AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery

Chemical prospecting, biological evaluation and use of molecular networking as tool for searching bioactive compounds in marine microrganisms

O ambiente marinho é considerado como uma fonte de produtos naturais bioativos singulares, altamente complexos, os quais são biossintetizados por uma diversidade de macro e microrganismos, muitas vezes via associações entre eles. Neste contexto, os fungos algícolas, aqueles associados a macroalgas e as cianobactérias marinhas destacam-se como fontes promissoras de novas substâncias bioativas. Dessa forma, um dos objetivos deste trabalho foi realizar a prospecção química e avaliar o potencial biológico do fungo Penicillium echinulatum isolado da macroalga antártica Adenocystis utricularis. Foram isoladas oito substâncias, identificadas como ciclopenina, ciclopenol, desidrociclopeptina, ciclopeptina, viridicatina e viridicatol, além de um par de diasteroisômeros inéditos. Para os ensaios antiparasitários, viridicatina e viridicatol apresentaram atividade leishmanicida frente a forma amastigota de Leishmania amazonensis, parasita causador da Leishmaniose; apenas viridicatina inibiu a proliferação do parasita Neospora caninum, agente etiológico da Neosporose e os metabólitos ciclopenina e desidrociclopeptina foram considerados ativo e moderadamente ativo, respectivamente, contra a cepa multirresistente de Plasmodium falciparum, principal parasita que causa Malária. Além disso, as substâncias viridicatina e viridicatol apresentaram potencial fotoprotetor e antioxidante e podem ser considerados uma nova classe de moléculas para fotoproteção. A viridicatina também foi capaz de modular a produção de espécies reativas de oxigênio (ERO) por neutrófilos humanos. Concomitantemente, foi realizado o cultivo misto entre o fungo marinho P. echinulatum e a linhagem de cianobactéria Geitlerinema sp. CENA 556, onde foi avaliada a interação química entre eles e a atividade larvicida dos extratos brutos obtidos das monoculturas e do cultivo misto contra larvas de Aedes aegypti, mosquito transmissor da Dengue. Os resultados demonstraram que houve interação química entre os organismos, visto que foi evidenciado atividade promissora do extrato bruto e de uma das frações obtidas a partir do cultivo misto quando comparados com o extrato e frações da monocultura de P. echinulatum. Ainda, a partir dos dados de perfil químico em conjunto com análise da rede molecular obtida foi possível sugerir que a atividade larvicida pode estar relacionada com a substância desidrociclopeptina. Adicionalmente, redes moleculares foram utilizadas para identificar classes de metabólitos com atividade antiparasitária contra Trypanosoma cruzi (parasita que causa a Doença de Chagas) de uma biblioteca de extratos e frações de cianobactérias pertencentes ao Prof. Dr. William H. Gerwick do Instituto de Oceanografia da Universidade da Califórnia, San Diego (EUA). Cerca de 2.800 amostras tiveram atividade tripanocida avaliada e dentre estas, dez frações apresentaram inibição do crescimento do parasita T. cruzi. A partir do estudo químico dessas frações mais ativas foi possível observar que os ácidos graxos e seus derivados foi a principal classe de substâncias relacionada com a atividade antiparasitária. Além disso, por meio da análise dos dados da rede molecular foram identificadas cinco substâncias conhecidas, como vatiamida C, curacina D, viequeamida A, aeruciclamida A e formidolida, além de clusters de moléculas desconhecidas que podem ser inéditas e bioativas. Os resultados deste trabalho acrescentam dados químicos e biológicos para as espécies estudadas, enriquecendo a área de química de produtos naturais marinhos.The marine environment is considered as unique, highly complex, bioactive natural products source, which are biosynthesized by a diversity of macro- and microorganisms, often via associations between them. In this context, algicolous fungi, those associated with macroalgae and marine cyanobacteria stand out as promising sources of new bioactive compounds. Thus, one of the objectives of this work was to perform a chemical prospecting and evaluate the biological potential of the fungus Penicillium echinulatum isolated from the Antarctic macroalgae Adenocystis utricularis. Eight compounds were isolated, identified as cyclopenin, cyclopenol, dehydrocyclopeptin, cyclopeptin, viridicatin, and viridicatol, in addition to a pair of novel diastereomers. For the antiparasitic assays, viridicatin and viridicatol showed leishmanicidal activity against the amastigote form of Leishmania amazonensis, the parasite that causes Leishmaniasis; only viridicatin inhibited the proliferation of the parasite Neospora caninum, the etiologic agent of Neosporosis, and the metabolites cyclopenine and dehydrocyclopeptin were considered active and moderately active, respectively, against the multidrug-resistant strain of Plasmodium falciparum, the main parasite that causes Malaria. In addition, viridicatin and viridicatol showed photoprotective and antioxidant potential and can be considered a new class of molecules for photoprotection. Viridicatin was also able to modulate the production of reactive oxygen species (ROS) by human neutrophils. Simultaneously, a mixed culture between the marine fungus P. echinulatum and the cyanobacterial strain Geitlerinema sp. CENA 556 was performed. The chemical interaction between them and the larvicidal activity of crude extracts obtained from monocultures and mixed cultures were evaluated against Aedes aegypti larvae, the mosquito that transmits Dengue. The results showed that there was chemical interaction between the organisms, since it was evidenced promising activity of the crude extract and of one of the fractions obtained from the mixed culture when compared with the extract and fractions of the monoculture of P. echinulatum. Furthermore, from the chemical profile data together with the molecular networking analysis obtained, it was possible to suggest that the larvicidal activity may be related to the compound dehydrocyclopeptin. Additionally, molecular networking analysis were used to identify classes of metabolites with antiparasitic activity against Trypanosoma cruzi (the parasite that causes Chagas Disease) from a library of cyanobacterial extracts and fractions belonging to Prof. Dr. William H. Gerwick of the Institute of Oceanography at the University of California, San Diego (USA). About 2,800 samples had trypanocidal activity evaluated, and among these, ten fractions showed inhibition of T. cruzi parasite growth. From the chemical study of these more active fractions, it was possible to observe that fatty acids and their derivatives was the main class of compounds related to antiparasitic activity. In addition, through the analysis of the molecular networking data, five known compounds were identified, such as vatiamide C, curacin D, viequeamide A, aerucyclamide A and formidolide, in addition to clusters of unknown molecules that may be novel and bioactive. The results of this work provide chemical and biological information about species studied, enriching the area of chemistry of marine natural products

Leaf anatomy of Cordiera sessilis (Vell.) Kuntze (Rubiaceae)

A study on the leaf anatomy of Cordiera sessilis (Rubiaceae), a native medicinal shrub from Brazilian Cerrado was carried out to contribute for species identification and provide support for future biochemical studies and medicinal application. Leaves were collected, fixed and processed by usual techniques, and studied by light and electron microscopy. Quantitative analyzes of stomata and trichomes were performed. The leaves showed typical characteristics of Rubiaceae family, like hypostomatic leaves, paracytic stomata, dorsiventral mesophyll and collateral bundles. Two types of vascular patterns were identified in the petiole: in distal part, the vascular system is arranged cylindrically surrounded by sclerenchyma sheath and in proximal part, the vascular system is arranged in U-shape coupled to sclerified cells. The micromorphological organization of leaf surface, epicuticular wax types, the petiole pattern and histochemical characteristics as the presence of druses, sand crystals and alkaloids and absence of raphids in the mesophyll, midrib and petiole are considerate representative characteristics of C. sessilis and may be useful in the species identification.A study on the leaf anatomy of Cordiera sessilis (Rubiaceae), a native medicinal shrub from Brazilian Cerrado was carried out to identify features that may be useful in species recognition. Leaves were collected, fixed and processed by usual techniques, and studied by light and electron microscopy. Quantitative analyzes of stomata and trichomes were performed. In addition to the typical anatomical characteristics of Rubiaceae leaves, two types of vascular patterns were identified in the petiole: in distal part, the vascular system is arranged cylindrically surrounded by sclerenchyma sheath and in proximal part the vascular system is arranged in U-shape coupled to sclerified cells. The micromorphological organization of leaf surface, epicuticular wax types, the petiole pattern and histochemical characteristics as the presence of druses, crystal sand and alkaloids and absence of raphides in the mesophyll, midrib and petiole are considerate representative characteristics of C. sessilis and may be useful in the species recognition.

Flavonoid-Rich Fractions of Bauhinia holophylla Leaves Inhibit Candida albicans Biofilm Formation and Hyphae Growth

This study evaluated the effect of the extract and fractions of Bauhinia holophylla on Candida albicans planktonic growth, biofilm formation, mature biofilm, and hyphae growth. Three C. albicans strains (SC5314, ATCC 18804, and ATCC 10231) were tested. The crude extract and the fractions were obtained by exhaustive percolation and liquid–liquid partition, respectively. Phytochemical analyses of B. holophylla extract and fractions were performed using high-performance liquid chromatography coupled with a diode-array detector and mass spectrometry (HPLC-DAD-MS). A microdilution assay was used to evaluate the effect of the B. holophylla extract and fractions on C. albicans planktonic growth, and crystal violet staining was used to measure the total biomass of the biofilm. Hyphae growth was analyzed using light microscopy. Thirteen flavonoids were identified, with a predominance of the flavonol-3-O-glycoside type based on quercetin, myricetin, and kaempferol. Flavonoid-rich fractions of B. holophylla leaves displayed antifungal activity and inhibited both biofilm formation and hyphae growth in all the tested strains, but were not effective on C. albicans planktonic growth and mature biofilm. This study indicates that flavonoid-rich fractions from B. holophylla leaves interfere with the virulence of Candida species and support the use of Bauhinia spp. in folk medicine to treat infections

Antiviral Activity of Flavonoids from <i>Bauhinia holophylla</i> Leaves against <i>Zika virus</i>

Zika virus (ZIKV) is involved in the etiology of serious nervous system pathologies. Currently, there are no specific and effective vaccines or antiviral drugs to prevent the diseases caused by ZIKV. This study aimed to assess the activity of flavonoids present in crude hydroethanolic extract (CHE) and fractions obtained from B. holophylla leaves against ZIKV. O-glycosylated flavonoids were characterized by high-performance liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS/MS). The cytotoxic concentration and the effective concentration for 50% of the cells (CC50 and EC50, respectively) were determined, and the selectivity index (SI) was calculated. Molecular networks were constructed based on the chemical composition of the samples and global antiviral activity data using the Global Natural Products Social Molecular Networking (GNPS) platform. Protein–ligand docking was performed in the NS2B-NS3 protease, NS3 helicase, and NS5 methyltransferase of the ZIKV. CHE showed greater antiviral activity at a multiplicity of infection (MOI) of 1.0, with an EC50 of 11.93 µg/mL, SI = 13.38, and reduced cytopathic effects. Molecular networks indicated that O-glycosylated flavonoids are responsible for the activity against ZIKV, being quercetin-O-deoxyhexoside more selective and effective. Molecular docking confirmed the inhibitory activity of quercetin-O-deoxyhexoside, which showed an affinity for the tested targets, especially for NS2B-NS3 protease. The results showed that B. holophylla has flavonoids with potential for future therapeutic applications against ZIKV

Bauhinia holophylla (Bong.) Steud. leaves-derived extracts as potent anti-dengue serotype 2

Dengue virus (DENV) is the most prevalent mosquito-borne viral pathogen and made the disease a major health concern worldwide. However, specific antiviral drugs against this arbovirose or vaccines are not yet available for treatment or prevention. Thus, here we aimed to study the antiviral activity of hydroethanolic extract, fraction ethyl acetate and subfractions of the leaves of Bauhinia holophylla (Fabaceae:Cercideae), a native plant of the Brazilian Cerrado, against DENV-2 by methylthiazolyldiphenyl-tetrazolium bromide (MTT) method in mammalian cells culture. As results, the hydroethanolic extract showed the most potent effect, with an inhibitory concentration (IC50) of 3.2 μg mL-1 and selectivity index (SI) of 27.6, approximately 16-times higher anti-DENV-2 activity than of the ribavirin (IC50 52.8 μg mL-1). Our results showed in this study appointed that B. holophylla has a promising anti-dengue activity, which was associated mainly with the presence of flavonoids.status: publishe