Antidiabetic Potential of a Trimeric Anthranilic Acid Peptide Isolated from Malbranchea flocciformis.

Compound 3, a trimeric anthranilic acid peptide, and another three metabolites were isolated from an organic extract from the culture medium of Malbranchea flocciformis ATCC 34530. The chemical structure proposed previously for 3 was unequivocally assigned via synthesis and X-ray diffraction analysis. Tripeptide 3 showed insulinotropic properties by decreasing the postprandial peak in healthy and hyperglycemic mice. It also increased glucose-induced insulin secretion in INS-1E at 5 µM, specifically at higher glucose concentrations. These results revealed that 3 might act as an insulin sensitizer and a non-classical insulin secretagogue. Altogether, these findings are in harmony with the in vivo oral glucose tolerance test and acute oral hypoglycemic assay. Finally, the chemical composition of the extract was established by the Global Natural Products Social Molecular Network platform. Phylogenetic analysis using the internal transcribed spacer region revealed that M. flocciformis ATCC 34530 is related to the Malbrancheaceae.

Encoding mu-opioid receptor biased agonism with interaction fingerprints.

Opioids are potent painkillers, however, their therapeutic use requires close medical monitoring to diminish the risk of severe adverse effects. The G-protein biased agonists of the µ-opioid receptor (MOR) have shown safer therapeutic profiles than non-biased ligands. In this work, we performed extensive all-atom molecular dynamics simulations of two markedly biased ligands and a balanced reference molecule. From those simulations, we identified a protein-ligand interaction fingerprint that characterizes biased ligands. Then, we built and virtually screened a database containing 68,740 ligands with proven or potential GPCR agonistic activity. Exemplary molecules that fulfill the interacting pattern for biased agonism are showcased, illustrating the usefulness of this work for the search of biased MOR ligands and how this contributes to the understanding of MOR biased signaling.

Network Pharmacology Uncovers Anticancer Activity of Mammea-Type Coumarins from Calophyllum brasiliense.

Mammea-type coumarins are a particular type of secondary metabolites biosynthesized by the tropical rainforest tree Calophyllum Brasiliense, which is distributed from South America to Mexico. Particularly, mammea A/BA and A/BB (alone or as a mixture) possess biological properties such as cytotoxic and antitumoral activities, however, most of its molecular targets remain unknown. In this context, novel bioinformatic approaches, such as network pharmacology analysis, have been successfully used in herbal medicine to accelerate research in this field, and the support of experimental validations has been shown to be quite robust. In the present study, we performed a network pharmacology analysis to assess the possible molecular biological networks that interact with mammea A/BA and A/BB. Moreover, we validated the most relevant networks experimentally in vitro on K562 cancer cells. The results of the network pharmacology analysis indicate that mammea A/BA and A/BB interacts with cell death, PI3K/AKT, MAPK, Ras, and cancer pathways. The in vitro model shows that mammea A/BA and A/BB induce apoptosis through the overexpression of the proapoptotic proteins Bax and Bak, disrupt the autophagic flux as seen by the cytosolic accumulation of LC3-II and p62, disrupting the mitochondria ultrastructure and concomitantly increase the intracellular calcium concentration. Additionally, docking analysis predicted a possible interaction with a rapamycin-binding domain of mTOR. In conclusion, we validated network pharmacology analysis and report, for the first time, that mammea A/BA and A/BB coumarins induce apoptosis through the inhibition of the autophagic flux, possibly interacting with mTOR.

α-Glucosidase Inhibitors from Preussia minimoides ‡.

Extensive fractionation of an extract from the grain-based culture of the endophytic fungus Preussia minimoides led to the isolation of two new polyketides with novel skeletons, minimoidiones A (1) and B (2), along with the known compounds preussochromone C (3), corymbiferone (4), and 5-hydroxy-2,7-dimethoxy-8-methylnaphthoquinone (5). The structures of 1 and 2 were elucidated using 1D and 2D NMR data analysis, along with DFT calculations of 1H NMR chemical shifts. The absolute configuration of 1 was established by a single-crystal X-ray diffraction analysis and TDDFT-ECD calculations. Compounds 1-4 significantly inhibited yeast α-glucosidase.

α-Glucosidase Inhibitors from Malbranchea flavorosea.

From an extract prepared from the grain-based culture of Malbranchea flavorosea two new polyketides, namely, 8-chloroxylarinol A (1) and flavoroseoside (2), along with the known compounds xylarinol A (3), xylarinol B (4), massarigenins B and C (5 and 6), and clavatol (7), were isolated. The structures of 1 and 2 were elucidated using spectroscopic methods and corroborated by single-crystal X-ray diffraction analysis. In the case of compound 2 the absolute configuration at the stereogenic centers was established according to the method of Flack. In addition, the X-ray structure of compound 6 is reported for the first time. Compounds 3, 4, and 6 significantly inhibited yeast α-glucosidase. Compound 6 also inhibited the postprandial peak during an oral sucrose tolerance assay when tested in vivo, using normal and NA/STZ-induced hyperglycemic mice.

Antidiabetic and Antihyperalgesic Effects of a Decoction and Compounds from Acourtia thurberi.

The purpose of this research was to examine the preclinical efficacy of a decoction from the roots of Acourtia thurberi as a hypoglycemic, antihyperglycemic, and antihyperalgesic agent using well-known experimental models in mice. Acute oral administration of A. thurberi decoction did not produce toxic effects in mice, according to the Lorke procedure. A. thurberi decoction (31.6-316.2 mg/kg, p. o.) decreased blood glucose levels during acute hypoglycemic and the oral glucose tolerance and oral sucrose tolerance tests, both in normoglycemic and hyperglycemic animals. Phytochemical analysis of A. thurberi roots led to the isolation of perezone (1), a mixture of α-pipitzol (2) and ß-pipitzol (3), and 8-ß-D-glucopyranosyloxy-4-methoxy-5-methyl-coumarin (4). A pharmacological evaluation of compounds 1-4 (3.2-31.6 mg/kg) using the same assays revealed their hypoglycemic and antihyperglycemic actions. Finally, local administration of A. thurberi decoction (31.6-316.2 µg/paw) and compounds 1-4 (3.2-31.6 µg/paw) produced significant inhibition on the licking time during the formalin test in healthy and hyperglycemic mice, demonstrating their antinociceptive and antihyperalgesic potential, respectively. Altogether, these results could be related to the use of A. thurberi for treating diabetes and painful complaints in contemporary Mexican folk medicine. A suitable UPLC-ESI/MS method was developed and successfully applied to quantify simultaneously compounds 1 and 4 in A. thurberi decoction.

Calmodulin inhibitors from natural sources: an update.

Calmodulin (CaM) plays a central role in regulating a myriad of cellular functions in physiological and pathophysiological processes, thus representing an important drug target. In previous reviews, our group has reported relevant information regarding natural anti-CaM compounds up to 2009. Natural sources continue to provide a diverse and unique reservoir of CaM inhibitors for drug and research tool discovery. This review provides an update of natural products with reported CaM inhibitory properties, which includes around 70 natural products and some synthetic analogues, belonging to different structural classes. Most of these natural inhibitors were isolated from fungi and plants and belong to the stilbenoid, polyketide, alkaloid, and peptide structural classes. These products were discovered mainly using a fluorescence-based method on rationally designed biosensors, which are highly specific, low-cost, and selective and have short reaction times. The effect of several antimitotic drugs on Ca(2+)-hCaM is also described.

Importance of the interaction protein-protein of the CaM-PDE1A and CaM-MLCK complexes in the development of new anti-CaM drugs.

Protein-protein interactions play central roles in physiological and pathological processes. The bases of the mechanisms of drug action are relevant to the discovery of new therapeutic targets. This work focuses on understanding the interactions in protein-protein-ligands complexes, using proteins calmodulin (CaM), human calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A active human (PDE1A), and myosin light chain kinase (MLCK) and ligands αII-spectrin peptide (αII-spec), and two inhibitors of CaM (chlorpromazine (CPZ) and malbrancheamide (MBC)). The interaction was monitored with a fluorescent biosensor of CaM (hCaM M124C-mBBr). The results showed changes in the affinity of CPZ and MBC depending on the CaM-protein complex under analysis. For the Ca(2+) -CaM, Ca(2+) -CaM-PDE1A, and Ca(2+) -CaM-MLCK complexes, CPZ apparent dissociation constants (Kds ) were 1.11, 0.28, and 0.55 µM, respectively; and for MBC Kds were 1.43, 1.10, and 0.61 µM, respectively. In competition experiments the addition of calmodulin binding peptide 1 (αII-spec) to Ca(2+) -hCaM M124C-mBBr quenched the fluorescence (Kd = 2.55 ± 1.75 pM) and the later addition of MBC (up to 16 µM) did not affect the fluorescent signal. Instead, the additions of αII-spec to a preformed Ca(2+) -hCaM M124C-mBBr-MBC complex modified the fluorescent signal. However, MBC was able to displace the PDE1A and MLCK from its complex with Ca(2+) -CaM. In addition, docking studies were performed for all complexes with both ligands showing an excellent correlation with experimental data. These experiments may help to explain why in vivo many CaM drugs target prefer only a subset of the Ca(2+) -CaM regulated proteins and adds to the understanding of molecular interactions between protein complexes and small ligands.

Absolute configuration of acremoxanthone C, a potent calmodulin inhibitor from Purpureocillium lilacinum.

Bioassay-guided fractionation of an extract prepared from the culture medium and mycelium of Purpureocillium lilacinum allowed the isolation of two calmodulin (CaM) inhibitors, namely, acremoxanthone C (1) and acremonidin A (2). The absolute configuration of 1 was established as 2R, 3R, 1'S, 11'S, and 14'R through extensive NMR spectroscopy and molecular modeling calculations at the DFT B3LYP/DGDZVP level, which included the comparison between theoretical and experimental specific rotation, ³J(C,H), and ³J(H,H) values. Compounds 1 and 2 bind to the human calmodulin (hCaM) biosensor hCaM M124C-mBBr, with dissociation constants (Kd) of 18.25 and 19.40 nM, respectively, 70-fold higher than that of chlorpromazine (Kd = 1.24 µM), used as positive control. Docking analysis using AutoDock 4.2 predicted that 1 and 2 bind to CaM at a similar site to that which KAR-2 binds, which is unusual. Furthermore, a novel, sensible, and specific fluorescent biosensor of hCaM, i.e., hCaM T110C-mBBr, was constructed; this device is labeled at a site where classical inhibitors do not interact and was successfully applied to measure the interaction of 1 with CaM. This is the first report of xanthone-anthraquinone heterodimers in species of Paecilomyces or Purpureocillium genera.

Discovery of inhibitors of protein tyrosine phosphatase 1B contained in a natural products library from Mexican medicinal plants and fungi using a combination of enzymatic and in silico methods*.

This work aimed to discover protein tyrosine phosphatase 1B (PTP1B) inhibitors from a small molecule library of natural products (NPs) derived from selected Mexican medicinal plants and fungi to find new hits for developing antidiabetic drugs. The products showing similar IC50 values to ursolic acid (UA) (positive control, IC50 = 26.5) were considered hits. These compounds were canophyllol (1), 5-O-(ß-D-glucopyranosyl)-7-methoxy-3',4'-dihydroxy-4-phenylcoumarin (2), 3,4-dimethoxy-2,5-phenanthrenediol (3), masticadienonic acid (4), 4',5,6-trihydroxy-3',7-dimethoxyflavone (5), E/Z vermelhotin (6), tajixanthone hydrate (7), quercetin-3-O-(6″-benzoyl)-ß-D-galactoside (8), lichexanthone (9), melianodiol (10), and confusarin (11). According to the double-reciprocal plots, 1 was a non-competitive inhibitor, 3 a mixed-type, and 6 competitive. The chemical space analysis of the hits (IC50 < 100 µM) and compounds possessing activity (IC50 in the range of 100-1,000 µM) with the BIOFACQUIM library indicated that the active molecules are chemically diverse, covering most of the known Mexican NPs' chemical space. Finally, a structure-activity similarity (SAS) map was built using the Tanimoto similarity index and PTP1B absolute inhibitory activity, which allows the identification of seven scaffold hops, namely, compounds 3, 5, 6, 7, 8, 9, and 11. Canophyllol (1), on the other hand, is a true analog of UA since it is an SAR continuous zone of the SAS map.

Subtle structural differences of nucleotide analogs may impact SARS-CoV-2 RNA-dependent RNA polymerase and exoribonuclease activity.

The rapid spread and public health impact of the novel SARS-CoV-2 variants that cause COVID-19 continue to produce major global impacts and social distress. Several vaccines were developed in record time to prevent and limit the spread of the infection, thus playing a pivotal role in controlling the pandemic. Although the repurposing of available drugs attempts to provide therapies of immediate access against COVID-19, there is still a need for developing specific treatments for this disease. Remdesivir, molnupiravir and Paxlovid remain the only evidence-supported antiviral drugs to treat COVID-19 patients, and only in severe cases. To contribute on the search of potential Covid-19 therapeutic agents, we targeted the viral RNA-dependent RNA polymerase (RdRp) and the exoribonuclease (ExoN) following two strategies. First, we modeled and analyzed nucleoside analogs sofosbuvir, remdesivir, favipiravir, ribavirin, and molnupiravir at three key binding sites on the RdRp-ExoN complex. Second, we curated and virtually screened a database containing 517 nucleotide analogs in the same binding sites. Finally, we characterized key interactions and pharmacophoric features presumably involved in viral replication halting at multiple sites. Our results highlight structural modifications that might lead to more potent SARS-CoV-2 inhibitors against an expansive range of variants and provide a collection of nucleotide analogs useful for screening campaigns.

Protein tyrosine phosphatase 1B inhibitory activity of compounds from Justicia spicigera (Acanthaceae).

An infusion from the aerial parts of Justicia spicigera Schltdl., an herb commonly used to treat diabetes, inhibited the activity of protein tyrosine phosphatase 1B (PTP1B). Two undescribed compounds, 2-N-(p-coumaroyl)-3H-phenoxazin-3-one, and 3″-O-acetyl-kaempferitrin, along with kaempferitrin, kaempferol 7-O-α-L-rhamnopyranoside, perisbivalvine B and 2,5-dimethoxy-p-benzoquinone were isolated from the active extract. Their structures were elucidated by a combination of spectroscopic and spectrometric methods. The isolates were evaluated for their inhibitory activity against PTP1B; the most active compounds were 2-N-(p-coumaroyl)-3H-phenoxazin-3-one, and perisbivalvine B with IC50 values of 159.1 ± 0.02 µM and 106.6 ± 0.01 µM, respectively. However, perisbivalvine B was unstable. Kinetic analysis of 2-N-(p-coumaroyl)-3H-phenoxazin-3-one and 2,5-dimethoxy-p-benzoquinone (obtained in good amounts) indicated that both compounds behaved as parabolic competitive inhibitors and bind to the enzyme forming complexes with 1:1 and 1:2 stoichiometry. Docking of 2-N-(p-coumaroyl)-3H-phenoxazin-3-one and 2,5-dimethoxy-p-benzoquinone to PTP1B1-400 predicted a good affinity of these compounds for PTP1B catalytic site and demonstrated that the binding of a second ligand is sterically possible. The 1:2 complex was also supported by the second docking analysis, which predicted an important contribution of π-stacking interactions to the stability of these 1:2 complexes. Finally, an UHPLC-MS method was developed and validated to quantify the content of kaempferitrin in the infusion of the plant.

Fluorescence, circular dichroism, NMR, and docking studies of the interaction of the alkaloid malbrancheamide with calmodulin.

A new malbrancheamide analogue, isomalbrancheamide B (3), along with three known compounds, malbrancheamide (1), isomalbrancheamide (2), and premalbrancheamide (4), were isolated in higher yields from the alkaloid fraction of the fungus Malbranchea aurantiaca. The interaction of the alkaloids 1-4 with calmodulin (CaM) was analyzed using different enzymatic, fluorescence, spectroscopic, nuclear magnetic resonance (NMR), and molecular modelling techniques. On the basis of the enzymatic and fluorescence experiments, malbrancheamides 1-3 are classical CaM inhibitors. Compound 4, however, did not quench the extrinsic fluorescence of the CaM biosensor indicating that it could be a functional inhibitor. Circular dichroism, NMR, and molecular modelling studies revealed that 1 binds to CaM in the same hydrophobic pocket than the chlorpromazine and trifluoperazine, two classical CaM inhibitors. Thus, malbrancheamide and related monochlorinated analogues are compounds with a high potential for the development of new therapeutic agents, involving CaM as their molecular target.

Predictive Global Models of Cruzain Inhibitors with Large Chemical Coverage.

Chagas disease affects 8-11 million people worldwide, most of them living in Latin America. Moreover, migratory phenomena have spread the infection beyond endemic areas. Efforts for the development of new pharmacological therapies are paramount as the pharmacological profile of the two marketed drugs currently available, nifurtimox and benznidazole, needs to be improved. Cruzain, a parasitic cysteine protease, is one of the most attractive biological targets due to its roles in parasite survival and immune evasion. In this work, we compiled and curated a database of diverse cruzain inhibitors previously reported in the literature. From this data set, quantitative structure-activity relationship (QSAR) models for the prediction of their pIC50 values were generated using k-nearest neighbors and random forest algorithms. Local and global models were calculated and compared. The statistical parameters for internal and external validation indicate a significant predictability, with q loo 2 values around 0.66 and 0.61 and external R 2 coefficients of 0.725 and 0.766. The applicability domain is quantitatively defined, according to QSAR good practices, using the leverage and similarity methods. The models described in this work are readily available in a Python script for the discovery of novel cruzain inhibitors.

DiaNat-DB: a molecular database of antidiabetic compounds from medicinal plants.

Natural products are an invaluable source of molecules with a large variety of biological activities. Interest in natural products in drug discovery is documented in an increasing number of publications of bioactive secondary metabolites. Among those, medicinal plants are one of the most studied for this endeavor. An ever thriving area of opportunity within the field concerns the discovery of antidiabetic natural products. As a result, a vast amount of secondary metabolites are isolated from medicinal plants used against diabetes mellitus but whose information has not been organized systematically yet. Several research articles enumerate antidiabetic compounds, but the lack of a chemical database for antidiabetic metabolites limits their application in drug development. In this work, we present DiaNat-DB, a comprehensive collection of 336 molecules from medicinal plants reported to have in vitro or in vivo antidiabetic activity. We also discuss a chemoinformatic analysis of DiaNat-DB to compare antidiabetic drugs and natural product databases. To further explore the antidiabetic chemical space based on DiaNat compounds, we searched for analogs in ZINC15, an extensive database listing commercially available compounds. This work will help future analyses, design, and development of new antidiabetic drugs. DiaNat-DB and its ZINC15 analogs are freely available at http://rdu.iquimica.unam.mx/handle/20.500.12214/1186.

DARK Classics in Chemical Neuroscience: Salvinorin A.

Salvinorin A is the main bioactive compound in Salvia divinorum, an endemic plant with ancestral use by the inhabitants of the Mazateca mountain range (Sierra Mazateca) in Oaxaca, México. The main use of la pastora, as locally known, is in spiritual rites due to its extraordinary hallucinogenic effects. Being the first known nonalkaloidal opioid-mediated psychotropic molecule, salvinorin A set new research areas in neuroscience. The absence of a protonated amine group, common to all previously known opioids, results in a fast metabolism with the concomitant fast elimination and swift loss of activity. The worldwide spread and psychotropic effects of salvinorin A account for its misuse and classification as a drug of abuse. Consequently, salvinorin A and Salvia divinorum are now banned in many countries. Several synthetic efforts have been focused on the improvement of physicochemical and biological properties of salvinorin A: from total synthesis to hundreds of analogues. In this Review, we discuss the impact of salvinorin A in chemistry and neuroscience covering the historical relevance, isolation from natural sources, synthetic efforts, and pharmacological and safety profiles. Altogether, the chemistry behind and the taboo that encloses salvinorin A makes it one of the most exquisite naturally occurring drugs.

The impact of chemoinformatics on drug discovery in the pharmaceutical industry.

Introduction: Even though there have been substantial advances in our understanding of biological systems, research in drug discovery is only just now beginning to utilize this type of information. The single-target paradigm, which exemplifies the reductionist approach, remains a mainstay of drug research today. A deeper view of the complexity involved in drug discovery is necessary to advance on this field.Areas covered: This perspective provides a summary of research areas where cheminformatics has played a key role in drug discovery, including of the available resources as well as a personal perspective of the challenges still faced in the field.Expert opinion: Although great strides have been made in the handling and analysis of biological and pharmacological data, more must be done to link the data to biological pathways. This is crucial if one is to understand how drugs modify disease phenotypes, although this will involve a shift from the single drug/single target paradigm that remains a mainstay of drug research. Moreover, such a shift would require an increased awareness of the role of physiology in the mechanism of drug action, which will require the introduction of new mathematical, computer, and biological methods for chemoinformaticians to be trained in.

Distribution of toxicity values across different species and modes of action of pesticides from PESTIMEP and PPDB databases.

The continuous use of compounds contained in commodities such as processed food, medicines, and pesticides, demands safety measures, in particular, for those in direct contact with humans and the environment. Safety measures have evolved and regulations are now in place around the globe. In the case of pesticides, attempts have been made to use toxicological data to inform of potentially harmful compounds either across species, on different routes of exposure, or entirely new chemicals. The generation of models, based on statistical and molecular modeling studies, allows for such predictions. However, the use of these models is framed by the available data, the experimental errors, the complexity of the measurement, and the available computational algorithms, among other factors. In this work, we present the methodologies used for extrapolation across different species and routes of administration and show the appropriateness of developing predictive models of pesticides based on their type and mode of action. The analyses include comparisons based on structural characteristics and physicochemical properties. Whenever possible, the scope and limitations of the methodologies are discussed. We expect that this work will serve as a useful introductory guide of the tools employed in the toxicity assessment of agrochemical compounds.

The OECD Principles for (Q)SAR Models in the Context of Knowledge Discovery in Databases (KDD).

The steps followed in the knowledge discovery in databases (KDD) process are well documented and are widely used in different areas where exploration of data is used for decision making. In turn, while different workflows for developing quantitative structure-activity relationship (QSAR) models have been proposed, including combinatorial use of QSAR, there is now agreement on common requirements for building trustable predictive models. In this work, we analyze and confront the steps involved in KDD and QSAR and present how they comply with the OECD principles for the validation, for regulatory purposes, of QSAR models.

Mu-Opioid receptor biased ligands: A safer and painless discovery of analgesics?

Biased activation of G-protein-coupled receptors (GPCRs) is shifting drug discovery efforts and appears promising for the development of safer drugs. The most effective analgesics to treat acute pain are agonists of the µ opioid receptor (µ-OR), a member of the GPCR superfamily. However, the analgesic use of opioid drugs, such as morphine, is hindered by adverse effects. Only a few µ-OR agonists have been reported to selectively activate the Gi over ß-arrestin signaling pathway, resulting in lower gastrointestinal dysfunction and respiratory suppression. Here, we discuss the strategies that led to the development of biased µ-OR agonists, and potential areas for improvement, with an emphasis on structural aspects of the ligand-receptor recognition process.