Pharmacophore modeling, molecular docking, and molecular dynamics studies to identify new 5-HT2AR antagonists with the potential for design of new atypical antipsychotics

Some important atypical antipsychotic drugs target the serotonergic receptor 2A (5-HT2AR). Currently, new therapeutic strategies are needed to offer faster onset of action with fewer side effects and, therefore, greater efficacy in a substantial proportion of patients with neuropsychological disorders such as Autism and Parkinson. The main objective of this work was to use SBDD methods to identify new hit compounds potentially useful as precursors of novel and selective 5-HT2AR antagonists. A structure-based pharmacophore screening study based on a selective antagonist was carried out in ten databases. The set obtained was refined using molecular docking, and the five most promising compounds were subjected to molecular dynamics simulations. The most stable and promising hit occupied a side pocket present in the 5-HT2AR, a site that can be explored to obtain selective ligands. Simulations against 5-HT2CR and D2R showed that the best hit could not form stable complexes with these targets, strengthening the hypothesis that the hit presents selective binding by the receptor of interest. The selected hits showed some predicted toxicity risk or violated some drug-likeness property. However, it can be concluded that the identified hits are the most promising for performing in vitro assays. Once the presence of activity is confirmed, they could become precursors of optimized and selective antagonists of 5-HT2AR. An SBDD study was carried out to identify new selective 5-HT2AR ligands potentially useful for designing selective atypical antipsychotics.

Multivariate QSAR, similarity search and ADMET studies based in a set of methylamine derivatives described as dopamine transporter inhibitors

The dopamine transporter (DAT), responsible for the regulation of dopaminergic neurotransmission, is implicated in the etiology of several neuropsychiatric disorders which, in turn, have contributed to high rates of disability and numerous deaths in recent years, significantly impacting the global health system. Although the research for new drugs for the treatment of neuropsychiatric disorders has evolved in recent years, the availability of DAT-selective drugs that do not generate the same psychostimulant effects observed in drugs of abuse remains scarce. Therefore, we performed a QSAR study based on a dataset of 36 methylamine derivatives described as DAT inhibitors. The model was obtained based only in descriptors derived from 2D structures, and it was validated and generated satisfactory results considering the metrics used for internal and external validation. Subsequently, a virtual screening step also based on 2D similarity was performed, where it was possible to identify a total of 1157 compounds. After a series of reductions of the set using toxicity filters, applicability domain evaluation, and pharmacokinetic properties in silico assessment, seven hit compounds were selected as the most promising to be used, in future studies, as new scaffolds for the development of new DAT inhibitors.

Naringenin-4'-glucuronide as a new drug candidate against the COVID-19 Omicron variant: a study based on molecular docking, molecular dynamics, MM/PBSA and MM/GBSA

This study aimed to identify natural bioactive compounds (NBCs) as potential inhibitors of the spike (S1) receptor binding domain (RBD) of the COVID-19 Omicron variant using computer simulations (in silico). NBCs with previously proven biological in vitro activity were obtained from the ZINC database and analyzed through virtual screening, molecular docking, molecular dynamics (MD), molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA), and molecular mechanics/generalized Born surface area (MM/GBSA). Remdesivir was used as a reference drug in docking and MD calculations. A total of 170,906 compounds were analyzed. Molecular docking screening revealed the top four NBCs with a high affinity with the spike (affinity energy <-7 kcal/mol) to be ZINC000045789238, ZINC000004098448, ZINC000008662732, and ZINC000003995616. In the MD analysis, the four ligands formed a complex with the highest dynamic equilibrium S1 (mean RMSD <0.3 nm), lowest fluctuation of the complex amino acid residues (RMSF <1.3), and solvent accessibility stability. However, the ZINC000045789238-spike complex (naringenin-4'-O glucuronide) was the only one that simultaneously had minus signal (-) MM/PBSA and MM/GBSA binding free energy values (-3.74 kcal/mol and -15.65 kcal/mol, respectively), indicating favorable binding. This ligand (naringenin-4'-O glucuronide) was also the one that produced the highest number of hydrogen bonds in the entire dynamic period (average = 4601 bonds per nanosecond). Six mutant amino acid residues formed these hydrogen bonds from the RBD region of S1 in the Omicron variant: Asn417, Ser494, Ser496, Arg403, Arg408, and His505. Naringenin-4'-O-glucuronide showed promising results as a potential drug candidate against COVID-19. In vitro and preclinical studies are needed to confirm these findings.Communicated by Ramaswamy H. Sarma.

Bioactive compounds as potential angiotensin-converting enzyme II inhibitors against COVID-19: a scoping review

Objective and design

The current study aimed to summarize the evidence of compounds contained in plant species with the ability to block the angiotensin-converting enzyme 2 (ACE-II), through a scoping review.

Methods

PubMed and Scopus electronic databases were used for the systematic search and a manual search was performed

Results

Studies included were characterized as in silico. Among the 200 studies retrieved, 139 studies listed after the exclusion of duplicates and 74 were included for the full read. Among them, 32 studies were considered eligible for the qualitative synthesis. The most evaluated class of secondary metabolites was flavonoids with quercetin and curcumin as most actives substances and terpenes (isothymol, limonin, curcumenol, anabsinthin, and artemisinin). Other classes that were also evaluated were alkaloid, saponin, quinone, substances found in essential oils, and primary metabolites as the aminoacid l-tyrosine and the lipidic compound 2-monolinolenin.

Conclusion

This review suggests the most active substance from each class of metabolites, which presented the strongest affinity to the ACE-II receptor, what contributes as a basis for choosing compounds and directing the further experimental and clinical investigation on the applications these compounds in biotechnological and health processes as in COVID-19 pandemic.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00011-022-01642-7.

SMILES-based 2D-QSAR and similarity search for identification of potential new scaffolds for development of SARS-CoV-2 MPRO inhibitors

COVID-19, whose etiological agent is the SARS-CoV-2 virus, has caused over 537.5 million cases and killed over 6.3 million people since its discovery in 2019. Despite the recent development of the first drugs indicated for treating people already infected, the great need to develop new anti-SARS-CoV-2 drugs still exists, mainly due to the possible emergence of new variants of this virus and resistant strains of the current variants. Thus, this work presents the results of QSAR and similarity search studies based only on 2D structures from a set of 32 bicycloproline derivatives, aiming to quickly, reproducibly, and reliably identify potentially useful compounds as scaffolds of new major protease inhibitors (M^pro) of the virus. The obtained QSAR model is based only on topological molecular descriptors. The model has good internal and external statistics, is robust, and does not present a chance correlation. This model was used as one of the tools to support the virtual screening stage carried out in the SwissADME web tool. Five molecules, from an initial set of 2695 molecules, proved to be the most promising, as they were within the model’s applicability domain and linearity range, with low potential to cause carcinogenic, teratogenic, and reproductive toxicity effects and promising pharmacokinetic properties. These five compounds were then selected as the most competent to generate, in future studies, new anti-SARS-CoV-2 agents with drug-likeness properties suitable for use in therapy.

Novel coumarins active against Trypanosoma cruzi and toxicity assessment using the animal model Caenorhabditis elegans

BACKGROUND

Chagas disease (CD) is a tropical parasitic disease. Although the number of people infected is very high, the only drugs available to treat CD, nifurtimox (Nfx) and benznidazole, are highly toxic, particularly in the chronic stage of the disease. Coumarins are a large class of compounds that display a wide range of interesting biological properties, such as antiparasitic. Hence, the aim of this work is to find a good antitrypanosomal drug with less toxicity. The use of simple organism models has become increasingly attractive for planning and simplifying efficient drug discovery. Within these models, Caenorhabditis elegans has emerged as a convenient and versatile tool with significant advantages for the toxicological potential identification for new compounds.

METHODS

Trypanocidal activity: Forty-two 4-methylamino-coumarins were assayed against the epimastigote form of Trypanosoma cruzi (Tulahuen 2 strain) by inhibitory concentration 50% (IC50). Toxicity assays: Lethal dose 50% (LD50) and Body Area were determined by Caenorhabditis elegans N2 strain (wild type) after acute exposure. Structure-activity relationship: A classificatory model was built using 3D descriptors.

RESULTS

Two of these coumarins demonstrated near equipotency to Nifurtimox (IC50 = 5.0 ± 1 μM), with values of: 11 h (LaSOM 266), (IC50 = 6.4 ± 1 μM) and 11 g (LaSOM 231), (IC50 = 8.2 ± 2.3 μM). In C. elegans it was possible to observe that Nfx showed greater toxicity in both the LD50 assay and the evaluation of the development of worms. It is possible to observe that the efficacy between Nfx and the synthesized compounds (11 h and 11 g) are similar. On the other hand, the toxicity of Nfx is approximately three times higher than that of the compounds. Results from the QSAR-3D study indicate that the volume and hydrophobicity of the substituents have a significant impact on the trypanocidal activities for derivatives that cause more than 50% of inhibition. These results show that the C. elegans model is efficient for screening potentially toxic compounds.

CONCLUSION

Two coumarins (11 h and 11 g) showed activity against T. cruzi epimastigote similar to Nifurtimox, however with lower toxicity in both LD50 and development of C. elegans assays. These two compounds may be a feasible starting point for the development of new trypanocidal drugs.

In silico study toward the identification of new and safe potential inhibitors of photosynthetic electron transport

To address the rising global demand for food, it is necessary to search for new herbicides that can control resistant weeds. We performed a 2D-quantitative structure-activity relationship (QSAR) study to predict compounds with photosynthesis-inhibitory activity. A data set of 44 compounds (quinolines and naphthalenes), which are described as photosynthetic electron transport (PET) inhibitors, was used. The obtained model was approved in internal and external validation tests. 2D Similarity-based virtual screening was performed and 64 compounds were selected from the ZINC database. By using the VEGA QSAR software, 48 compounds were shown to have potential toxic effects (mutagenicity and carcinogenicity). Therefore, the model was also tested using a set of 16 molecules obtained by a similarity search of the ZINC database. Six compounds showed good predicted inhibition of PET. The obtained model shows potential utility in the design of new PET inhibitors, and the hit compounds found by virtual screening are novel bicyclic scaffolds of this class.

A best​ comprehension about the toxicity of phenylsulfonyl carboxylates in Vibrio fischeri using quantitative structure activity/property relationship methods

Aromatic sulfones comprise a class of chemicals used in agrochemical and pharmaceutical industries and as floatation and extractant agents in petrochemical and metallurgy industries. In this study, new QSA(P)R studies were carried out to predict the toxicity against Vibrio fischeri of a set of 52 aromatic sulfones. The same approach was used to evaluate the relationship between these endpoint and the water solubility, another important environmental endpoint. The study resulted in models of good statistical quality and mechanistic interpretation with a possible correlation between the two endpoints, but the toxic effect is also likely to depend on other physicochemical properties. The use of the PLS2, a method not commonly used in QSA(P)R studies, also produced models of greater reliability, and the relationship between the two endpoints was reinforced to some degree. These results are useful for better understanding the process by which these compounds exert their environmental toxicity, thus aiding in the development of industrially useful compounds with less potential environmental damage.

Correction: A structure-activity relationship study of the toxicity of ionic liquids using an adapted Ferreira-Kiralj hydrophobicity parameter

Correction for 'A structure-activity relationship study of the toxicity of ionic liquids using an adapted Ferreira-Kiralj hydrophobicity parameter' by Eduardo Borges de Melo et al., Phys. Chem. Chem. Phys., 2015, 17, 4516-4523.

1,2,3-Triazole-based analogue of benznidazole displays remarkable activity against Trypanosoma cruzi

The current treatment of Chagas disease is based on the use of two drugs, nifurtimox and benznidazole, which present limited efficacy in the chronic stage of the disease and toxic side effects. Although some progress has been made in the development of new drugs to treat this disease, the discovery of novel compounds is urgently required. In this work we report the synthesis and biological evaluation of 1,2,3-triazole-based analogues of benznidazole. A small series of 27 compounds was successfully synthesized via microwave-assisted copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and ruthenium-catalyzed azide-alkyne cycloaddition (RuAAC) from N-benzyl-2-azidoacetamide (1) and a set of commercial terminal alkynes. Analogues 24 (IC50 40 μM) and 28 (IC50 50 μM) showed comparable activities to benznidazole (IC50 34 μM) against trypomastigote form and analogue 15 (IC50 7 μM) was found to be the most active. Regarding the cytotoxicity assessment of the series, most compounds were not cytotoxic. This work shows that the designed strategy is efficiently capable of generating novel benzindazole analogues and reveals one analogue is more active than benznidazole.

A structure–activity relationship study of the toxicity of ionic liquids using an adapted Ferreira–Kiralj hydrophobicity parameter

An alternative molecular descriptor for characterizing the hydrophobicity of ionic liquids, W_cAdap, is presented in this study.

An alternative approach for the use of water solubility of nonionic pesticides in the modeling of the soil sorption coefficients

The collection of data to study the damage caused by pesticides to the environment and its ecosystems is slowly acquired and costly. Large incentives have been established to encourage research projects aimed at building mathematical models for predicting physical, chemical or biological properties of environmental interest. The organic carbon normalized soil sorption coefficient (K(oc)) is an important physicochemical property used in environmental risk assessments for compounds released into the environment. Many models for predicting logK(oc) that have used the parameters logP or logS as descriptors have been published in recent decades. The strong correlation between these properties (logP and logS) prevents them from being used together in multiple linear regressions. Because the sorption of a chemical compound in soil depends on both its water solubility and its water/organic matter partitioning, we assume that models capable of combining these two properties can generate more realistic results. Therefore, the objective of this study was to propose an alternative approach for modeling logK(oc), using a simple descriptor of solubility, here designated as the logarithm of solubility corrected by octanol/water partitioning (logS(P)). Thus, different models were built with this descriptor and with the conventional descriptors logP and logS, alone or associated with other explanatory variables representing easy-to-interpret physicochemical properties. The obtained models were validated according to current recommendations in the literature, and they were compared with other previously published models. The results showed that the use of logS(p) instead of conventional descriptors led to simple models with greater statistical quality and predictive power than other more complex models found in the literature. Therefore, logS(P) can be a good alternative to consider for the modeling of logK(oc) and other properties that relate to both solubility and water/organic matter partitioning.

The effect of different log P algorithms on the modeling of the soil sorption coefficient of nonionic pesticides

Collecting data on the effects of pesticides on the environment is a slow and costly process. Therefore, significant efforts have been focused on the development of models that predict physical, chemical or biological properties of environmental interest. The soil sorption coefficient normalized to the organic carbon content (Koc) is a key parameter that is used in environmental risk assessments. Thus, several log Koc prediction models that use the hydrophobic parameter log P as a descriptor have been reported in the literature. Often, algorithms are used to calculate the value of log P due to the lack of experimental values for this property. Despite the availability of various algorithms, previous studies fail to describe the procedure used to select the appropriate algorithm. In this study, models that correlate log Koc with log P were developed for a heterogeneous group of nonionic pesticides using different freeware algorithms. The statistical qualities and predictive power of all of the models were evaluated. Thus, this study was conducted to assess the effect of the log P algorithm choice on log Koc modeling. The results clearly demonstrate that the lack of a selection criterion may result in inappropriate prediction models. Seven algorithms were tested, of which only two (ALOGPS and KOWWIN) produced good results. A sensible choice may result in simple models with statistical qualities and predictive power values that are comparable to those of more complex models. Therefore, the selection of the appropriate log P algorithm for modeling log Koc cannot be arbitrary but must be based on the chemical structure of compounds and the characteristics of the available algorithms.

A QSAR Study of Matrix Metalloproteinases Type 2 (MMP-2) Inhibitors with Cinnamoyl Pyrrolidine Derivatives

A multivariate PLS-QSAR study with a data set of 31 cinnamoyl pyrrolidine derivatives described as type 2 matrix metalloproteinases (MMP-2) inhibitors is presented in this paper. The variable selection was performed with the Ordered Predictors Selection (OPS) algorithm. The PLS model presented six descriptors and three Latent Variables (LV) that cumulated 71.845% of variance. Leave-N-out (LNO) cross validation and y-randomization tests showed that the model presented robustness and no chance correlation, respectively. The descriptors indicated that MMP-2 inhibition depends mainly on the electronic properties of the compounds. The model obtained can be useful as a support tool in the design of new MMP-2 inhibitors.

A new quantitative structure-property relationship model to predict bioconcentration factors of polychlorinated biphenyls (PCBs) in fishes using E-state index and topological descriptors

A quantitative structure-property relationship (QSPR) study for predicting the logarithm of bioconcentration factors (LogBCF) of polychlorinated biphenyls (PCBs) is presented in this work. For this, the descriptors were obtained using only the Simplified Molecular Input Line Entry System (SMILES) strings in the free web server Parameter Client. The model was built using the Partial Least Squares (PLS) regression method. The best model presented five descriptors (one E-state index and four topological descriptors) and a high quality for fit, internal, and external predictions. The leave-N-out (LNO) cross validation and the y-randomization test showed the model is robust and has no shown chance correlation. With a second test set, the model was compared to other models and presented a root mean square error (RMSE) very close to the best model. The mechanistic interpretation was corroborated by other works in the literature and by the descriptors' theory. Thus, the results meet the five Organization for Economic Co-operation and Development (OECD) principles for validation of QSA(P)R models, and it is expected the model can effectively predict the BCF values in fishes of the PCB congeners without highly reliable experimental BCF.

Qualidade de medicamentos isentos de prescrição: um estudo com marcas de dipirona comercializadas em uma drogaria de Cascavel (PR, Brasil)

A dipirona é um fármaco muito utilizado pela população brasileira. É considerado seguro mesmo em gestantes, lactentes e crianças, mas é proibido em alguns países do mundo pelo suposto papel de causar agranulocitose e anemia aplástica. Em 2001, a Agência Nacional de Vigilância Sanitária (Anvisa) considerou que os medicamentos com esse fármaco apresentavam bom risco-benefício em relação a outros de indicação semelhante. Porém, de nada adianta segurança no uso de um medicamento se este é de baixa qualidade. É comum encontrar no mercado brasileiro medicamentos fora dos padrões, o que se constitui em um risco para a população em geral. Dessa forma, foram analisadas sete amostras de marcas diferentes de dipirona solução oral comercializados em uma farmácia de Cascavel (PR). Os resultados demonstram que a fiscalização quanto à qualidade de medicamentos similares precisa ser aprimorada, pois eles foram os que mais apresentaram desvios de qualidade.

Multivariate QSAR study on the antimutagenic activity of flavonoids against 3-NFA on Salmonella typhimurium TA98

A quantitative structure-activity relationship (QSAR) study of twenty flavonoid derivatives with antimutagenic activity against 3-nitrofluoranthene (3-NFA) was performed by Partial Least Squares (PLS), using Ordered Predictors Selection (OPS) algorithm for variable selection. Four descriptors (PJI2, Mor27m, G1e and R4u+) were selected and a good model (n = 19; R(2) = 0.747; SEC = 0.332; PRESS(cal) = 1.768; F((2,27)) = 23.585; Q(LOO)(2) = 0.590; SEV = 0.388; PRESS(val) = 2.858; R(pred)(2) = 0.591; SEP = 0.394; ARE(pred) = 5.230%; k = 1.005; k' = 0.990; |R(02) - R'(02)| = 0.109) was built with two latent variables describing 83.410% of the original information. Leave-N-out cross validation (LNO) and y-randomization were performed in order to confirm the robustness of the model. The topological descriptors selected indicate that the antimutagenic activity against 3-NFA depends on molecular size, shape and Sanderson electronegativity of flavonoids. The proposed model may provide a better understanding of the antimutagenic activity of flavonoids and can be used as a guidance for proposition of new chemopreventive agents.

[Description of attempts to obtain approval for selling medications at ordinary Brazilian establishments after the introduction of the Real Economic Stabilization Plan]

Although not legal, the practice of selling medications through unlicensed outlets such as stores and supermarkets has long been common in Brazil. Introducing the Real Economic Stabilization Plan, Provisional Measure 592/94 allowed the sale of non-prescription medications (anodynes) in such establishments. However, this item was suppressed when this Provisional Measure was enacted as Law N masculine 9,069/95. Since then, other attempts have been made to establish this type of trade in medications, forbidden in 2004 through a decision handed down by the Superior Court of Justice. Nevertheless, this unlawful trade in medications still continues. Due to the scarcity of publications on this specific issue, this paper offers an updated overview for druggists, pharmacists, academics and researchers, describing the events that took place between 1994 and 2006.