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1.
Chem Res Toxicol ; 37(6): 910-922, 2024 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-38781421

RESUMO

The human Ether-à-go-go-Related Gene (hERG) is a transmembrane protein that regulates cardiac action potential, and its inhibition can induce a potentially deadly cardiac syndrome. In vitro tests help identify hERG blockers at early stages; however, the high cost motivates searching for alternative, cost-effective methods. The primary goal of this study was to enhance the Pred-hERG tool for predicting hERG blockage. To achieve this, we developed new QSAR models that incorporated additional data, updated existing classificatory and multiclassificatory models, and introduced new regression models. Notably, we integrated SHAP (SHapley Additive exPlanations) values to offer a visual interpretation of these models. Utilizing the latest data from ChEMBL v30, encompassing over 14,364 compounds with hERG data, our binary and multiclassification models outperformed both the previous iteration of Pred-hERG and all publicly available models. Notably, the new version of our tool introduces a regression model for predicting hERG activity (pIC50). The optimal model demonstrated an R2 of 0.61 and an RMSE of 0.48, surpassing the only available regression model in the literature. Pred-hERG 5.0 now offers users a swift, reliable, and user-friendly platform for the early assessment of chemically induced cardiotoxicity through hERG blockage. The tool provides versatile outcomes, including (i) classificatory predictions of hERG blockage with prediction reliability, (ii) multiclassificatory predictions of hERG blockage with reliability, (iii) regression predictions with estimated pIC50 values, and (iv) probability maps illustrating the contribution of chemical fragments for each prediction. Furthermore, we implemented explainable AI analysis (XAI) to visualize SHAP values, providing insights into the contribution of each feature to binary classification predictions. A consensus prediction calculated based on the predictions of the three developed models is also present to assist the user's decision-making process. Pred-hERG 5.0 has been designed to be user-friendly, making it accessible to users without computational or programming expertise. The tool is freely available at http://predherg.labmol.com.br.


Assuntos
Canais de Potássio Éter-A-Go-Go , Relação Quantitativa Estrutura-Atividade , Humanos , Canais de Potássio Éter-A-Go-Go/antagonistas & inibidores , Canais de Potássio Éter-A-Go-Go/metabolismo , Medição de Risco , Análise de Regressão , Bloqueadores dos Canais de Potássio/farmacologia , Bloqueadores dos Canais de Potássio/química
2.
J Med Chem ; 66(18): 12828-12839, 2023 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-37677128

RESUMO

Hits from high-throughput screening (HTS) of chemical libraries are often false positives due to their interference with assay detection technology. In response, we generated the largest publicly available library of chemical liabilities and developed "Liability Predictor," a free web tool to predict HTS artifacts. More specifically, we generated, curated, and integrated HTS data sets for thiol reactivity, redox activity, and luciferase (firefly and nano) activity and developed and validated quantitative structure-interference relationship (QSIR) models to predict these nuisance behaviors. The resulting models showed 58-78% external balanced accuracy for 256 external compounds per assay. QSIR models developed and validated herein identify nuisance compounds among experimental hits more reliably than do popular PAINS filters. Both the models and the curated data sets were implemented in "Liability Predictor," publicly available at https://liability.mml.unc.edu/. "Liability Predictor" may be used as part of chemical library design or for triaging HTS hits.


Assuntos
Artefatos , Ensaios de Triagem em Larga Escala , Ensaios de Triagem em Larga Escala/métodos , Bibliotecas de Moléculas Pequenas/química
3.
Toxicol Sci ; 189(2): 250-259, 2022 09 24.
Artigo em Inglês | MEDLINE | ID: mdl-35916740

RESUMO

In the United States, a pre-market regulatory submission for any medical device that comes into contact with either a patient or the clinical practitioner must include an adequate toxicity evaluation of chemical substances that can be released from the device during its intended use. These substances, also referred to as extractables and leachables, must be evaluated for their potential to induce sensitization/allergenicity, which traditionally has been done in animal assays such as the guinea pig maximization test (GPMT). However, advances in basic and applied science are continuously presenting opportunities to employ new approach methodologies, including computational methods which, when qualified, could replace animal testing methods to support regulatory submissions. Herein, we developed a new computational tool for rapid and accurate prediction of the GPMT outcome that we have named PreS/MD (predictor of sensitization for medical devices). To enable model development, we (1) collected, curated, and integrated the largest publicly available dataset for GPMT results; (2) succeeded in developing externally predictive (balanced accuracy of 70%-74% as evaluated by both 5-fold external cross-validation and testing of novel compounds) quantitative structure-activity relationships (QSAR) models for GPMT using machine learning algorithms, including deep learning; and (3) developed a publicly accessible web portal integrating PreS/MD models that can predict GPMT outcomes for any molecule of interest. We expect that PreS/MD will be used by both industry and regulatory scientists in medical device safety assessments and help replace, reduce, or refine the use of animals in toxicity testing. PreS/MD is freely available at https://presmd.mml.unc.edu/.


Assuntos
Alérgenos , Testes de Toxicidade , Algoritmos , Animais , Cobaias , Aprendizado de Máquina , Relação Quantitativa Estrutura-Atividade , Testes de Toxicidade/métodos
4.
Environ Health Perspect ; 130(2): 27012, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-35192406

RESUMO

BACKGROUND: Modern chemical toxicology is facing a growing need to Reduce, Refine, and Replace animal tests (Russell 1959) for hazard identification. The most common type of animal assays for acute toxicity assessment of chemicals used as pesticides, pharmaceuticals, or in cosmetic products is known as a "6-pack" battery of tests, including three topical (skin sensitization, skin irritation and corrosion, and eye irritation and corrosion) and three systemic (acute oral toxicity, acute inhalation toxicity, and acute dermal toxicity) end points. METHODS: We compiled, curated, and integrated, to the best of our knowledge, the largest publicly available data sets and developed an ensemble of quantitative structure-activity relationship (QSAR) models for all six end points. All models were validated according to the Organisation for Economic Co-operation and Development (OECD) QSAR principles, using data on compounds not included in the training sets. RESULTS: In addition to high internal accuracy assessed by cross-validation, all models demonstrated an external correct classification rate ranging from 70% to 77%. We established a publicly accessible Systemic and Topical chemical Toxicity (STopTox) web portal (https://stoptox.mml.unc.edu/) integrating all developed models for 6-pack assays. CONCLUSIONS: We developed STopTox, a comprehensive collection of computational models that can be used as an alternative to in vivo 6-pack tests for predicting the toxicity hazard of small organic molecules. Models were established following the best practices for the development and validation of QSAR models. Scientists and regulators can use the STopTox portal to identify putative toxicants or nontoxicants in chemical libraries of interest. https://doi.org/10.1289/EHP9341.


Assuntos
Alternativas aos Testes com Animais , Simulação por Computador , Substâncias Perigosas , Animais , Cosméticos/toxicidade , Substâncias Perigosas/toxicidade , Praguicidas/toxicidade , Preparações Farmacêuticas , Relação Quantitativa Estrutura-Atividade
5.
Front Chem ; 9: 662688, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33996755

RESUMO

Natural products are continually explored in the development of new bioactive compounds with industrial applications, attracting the attention of scientific research efforts due to their pharmacophore-like structures, pharmacokinetic properties, and unique chemical space. The systematic search for natural sources to obtain valuable molecules to develop products with commercial value and industrial purposes remains the most challenging task in bioprospecting. Virtual screening strategies have innovated the discovery of novel bioactive molecules assessing in silico large compound libraries, favoring the analysis of their chemical space, pharmacodynamics, and their pharmacokinetic properties, thus leading to the reduction of financial efforts, infrastructure, and time involved in the process of discovering new chemical entities. Herein, we discuss the computational approaches and methods developed to explore the chemo-structural diversity of natural products, focusing on the main paradigms involved in the discovery and screening of bioactive compounds from natural sources, placing particular emphasis on artificial intelligence, cheminformatics methods, and big data analyses.

6.
Chem Res Toxicol ; 34(2): 258-267, 2021 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-32673477

RESUMO

Safety assessment is an essential component of the regulatory acceptance of industrial chemicals. Previously, we have developed a model to predict the skin sensitization potential of chemicals for two assays, the human patch test and murine local lymph node assay, and implemented this model in a web portal. Here, we report on the substantially revised and expanded freely available web tool, Pred-Skin version 3.0. This up-to-date version of Pred-Skin incorporates multiple quantitative structure-activity relationship (QSAR) models developed with in vitro, in chemico, and mice and human in vivo data, integrated into a consensus naïve Bayes model that predicts human effects. Individual QSAR models were generated using skin sensitization data derived from human repeat insult patch tests, human maximization tests, and mouse local lymph node assays. In addition, data for three validated alternative methods, the direct peptide reactivity assay, KeratinoSens, and the human cell line activation test, were employed as well. Models were developed using open-source tools and rigorously validated according to the best practices of QSAR modeling. Predictions obtained from these models were then used to build a naïve Bayes model for predicting human skin sensitization with the following external prediction accuracy: correct classification rate (89%), sensitivity (94%), positive predicted value (91%), specificity (84%), and negative predicted value (89%). As an additional assessment of model performance, we identified 11 cosmetic ingredients known to cause skin sensitization but were not included in our training set, and nine of them were accurately predicted as sensitizers by our models. Pred-Skin can be used as a reliable alternative to animal tests for predicting human skin sensitization.


Assuntos
Cosméticos/efeitos adversos , Testes Cutâneos , Pele/efeitos dos fármacos , Animais , Teorema de Bayes , Cosméticos/química , Humanos , Camundongos , Relação Quantitativa Estrutura-Atividade
7.
J Chem Inf Model ; 60(8): 4056-4063, 2020 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-32678597

RESUMO

Small, colloidally aggregating molecules (SCAMs) are the most common source of false positives in high-throughput screening (HTS) campaigns. Although SCAMs can be experimentally detected and suppressed by the addition of detergent in the assay buffer, detergent sensitivity is not routinely monitored in HTS. Computational methods are thus needed to flag potential SCAMs during HTS triage. In this study, we have developed and rigorously validated quantitative structure-interference relationship (QSIR) models of detergent-sensitive aggregation in several HTS campaigns under various assay conditions and screening concentrations. In particular, we have modeled detergent-sensitive aggregation in an AmpC ß-lactamase assay, the preferred HTS counter-screen for aggregation, as well as in another assay that measures cruzain inhibition. Our models increase the accuracy of aggregation prediction by ∼53% in the ß-lactamase assay and by ∼46% in the cruzain assay compared to previously published methods. We also discuss the importance of both assay conditions and screening concentrations in the development of QSIR models for various interference mechanisms besides aggregation. The models developed in this study are publicly available for fast prediction within the SCAM detective web application (https://scamdetective.mml.unc.edu/).


Assuntos
Ensaios de Triagem em Larga Escala
8.
Drug Discov Today ; 25(5): 928-941, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32320852

RESUMO

In the past decade we have seen two major Ebola virus outbreaks in Africa, the Zika virus in Brazil and the Americas and the current pandemic of coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There is a strong sense of déjà vu because there are still no effective treatments. In the COVID-19 pandemic, despite being a new virus, there are already drugs suggested as active in in vitro assays that are being repurposed in clinical trials. Promising SARS-CoV-2 viral targets and computational approaches are described and discussed. Here, we propose, based on open antiviral drug discovery approaches for previous outbreaks, that there could still be gaps in our approach to drug discovery.


Assuntos
Antivirais/farmacologia , Antivirais/uso terapêutico , Betacoronavirus/efeitos dos fármacos , Infecções por Coronavirus/tratamento farmacológico , Descoberta de Drogas , Pneumonia Viral/tratamento farmacológico , Enzima de Conversão de Angiotensina 2 , Animais , Betacoronavirus/metabolismo , COVID-19 , Chlorocebus aethiops , Simulação por Computador , Reposicionamento de Medicamentos , Doença pelo Vírus Ebola/tratamento farmacológico , Humanos , Técnicas In Vitro , Coronavírus da Síndrome Respiratória do Oriente Médio , Simulação de Acoplamento Molecular , Pandemias , Peptidil Dipeptidase A/metabolismo , Coronavírus Relacionado à Síndrome Respiratória Aguda Grave , SARS-CoV-2 , Síndrome Respiratória Aguda Grave/tratamento farmacológico , Glicoproteína da Espícula de Coronavírus/metabolismo , Células Vero , Infecção por Zika virus/tratamento farmacológico , Tratamento Farmacológico da COVID-19
9.
PLoS Comput Biol ; 16(2): e1007025, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-32069285

RESUMO

Malaria is an infectious disease that affects over 216 million people worldwide, killing over 445,000 patients annually. Due to the constant emergence of parasitic resistance to the current antimalarial drugs, the discovery of new drug candidates is a major global health priority. Aiming to make the drug discovery processes faster and less expensive, we developed binary and continuous Quantitative Structure-Activity Relationships (QSAR) models implementing deep learning for predicting antiplasmodial activity and cytotoxicity of untested compounds. Then, we applied the best models for a virtual screening of a large database of chemical compounds. The top computational predictions were evaluated experimentally against asexual blood stages of both sensitive and multi-drug-resistant Plasmodium falciparum strains. Among them, two compounds, LabMol-149 and LabMol-152, showed potent antiplasmodial activity at low nanomolar concentrations (EC50 <500 nM) and low cytotoxicity in mammalian cells. Therefore, the computational approach employing deep learning developed here allowed us to discover two new families of potential next generation antimalarial agents, which are in compliance with the guidelines and criteria for antimalarial target candidates.


Assuntos
Antimaláricos/química , Antimaláricos/uso terapêutico , Aprendizado Profundo , Descoberta de Drogas/métodos , Malária/tratamento farmacológico , Humanos , Relação Quantitativa Estrutura-Atividade , Reprodutibilidade dos Testes , Relação Estrutura-Atividade
10.
Anticancer Agents Med Chem ; 19(5): 667-676, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30734686

RESUMO

BACKGROUND: It was recently demonstrated that the phthalimide N-(4-methyl-phenyl)-4- methylphthalimide (MPMPH-1) has important effects against acute and chronic pain in mice, with a mechanism of action correlated to adenylyl cyclase inhibition. Furthermore, it was also demonstrated that phthalimide derivatives presented antiproliferative and anti-tumor effects. Considering the literature data, the present study evaluated the effects of MPMPH-1 on breast cancer bone metastasis and correlated painful symptom, and provided additional toxicological information about the compound and its possible metabolites. METHODS: In silico toxicological analysis was supported by in vitro and in vivo experiments to demonstrate the anti-tumor and anti-hypersensitivity effects of the compound. RESULTS: The data obtained with the in silico toxicological analysis demonstrated that MPMPH-1 has mutagenic potential, with a low to moderate level of confidence. The mutagenicity potential was in vivo confirmed by micronucleus assay. MPMPH-1 treatments in the breast cancer bone metastasis model were able to prevent the osteoclastic resorption of bone matrix. Regarding cartilage, degradation was considerably reduced within the zoledronic acid group, while in MPMPH-1, chondrocyte multiplication was observed in random areas, suggesting bone regeneration. Additionally, the repeated treatment of mice with MPMPH-1 (10 mg/kg, i.p.), once a day for up to 36 days, significantly reduces the hypersensitivity in animals with breast cancer bone metastasis. CONCLUSION: Together, the data herein obtained show that MPMPH-1 is relatively safe, and significantly control the cancer growth, allied to the reduction in bone reabsorption and stimulation of bone and cartilage regeneration. MPMPH-1 effects may be linked, at least in part, to the ability of the compound to interfere with adenylylcyclase pathway activation.


Assuntos
Antineoplásicos/uso terapêutico , Neoplasias Ósseas/tratamento farmacológico , Neoplasias da Mama/patologia , Ftalimidas/uso terapêutico , Animais , Antineoplásicos/toxicidade , Neoplasias Ósseas/secundário , Modelos Animais de Doenças , Feminino , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Ftalimidas/toxicidade
11.
Eur J Med Chem ; 163: 649-659, 2019 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-30562700

RESUMO

Chagas disease is a neglected tropical disease (NTD) caused by the protozoan parasite Trypanosoma cruzi and is primarily transmitted to humans by the feces of infected Triatominae insects during their blood meal. The disease affects 6-8 million people, mostly in Latin America countries, and kills more people in the region each year than any other parasite-born disease, including malaria. Moreover, patient numbers are currently increasing in non-endemic, developed countries, such as Australia, Japan, Canada, and the United States. The treatment is limited to one drug, benznidazole, which is only effective in the acute phase of the disease and is very toxic. Thus, there is an urgent need to develop new, safer, and effective drugs against the chronic phase of Chagas disease. Using a QSAR-based virtual screening followed by in vitro experimental evaluation, we report herein the identification of novel potent and selective hits against T. cruzi intracellular stage. We developed and validated binary QSAR models for prediction of anti-trypanosomal activity and cytotoxicity against mammalian cells using the best practices for QSAR modeling. These models were then used for virtual screening of a commercial database, leading to the identification of 39 virtual hits. Further in vitro assays showed that seven compounds were potent against intracellular T. cruzi at submicromolar concentrations (EC50 < 1 µM) and were very selective (SI > 30). Furthermore, other six compounds were also inside the hit criteria for Chagas disease, which presented activity at low micromolar concentrations (EC50 < 10 µM) against intracellular T. cruzi and were also selective (SI > 15). Moreover, we performed a multi-parameter analysis for the comparison of tested compounds regarding their balance between potency, selectivity, and predicted ADMET properties. In the next studies, the most promising compounds will be submitted to additional in vitro and in vivo assays in acute model of Chagas disease, and can be further optimized for the development of new promising drug candidates against this important yet neglected disease.


Assuntos
Doença de Chagas/tratamento farmacológico , Descoberta de Drogas , Relação Quantitativa Estrutura-Atividade , Trypanosoma cruzi/efeitos dos fármacos , Avaliação Pré-Clínica de Medicamentos/métodos , Humanos , Tripanossomicidas/química
12.
Front Pharmacol ; 9: 1275, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30524275

RESUMO

Virtual screening (VS) has emerged in drug discovery as a powerful computational approach to screen large libraries of small molecules for new hits with desired properties that can then be tested experimentally. Similar to other computational approaches, VS intention is not to replace in vitro or in vivo assays, but to speed up the discovery process, to reduce the number of candidates to be tested experimentally, and to rationalize their choice. Moreover, VS has become very popular in pharmaceutical companies and academic organizations due to its time-, cost-, resources-, and labor-saving. Among the VS approaches, quantitative structure-activity relationship (QSAR) analysis is the most powerful method due to its high and fast throughput and good hit rate. As the first preliminary step of a QSAR model development, relevant chemogenomics data are collected from databases and the literature. Then, chemical descriptors are calculated on different levels of representation of molecular structure, ranging from 1D to nD, and then correlated with the biological property using machine learning techniques. Once developed and validated, QSAR models are applied to predict the biological property of novel compounds. Although the experimental testing of computational hits is not an inherent part of QSAR methodology, it is highly desired and should be performed as an ultimate validation of developed models. In this mini-review, we summarize and critically analyze the recent trends of QSAR-based VS in drug discovery and demonstrate successful applications in identifying perspective compounds with desired properties. Moreover, we provide some recommendations about the best practices for QSAR-based VS along with the future perspectives of this approach.

13.
Drug Discov Today ; 23(11): 1833-1847, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-29935345

RESUMO

Despite the recent outbreak of Zika virus (ZIKV), there are still no approved treatments, and early-stage compounds are probably many years away from approval. A comprehensive A-Z review of the recent advances in ZIKV drug discovery efforts is presented, highlighting drug repositioning and computationally guided compounds, including discovered viral and host cell inhibitors. Promising ZIKV molecular targets are also described and discussed, as well as targets belonging to the host cell, as new opportunities for ZIKV drug discovery. All this knowledge is not only crucial to advancing the fight against the Zika virus and other flaviviruses but also helps us prepare for the next emerging virus outbreak to which we will have to respond.


Assuntos
Antivirais/farmacologia , Descoberta de Drogas , Terapia de Alvo Molecular/métodos , Infecção por Zika virus/tratamento farmacológico , Zika virus/efeitos dos fármacos , Antivirais/química , Antivirais/uso terapêutico , Humanos , Modelos Biológicos , Estrutura Molecular
14.
Front Pharmacol ; 9: 146, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29559909

RESUMO

Malaria is a life-threatening infectious disease caused by parasites of the genus Plasmodium, affecting more than 200 million people worldwide every year and leading to about a half million deaths. Malaria parasites of humans have evolved resistance to all current antimalarial drugs, urging for the discovery of new effective compounds. Given that the inhibition of deoxyuridine triphosphatase of Plasmodium falciparum (PfdUTPase) induces wrong insertions in plasmodial DNA and consequently leading the parasite to death, this enzyme is considered an attractive antimalarial drug target. Using a combi-QSAR (quantitative structure-activity relationship) approach followed by virtual screening and in vitro experimental evaluation, we report herein the discovery of novel chemical scaffolds with in vitro potency against asexual blood stages of both P. falciparum multidrug-resistant and sensitive strains and against sporogonic development of P. berghei. We developed 2D- and 3D-QSAR models using a series of nucleosides reported in the literature as PfdUTPase inhibitors. The best models were combined in a consensus approach and used for virtual screening of the ChemBridge database, leading to the identification of five new virtual PfdUTPase inhibitors. Further in vitro testing on P. falciparum multidrug-resistant (W2) and sensitive (3D7) parasites showed that compounds LabMol-144 and LabMol-146 demonstrated fair activity against both strains and presented good selectivity versus mammalian cells. In addition, LabMol-144 showed good in vitro inhibition of P. berghei ookinete formation, demonstrating that hit-to-lead optimization based on this compound may also lead to new antimalarials with transmission blocking activity.

15.
Artigo em Inglês | MEDLINE | ID: mdl-29203486

RESUMO

Five bis-arylimidamides were assayed as anti-Trypanosoma cruzi agents by in vitro, in silico, and in vivo approaches. None were considered to be pan-assay interference compounds. They had a favorable pharmacokinetic landscape and were active against trypomastigotes and intracellular forms, and in combination with benznidazole, they gave no interaction. The most selective agent (28SMB032) tested in vivo led to a 40% reduction in parasitemia (0.1 mg/kg of body weight/5 days intraperitoneally) but without mortality protection. In silico target fishing suggested DNA as the main target, but ultrastructural data did not match.


Assuntos
Amidinas/farmacologia , Tripanossomicidas/farmacologia , Trypanosoma cruzi/efeitos dos fármacos , Animais , Doença de Chagas/tratamento farmacológico , Masculino , Camundongos , Nitroimidazóis/farmacologia , Parasitemia/tratamento farmacológico , Testes de Sensibilidade Parasitária/métodos
16.
Eur J Med Chem ; 137: 126-138, 2017 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-28582669

RESUMO

New anti-tuberculosis (anti-TB) drugs are urgently needed to battle drug-resistant Mycobacterium tuberculosis strains and to shorten the current 6-12-month treatment regimen. In this work, we have continued the efforts to develop chalcone-based anti-TB compounds by using an in silico design and QSAR-driven approach. Initially, we developed SAR rules and binary QSAR models using literature data for targeted design of new heteroaryl chalcone compounds with anti-TB activity. Using these models, we prioritized 33 compounds for synthesis and biological evaluation. As a result, 10 heteroaryl chalcone compounds (4, 8, 9, 11, 13, 17-20, and 23) were found to exhibit nanomolar activity against replicating mycobacteria, low micromolar activity against nonreplicating bacteria, and nanomolar and micromolar against rifampin (RMP) and isoniazid (INH) monoresistant strains (rRMP and rINH) (<1 µM and <10 µM, respectively). The series also show low activity against commensal bacteria and generally show good selectivity toward M. tuberculosis, with very low cytotoxicity against Vero cells (SI = 11-545). Our results suggest that our designed heteroaryl chalcone compounds, due to their high potency and selectivity, are promising anti-TB agents.


Assuntos
Antituberculosos/farmacologia , Chalcona/farmacologia , Descoberta de Drogas , Mycobacterium tuberculosis/efeitos dos fármacos , Relação Quantitativa Estrutura-Atividade , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Animais , Antituberculosos/síntese química , Antituberculosos/química , Chalcona/síntese química , Chalcona/química , Chlorocebus aethiops , Relação Dose-Resposta a Droga , Desenho de Fármacos , Testes de Sensibilidade Microbiana , Estrutura Molecular , Células Vero
17.
J Chem Inf Model ; 57(5): 1013-1017, 2017 05 22.
Artigo em Inglês | MEDLINE | ID: mdl-28459556

RESUMO

Chemically induced skin sensitization is a complex immunological disease with a profound impact on quality of life and working ability. Despite some progress in developing alternative methods for assessing the skin sensitization potential of chemical substances, there is no in vitro test that correlates well with human data. Computational QSAR models provide a rapid screening approach and contribute valuable information for the assessment of chemical toxicity. We describe the development of a freely accessible web-based and mobile application for the identification of potential skin sensitizers. The application is based on previously developed binary QSAR models of skin sensitization potential from human (109 compounds) and murine local lymph node assay (LLNA, 515 compounds) data with good external correct classification rate (0.70-0.81 and 0.72-0.84, respectively). We also included a multiclass skin sensitization potency model based on LLNA data (accuracy ranging between 0.73 and 0.76). When a user evaluates a compound in the web app, the outputs are (i) binary predictions of human and murine skin sensitization potential; (ii) multiclass prediction of murine skin sensitization; and (iii) probability maps illustrating the predicted contribution of chemical fragments. The app is the first tool available that incorporates quantitative structure-activity relationship (QSAR) models based on human data as well as multiclass models for LLNA. The Pred-Skin web app version 1.0 is freely available for the web, iOS, and Android (in development) at the LabMol web portal ( http://labmol.com.br/predskin/ ), in the Apple Store, and on Google Play, respectively. We will continuously update the app as new skin sensitization data and respective models become available.


Assuntos
Alérgenos , Dermatite de Contato , Internet , Pele , Software , Alérgenos/toxicidade , Animais , Simulação por Computador , Bases de Dados de Compostos Químicos , Humanos , Ensaio Local de Linfonodo , Camundongos , Relação Quantitativa Estrutura-Atividade , Pele/efeitos dos fármacos , Pele/patologia , Fatores de Tempo
18.
Biochem Biophys Res Commun ; 492(4): 643-651, 2017 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-28341122

RESUMO

America is still suffering with the outbreak of Zika virus (ZIKV) infection. Congenital ZIKV syndrome has already caused a public health emergency of international concern. However, there are still no vaccines to prevent or drugs to treat the infection caused by ZIKV. The ZIKV NS3 helicase (NS3h) protein is a promising target for drug discovery due to its essential role in viral genome replication. NS3h unwinds the viral RNA to enable the replication of the viral genome by the NS5 protein. NS3h contains two important binding sites: the NTPase binding site and the RNA binding site. Here, we used molecular dynamics (MD) simulations to study the molecular behavior of ZIKV NS3h in the presence and absence of ssRNA and the potential implications for NS3h activity and inhibition. Although there is conformational variability and poor electron densities of the RNA binding loop in various apo flaviviruses NS3h crystallographic structures, the MD trajectories of NS3h-ssRNA demonstrated that the RNA binding loop becomes more stable when NS3h is occupied by RNA. Our results suggest that the presence of RNA generates important interactions with the RNA binding loop, and these interactions stabilize the loop sufficiently that it remains in a closed conformation. This closed conformation likely keeps the ssRNA bound to the protein for a sufficient duration to enable the unwinding/replication activities of NS3h to occur. In addition, conformational changes of this RNA binding loop can change the nature and location of the optimal ligand binding site, according to ligand binding site prediction results. These are important findings to help guide the design and discovery of new inhibitors of NS3h as promising compounds to treat the ZIKV infection.


Assuntos
Modelos Químicos , Simulação de Dinâmica Molecular , RNA Viral/química , RNA Viral/ultraestrutura , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/ultraestrutura , Zika virus/enzimologia , Sítios de Ligação , Ativação Enzimática , Conformação de Ácido Nucleico , Ligação Proteica , Conformação Proteica , RNA Helicases/química , RNA Helicases/ultraestrutura , Serina Endopeptidases/química , Serina Endopeptidases/ultraestrutura
19.
Eur J Med Chem ; 129: 287-302, 2017 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-28235702

RESUMO

A new generation of potent hDHODH inhibitors designed by a scaffold-hopping replacement of the quinolinecarboxylate moiety of brequinar, one of the most potent known hDHODH inhibitors, is presented here. Their general structure is characterized by a biphenyl moiety joined through an amide bridge with an acidic hydroxyazole scaffold (hydroxylated thiadiazole, pyrazole and triazole). Molecular modelling suggested that these structures should adopt a brequinar-like binding mode involving interactions with subsites 1, 2 and 4 of the hDHODH binding site. Initially, the inhibitory activity of the compounds was studied on recombinant hDHODH. The most potent compound of the series in the enzymatic assays was the thiadiazole analogue 4 (IC50 16 nM). The activity was found to be dependent on the fluoro substitution pattern at the biphenyl moiety as well as on the choice/substitution of the heterocyclic ring. Structure determination of hDHODH co-crystallized with one representative compound from each series (4, 5 and 6) confirmed the brequinar-like binding mode as suggested by modelling. The specificity of the observed effects of the compound series was tested in cell-based assays for antiproliferation activity using Jurkat cells and PHA-stimulated PBMC. These tests were also verified by addition of exogenous uridine to the culture medium. In particular, the triazole analogue 6 (IC50 against hDHODH: 45 nM) exerted potent in vitro antiproliferative and immunosuppressive activity without affecting cell survival.


Assuntos
Azóis/química , Inibidores Enzimáticos/química , Oxirredutases atuantes sobre Doadores de Grupo CH-CH/antagonistas & inibidores , Sítios de Ligação , Proliferação de Células/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Células Cultivadas , Di-Hidro-Orotato Desidrogenase , Desenho de Fármacos , Inibidores Enzimáticos/farmacologia , Humanos , Hidroxilação , Terapia de Imunossupressão , Células Jurkat , Modelos Moleculares , Estrutura Molecular , Relação Estrutura-Atividade , Difração de Raios X
20.
J Med Chem ; 59(15): 7075-88, 2016 Aug 11.
Artigo em Inglês | MEDLINE | ID: mdl-27396732

RESUMO

Schistosomiasis is a debilitating neglected tropical disease, caused by flatworms of Schistosoma genus. The treatment relies on a single drug, praziquantel (PZQ), making the discovery of new compounds extremely urgent. In this work, we integrated QSAR-based virtual screening (VS) of Schistosoma mansoni thioredoxin glutathione reductase (SmTGR) inhibitors and high content screening (HCS) aiming to discover new antischistosomal agents. Initially, binary QSAR models for inhibition of SmTGR were developed and validated using the Organization for Economic Co-operation and Development (OECD) guidance. Using these models, we prioritized 29 compounds for further testing in two HCS platforms based on image analysis of assay plates. Among them, 2-[2-(3-methyl-4-nitro-5-isoxazolyl)vinyl]pyridine and 2-(benzylsulfonyl)-1,3-benzothiazole, two compounds representing new chemical scaffolds have activity against schistosomula and adult worms at low micromolar concentrations and therefore represent promising antischistosomal hits for further hit-to-lead optimization.


Assuntos
Descoberta de Drogas , Relação Quantitativa Estrutura-Atividade , Schistosoma mansoni/efeitos dos fármacos , Esquistossomose/tratamento farmacológico , Esquistossomicidas/farmacologia , Animais , Relação Dose-Resposta a Droga , Avaliação Pré-Clínica de Medicamentos , Humanos , Modelos Moleculares , Estrutura Molecular , Esquistossomicidas/síntese química , Esquistossomicidas/química
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