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Item QSAR-Driven design and discovery of novel compounds with antiplasmodial and transmission blocking activities(2018) Lima, Marília Nunes do Nascimento; Melo Filho, Cleber Camilo do; Cassiano, Gustavo Capatti; Neves, Bruno Junior; Alves, Vinícius de Medeiros; Braga, Rodolpho de Campos; Cravo, Pedro Vitor Lemos; Muratov, Eugene; Paim, Juliana Calit; Bargieri, Daniel Youssef; Costa, Fabio Trindade Maranhão; Andrade, Carolina HortaMalaria 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.Item Development of Web and mobile applications for chemical toxicity prediction(2018) Alves, Vinícius de Medeiros; Braga, Rodolpho de Campos; Muratov, Eugene; Andrade, Carolina HortaComputational tools are recognized to provide high-quality predictions for the assessment of chemical toxicity. In the recent years, mobile devices have become ubiquitous, allowing for the development of innovative and useful models implemented as chemical software applications. Here, we will briefly discuss this recent uptick in the development of web-based and mobile applications for chemical problems, focusing on best practices, development, usage and interpretation. As an example, we also describe two innovative apps (Pred-hERG and Pred-Skin) for chemical toxicity prediction developed in our laboratory. These applications are based on predictive quantitative structure-activity relationships (QSAR) models developed using the largest publicly available datasets of structurally diverse compounds. The developed tools ensure both highly accurate predictions and easy interpretation of the models, allowing users to discriminate potential toxicants and to purpose structural modifications to design safer chemicals.Item Quimioinformática: uma introdução(2018) Alves, Vinícius de Medeiros; Braga, Rodolpho de Campos; Muratova, Eugene; Andrade, Carolina HortaCheminformatics is an interdisciplinary field between chemistry and informatics, which has evolved considerably since its inception in the 1960s. Initially, the cheminformatics community dealt primarily with practical and technical aspects of chemical structure representation, manipulation, and processing, while modern research explores a new role: the exploration and interpretation of large chemical databases and the discovery of new compounds with desired activity and safety profiles. Despite the recent release of several hallmark reviews addressing methods and application of cheminformatics written in Portuguese, so far there are no scientific articles presenting cheminformatics research to the Brazilian scientific community yet. To address this gap, we aim to introduce the field of cheminformatics to both students and researchers in a simple and didactic way by narrating important historical facts and contextualizing information within the scope of various applications.Item Perspectivas da química medicinal para o século XXI: desafios e oportunidades(2018) Andrade, Carolina Horta; Kümmerle, Arthur Eugen; Guido, Rafael Victorio CarvalhoIn the 21st century, medicinal chemists will face many challenges to improve the quality of life of populations. The challenges consist of emerging infectious (ex. bacterial, viral and parasite infections) and non-communicable diseases (ex. autoimmune, Alzheimer disease, Parkinson’s disease) that will require innovative technologies (ex. microfluidics, nanotechnology, biotechnology) to be fully understood and combated. In this work, we indicate trends, perspectives and opportunities related to drug discovery as well as highlight the tools and strategies that could be used in drug discovery of the 21st centuryItem OpenZika: an IBM world community grid project to accelerate Zika virus drug discovery(2016) Ekins, Sean; Perryman, Alexander Luke; Andrade, Carolina HortaThe Zika virus outbreak in the Americas has caused global concern. To help accelerate this fight against Zika, we launched the OpenZika project. OpenZika is an IBM World Community Grid Project that uses distributed computing on millions of computers and Android devices to run docking experiments, in order to dock tens of millions of drug-like compounds against crystal structures and homology models of Zika proteins (and other related flavivirus targets). This will enable the identification of new candidates that can then be tested in vitro, to advance the discovery and development of new antiviral drugs against the Zika virus. The docking data is being made openly accessible so that all members of the global research community can use it to further advance drug discovery studies against Zika and other related flaviviruses.Item The antidepressant drug paroxetine as a new lead candidate in schistosome drug discovery(2016) Neves, Bruno Junior; Dantas, Rafael Ferreira; Senger, Mário Roberto; Valente, Walter César Góes; Rezende Neto, João de Mello; Chaves, Willian Távora; Kamentsky, Lee; Carpenter, Anne; Silva Junior, Floriano Paes; Andrade, Carolina HortaRecently, our in silico repositioning-chemogenomics approach predicted paroxetine (PAR), an antidepressant drug, as a inhibitor of Schistosoma mansoni serotonin transporters (SmSERTs), and consequently, a new anti-schistosomal candidate. With the aim of determining the anti-schistosomal activity of this drug, we initially used a spectrophotometric assay to determine activity against schistosomula worms. During this investigation, we verified that PAR showed a pronounced effect on schistosomula viability (IC50 = 2.5 μM) after 72 h of incubation. Then, we performed ex vivo studies with adult S. mansoni worms using a new automated image-based assay to accurately measure worm motility. As expected from the PAR's predicted mechanism of action, both male and female worms treated with low concentrations of PAR exhibited enhanced motility followed by reduction in motility as incubation time increased. PAR EC50 values for motility reduction in male and female worms were 5.1 μM and 9.9 μM after 24 h of exposure, respectively, and this effect was maintained until the end of the experiment (72 h). Lastly, homology modeling and docking studies with SmSERT-A and human SERT (hSERT) revealed insights into the chemical basis of PAR anti-schistosomal activity. These results provide crucial guidance for further studies to optimize PAR in terms of potency and selectivity.Item A evolução da química medicinal no Brasil: avanços nos 40 anos da Sociedade Brasileira de Química(2017) Amaral, Antonia Tavares do; Andrade, Carolina Horta; Kummerle, Arthur Eugen; Guido, Rafael Victorio CarvalhoMEDICINAL CHEMISTRY PROGRESS IN BRAZIL: ADVANCES IN THE 40 YEARS OF THE BRAZILIAN CHEMICAL SOCIETY. Medicinal Chemistry includes the invention, discovery, design, identification, and interpretation of the molecular mechanism of action of biologically active compounds. In addition to the discovery of bioactive molecules, Medicinal Chemistry investigates drug metabolism and the relationships between chemical structure and biological activity. The advances achieved in the 20th century have significantly contributed to the better understanding of pathophysiological processes as well as the development of new, safer and more effective drugs for many diseases. In this article, we review the evolution of Medicinal Chemistry in Brazil during the last 40 years and evaluate the impact of the Brazilian contributions in the international context. The analyzed data revealed that Medicinal Chemistry research in Brazil has increased exponentially in the last two decades, the research groups became more well-distributed across the Brazilian regions and our scientific contributions have significant impact in the main journals of the field. Therefore, aiming at evolving steadily and striving for excellence in drug discovery and development, we shall focus on national and international collaborations and investment in translational research, as well.Item A diarylamine derived from anthranilic acid inhibits ZIKV replication(2019) Silva, Suely da; Shimizu, Jacqueline Farinha; Oliveira, Débora Moraes; Assis, Leticia Ribeiro de; Oliva, Cíntia Bittar; Mottin, Melina; Sousa, Bruna Katiele de Paula; Mesquita, Nathalya Cristina de Moraes Roso; Regasini, Luis Octávio; Rahal, Paula; Andrade, Carolina HortaZika virus (ZIKV) is a mosquito-transmitted Flavivirus, originally identified in Uganda in 1947 and recently associated with a large outbreak in South America. Despite extensive efforts there are currently no approved antiviral compounds for treatment of ZIKV infection. Here we describe the antiviral activity of diarylamines derived from anthranilic acid (FAMs) against ZIKV. A synthetic FAM (E3) demonstrated anti-ZIKV potential by reducing viral replication up to 86%. We analyzed the possible mechanisms of action of FAM E3 by evaluating the intercalation of this compound into the viral dsRNA and its interaction with the RNA polymerase of bacteriophage SP6. However, FAM E3 did not act by these mechanisms. In silico results predicted that FAM E3 might bind to the ZIKV NS3 helicase suggesting that this protein could be one possible target of this compound. To test this, the thermal stability and the ATPase activity of the ZIKV NS3 helicase domain (NS3Hel) were investigated in vitro and we demonstrated that FAM E3 could indeed bind to and stabilize NS3Hel.Item Cheminformatics-driven discovery of polymeric micelle formulations for poorly soluble drugs(2019) Alves, Vinícius de Medeiros; Hwang, Duhyeong; Muratov, Eugene; Sokolsky-Papkov, Marina; Varlamova, Ekaterina; Vinod, Natasha; Chaemin, Lim; Andrade, Carolina Horta; Tropsha, Alexander; Kabanov, Alexander V.Many drug candidates fail therapeutic development because of poor aqueous solubility. We have conceived a computer-aided strategy to enable polymeric micelle-based delivery of poorly soluble drugs. We built models predicting both drug loading efficiency (LE) and loading capacity (LC) using novel descriptors of drug-polymer complexes. These models were employed for virtual screening of drug libraries, and eight drugs predicted to have either high LE and high LC or low LE and low LC were selected. Three putative positives, as well as three putative negative hits, were confirmed experimentally (implying 75% prediction accuracy). Fortuitously, simvastatin, a putative negative hit, was found to have the desired micelle solubility. Podophyllotoxin and simvastatin (LE of 95% and 87% and LC of 43% and 41%, respectively) were among the top five polymeric micelle-soluble compounds ever studied experimentally. The success of the strategy described herein suggests its broad utility for designing drug delivery systems.Item QSAR-driven discovery of novel chemical scaffolds active against schistosoma mansoni(2016) Melo Filho, Cleber Camilo; Dantas, Rafael Ferreira; Braga, Rodolpho de Campos; Neves, Bruno Junior; Senger, Mário Roberto; Valente, Walter César Góes; Rezende Neto, João de Mello; Chaves, Willian Távaro; Muratov, Eugene; Paveley, Ross; Andrade, Carolina HortaSchistosomiasis is a neglected tropical disease that affects millions of people worldwide. Thioredoxin glutathione reductase of Schistosoma mansoni (SmTGR) is a validated drug target that plays a crucial role in the redox homeostasis of the parasite. We report the discovery of new chemical scaffolds against S. mansoni using a combi-QSAR approach followed by virtual screening of a commercial database and confirmation of top ranking compounds by in vitro experimental evaluation with automated imaging of schistosomula and adult worms. We constructed 2D and 3D quantitative structure–activity relationship (QSAR) models using a series of oxadiazoles-2-oxides reported in the literature as SmTGR inhibitors and combined the best models in a consensus QSAR model. This model was used for a virtual screening of Hit2Lead set of ChemBridge database and allowed the identification of ten new potential SmTGR inhibitors. Further experimental testing on both shistosomula and adult worms showed that 4-nitro-3,5-bis(1-nitro-1H-pyrazol-4-yl)-1H-pyrazole (LabMol-17) and 3-nitro-4-{[(4-nitro-1,2,5-oxadiazol-3-yl)oxy]methyl}-1,2,5-oxadiazole (LabMol-19), two compounds representing new chemical scaffolds, have high activity in both systems. These compounds will be the subjects for additional testing and, if necessary, modification to serve as new schistosomicidal agents.Item Open drug discovery for the Zika virus(2016) Ekins, Sean; Mietchen, Daniel; Coffee, Megan; Stratton, Thomas P.; Freundlich, Joel S.; Freitas Junior, Lucio; Muratov, Eugene; Siqueira Neto, Jair; Williams, Antony; Andrade, Carolina HortaThe Zika virus (ZIKV) outbreak in the Americas has caused global concern that we may be on the brink of a healthcare crisis. The lack of research on ZIKV in the over 60 years that we have known about it has left us with little in the way of starting points for drug discovery. Our response can build on previous efforts with virus outbreaks and lean heavily on work done on other flaviviruses such as dengue virus. We provide some suggestions of what might be possible and propose an open drug discovery effort that mobilizes global science efforts and provides leadership, which thus far has been lacking. We also provide a listing of potential resources and molecules that could be prioritized for testing as in vitro assays for ZIKV are developed. We propose also that in order to incentivize drug discovery, a neglected disease priority review voucher should be available to those who successfully develop an FDA approved treatment. Learning from the response to the ZIKV, the approaches to drug discovery used and the success and failures will be critical for future infectious disease outbreaks.Item Unveiling the kinomes of Leishmania infantum and L. braziliensis empowers the discovery of new kinase targets and antileishmanial compounds(2019) Borba, Joyce Villa Verde Bastos; Silva, Arthur de Carvalho e; Pereira, Pablo Ivan; Grazzia, Nathalia; Miguel, Danilo Ciccone; Muratov, Eugene; Furnham, Nicholas; Andrade, Carolina HortaLeishmaniasis is a neglected tropical disease caused by parasites of the genus Leishmania (NTD) endemic in 98 countries. Although some drugs are available, current treatments deal with issues such as toxicity, low efficacy, and emergence of resistance. Therefore, there is an urgent need to identify new targets for the development of new antileishmanial drugs. Protein kinases (PKs), which play an essential role in many biological processes, have become potential drug targets for many parasitic diseases. A refined bioinformatics pipeline was applied in order to define and compare the kinomes of L. infantum and L. braziliensis, species that cause cutaneous and visceral manifestations of leishmaniasis in the Americas, the latter being potentially fatal if untreated. Respectively, 224 and 221 PKs were identified in L. infantum and L. braziliensis overall. Almost all unclassified eukaryotic PKs were assigned to six of nine major kinase groups and, consequently, most have been classified into family and subfamily. Furthermore, revealing the kinomes for both Leishmania species allowed for the prioritization of potential drug targets that could be explored for discovering new drugs against leishmaniasis. Finally, we used a drug repurposing approach and prioritized seven approved drugs and investigational compounds to be experimentally tested against Leishmania. Trametinib and NMS-1286937 inhibited the growth of L. infantum and L. braziliensis promastigotes and amastigotes and therefore might be good candidates for the drug repurposing pipeline.Item CoMPARA: collaborative modeling project for androgen receptor activity(2020) Mansouri, Kamel; Kleinstreuer, Nicole; Abdelaziz , Ahmed M.; Alberga, Domenico; Alves, Vinícius de Medeiros; Andersson, Patrik L.; Andrade, Carolina Horta; Fang, Bai; Balabin, Ilya; Ballabio, DavideBackground: Endocrine disrupting chemicals (EDCs) are xenobiotics that mimic the interaction of natural hormones and alter synthesis, transport, or metabolic pathways. The prospect of EDCs causing adverse health effects in humans and wildlife has led to the development of scientific and regulatory approaches for evaluating bioactivity. This need is being addressed using high-throughput screening (HTS) in vitro approaches and computational modeling. Objectives: In support of the Endocrine Disruptor Screening Program, the U.S. Environmental Protection Agency (EPA) led two worldwide consortiums to virtually screen chemicals for their potential estrogenic and androgenic activities. Here, we describe the Collaborative Modeling Project for Androgen Receptor Activity (CoMPARA) efforts, which follows the steps of the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP). Methods: The CoMPARA list of screened chemicals built on CERAPP’s list of 32,464 chemicals to include additional chemicals of interest, as well as simulated ToxCast™ metabolites, totaling 55,450 chemical structures. Computational toxicology scientists from 25 international groups contributed 91 predictive models for binding, agonist, and antagonist activity predictions. Models were underpinned by a common training set of 1,746 chemicals compiled from a combined data set of 11 ToxCast™/Tox21 HTS in vitro assays. Results: The resulting models were evaluated using curated literature data extracted from different sources. To overcome the limitations of single-model approaches, CoMPARA predictions were combined into consensus models that provided averaged predictive accuracy of approximately 80% for the evaluation set. Discussion: The strengths and limitations of the consensus predictions were discussed with example chemicals; then, the models were implemented into the free and open-source OPERA application to enable screening of new chemicals with a defined applicability domain and accuracy assessment. This implementation was used to screen the entire EPA DSSTox database of ∼875,000 chemicals, and their predicted AR activities have been made available on the EPA CompTox Chemicals dashboard and National Toxicology Program’s Integrated Chemical Environment.Item Novel computational models offer alternatives to animal testing for assessing eye irritation and corrosion potential of chemicals(2021) Silva, Arthur de Carvalho e; Borba, Joyce Villa Verde Bastos; Alves, Vinícius de Medeiros; Hall, Steven Umuale Silva; Furnham, Nicholas; Kleinstreuer, Nicole; Muratov, Eugene; Tropsha, Alexander; Andrade, Carolina HortaEye irritation and corrosion are fundamental considerations in developing chemicals to be used in or near the eye, from cleaning products to ophthalmic solutions. Unfortunately, animal testing is currently the standard method to identify compounds that cause eye irritation or corrosion. Yet, there is growing pressure on the part of regulatory agencies both in the USA and abroad to develop New Approach Methodologies (NAMs) that help reduce the need for animal testing and address unmet need to modernize safety evaluation of chemical hazards. In furthering the development and applications of computational NAMs in chemical safety assessment, in this study we have collected the largest expertly curated dataset of compounds tested for eye irritation and corrosion, and employed this data to build and validate binary and multi-classification Quantitative Structure-Activity Relationships (QSAR) models that can reliably assess eye irritation/corrosion potential of novel untested compounds. QSAR models were generated with Random Forest (RF) and Multi-Descriptor Read Across (MuDRA) machine learning (ML) methods, and validated using a 5-fold external cross-validation protocol. These models demonstrated high balanced accuracy (CCR of 0.68–0.88), sensitivity (SE of 0.61–0.84), positive predictive value (PPV of 0.65–0.90), specificity (SP of 0.56–0.91), and negative predictive value (NPV of 0.68–0.85). Overall, MuDRA models outperformed RF models and were applied to predict compounds’ irritation/corrosion potential from the Inactive Ingredient Database, which contains components present in FDA-approved drug products, and from the Cosmetic Ingredient Database, the European Commission source of information on cosmetic substances. All models built and validated in this study are publicly available at the STopTox web portal (https://stoptox.mml.unc.edu/). These models can be employed as reliable tools for identifying potential eye irritant/corrosive compounds.Item CATMoS: collaborative acute toxicity modeling suite(2021) Mansour, Kamel; Karmaus, Agnes L.; Fitzpatrick, Jeremy; Patlewicz, Grace; Pradeep, Prachi; Alberga, Domenico; Alepee, Nathalie; Allen, Timothy E. H.; Allen, Dave; Alves, Vinícius de Medeiros; Andrade, Carolina HortaBackground: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. Objectives: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50≤50mg/kg)], and nontoxic chemicals (LD50>2,000mg/kg). Methods: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. Results: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results. Discussion: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program’s Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made.Item A critical overview of computational approaches employed for COVID-19 drug discovery(2021) Muratov, Eugene; Amaro, Rommie E.; Andrade, Carolina Horta; Brown, Nathan; Ekins, Sean; Isayev, Olexandr; Fourches, Denis; Kozakov, Dima; Franco, José Luis Medina; Merz, Kenneth Malcolm; Oprea, Tudor I.COVID-19 has resulted in huge numbers of infections and deaths worldwide and brought the most severe disruptions to societies and economies since the Great Depression. Massive experimental and computational research effort to understand and characterize the disease and rapidly develop diagnostics, vaccines, and drugs has emerged in response to this devastating pandemic and more than 130 000 COVID-19-related research papers have been published in peer-reviewed journals or deposited in preprint servers. Much of the research effort has focused on the discovery of novel drug candidates or repurposing of existing drugs against COVID-19, and many such projects have been either exclusively computational or computer-aided experimental studies. Herein, we provide an expert overview of the key computational methods and their applications for the discovery of COVID-19 small-molecule therapeutics that have been reported in the research literature. We further outline that, after the first year the COVID-19 pandemic, it appears that drug repurposing has not produced rapid and global solutions. However, several known drugs have been used in the clinic to cure COVID-19 patients, and a few repurposed drugs continue to be considered in clinical trials, along with several novel clinical candidates. We posit that truly impactful computational tools must deliver actionable, experimentally testable hypotheses enabling the discovery of novel drugs and drug combinations, and that open science and rapid sharing of research results are critical to accelerate the development of novel, much needed therapeutics for COVID-19.Item Repurposing the Ebola and marburg virus inhibitors tilorone, quinacrine, and pyronaridine: in vitro activity against SARS-CoV-2 and potential mechanisms(2021) Puhl, Ana Cristina; Fritch, Ethan J.; Lane, Thomas R.; Tse, Longping V.; Sacramento, Carolina de Queiroz; Yount, Boyd L.; Rodrigues, Natalia Fintelman; Tavella, Tatyana Almeida; Costa, Fabio Trindade Maranhão; Weston, Stuart; Andrade, Carolina HortaSevere acute respiratory coronavirus 2 (SARS-CoV-2) is a newly identified virus that has resulted in over 2.5 million deaths globally and over 116 million cases globally in March, 2021. Small-molecule inhibitors that reverse disease severity have proven difficult to discover. One of the key approaches that has been widely applied in an effort to speed up the translation of drugs is drug repurposing. A few drugs have shown in vitro activity against Ebola viruses and demonstrated activity against SARS-CoV-2 in vivo. Most notably, the RNA polymerase targeting remdesivir demonstrated activity in vitro and efficacy in the early stage of the disease in humans. Testing other small-molecule drugs that are active against Ebola viruses (EBOVs) would appear a reasonable strategy to evaluate their potential for SARS-CoV-2. We have previously repurposed pyronaridine, tilorone, and quinacrine (from malaria, influenza, and antiprotozoal uses, respectively) as inhibitors of Ebola and Marburg viruses in vitro in HeLa cells and mouse-adapted EBOV in mice in vivo. We have now tested these three drugs in various cell lines (VeroE6, Vero76, Caco-2, Calu-3, A549-ACE2, HUH-7, and monocytes) infected with SARS-CoV-2 as well as other viruses (including MHV and HCoV 229E). The compilation of these results indicated considerable variability in antiviral activity observed across cell lines. We found that tilorone and pyronaridine inhibited the virus replication in A549-ACE2 cells with IC50 values of 180 nM and IC50 198 nM, respectively. We used microscale thermophoresis to test the binding of these molecules to the spike protein, and tilorone and pyronaridine bind to the spike receptor binding domain protein with Kd values of 339 and 647 nM, respectively. Human Cmax for pyronaridine and quinacrine is greater than the IC50 observed in A549-ACE2 cells. We also provide novel insights into the mechanism of these compounds which is likely lysosomotropic.Item QSAR-based virtual screening of natural products database for identification of potent antimalarial hits(2021) Ferreira, Letícia Tiburcio; Borba, Joyce Villa Verde Bastos; Moreira Filho, José Teófilo; Ribeiro, Aline Rimoldi; Andrade, Carolina Horta; Costa, Fabio Trindade MaranhãoWith about 400,000 annual deaths worldwide, malaria remains a public health burden in tropical and subtropical areas, especially in low-income countries. Selection of drug-resistant Plasmodium strains has driven the need to explore novel antimalarial compounds with diverse modes of action. In this context, biodiversity has been widely exploited as a resourceful channel of biologically active compounds, as exemplified by antimalarial drugs such as quinine and artemisinin, derived from natural products. Thus, combining a natural product library and quantitative structure–activity relationship (QSAR)-based virtual screening, we have prioritized genuine and derivative natural compounds with potential antimalarial activity prior to in vitro testing. Experimental validation against cultured chloroquine-sensitive and multi-drug-resistant P. falciparum strains confirmed the potent and selective activity of two sesquiterpene lactones (LDT-597 and LDT-598) identified in silico. Quantitative structure–property relationship (QSPR) models predicted absorption, distribution, metabolism, and excretion (ADME) and physiologically based pharmacokinetic (PBPK) parameters for the most promising compound, showing that it presents good physiologically based pharmacokinetic properties both in rats and humans. Altogether, the in vitro parasite growth inhibition results obtained from in silico screened compounds encourage the use of virtual screening campaigns for identification of promising natural compound-based antimalarial molecules.Item Violacein-induced chaperone system collapse underlies multistage antiplasmodial activity(2021) Tavella, Tatyana Almeida; Silva, Noeli Soares Melo da; Spillman, Natalie; Andrade, Ana Carolina; Kayano, Vitor; Cassiano, Gustavo Capatti; Vasconcelos, Adrielle Ayumi; Camargo, Antônio Pedro de Castello Branco da Rocha; Silva, Djane Clarys Baia da; Fontinha, Diana; Salazar Alvarez, Luis Carlos; Ferreira, Letícia Tiburcio; Peralis Tomaz, Kaira Cristina; Neves, Bruno Junior; Andrade, Carolina HortaAntimalarial drugs with novel modes of action and wide therapeutic potential are needed to pave the way for malaria eradication. Violacein is a natural compound known for its biological activity against cancer cells and several pathogens, including the malaria parasite, Plasmodium falciparum (Pf). Herein, using chemical genomic profiling (CGP), we found that violacein affects protein homeostasis. Mechanistically, violacein binds Pf chaperones, PfHsp90 and PfHsp70-1, compromising the latter’s ATPase and chaperone activities. Additionally, violacein-treated parasites exhibited increased protein unfolding and proteasomal degradation. The uncoupling of the parasite stress response reflects the multistage growth inhibitory effect promoted by violacein. Despite evidence of proteotoxic stress, violacein did not inhibit global protein synthesis via UPR activation—a process that is highly dependent on chaperones, in agreement with the notion of a violacein-induced proteostasis collapse. Our data highlight the importance of a functioning chaperone–proteasome system for parasite development and differentiation. Thus, a violacein-like small molecule might provide a good scaffold for development of a novel probe for examining the molecular chaperone network and/or antiplasmodial drug design.Item Update and elucidation of Plasmodium kinomes: prioritization of kinases as potential drug targets for malaria(2022) Borba, Joyce Villa Verde Bastos; Silva, Arthur de Carvalho e; Nascimento, Marília Nunes do; Ferreira, Letícia Tiburcio; Ribeiro, Aline Rimoldi; Starling, Luísa Caldas; Ramos, Pablo Ivan Pereira; Costa, Fabio Trindade Maranhão; Andrade, Carilona HortaMalaria is a tropical disease caused by Plasmodium spp. and transmitted by the bite of infected Anopheles mosquitoes. Protein kinases (PKs) play key roles in the life cycle of the etiological agent of malaria, turning these proteins attractive targets for antimalarial drug discovery campaigns. As part of an effort to understand parasite signaling functions, we report the results of a bioinformatics pipeline analysis of PKs of eight Plasmodium species. To date, no P. malariae and P. ovale kinome assemble has been conducted. We classified, curated and annotated predicted kinases to update P. falciparum, P. vivax, P. yoelii, P. berghei, P. chabaudi, and P. knowlesi kinomes published to date, as well as report for the first time the kinomes of P. malariae and P. ovale. Overall, from 76 to 97 PKs were identified among all Plasmodium spp. kinomes. Most of the kinases were assigned to seven of nine major kinase groups: AGC, CAMK, CMGC, CK1, STE, TKL, OTHER; and the Plasmodium-specific group FIKK. About 30% of kinases have been deeply classified into group, family and subfamily levels and only about 10% remained unclassified. Furthermore, updating and comparing the kinomes of P. vivax and P. falciparum allowed for the prioritization and selection of kinases as potential drug targets that could be explored for discovering new drugs against malaria. This integrated approach resulted in the selection of 37 protein kinases as potential targets and the identification of investigational compounds with moderate in vitro activity against asexual P. falciparum (3D7 and Dd2 strains) stages that could serve as starting points for the search of potent antimalarial leads in the future.