical scoring system that builds upon the principle underlying Fsp3 and FCstereo and expresses the spacial complexity of a compound in a uniform manner on a highly granular scale. The size-normalized SPS (nSPS) can differentiate distributions of natural products and synthetic compounds and is applicable in the analysis of biological activity data. Analysis of the ChEMBL database revealed general trends of increasing selectivity and potency with increasing nSPS. SPS can also be used advantageously in planning and analysis of synthesis programs for direct comparison of chemical transformations and intermediates in reaction sequences.

A chemoinformatic analysis on natural glycosides with respect to biological origin and structural class

Covering: up to 202216.19% of reported natural products (NPs) in the Dictionary of Natural Products (DNP) are glycosides. As one of the most important NPs' structural modifications, glycosylation can change the NPs' polarity, making the aglycones more amphipathic. However, until now, little is known about the general distribution profile of the natural glycosides in different biological sources or structural types. The reason, structural or species preferences of the natural glycosylation remain unclear. In this highlight, chemoinformatic methods were employed to analyze the natural glycosides from DNP, the most comprehensively annotated NP database. We found that the glycosylation ratios of NPs from plants, bacteria, animals and fungi decrease successively, which are 24.99%, 20.84%, 8.40% and 4.48%, respectively. Echinoderm-derived NPs (56.11%) are the most frequently glycosylated, while those produced by molluscs (1.55%), vertebrates (2.19%) and Rhodophyta (3.00%) are the opposite. Among the diverse structural types, a large proportion of steroids (45.19%), tannins (44.78%) and flavonoids (39.21%) are glycosides, yet aminoacids and peptides (5.16%), alkaloids (5.66%) are comparatively less glycosylated. Even within the same biological source or structural type, their glycosylation rates fluctuate drastically between sub- or cross-categories. The substitute patterns of flavonoid and terpenoid glycosides and the most frequently glycosylated scaffolds were identified. NPs with different glycosylation levels occupy different chemical spaces of physicochemical property and scaffold. These findings could help us to interpret the preference of NPs' glycosylation and investigate how NP glycosylation could aid NP-based drug discovery.

In silico modeling-based new alternative methods to predict drug and herb-induced liver injury: A review

New approach methods (NAMs) have been developed to predict a wide range of toxicities through innovative technologies. Liver injury is one of the most extensively studied endpoints due to its severity and frequency, occurring among populations that consume drugs or dietary supplements. In this review, we focus on recent developments of in silico modeling for liver injury prediction using deep learning and in vitro data based on adverse outcome pathways (AOPs). Despite these models being mainly developed using datasets generated from drug-like molecules, they were also applied to the prediction of hepatotoxicity caused by herbal products. As deep learning has achieved great success in many different fields, advanced machine learning algorithms have been actively applied to improve the accuracy of in silico models. Additionally, the development of liver AOPs, combined with big data in toxicology, has been valuable in developing in silico models with enhanced predictive performance and interpretability. Specifically, one approach involves developing structure-based models for predicting molecular initiating events of liver AOPs, while others use in vitro data with structure information as model inputs for making predictions. Even though liver injury remains a difficult endpoint to predict, advancements in machine learning algorithms and the expansion of in vitro databases with relevant biological knowledge have made a huge impact on improving in silico modeling for drug-induced liver injury prediction.

Modified Rice Bran Arabinoxylan by Lentinus edodes Mycelial Enzyme as an Immunoceutical for Health and Aging-A Comprehensive Literature Review

Rice bran arabinoxylan compound (RBAC) is derived from defatted rice bran enzymatically treated with Lentinus edodes mycelium. This review explores biologically active compounds and mechanisms of action that support RBAC as an immunomodulating nutraceutical in generally healthy and/or aging individuals. Thirty-seven (n = 37) primary research articles fulfilled the selection criteria for review. Most research is based on Biobran MGN-3, which consists of complex heteropolysaccharides with arabinoxylan as its primary structure while also containing galactan and glucan. RBAC was found to invoke immunological activities through direct absorption via the digestive tract and interaction with immune cells at the Peyer's patches. RBAC was shown to promote innate defence by upregulating macrophage phagocytosis and enhancing natural killer cell activity while lowering oxidative stress. Through induction of dendritic cell maturation, RBAC also augments adaptive immunity by promoting T and B lymphocyte proliferation. RBAC acts as an immunomodulator by inhibiting mast cell degranulation during allergic reactions, attenuating inflammation, and downregulating angiogenesis by modulating cytokines and growth factors. RBAC has been shown to be a safe and effective nutraceutical for improving immune health, notably in aging individuals with reduced immune function. Human clinical trials with geriatric participants have demonstrated RBAC to have prophylactic benefits against viral infection and may improve their quality of life. Further research should explore RBAC's bioavailability, pharmacodynamics, and pharmacokinetics of the complex heteropolysaccharides within. Translational research to assess RBAC as a nutraceutical for the aging population is still required, particularly in human studies with larger sample sizes and cohort studies with long follow-up periods.

Marine diterpenoid targets STING palmitoylation in mammalian cells

Natural products are important sources of therapeutic agents and useful drug discovery tools. The fused macrocycles and multiple stereocenters of briarane-type diterpenoids pose a major challenge to total synthesis and efforts to characterize their biological activities. Harnessing a scalable source of excavatolide B (excB) from cultured soft coral Briareum stechei, we generated analogs by late-stage diversification and performed structure-activity analysis, which was critical for the development of functional excB probes. We further used these probes in a chemoproteomic strategy to identify Stimulator of Interferon Genes (STING) as a direct target of excB in mammalian cells. We showed that the epoxylactone warhead of excB is required to covalently engage STING at its membrane-proximal Cys91, inhibiting STING palmitoylation and signaling. This study reveals a possible mechanism-of-action of excB, and expands the repertoire of covalent STING inhibitors.

Applications of machine learning in microbial natural product drug discovery

INTRODUCTION

Natural products (NPs) are a desirable source of new therapeutics due to their structural diversity and evolutionarily optimized bioactivities. NPs and their derivatives account for roughly 70% of approved pharmaceuticals. However, the rate at which novel NPs are discovered has decreased. To accelerate the microbial NP discovery process, machine learning (ML) is being applied to numerous areas of NP discovery and development.

AREAS COVERED

This review explores the utility of ML at various phases of the microbial NP drug discovery pipeline, discussing concrete examples throughout each major phase: genome mining, dereplication, and biological target prediction. Moreover, the authors discuss how ML approaches can be applied to semi-synthetic approaches to drug discovery.

EXPERT OPINION

Despite the important role that microbial NPs play in the development of novel drugs, their discovery has declined due to challenges associated with the conventional discovery process. ML is positioned to overcome these limitations given its ability to model complex datasets and generalize to novel chemical and sequence space. Unsurprisingly, ML comes with its own limitations that must be considered for its successful implementation. The authors stress the importance of continuing to build high quality and open access NP datasets to further increase the utility of ML in NP discovery.

Chemoenzymatic Synthesis of Novel Cytotoxic Epoxyketones Using the Eponemycin Biosynthetic Enzyme EpnF

Eponemycin is an α,β-epoxyketone natural product that inhibits the proteasome via covalent interaction of the epoxyketone warhead with catalytic N-terminal threonine residues. The epoxyketone warhead is biosynthesized from a β-ketoacid substrate by EpnF, a recently identified flavin-dependent acyl-CoA dehydrogenase-like enyzme. Herein, we report biochemical characterization of EpnF kinetics and substrate scope using a series of synthetic β-ketoacid substrates. These studies indicate that epoxide formation likely occurs prior to other tailoring reactions in the biosynthetic pathway, and have led to the identification of novel epoxyketone analogues with potent anticancer activity.

Bioactivity-guided isolation of trypanocidal coumarins and dihydro-pyranochromones from selected Apiaceae plant species

Bioactivity-guided isolation of natural products from plant matrices is widely used in drug discovery. Here, this strategy was applied to identify trypanocidal coumarins effective against the parasite Trypanosoma cruzi, the etiologic agent of Chagas disease (American trypanosomiasis). Previously, phylogenetic relationships of trypanocidal activity revealed a coumarin-associated antichagasic hotspot in the Apiaceae. In continuation, a total of 35 ethyl acetate extracts of different Apiaceae species were profiled for selective cytotoxicity against T. cruzi epimastigotes over host CHO-K1 and RAW264.7 cells at 10 μg/mL. A flow cytometry-based T. cruzi trypomastigote cellular infection assay was employed to measure toxicity against the intracellular amastigote stage. Among the tested extracts, Seseli andronakii aerial parts, Portenschlagiella ramosissima and Angelica archangelica subsp. litoralis roots exhibited selective trypanocidal activity and were subjected to bioactivity-guided fractionation and isolation by countercurrent chromatography. The khellactone ester isosamidin isolated from the aerial parts of S. andronakii emerged as a selective trypanocidal molecule (selectivity index ∼9) and inhibited amastigote replication in CHO-K1 cells, though it was significantly less potent than benznidazole. The khellactone ester praeruptorin B and the linear dihydropyranochromones 3'-O-acetylhamaudol and ledebouriellol isolated from the roots of P. ramosissima were more potent and efficiently inhibited the intracellular amastigote replication at < 10 μM. The furanocoumarins imperatorin, isoimperatorin and phellopterin from A. archangelica inhibited T. cruzi replication in host cells only in combination, indicative of superadditive effects, while alloimperatorin was more active in fractions. Our study reports preliminary structure-activity relationships of trypanocidal coumarins and shows that pyranocoumarins and dihydropyranochromones are potential chemical scaffolds for antichagasic drug discovery.

Putative target sites in synganglion for novel ixodid tick control strategies

Acaricide resistance is a global problem that has impacts worldwide. Tick populations with broad resistance to all commercially available acaricides have been reported. Since resistance selection in ticks and their role in pathogen transmission to animals and humans result in important economic and public health burden, it is essential to develop new strategies for their control (i.e., novel chemical compounds, vaccines, biological control). The synganglion is the tick central nervous system and it is responsible for synthesizing and releasing signaling molecules with different physiological functions. Synganglion proteins are the targets of the majority of available acaricides. In this review we provide an overview of the mode-of-action and resistance mechanisms against neurotoxic acaricides in ticks, as well as putative target sites in synganglion, as a supporting tool to identify new target proteins and to develop new strategies for tick control.

Characterization of the hydrochloride salt hemihydrate as a new salt of the antifungal agent tioconazole

Tioconazole is an effective antifungal agent, which has a very low solubility in aqueous media, that limits its bioavailability and efficacy. In an effort to overcome the drug limitations by improving its solubility, the hydrochloride salt was prepared in methanolic 1M HCl and obtained as the hemihydrate, as demonstrated by elemental analysis. Single crystals were grown by slow evaporation from an aqueous 1M HCl solution and their structure was determined using single-crystal X-ray diffraction at 302 K. The structures resulting from dehydration and further rehydration were also assessed, at 333 and 283 K, respectively. The morphology of the crystal, which exhibited birefringence under polarized light, was verified by hot stage microscopy. The solid was characterized by additional means, including thermal analysis (melting point, differential scanning calorimetry and thermogravimetry), spectroscopic methods (mid infrared, near infrared, ¹H, ¹³C and ¹⁵N nuclear magnetic resonance in solution, as well as ¹³C and ¹⁵N solid state with spinning at the magic angle) and X-ray diffraction techniques. Functional evaluation tests, including the intrinsic dissolution rate and the dissolution of powders were also performed. In the intrinsic dissolution rate test, the salt proved to dissolve over 2000 times faster than tioconazole. The results suggest that the new salt has physicochemical and performance properties which may support its use as a replacement of the free base in certain applications, especially where improved dissolution rate, solubility or bioavailability of the drug would be desired.

Rapid and Efficient Access to Novel Bio-Inspired 3-Dimensional Tricyclic SpiroLactams as Privileged Structures via Meyers’ Lactamization

The concept of privileged structure has been used as a fruitful approach for the discovery of novel biologically active molecules. A privileged structure is defined as a semi-rigid scaffold able to display substituents in multiple spatial directions and capable of providing potent and selective ligands for different biological targets through the modification of those substituents. On average, these backbones tend to exhibit improved drug-like properties and therefore represent attractive starting points for hit-to-lead optimization programs. This article promotes the rapid, reliable, and efficient synthesis of novel, highly 3-dimensional, and easily functionalized bio-inspired tricyclic spirolactams, as well as an analysis of their drug-like properties.

Antiparasitic Activity of Hippeastrum Species and Synergistic Interaction between Montanine and Benznidazole against Trypanosoma cruzi

BACKGROUND

Hippeastrum species have a wide range of biological properties. In Argentina, this genus comprises ten widely distributed species.

PURPOSE

To evaluate the antiparasitic and anticholinesterase activities and chemical profiles of seven Argentinean Hippeastrum species and determine the synergism between the major isolated alkaloid-montanine-and benznidazole in anti-Trypanosoma cruzi activity.

METHODS

The antiparasitic activity was evaluated through antiproliferative and viability assays against T. cruzi epimastigotes. Synergism assays were performed using the Chou-Talalay method. AChE and BuChE inhibitory activities were also assessed. The alkaloid composition was obtained using GC-MS analysis.

RESULTS

All extracts showed strong growth inhibition of T. cruzi epimastigote proliferation. The extracts from H. aglaiae, H. aulicum, and H. hybrid stand out for their potent and total growth inhibition, which was comparable to benznidazole. The H. reticulatum extract showed strong Acetylcholinesterase (AChE) inhibitory activities, while five species showed moderate Butyrylcholinesterase (BuChE) inhibition. Fifteen alkaloids were identified by means of GC-MS. Regarding the synergism assessment, the highest synergistic effect was obtained from the combination of montanine and benznidazole.

CONCLUSION

Hippeastrum species bulb extracts from Argentina were shown to be a good source of antiparasitic alkaloids and cholinesterase inhibitors. The synergism between montanine and benznidazole emerges as a potential combination for future studies to treat Chagas disease.

Trends in development and quality assessment of pharmaceutical formulations - F2α analogues in the glaucoma treatment

The ocular delivery route presents a number of challenges in terms of drug administration and bioavailability. The low bioavailability following topical ophthalmic administration shows that there is a clear need for in-depth research aimed at finding both more efficacious molecules and formulations precisely targeted at the site of action. Continuous technological development will eventually result in improved bioavailability, lower dosages, reduced toxicity, fewer adverse effects, and thus better patient compliance and treatment efficacy. Technological development, as well as increasingly stringent quality requirements, help stimulate analytical progress. This is also clearly evident in the case of medicinal products used in the treatment of glaucoma, which are the subject of this review. Impurity profiling of PGF2α analogues, either in the pure substance or in the finished formulation, is a crucial step in assessing their quality. The development of specific, accurate and precise stability-indicating analytical methods for determining the content and related substances seems to be an important issue in relation to this tasks. A total of 27 official and in-house analytical methods are presented that are used for the analysis of latanoprost, travoprost and bimatoprost. The conditions for chromatographic separation with UV or MS/MS detection and the available results obtained during method validation are described. In addition, several aspects are discussed, with particular emphasis on the instability of the analogues in aqueous solution and the phenomenon of isomerism, which affects a potentially large number of degradation products.

Antioxidant Efficacy of Esculetin against Tert-Butyl Hydroperoxide-Induced Oxidative Stress in HEK293 Cells

Esculetin is an antioxidant and anti-inflammatory compound derived from coumarin. Oxidative stress can cause overproduction of reactive oxygen species (ROS), which can lead to the development of chronic kidney failure. In this study, human embryonic kidney 293 (HEK293) cells were treated with tert-butyl hydroperoxide (t-BHP) to determine the antioxidant effects of esculetin. HEK293 cells were treated with t-BHP to validate changes in cell viability, ROS production, and apoptosis, and then treated with esculetin to evaluate the changes. Changes in mRNA and protein levels were analyzed using a proteome kit, PCR, and Western blotting. Esculetin improved HEK293 cell viability and reduced apoptosis caused by t-BHP-induced oxidative stress. At the mRNA and protein levels, esculetin decreased pro-apoptotic factor expression as well as increased anti-apoptotic factor expression. The antioxidant efficacy of esculetin was validated when it inhibited the apoptosis caused by t-BHP-induced oxidative stress in HEK293 cells.

Destroying the Shield of Cancer Stem Cells: Natural Compounds as Promising Players in Cancer Therapy

In a scenario where eco-sustainability and a reduction in chemotherapeutic drug waste are certainly a prerogative to safeguard the biosphere, the use of natural products (NPs) represents an alternative therapeutic approach to counteract cancer diseases. The presence of a heterogeneous cancer stem cell (CSC) population within a tumor bulk is related to disease recurrence and therapy resistance. For this reason, CSC targeting presents a promising strategy for hampering cancer recurrence. Increasing evidence shows that NPs can inhibit crucial signaling pathways involved in the maintenance of CSC stemness and sensitize CSCs to standard chemotherapeutic treatments. Moreover, their limited toxicity and low costs for large-scale production could accelerate the use of NPs in clinical settings. In this review, we will summarize the most relevant studies regarding the effects of NPs derived from major natural sources, e.g., food, botanical, and marine species, on CSCs, elucidating their use in pre-clinical and clinical studies.

Biotechnology and In Vitro Culture as an Alternative System for Secondary Metabolite Production

Medicinal plants are rich sources of bioactive compounds widely used as medicaments, food additives, perfumes, and agrochemicals. These secondary compounds are produced under stress conditions to carry out physiological tasks in plants. Secondary metabolites have a complex chemical structure with pharmacological properties. The widespread use of these metabolites in a lot of industrial sectors has raised the need to increase the production of secondary metabolites. Biotechnological methods of cell culture allow the conservation of plants, as well as the improvement of metabolite biosynthesis and the possibility to modify the synthesis pathways. The objective of this review is to outline the applications of different in vitro culture systems with previously reported relevant examples for the optimal production of plant-derived secondary metabolites.

Synthesis of psychotropic alkaloids from Galbulimima

Efficient syntheses of valuable natural products open gateways from kind learning environments to wicked worlds, where long-term, interdisciplinary research questions can be asked and answered. In this Perspective, we discuss the Galbulimima (GB) alkaloids, metabolites of a rainforest canopy tree that exhibit potent but poorly understood effects in humans, including accounts of hallucination. Recent syntheses from our group have opened up GB alkaloid chemical space for investigation by way of new cross-coupling reactions and gram-scale target production. Although natural product synthesis can be challenging, its objective is obvious. Realization of long-term, enabling goals will be a circuitous journey at the interface of chemistry, pharmacology and neuroscience-a potent mix to foster discovery in the coming century.

Direct α-C-H Alkylation of Structurally Diverse Alcohols via Combined Tavaborole and Photoredox Catalysis

Herein, we report a method that uses antifungal tavaborole as a co-catalyst for direct α-C-H alkylation of structurally diverse alcohols through photoredox catalysis. The protocol features mild conditions, remarkable scope, and wide functional group tolerance, which allows for the construction of a wide array of highly functionalized alcohols, including homoserine derivatives and C-glycosyl amino acids. We also demonstrate the synthetic applications of this methodology to the late-stage functionalization of pharmaceuticals and natural products.

Virtual Screening of Alkaloid and Terpenoid Inhibitors of SMT Expressed in Naegleria sp

The pathogenic form of thermophilic Naegleria sp. i.e., Naegleria fowleri, also known as brain eating amoeba, causes primary amoebic encephalitis (PAM) with a >97% fatality rate. To date, there are no specific drugs identified to treat this disease specifically. The present antimicrobial combinatorial chemotherapy is hard on many patients, especially children. Interestingly, Naegleria fowleri has complex lipid biosynthesis pathways like other protists and also has a strong preference to utilize absorbed host lipids for generating energy. The ergosterol biosynthesis pathway provides a unique drug target opportunity, as some of the key enzymes involved in this pathway are absent in humans. Sterol 24-C Methyltransferase (SMT) is one such enzyme that is not found in humans. To select novel inhibitors for this enzyme, alkaloids and terpenoids inhibitors were screened and tested against two isozymes of SMT identified in N. gruberi (non-pathogenic) as well as its homolog found in yeast, i.e., ERG6. Five natural product derived inhibitors i.e., Cyclopamine, Chelerythrine, Berberine, Tanshinone 2A, and Catharanthine have been identified as potential drug candidates based on multiple criteria including binding affinity, ADME scores, absorption, and, most importantly, its ability to cross the blood brain barrier. This study provides multiple leads for future drug exploration against Naegleria fowleri.

Engineering site-selective incorporation of fluorine into polyketides

Although natural products and synthetic small molecules both serve important medicinal functions, their structures and chemical properties are relatively distinct. To expand the molecular diversity available for drug discovery, one strategy is to blend the effective attributes of synthetic and natural molecules. A key feature found in synthetic compounds that is rare in nature is the use of fluorine to tune drug behavior. We now report a method to site-selectively incorporate fluorine into complex structures to produce regioselectively fluorinated full-length polyketides. We engineered a fluorine-selective trans-acyltransferase to produce site-selectively fluorinated erythromycin precursors in vitro. We further demonstrated that these analogs could be produced in vivo in Escherichia coli on engineering of the fluorinated extender unit pool. By using engineered microbes, elaborate fluorinated compounds can be produced by fermentation, offering the potential for expanding the identification and development of bioactive fluorinated small molecules.

Plant-based engineering for production of high-valued natural products

Covering: up to March 2022Plants are a unique source of complex specialized metabolites, many of which play significant roles in human society. In many cases, however, the availability of these metabolites from naturally occurring sources fails to meet current demands. Thus, there is much interest in expanding the production capacity of target plant molecules. Traditionally, plant breeding, chemical synthesis, and microbial fermentation are considered the primary routes towards large scale production of natural products. Here, we explore the advances, challenges, and future of plant engineering as a complementary path. Although plants are an integral part of our food and agricultural systems and sustain an extensive array of chemical constituents, their complex genetics and physiology have prevented the optimal exploitation of plants as a production chassis. We highlight emerging engineering tools and scientific advances developed in recent years that have improved the prospects of using plants as a sustainable and scalable production platform. We also discuss technological limitations and overall economic outlook of plant-based production of natural products.

Theoretical Prediction of Gastrointestinal Absorption of Phytochemicals

The discovery of bioactive compounds for non-invasive therapy has been the goal of research groups focused on pharmacotherapy. Phytonutrients have always been attractive for researchers because they are a significant source of bioactive phytochemicals. Still, it is challenging to determine which components show high biomedical activity and bioavailability after administration. However, based on the chemical structure of these phytochemicals, their physicochemical properties can be calculated to predict the probability of gastrointestinal (GI) absorption after oral administration. Indeed, different researchers have proposed several rules (e.g., Lipinski’s, Veber’s, Ghose’s, and Muegge’s rules) to attain these predictions, but only for synthetic compounds. Most phytochemicals do not fully comply with these rules even though they show high bioactivity and high GI absorption experimentally. Here, we propose a detailed methodology using scientifically validated web-based platforms to determine the physicochemical properties of five phytochemicals found in ginger, echinacea, and tobacco. Furthermore, we analyzed the calculated data and established a protocol based on the integration of these classical rules, plus other extended parameters, that we called the Phytochemical Rule, to obtain a more reliable prediction of the GI absorption of natural compounds. This methodology can help evaluate bioactive phytochemicals as potential drug candidates and predict their oral bioavailability in patients.

Ring systems in natural products: structural diversity, physicochemical properties, and coverage by synthetic compounds

Covering: up to 2021The structural core of most small-molecule drugs is formed by a ring system, often derived from natural products. However, despite the importance of natural product ring systems in bioactive small molecules, there is still a lack of a comprehensive overview and understanding of natural product ring systems and how their full potential can be harnessed in drug discovery and related fields. Herein, we present a comprehensive cheminformatic analysis of the structural and physicochemical properties of 38 662 natural product ring systems, and the coverage of natural product ring systems by readily purchasable, synthetic compounds that are commonly explored in virtual screening and high-throughput screening. The analysis stands out by the use of comprehensive, curated data sets, the careful consideration of stereochemical information, and a robust analysis of the 3D molecular shape and electrostatic properties of ring systems. Among the key findings of this study are the facts that only about 2% of the ring systems observed in NPs are present in approved drugs but that approximately one in two NP ring systems are represented by ring systems with identical or related 3D shape and electrostatic properties in compounds that are typically used in (high-throughput) screening.

AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials

Antibiotic resistance is a major threat to public health. The development of chemo-informatic tools to guide medicinal chemistry campaigns in the efficint design of antibacterial libraries is urgently needed. We present AB-DB, an open database of all-atom force-field parameters, molecular dynamics trajectories, quantum-mechanical properties, and curated physico-chemical descriptors of antimicrobial compounds. We considered more than 300 molecules belonging to 25 families that include the most relevant antibiotic classes in clinical use, such as β-lactams and (fluoro)quinolones, as well as inhibitors of key bacterial proteins. We provide traditional descriptors together with properties obtained with Density Functional Theory calculations. Noteworthy, AB-DB contains less conventional descriptors extracted from μs-long molecular dynamics simulations in explicit solvent. In addition, for each compound we make available force-field parameters for the major micro-species at physiological pH. With the rise of multi-drug-resistant pathogens and the consequent need for novel antibiotics, inhibitors, and drug re-purposing strategies, curated databases containing reliable and not straightforward properties facilitate the integration of data mining and statistics into the discovery of new antimicrobials.

Measurement(s)	molecular physical property analysis objective
Technology Type(s)	Computer Modeling

Natural-Product-Directed Catalytic Stereoselective Synthesis of Functionalized Fused Borane Cluster-Oxazoles for the Discovery of Bactericidal Agents

The identification of an alternative chemical space in order to address the global challenge posed by emerging antimicrobial resistance is very much needed for the discovery of novel antimicrobial lead compounds. Boron clusters are currently being explored in drug discovery due to their unique steric and electronic properties. However, the challenges associated with the synthesis and derivatization techniques of these compounds have limited their utility in the rapid construction of a library of molecules for screening against various biological targets as an alternative molecular platform. Herein, we report a transition-metal-catalyzed regioselective direct B-H alkylation-annulation of the closo-dodecaborate anion with natural products such as menthol and camphor as the directing groups. This method allowed the rapid construction of a library of 1,2,3-trisubstituted clusters, which were evaluated in terms of their antibacterial activity against WHO priority pathogens. Several of the synthesized dodecaborate derivatives displayed medium- to high-level bactericidal activity against Gram-positive and Gram-negative bacteria.

Antiproliferative and cytotoxic activity of Geraniaceae plant extracts against five tumor cell lines

Aim: To determine the antiproliferative and cytotoxic activities of Geranium and Erodium species against human cancer and noncancer cell lines, respectively. Methods: Twenty-one species of Geranium and Erodium were extracted and screened against cancerous and noncancerous human cell lines. Results: In a dose-response manner, G. glaberrimum, G. asphodeloides, E. brandianum and E. leucanthum were able, with variable potency, to inhibit cellular proliferation. Except for  E. brandianum, all extracts induced cellular autophagy in tumor cells with similar levels to that of rapamycin; but, only E. brandianum induced cellular apoptosis, likely through Bcl2 and BAX protein expressions. Discussion: This is the first study to report the potential antiproliferative effects of ethanol extracts of several Geraniaceae species.

Oncopreventive and oncotherapeutic potential of licorice triterpenoid compound glycyrrhizin and its derivatives: Molecular insights

Licorice (Glycyrrhiza glabra) is a well-known natural herb used to treat different ailments since ancient times. Glycyrrhizin (GL), which is the primary triterpenoid compound of licorice extract, has been known to have broad-spectrum pharmacological effects. GL is cleaved into glucuronide and the aglycone, glycyrrhetinic acid (GA), which exists in two stereoisomeric forms: 18α- and 18β-GA. It is well documented that GL and GA have great potential as anti-inflammatory, anticancer, antiviral, anti-diabetic, antioxidant, and hepatoprotective agents. Studies undertaken during the coronavirus disease 2019 pandemic suggest that GL is effective at inhibiting the viral replication of severe acute respiratory syndrome coronavirus 2. The anticancer effects of GL and GA involve modulating various signaling pathways, such as the phosphatase and tensin homolog/phosphatidylinositol 3-kinase/protein kinase B pathway, the mitogen-activated protein kinase, and the mammalian target of rapamycin/signal transducer and activator of transcription 3, which are mainly involved in regulating cancer cell death, oxidative stress, and inflammation. The potential of GL and GA in preventing cancer development and suppressing the growth and invasion of different cancer types has been reviewed in this paper. This review also provides molecular insights on the mechanism of action for the oncopreventive and oncotherapeutic effects of GL and its derivative, GA, which could help develop more specific forms of these agents for clinical use.

Cheminformatic analysis of natural product-based drugs and chemical probes

Covering: 1981 to 2019Natural products continue to play a major role in drug discovery, with half of new chemical entities based structurally on a natural product. Herein, we report a cheminformatic analysis of the structural and physicochemical properties of natural product-based drugs in comparison to top-selling brand-name synthetic drugs, and a selection of chemical probes recently discovered from diversity-oriented synthesis libraries. In this analysis, natural product-based drugs covered a broad range of chemical space based on size, polarity, and three-dimensional structure. Natural product-based structures were also more prevalent in top-selling drugs of 2018 compared to 2006. Further, the drugs clustered well according to biosynthetic origins, but less so based on therapeutic classes. Macrocycles occupied distinctive and relatively underpopulated regions of chemical space, while chemical probes largely overlapped with synthetic drugs. This analysis highlights the continued opportunities to leverage natural products and their pharmacophores in modern drug discovery.

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.

Bioactive Marine Xanthones: A Review

The marine environment is an important source of specialized metabolites with valuable biological activities. Xanthones are a relevant chemical class of specialized metabolites found in this environment due to their structural variety and their biological activities. In this work, a comprehensive literature review of marine xanthones reported up to now was performed. A large number of bioactive xanthone derivatives (169) were identified, and their structures, biological activities, and natural sources were described. To characterize the chemical space occupied by marine-derived xanthones, molecular descriptors were calculated. For the analysis of the molecular descriptors, the xanthone derivatives were grouped into five structural categories (simple, prenylated, O-heterocyclic, complex, and hydroxanthones) and six biological activities (antitumor, antibacterial, antidiabetic, antifungal, antiviral, and miscellaneous). Moreover, the natural product-likeness and the drug-likeness of marine xanthones were also assessed. Marine xanthone derivatives are rewarding bioactive compounds and constitute a promising starting point for the design of other novel bioactive molecules.

In Vitro Evaluation of the Anti-Diabetic Potential of Aqueous Acetone Helichrysum petiolare Extract (AAHPE) with Molecular Docking Relevance in Diabetes Mellitus

Diabetes mellitus (DM) is a chronic metabolic condition that can lead to significant complications and a high fatality rate worldwide. Efforts are ramping up to find and develop novel α-glucosidase and α-amylase inhibitors that are both effective and potentially safe. Traditional methodologies are being replaced with new techniques that are less complicated and less time demanding; yet, both the experimental and computational strategies are viable and complementary in drug discovery and development. As a result, this study was conducted to investigate the in vitro anti-diabetic potential of aqueous acetone Helichrysum petiolare and B.L Burtt extract (AAHPE) using a 2-NBDG, 2-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl) amino)-2-deoxy-d-glucose uptake assay. In addition, we performed molecular docking of the flavonoid constituents identified and quantified by liquid chromatography-mass spectrometry (LC-MS) from AAHPE with the potential to serve as effective and safe α-amylase and α-glucosidase inhibitors, which are important in drug discovery and development. The results showed that AAHPE is a potential inhibitor of both α-amylase and α-glucosidase, with IC₅₀ values of 46.50 ± 6.17 (µg/mL) and 37.81 ± 5.15 (µg/mL), respectively. This is demonstrated by a significant increase in the glucose uptake activity percentage in a concentration-dependent manner compared to the control, with the highest AAHPE concentration of 75 µg/mL of glucose uptake activity being higher than metformin, a standard anti-diabetic drug, in the insulin-resistant HepG2 cell line. The molecular docking results displayed that the constituents strongly bind α-amylase and α-glucosidase while achieving better binding affinities that ranged from ΔG = -7.2 to -9.6 kcal/mol (compared with acarbose ΔG = -6.1 kcal/mol) for α-amylase, and ΔG = -7.3 to -9.0 kcal/mol (compared with acarbose ΔG = -6.3 kcal/mol) for α-glucosidase. This study revealed the potential use of the H. petiolare plant extract and its phytochemicals, which could be explored to develop potent and safe α-amylase and α-glucosidase inhibitors to treat postprandial glycemic levels in diabetic patients.

Modulation of biopharmaceutical properties of acidic drugs using cationic counterions: A critical analysis of FDA-approved pharmaceutical salts

Salification has a successful track record in modulating the biopharmaceutical properties of drugs. This is evident from the significant share (40%) of pharmaceutical salts in FDA-approved drugs in the past 80-years. Based on the ionic nature of drugs, the corresponding cationic or anionic counterions are employed for salification. This review aims to provide the contribution of cationic counterions in FDA-approved drugs from 1939 to 2020. The analysis of 80-years data has shown that the 7.1% of the FDA-approved drugs comprise cationic counterions (98 pharmaceutical salts). Heparin sodium is the pioneering drug in the history of pharmaceutical salts that was approved in 1939 as an anticoagulant medication. Inorganic (sodium, calcium, potassium, magnesium, silver), as well as organic (tromethamine, meglumine, erbumine) cationic counterions, were used in FDA-approved drugs with a major share by sodium (76 drugs). The technical superiority of cationic salts over other salt forms and the parent drug is also exemplified using case studies.

Synthesis of N-Arylcytisine Derivatives Using the Copper-Catalyzed Chan-Lam Coupling

N-Arylcytisine derivatives are quite rare. We report here a practical methodology to obtain these compounds. Using the copper-catalyzed Chan-Lam coupling, we synthesized new N-arylcytisine derivatives at room temperature, in air and using inexpensive phenylboronic acids. Cytisine and 3,5-dihalocytisines can act as substrates, and among the products, the p-Br-derivative 2r was used as a substrate to obtain biaryl derivatives under Pd-coupling conditions; ester 2j was converted into its acid and amide derivatives using classical carbodiimide conditions. This shows that the Chan-Lam cross-coupling reaction can be included as a versatile synthetic tool in the derivatization of natural products.

Medical Species Used in Russia for the Management of Diabetes and Related Disorders

Background: Polyherbal mixtures called "medical species" are part of traditional and officinal medicine in Russia. This review aimed to analyze medical species used in Russia for the treatment of diabetes and related disorders. The information relevant to medical species, diabetes, and obesity was collected from local libraries, the online service E-library.ru, and Google Scholar. The prediction of the antidiabetic activity for the principal compounds identified in plants was performed using the free web resource PASS Online. Results: We collected and analyzed information about the compositions, specificities of use, and posology of 227 medical species. The medical species represent mixtures of 2-15 plants, while the most frequently mentioned in the literature are species comprising 3-6 plants. The top 10 plants among the 158 mentioned in the literature include Vaccinium myrtillus L., Phaseolus vulgaris L., Taraxacum campylodes G.E. Haglund., Urtica dioica L., Rosa spp., Hypericum spp., Galega officinalis L., Mentha × piperita L., Arctium spp, and Fragaria vesca L. The leading binary combination found in medical species comprises the leaves of V. myrtillus and pericarp of P. vulgaris; leaves of V. myrtillus and leaves of U. dioica; and leaves of V. myrtillus and aerial parts of G. officinalis. In triple combinations, in addition to the above-mentioned components, the roots of T. campylodes are often used. These combinations can be regarded as basic mixtures. Other plants are added to improve the efficacy, treat associated disorders, improve gastrointestinal function, prevent allergic reactions, etc. Meanwhile, an increase in plants in the mixture necessitates advanced techniques for quality control. A feature of medical species in Russia is the addition of fresh juices, birch sap, seaweeds, and adaptogenic plants. Modern studies of the mechanisms of action and predicted activities of the principal compounds from medicinal plants support the rationality of polyherbal mixtures. Nevertheless, the mechanisms are not well studied and reported due to the limited number of compounds. Further investigations with calculations of synergistic or additive indices are important for strengthening the scientific fundamentals for the wider use of medical species in the therapy of diabetes. Two medical species, "Arfazetin" (7 medicinal plants) and "Myrphasinum" (12 medicinal plants), are approved for use in officinal medicine. The efficacy of these species was confirmed in several in vivo experiments and clinical trials. According to modern regulatory rules, additional experiments and clinical trials are required for more detailed investigations of the mechanisms of action and confirmation of efficacy. Conclusion: We believe that the scientifically based utilization of rich plant resources and knowledge of Russian herbal medicine can significantly contribute to the local economy as well as to the sectors seeking natural healing products.

Limonin as a Starting Point for the Construction of Compounds with High Scaffold Diversity

Structurally complex natural products have been a fruitful source for the discovery and development of new drugs. In an effort to construct a compound collection populated by architecturally complex members with unique scaffolds, we have used the natural product limonin as a starting point. Limonin is an abundant triterpenoid natural product and, through alteration of its heptacyclic core ring system using short synthetic sequences, a collection of 98 compounds was created, including multiple members with novel ring systems. The reactions leveraged in the construction of these compounds include novel ring cleavage, rearrangements, and cyclizations, and this work is highlighted by the discovery of a novel B-ring cleavage reaction, a unique B/C-ring rearrangement, an atypical D-ring cyclization, among others. Computational analysis shows that 52 different scaffolds/ring systems were produced during the course of this work, of which 36 are unprecedented. Phenotypic screening and structure-activity relationships identified compounds with activity against a panel of cancer cell lines.

NP Navigator: A New Look at the Natural Product Chemical Space

Natural products (NPs), being evolutionary selected over millions of years to bind to biological macromolecules, remained an important source of inspiration for medicinal chemists even after the advent of efficient drug discovery technologies such as combinatorial chemistry and high-throughput screening. Thus, there is a strong demand for efficient and user-friendly computational tools that allow to analyze large libraries of NPs. In this context, we introduce NP Navigator - a freely available intuitive online tool for visualization and navigation through the chemical space of NPs and NP-like molecules. It is based on the hierarchical ensemble of generative topographic maps, featuring NPs from the COlleCtion of Open NatUral producTs (COCONUT), bioactive compounds from ChEMBL and commercially available molecules from ZINC. NP Navigator allows to efficiently analyze different aspects of NPs - chemotype distribution, physicochemical properties, biological activity and commercial availability of NPs. The latter concerns not only purchasable NPs but also their close analogs that can be considered as synthetic mimetics of NPs or pseudo-NPs.

Cheminformatic Profiling and Hit Prioritization of Natural Products with Activities against Methicillin-Resistant Staphylococcus aureus (MRSA)

Several natural products (NPs) have displayed varying in vitro activities against methicillin-resistant Staphylococcus aureus (MRSA). However, few of these compounds have not been developed into potential antimicrobial drug candidates. This may be due to the high cost and tedious and time-consuming process of conducting the necessary preclinical tests on these compounds. In this study, cheminformatic profiling was performed on 111 anti-MRSA NPs (AMNPs), using a few orally administered conventional drugs for MRSA (CDs) as reference, to identify compounds with prospects to become drug candidates. This was followed by prioritizing these hits and identifying the liabilities among the AMNPs for possible optimization. Cheminformatic profiling revealed that most of the AMNPs were within the required drug-like region of the investigated properties. For example, more than 76% of the AMNPs showed compliance with the Lipinski, Veber, and Egan predictive rules for oral absorption and permeability. About 34% of the AMNPs showed the prospect to penetrate the blood–brain barrier (BBB), an advantage over the CDs, which are generally non-permeant of BBB. The analysis of toxicity revealed that 59% of the AMNPs might have negligible or no toxicity risks. Structure–activity relationship (SAR) analysis revealed chemical groups that may be determinants of the reported bioactivity of the compounds. A hit prioritization strategy using a novel “desirability scoring function” was able to identify AMNPs with the desired drug-likeness. Hit optimization strategies implemented on AMNPs with poor desirability scores led to the design of two compounds with improved desirability scores.

Predicting biochemical and physiological effects of natural products from molecular structures using machine learning

Covering: 2016 to 2021Discovery of novel natural products has been greatly facilitated by advances in genome sequencing, genome mining and analytical techniques. As a result, the volume of data for natural products has increased over the years, which started to serve as ingredients for developing machine learning models. In the past few years, a number of machine learning models have been developed to examine various aspects of a molecule by effectively processing its molecular structure. Understanding of the biological effects of natural products can benefit from such machine learning approaches. In this context, this Highlight reviews recent studies on machine learning models developed to infer various biological effects of molecules. A particular attention is paid to molecular featurization, or computational representation of a molecular structure, which is an essential process during the development of a machine learning model. Technical challenges associated with the use of machine learning for natural products are further discussed.