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Andrade C, Sousa BKDP, Sigurdardóttir S, Bourgard C, Borba J, Clementino L, Salazar-Alvarez LC, Groustra S, Zigweid R, Khim M, Staker B, Costa F, Eriksson L, Sunnerhagen P. Selective Bias Virtual Screening for Discovery of Promising Antimalarial Candidates targeting Plasmodium N-Myristoyltransferase. RESEARCH SQUARE 2024:rs.3.rs-3963523. [PMID: 38463971 PMCID: PMC10925453 DOI: 10.21203/rs.3.rs-3963523/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Malaria remains a significant public health challenge, with Plasmodium vivax being the species responsible for the most prevalent form of the disease. Given the limited therapeutic options available, the search for new antimalarials against P. vivax is urgent. This study aims to identify new inhibitors for P. vivax N-myristoyltransferase (PvNMT), an essential drug target against malaria. Through a validated virtual screening campaign, we prioritized 23 candidates for further testing. In the yeast NMT system, seven compounds exhibit a potential inhibitor phenotype. In vitro antimalarial phenotypic assays confirmed the activity of four candidates while demonstrating an absence of cytotoxicity. Enzymatic assays reveal LabMol-394 as the most promising inhibitor, displaying selectivity against the parasite and a strong correlation within the yeast system. Furthermore, molecular dynamics simulations shed some light into its binding mode. This study constitutes a substantial contribution to the exploration of a selective quinoline scaffold and provides valuable insights into the development of new antimalarial candidates.
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de Souza Neto LR, Montoya BO, Brandão-Neto J, Verma A, Bowyer S, Moreira-Filho JT, Dantas RF, Neves BJ, Andrade CH, von Delft F, Owens RJ, Furnham N, Silva-Jr FP. Fragment library screening by X-ray crystallography and binding site analysis on thioredoxin glutathione reductase of Schistosoma mansoni. Sci Rep 2024; 14:1582. [PMID: 38238498 PMCID: PMC10796382 DOI: 10.1038/s41598-024-52018-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
Schistosomiasis is caused by parasites of the genus Schistosoma, which infect more than 200 million people. Praziquantel (PZQ) has been the main drug for controlling schistosomiasis for over four decades, but despite that it is ineffective against juvenile worms and size and taste issues with its pharmaceutical forms impose challenges for treating school-aged children. It is also important to note that PZQ resistant strains can be generated in laboratory conditions and observed in the field, hence its extensive use in mass drug administration programs raises concerns about resistance, highlighting the need to search for new schistosomicidal drugs. Schistosomes survival relies on the redox enzyme thioredoxin glutathione reductase (TGR), a validated target for the development of new anti-schistosomal drugs. Here we report a high-throughput fragment screening campaign of 768 compounds against S. mansoni TGR (SmTGR) using X-ray crystallography. We observed 49 binding events involving 35 distinct molecular fragments which were found to be distributed across 16 binding sites. Most sites are described for the first time within SmTGR, a noteworthy exception being the "doorstop pocket" near the NADPH binding site. We have compared results from hotspots and pocket druggability analysis of SmTGR with the experimental binding sites found in this work, with our results indicating only limited coincidence between experimental and computational results. Finally, we discuss that binding sites at the doorstop/NADPH binding site and in the SmTGR dimer interface, should be prioritized for developing SmTGR inhibitors as new antischistosomal drugs.
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Affiliation(s)
- Lauro Ribeiro de Souza Neto
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bogar Omar Montoya
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - José Brandão-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Harwell, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, UK
| | - Anil Verma
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sebastian Bowyer
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - José Teófilo Moreira-Filho
- LabMol - Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Rafael Ferreira Dantas
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bruno Junior Neves
- Laboratory of Cheminformatics, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Design, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Brazil
- CRAFT - Center for Research and Advancement of Fragments and Molecular Targets, University of São Paulo, São Paulo, Brazil
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Harwell, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Raymond J Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Structural Biology, Rosalind Franklin Institute, Harwell, UK.
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Floriano Paes Silva-Jr
- LaBECFar - Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
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Moreira-Filho JT, Neves BJ, Cajas RA, Moraes JD, Andrade CH. Artificial intelligence-guided approach for efficient virtual screening of hits against Schistosoma mansoni. Future Med Chem 2023; 15:2033-2050. [PMID: 37937522 DOI: 10.4155/fmc-2023-0152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
Background: The impact of schistosomiasis, which affects over 230 million people, emphasizes the urgency of developing new antischistosomal drugs. Artificial intelligence is vital in accelerating the drug discovery process. Methodology & results: We developed classification and regression machine learning models to predict the schistosomicidal activity of compounds not experimentally tested. The prioritized compounds were tested on schistosomula and adult stages of Schistosoma mansoni. Four compounds demonstrated significant activity against schistosomula, with 50% effective concentration values ranging from 9.8 to 32.5 μM, while exhibiting no toxicity in animal and human cell lines. Conclusion: These findings represent a significant step forward in the discovery of antischistosomal drugs. Further optimization of these active compounds can pave the way for their progression into preclinical studies.
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Affiliation(s)
- José Teófilo Moreira-Filho
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, 74605-170, Brazil
| | - Bruno Junior Neves
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, 74605-170, Brazil
| | - Rayssa Araujo Cajas
- Research Center on Neglected Diseases (NPDN), Universidade Guarulhos, Guarulhos, 07023-070, Brazil
| | - Josué de Moraes
- Research Center on Neglected Diseases (NPDN), Universidade Guarulhos, Guarulhos, 07023-070, Brazil
| | - Carolina Horta Andrade
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, 74605-170, Brazil
- Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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Azevedo CM, Meira CS, da Silva JW, Moura DMN, de Oliveira SA, da Costa CJ, Santos EDS, Soares MBP. Therapeutic Potential of Natural Products in the Treatment of Schistosomiasis. Molecules 2023; 28:6807. [PMID: 37836650 PMCID: PMC10574020 DOI: 10.3390/molecules28196807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 10/15/2023] Open
Abstract
It is estimated that 250 million people worldwide are affected by schistosomiasis. Disease transmission is related to the poor sanitation and hygiene habits that affect residents of impoverished regions in tropical and subtropical countries. The main species responsible for causing disease in humans are Schistosoma Mansoni, S. japonicum, and S. haematobium, each with different geographic distributions. Praziquantel is the drug predominantly used to treat this disease, which offers low effectiveness against immature and juvenile parasite forms. In addition, reports of drug resistance prompt the development of novel therapeutic approaches. Natural products represent an important source of new compounds, especially those obtained from plant sources. This review compiles data from several in vitro and in vivo studies evaluating various compounds and essential oils derived from plants with cercaricidal and molluscicidal activities against both juvenile and adult forms of the parasite. Finally, this review provides an important discussion on recent advances in molecular and computational tools deemed fundamental for more rapid and effective screening of new compounds, allowing for the optimization of time and resources.
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Affiliation(s)
- Carine Machado Azevedo
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador 40296-710, Brazil; (C.M.A.); (C.S.M.)
| | - Cássio Santana Meira
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador 40296-710, Brazil; (C.M.A.); (C.S.M.)
- SENAI Institute of Innovation in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (J.W.d.S.); (E.d.S.S.)
| | - Jaqueline Wang da Silva
- SENAI Institute of Innovation in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (J.W.d.S.); (E.d.S.S.)
| | - Danielle Maria Nascimento Moura
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation (IAM-FIOCRUZ/PE), Recife 50740-465, Brazil; (D.M.N.M.); (S.A.d.O.); (C.J.d.C.)
| | - Sheilla Andrade de Oliveira
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation (IAM-FIOCRUZ/PE), Recife 50740-465, Brazil; (D.M.N.M.); (S.A.d.O.); (C.J.d.C.)
| | - Cícero Jádson da Costa
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation (IAM-FIOCRUZ/PE), Recife 50740-465, Brazil; (D.M.N.M.); (S.A.d.O.); (C.J.d.C.)
| | - Emanuelle de Souza Santos
- SENAI Institute of Innovation in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (J.W.d.S.); (E.d.S.S.)
| | - Milena Botelho Pereira Soares
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador 40296-710, Brazil; (C.M.A.); (C.S.M.)
- SENAI Institute of Innovation in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador 41650-010, Brazil; (J.W.d.S.); (E.d.S.S.)
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Gomes BF, Senger MR, Moreira-Filho JT, de Vasconcellos FJ, Dantas RF, Owens R, Andrade CH, Neves BJ, Silva-Junior FP. Discovery of new Schistosoma mansoni aspartyl protease inhibitors by structure-based virtual screening. Mem Inst Oswaldo Cruz 2023; 118:e230031. [PMID: 37672425 PMCID: PMC10481938 DOI: 10.1590/0074-02760230031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/01/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Schistosomiasis is a neglected tropical disease caused by trematodes of the genus Schistosoma, with a limited treatment, mainly based on the use of praziquantel (PZQ). Currently, several aspartic proteases genes have already been identified within the genome of Schistosoma species. At least one enzyme encoded from this gene family (SmAP), named SmCD1, has been validated for the development of schistosomicidal drugs, since it has a key role in haemoglobin digestion by worms. OBJECTIVE In this work, we integrated a structure-based virtual screening campaign, enzymatic assays and adult worms ex vivo experiments aiming to discover the first classes of SmCD1 inhibitors. METHODS Initially, the 3D-structures of SmCD1, SmCD2 and SmCD3 were generated using homology modelling approach. Using these models, we prioritised 50 compounds from 20,000 compounds from ChemBridge database for further testing in adult worm aqueous extract (AWAE) and recombinant SmCD1 using enzymatic assays. FINDINGS Seven compounds were confirmed as hits and among them, two compounds representing new chemical scaffolds, named 5 and 19, had IC50 values against SmCD1 close to 100 μM while presenting binding efficiency indexes comparable to or even higher than pepstatin, a classical tight-binding peptide inhibitor of aspartyl proteases. Upon activity comparison against mammalian enzymes, compound 50 was selective and the most potent against the AWAE aspartic protease activity (IC50 = 77.7 μM). Combination of computational and experimental results indicate that compound 50 is a selective inhibitor of SmCD2. Compounds 5, 19 and 50 tested at low concentrations (10 uM) were neither cytotoxic against WSS-1 cells (48 h) nor could kill adult worms ex-vivo, although compounds 5 and 50 presented a slight decrease on female worms motility on late incubations times (48 or 72 h). MAIN CONCLUSION Overall, the inhibitors identified in this work represent promising hits for further hit-to-lead optimisation.
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Affiliation(s)
- Bárbara Figueira Gomes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ, Brasil
| | - Mario Roberto Senger
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ, Brasil
| | - José Teófilo Moreira-Filho
- Universidade Federal de Goiás, Faculdade de Farmácia, Laboratório de Planejamento de Fármacos e Modelagem Molecular, Goiânia, GO, Brasil
| | - Fabio Jorge de Vasconcellos
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ, Brasil
| | - Rafael Ferreira Dantas
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ, Brasil
| | - Raymond Owens
- University of Oxford and Rosalind Franklin Institute, Oxfordshire, UK
| | - Carolina Horta Andrade
- Universidade Federal de Goiás, Faculdade de Farmácia, Laboratório de Planejamento de Fármacos e Modelagem Molecular, Goiânia, GO, Brasil
| | - Bruno Junior Neves
- Universidade Federal de Goiás, Faculdade de Farmácia, Laboratório de Quimioinformática, Goiânia, GO, Brasil
| | - Floriano Paes Silva-Junior
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ, Brasil
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Identification of a Family of Glycoside Derivatives Biologically Active against Acinetobacter baumannii and Other MDR Bacteria Using a QSPR Model. Pharmaceuticals (Basel) 2023. [DOI: 10.3390/ph16020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
As the rate of discovery of new antibacterial compounds for multidrug-resistant bacteria is declining, there is an urge for the search for molecules that could revert this tendency. Acinetobacter baumannii has emerged as a highly virulent Gram-negative bacterium that has acquired multiple resistance mechanisms against antibiotics and is considered of critical priority. In this work, we developed a quantitative structure-property relationship (QSPR) model with 592 compounds for the identification of structural parameters related to their property as antibacterial agents against A. baumannii. QSPR mathematical validation (R2 = 70.27, RN = −0.008, a(R2) = 0.014, and δK = 0.021) and its prediction ability (Q2LMO = 67.89, Q2EXT = 67.75, a(Q2) = −0.068, δQ = 0.0, rm2¯ = 0.229, and Δrm2 = 0.522) were obtained with different statistical parameters; additional validation was done using three sets of external molecules (R2 = 72.89, 71.64 and 71.56). We used the QSPR model to perform a virtual screening on the BIOFACQUIM natural product database. From this screening, our model showed that molecules 32 to 35 and 54 to 68, isolated from different extracts of plants of the Ipomoea sp., are potential antibacterials against A. baumannii. Furthermore, biological assays showed that molecules 56 and 60 to 64 have a wide antibacterial activity against clinically isolated strains of A. baumannii, as well as other multidrug-resistant bacteria, including Staphylococcus aureus, Escherichia coli, Klebsiella pneumonia, and Pseudomonas aeruginosa. Finally, we propose 60 as a potential lead compound due to its broad-spectrum activity and its structural simplicity. Therefore, our QSPR model can be used as a tool for the investigation and search for new antibacterial compounds against A. baumannii.
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Gupta MK, Gouda G, Sultana S, Punekar SM, Vadde R, Ravikiran T. Structure-related relationship: Plant-derived antidiabetic compounds. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2023:241-295. [DOI: 10.1016/b978-0-323-91294-5.00008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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Girod V, Houssier R, Sahmer K, Ghoris MJ, Caby S, Melnyk O, Dissous C, Senez V, Vicogne J. A self-purifying microfluidic system for identifying drugs acting against adult schistosomes. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220648. [PMID: 36465675 PMCID: PMC9709518 DOI: 10.1098/rsos.220648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
The discovery of novel antihelmintic molecules to combat the development and spread of schistosomiasis, a disease caused by several Schistosoma flatworm species, mobilizes significant research efforts worldwide. With a limited number of biochemical assays for measuring the viability of adult worms, the antischistosomicidal activity of molecules is usually evaluated by a microscopic observation of worm mobility and/or integrity upon drug exposure. Even if these phenotypical assays enable multiple parameters analysis, they are often conducted during several days and need to be associated with image-based analysis to minimized subjectivity. We describe here a self-purifying microfluidic system enabling the selection of healthy adult worms and the identification of molecules acting instantly on the parasite. The worms are assayed in a dynamic environment that eliminates unhealthy worms that cannot attach firmly to the chip walls prior to being exposed to the drug. The detachment of the worms is also used as second step readout for identifying active compounds. We have validated this new fluidic screening approach using the two major antihelmintic drugs, praziquantel and artemisinin. The reported dynamic system is simple to produce and to parallelize. Importantly, it enables a quick and sensitive detection of antischistosomal compounds in no more than one hour.
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Affiliation(s)
- Vincent Girod
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
- CNRS, University of Tokyo, IRL2820 – LIMMS, Lille F-59000, France
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
- University of Lille, CNRS, UPHF, JUNIA, CLI, UMR 8520 – IEMN – Institut d'Electronique, de Microélectronique et de Nanotechnologie, Villeneuve d'Ascq F-59650, France
| | - Robin Houssier
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Karin Sahmer
- University of Lille, IMT Lille Douai, University of Artois, JUNIA, ULR 4515 – LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000 Lille, France
| | - Marie-José Ghoris
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Stéphanie Caby
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Oleg Melnyk
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Colette Dissous
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Vincent Senez
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 – CANTHER – Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
- CNRS, University of Tokyo, IRL2820 – LIMMS, Lille F-59000, France
| | - Jérôme Vicogne
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017 – Center for Infection and Immunity of Lille, F-59000 Lille, France
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Monteiro NR, Oliveira JL, Arrais JP. DTITR: End-to-end drug–target binding affinity prediction with transformers. Comput Biol Med 2022; 147:105772. [DOI: 10.1016/j.compbiomed.2022.105772] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/07/2022] [Accepted: 06/19/2022] [Indexed: 11/03/2022]
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Mtemeli FL, Ndlovu J, Mugumbate G, Makwikwi T, Shoko R. Advances in schistosomiasis drug discovery based on natural products. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2080281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- F. L. Mtemeli
- Department of Biology, School of Natural Sciences and Mathematics Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - J. Ndlovu
- Department of Biology, School of Natural Sciences and Mathematics Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - G. Mugumbate
- Department of Chemical Technology, Midlands State University, Gweru, Zimbabwe
| | - T. Makwikwi
- Department of Pharmaceutical Sciences, Tshwane University of Technology, Pretoria, South Africa
| | - R. Shoko
- Department of Biology, School of Natural Sciences and Mathematics Chinhoyi University of Technology, Chinhoyi, Zimbabwe
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Guevara‐Pulido J, Jiménez RA, Morantes SJ, Jaramillo DN, Acosta‐Guzmán P. Design, Synthesis, and Development of 4‐[(7‐Chloroquinoline‐4‐yl)amino]phenol as a Potential SARS‐CoV‐2 Mpro Inhibitor. ChemistrySelect 2022; 7:e202200125. [PMID: 35601684 PMCID: PMC9111044 DOI: 10.1002/slct.202200125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
A series of chloroquine analogs were designed to search for a less toxic chloroquine derivative as a potential SARS‐CoV‐2 Mpro inhibitor. Herein, an ANN‐based QSAR model was built to predict the IC50 values of each analog using the experimental values of other 4‐aminoquinolines as the training set. Subsequently, molecular docking was used to evaluate each analog's binding affinity to Mpro. The analog that showed the greatest affinity and lowest IC50 values was synthesized and characterized for its posterior incorporation into a polycaprolactone‐based nanoparticulate system. After characterizing the loaded nanoparticles, an in vitro drug release assay was carried out, and the cytotoxicity of the analog and loaded nanoparticles was evaluated using murine fibroblast (L929) and human lung adenocarcinoma (A549) cell lines. Results show that the synthesized analog is much less toxic than chloroquine and that the nanoparticulate system allowed for the prolonged release of the analog without evidence of adverse effects on the cell lines used; therefore, suggesting that the analog could be a potential therapeutic option for COVID‐19.
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12
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First In Silico Screening of Insect Molecules for Identification of Novel Anti-Parasitic Compounds. Pharmaceuticals (Basel) 2022; 15:ph15020119. [PMID: 35215232 PMCID: PMC8877563 DOI: 10.3390/ph15020119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 02/01/2023] Open
Abstract
Schistosomiasis is a neglected tropical disease caused by blood flukes of the genus Schistosoma. In silico screenings of compounds for the identification of novel anti-parasitic drug candidates have received considerable attention in recent years, including the screening of natural compounds. For the first time, we investigated molecules from insects, a rather neglected source in drug discovery, in an in silico screening approach to find novel antischistosomal compounds. Based on the Dictionary of Natural Products (DNP), we created a library of 1327 insect compounds suitable for molecular docking. A structure-based virtual screening against the crystal structure of a known druggable target in Schistosoma mansoni, the thioredoxin glutathione reductase (SmTGR), was performed. The top ten compounds predominantly originated from beetles and were predicted to interact particularly with amino acids in the doorstop pocket of SmTGR. For one compound from a jewel beetle, buprestin H, we tested and confirmed antischistosomal activity against adult and juvenile parasites in vitro. At concentrations with anti-parasitic activity, we could also exclude any unspecific cytotoxic activity against human HepG2 cells. This study highlights the potential of insect molecules for the identification of novel antischistosomal compounds. Our library of insect-derived molecules could serve not only as basis for future in silico screenings against additional target proteins of schistosomes, but also of other parasites.
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Spiegel J, Senderowitz H. A Comparison between Enrichment Optimization Algorithm (EOA)-Based and Docking-Based Virtual Screening. Int J Mol Sci 2021; 23:43. [PMID: 35008467 PMCID: PMC8744642 DOI: 10.3390/ijms23010043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 12/30/2022] Open
Abstract
Virtual screening (VS) is a well-established method in the initial stages of many drug and material design projects. VS is typically performed using structure-based approaches such as molecular docking, or various ligand-based approaches. Most docking tools were designed to be as global as possible, and consequently only require knowledge on the 3D structure of the biotarget. In contrast, many ligand-based approaches (e.g., 3D-QSAR and pharmacophore) require prior development of project-specific predictive models. Depending on the type of model (e.g., classification or regression), predictive ability is typically evaluated using metrics of performance on either the training set (e.g.,QCV2) or the test set (e.g., specificity, selectivity or QF1/F2/F32). However, none of these metrics were developed with VS in mind, and consequently, their ability to reliably assess the performances of a model in the context of VS is at best limited. With this in mind we have recently reported the development of the enrichment optimization algorithm (EOA). EOA derives QSAR models in the form of multiple linear regression (MLR) equations for VS by optimizing an enrichment-based metric in the space of the descriptors. Here we present an improved version of the algorithm which better handles active compounds and which also takes into account information on inactive (either known inactive or decoy) compounds. We compared the improved EOA in small-scale VS experiments with three common docking tools, namely, Glide-SP, GOLD and AutoDock Vina, employing five molecular targets (acetylcholinesterase, human immunodeficiency virus type 1 protease, MAP kinase p38 alpha, urokinase-type plasminogen activator, and trypsin I). We found that EOA consistently outperformed all docking tools in terms of the area under the ROC curve (AUC) and EF1% metrics that measured the overall and initial success of the VS process, respectively. This was the case when the docking metrics were calculated based on a consensus approach and when they were calculated based on two different sets of single crystal structures. Finally, we propose that EOA could be combined with molecular docking to derive target-specific scoring functions.
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Affiliation(s)
| | - Hanoch Senderowitz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel;
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14
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Pantaleão SQ, Fernandes PO, Gonçalves JE, Maltarollo VG, Honorio KM. Recent Advances in the Prediction of Pharmacokinetics Properties in Drug Design Studies: A Review. ChemMedChem 2021; 17:e202100542. [PMID: 34655454 DOI: 10.1002/cmdc.202100542] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/07/2021] [Indexed: 12/11/2022]
Abstract
This review presents the main aspects related to pharmacokinetic properties, which are essential for the efficacy and safety of drugs. This topic is very important because the analysis of pharmacokinetic aspects in the initial design stages of drug candidates can increase the chances of success for the entire process. In this scenario, experimental and in silico techniques have been widely used. Due to the difficulties encountered with the use of some experimental tests to determine pharmacokinetic properties, several in silico tools have been developed and have shown promising results. Therefore, in this review, we address the main free tools/servers that have been used in this area, as well as some cases of application. Finally, we present some studies that employ a multidisciplinary approach with synergy between in silico, in vitro, and in vivo techniques to assess ADME properties of bioactive substances, achieving successful results in drug discovery and design.
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Affiliation(s)
- Simone Q Pantaleão
- Centro de Ciências Naturais e Humanas, Institution Universidade Federal do ABC, 09210-580, Santo André, SP, Brazil
| | - Philipe O Fernandes
- Departamento de Produtos Farmacêuticos, Universidade Federal de Minas Gerais, 31270-901, Pampulha, MG, Brazil
| | - José Eduardo Gonçalves
- Departamento de Produtos Farmacêuticos, Universidade Federal de Minas Gerais, 31270-901, Pampulha, MG, Brazil
| | - Vinícius G Maltarollo
- Departamento de Produtos Farmacêuticos, Universidade Federal de Minas Gerais, 31270-901, Pampulha, MG, Brazil
| | - Kathia Maria Honorio
- Centro de Ciências Naturais e Humanas, Institution Universidade Federal do ABC, 09210-580, Santo André, SP, Brazil.,Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, 03828-000, São Paulo, SP, Brazil
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15
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Prediction of antischistosomal small molecules using machine learning in the era of big data. Mol Divers 2021; 26:1597-1607. [PMID: 34351547 DOI: 10.1007/s11030-021-10288-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/24/2021] [Indexed: 12/13/2022]
Abstract
Schistosomiasis is a neglected tropical disease caused by helminths of the Schistosoma genus. Despite its high morbidity and socio-economic burden, therapeutics are just a handful with praziquantel being the main drug. Praziquantel is an old drug registered for human use in 1982 and has since been administered en masse for chemotherapy, risking the development of resistance, thus the need for new drugs with different mechanisms of action. This review examines the use of machine learning (ML) in this era of big data to aid in the prediction of novel antischistosomal molecules. It first discusses the challenges of drug discovery in schistosomiasis. Explanations are then offered for big data, its characteristics and then, some open databases where large biochemical data on schistosomiasis can be obtained for ML model development are examined. The concepts of artificial intelligence, ML, and deep learning and their drug applications are explored in schistosomiasis. The use of binary classification in predicting antischistosomal compounds and some algorithms that have been applied including random forest and naive Bayesian are discussed. For this review, some deep learning algorithms (deep neural networks) are proposed as novel algorithms for predicting antischistosomal molecules via binary classification. Databases specifically designed for housing bioactivity data on antischistosomal molecules enriched with functional genomic datasets and ontologies are thus urgently needed for developing predictive ML models. This shows the application of machine learning techniques for the discovery of novel antischistosomal small molecules via binary classification in the era of big data.
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16
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Gawriljuk VO, Foil DH, Puhl AC, Zorn KM, Lane TR, Riabova O, Makarov V, Godoy AS, Oliva G, Ekins S. Development of Machine Learning Models and the Discovery of a New Antiviral Compound against Yellow Fever Virus. J Chem Inf Model 2021; 61:3804-3813. [PMID: 34286575 DOI: 10.1021/acs.jcim.1c00460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Yellow fever (YF) is an acute viral hemorrhagic disease transmitted by infected mosquitoes. Large epidemics of YF occur when the virus is introduced into heavily populated areas with high mosquito density and low vaccination coverage. The lack of a specific small molecule drug treatment against YF as well as for homologous infections, such as zika and dengue, highlights the importance of these flaviviruses as a public health concern. With the advancement in computer hardware and bioactivity data availability, new tools based on machine learning methods have been introduced into drug discovery, as a means to utilize the growing high throughput screening (HTS) data generated to reduce costs and increase the speed of drug development. The use of predictive machine learning models using previously published data from HTS campaigns or data available in public databases, can enable the selection of compounds with desirable bioactivity and absorption, distribution, metabolism, and excretion profiles. In this study, we have collated cell-based assay data for yellow fever virus from the literature and public databases. The data were used to build predictive models with several machine learning methods that could prioritize compounds for in vitro testing. Five molecules were prioritized and tested in vitro from which we have identified a new pyrazolesulfonamide derivative with EC50 3.2 μM and CC50 24 μM, which represents a new scaffold suitable for hit-to-lead optimization that can expand the available drug discovery candidates for YF.
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Affiliation(s)
- Victor O Gawriljuk
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Santa Angelina, São Carlos, São Paulo 13563-120, Brazil
| | - Daniel H Foil
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Ana C Puhl
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Thomas R Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Olga Riabova
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071 Moscow, Russia
| | - Vadim Makarov
- Research Center of Biotechnology RAS, Leninsky Prospekt 33-2, 119071 Moscow, Russia
| | - Andre S Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Santa Angelina, São Carlos, São Paulo 13563-120, Brazil
| | - Glaucius Oliva
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Santa Angelina, São Carlos, São Paulo 13563-120, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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17
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Zhang X, Zhao P, Wang Z, Xu X, Liu G, Tang Y, Li W. In Silico Prediction of CYP2C8 Inhibition with Machine-Learning Methods. Chem Res Toxicol 2021; 34:1850-1859. [PMID: 34255486 DOI: 10.1021/acs.chemrestox.1c00078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cytochrome P450 2C8 (CYP2C8) is a major drug-metabolizing enzyme in humans and is responsible for the metabolism of ∼5% drugs in clinical use. Thus, inhibition of CYP2C8, which causes potential adverse drug events, cannot be neglected. The in vitro drug interaction studies guidelines for industry issued by the FDA also point out that it needs to be determined whether investigated drugs are CYP2C8 inhibitors before clinical trials. However, current studies mainly focus on predicting the inhibitors of other major P450 enzymes, and the importance of CYP2C8 inhibition has been overlooked. Therefore, there is a need to develop models for identifying potential CYP2C8 inhibition. In this study, in silico classification models for predicting CYP2C8 inhibition were built by five machine-learning methods combined with nine molecular fingerprints. The performance of the models built was evaluated by test and external validation sets. The best model had AUC values of 0.85 and 0.90 for the test and external validation sets, respectively. The applicability domain was analyzed based on the molecular similarity and exhibited an impact on the improvement of prediction accuracy. Furthermore, several representative privileged substructures such as 1H-benzo[d]imidazole, 1-phenyl-1H-pyrazole, and quinoline were identified by information gain and substructure frequency analysis. Overall, our results would be helpful for the prediction of CYP2C8 inhibition.
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Affiliation(s)
- Xiaoxiao Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Piaopiao Zhao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhiyuan Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuan Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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18
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Wang R, Xu H, Zhang Y, Hu Y, Wei Y, Du X, Zhao H. Ag-Cu copromoted direct C2-H bond thiolation of azoles with Bunte salts as sulfur sources. Org Biomol Chem 2021; 19:5899-5904. [PMID: 34132728 DOI: 10.1039/d1ob00823d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A direct C2-H thiolation of azoles with Bunte salts was achieved under the combined action of copper and silver salts. This protocol could furnish various substituted 2-thioazoles in moderate to good yields. This method has a broad substrate scope and shows good functional group tolerance.
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Affiliation(s)
- Rui Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China.
| | - Hongyan Xu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China.
| | - Ying Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China.
| | - Yuntao Hu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China.
| | - Yingsu Wei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China.
| | - Xiao Du
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China.
| | - Huaiqing Zhao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, China. and State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
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19
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Molecular insights on ABL kinase activation using tree-based machine learning models and molecular docking. Mol Divers 2021; 25:1301-1314. [PMID: 34191245 PMCID: PMC8241884 DOI: 10.1007/s11030-021-10261-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022]
Abstract
Abelson kinase (c-Abl) is a non-receptor tyrosine kinase involved in several biological processes essential for cell differentiation, migration, proliferation, and survival. This enzyme's activation might be an alternative strategy for treating diseases such as neutropenia induced by chemotherapy, prostate, and breast cancer. Recently, a series of compounds that promote the activation of c-Abl has been identified, opening a promising ground for c-Abl drug development. Structure-based drug design (SBDD) and ligand-based drug design (LBDD) methodologies have significantly impacted recent drug development initiatives. Here, we combined SBDD and LBDD approaches to characterize critical chemical properties and interactions of identified c-Abl's activators. We used molecular docking simulations combined with tree-based machine learning models—decision tree, AdaBoost, and random forest to understand the c-Abl activators' structural features required for binding to myristoyl pocket, and consequently, to promote enzyme and cellular activation. We obtained predictive and robust models with Matthews correlation coefficient values higher than 0.4 for all endpoints and identified characteristics that led to constructing a structure–activity relationship model (SAR).
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20
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Moreira-Filho JT, Silva AC, Dantas RF, Gomes BF, Souza Neto LR, Brandao-Neto J, Owens RJ, Furnham N, Neves BJ, Silva-Junior FP, Andrade CH. Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. Front Immunol 2021; 12:642383. [PMID: 34135888 PMCID: PMC8203334 DOI: 10.3389/fimmu.2021.642383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022] Open
Abstract
Schistosomiasis is a parasitic disease caused by trematode worms of the genus Schistosoma and affects over 200 million people worldwide. The control and treatment of this neglected tropical disease is based on a single drug, praziquantel, which raises concerns about the development of drug resistance. This, and the lack of efficacy of praziquantel against juvenile worms, highlights the urgency for new antischistosomal therapies. In this review we focus on innovative approaches to the identification of antischistosomal drug candidates, including the use of automated assays, fragment-based screening, computer-aided and artificial intelligence-based computational methods. We highlight the current developments that may contribute to optimizing research outputs and lead to more effective drugs for this highly prevalent disease, in a more cost-effective drug discovery endeavor.
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Affiliation(s)
- José T. Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Arthur C. Silva
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Rafael F. Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Barbara F. Gomes
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lauro R. Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Didcot, United Kingdom
- Research Complex at Harwell, Didcot, United Kingdom
| | - Raymond J. Owens
- The Rosalind Franklin Institute, Harwell, United Kingdom
- Division of Structural Biology, The Wellcome Centre for Human Genetic, University of Oxford, Oxford, United Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bruno J. Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Floriano P. Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina H. Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
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21
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Ferreira LT, Borba JVB, Moreira-Filho JT, Rimoldi A, Andrade CH, Costa FTM. QSAR-Based Virtual Screening of Natural Products Database for Identification of Potent Antimalarial Hits. Biomolecules 2021; 11:biom11030459. [PMID: 33808643 PMCID: PMC8003391 DOI: 10.3390/biom11030459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 01/15/2023] Open
Abstract
With 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.
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Affiliation(s)
- Letícia Tiburcio Ferreira
- Laboratory of Tropical Diseases Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP 13083-864, Brazil; (L.T.F.); (J.V.B.B.); (A.R.)
| | - Joyce V. B. Borba
- Laboratory of Tropical Diseases Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP 13083-864, Brazil; (L.T.F.); (J.V.B.B.); (A.R.)
- Laboratory of Molecular Modeling and Drug Design, LabMol, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO 74605-170, Brazil; (J.T.M.-F.); (C.H.A.)
| | - José Teófilo Moreira-Filho
- Laboratory of Molecular Modeling and Drug Design, LabMol, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO 74605-170, Brazil; (J.T.M.-F.); (C.H.A.)
| | - Aline Rimoldi
- Laboratory of Tropical Diseases Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP 13083-864, Brazil; (L.T.F.); (J.V.B.B.); (A.R.)
| | - Carolina Horta Andrade
- Laboratory of Molecular Modeling and Drug Design, LabMol, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO 74605-170, Brazil; (J.T.M.-F.); (C.H.A.)
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP 13083-864, Brazil; (L.T.F.); (J.V.B.B.); (A.R.)
- Correspondence: ; Tel.: +55-19-3521-6288
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22
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Rosas-Jimenez JG, Garcia-Revilla MA, Madariaga-Mazon A, Martinez-Mayorga K. Predictive Global Models of Cruzain Inhibitors with Large Chemical Coverage. ACS OMEGA 2021; 6:6722-6735. [PMID: 33748586 PMCID: PMC7970485 DOI: 10.1021/acsomega.0c05645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Chagas disease affects 8-11 million people worldwide, most of them living in Latin America. Moreover, migratory phenomena have spread the infection beyond endemic areas. Efforts for the development of new pharmacological therapies are paramount as the pharmacological profile of the two marketed drugs currently available, nifurtimox and benznidazole, needs to be improved. Cruzain, a parasitic cysteine protease, is one of the most attractive biological targets due to its roles in parasite survival and immune evasion. In this work, we compiled and curated a database of diverse cruzain inhibitors previously reported in the literature. From this data set, quantitative structure-activity relationship (QSAR) models for the prediction of their pIC50 values were generated using k-nearest neighbors and random forest algorithms. Local and global models were calculated and compared. The statistical parameters for internal and external validation indicate a significant predictability, with q loo 2 values around 0.66 and 0.61 and external R 2 coefficients of 0.725 and 0.766. The applicability domain is quantitatively defined, according to QSAR good practices, using the leverage and similarity methods. The models described in this work are readily available in a Python script for the discovery of novel cruzain inhibitors.
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Affiliation(s)
- Jose Guadalupe Rosas-Jimenez
- Division
de Ciencias Naturales y Exactas, Universidad
de Guanajuato, Guanajuato 36050, Mexico
- Instituto
de Quimica, Universidad Nacional Autonoma
de Mexico, Mexico
City 04510, Mexico
| | - Marco A. Garcia-Revilla
- Division
de Ciencias Naturales y Exactas, Universidad
de Guanajuato, Guanajuato 36050, Mexico
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Pereira ES, Rodrigues GLS, Rocha WR. Electronic structure and mechanism for the uptake of nitric oxide by the Ru(iii) antitumor complex NAMI-A. RSC Adv 2021; 11:7381-7390. [PMID: 35423255 PMCID: PMC8695036 DOI: 10.1039/d0ra10622d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/05/2021] [Indexed: 11/24/2022] Open
Abstract
Nitric oxide (NO) has well known vasodilation effects in living organisms and its participation in the metastasis of cancer cells through the angiogenesis process has been demonstrated experimentally. Therefore, the uptake of NO has become one focus of investigation to produce anti-metastatic drugs. In this article we have investigated the uptake of NO by the ruthenium based metallodrug trans-tetrachloride(dimethylsulfoxide)imidazole ruthenate(iii) [Im]trans-[RuCl4(Im)(DMSO)], known as New Anti-tumor Metastasis Inhibitor-A (NAMI-A). Electronic structure calculations using Density Functional Theory, DFT, and State-Averaged Complete Active Space Self Consistent Field, SA-CASSCF, with second order perturbation theory corrections, NEVPT2 were carried out to investigate the mechanism involved in the uptake of NO by the Ru-based anticancer metallodrug NAMI-A. The calculations revealed that the reaction takes place at the triplet potential energy surface, with the singlet surface being ∼15 kcal mol-1 shifted to higher energies, and there is a surface crossing to form the most stable singlet product after the reaction takes place at the triplet surface. The spin pairing and electron transfer from the nitric oxide to the metallic fragment takes place at the region of the minimum energy crossing point between the two surfaces. The Ru-NO bond in the {Ru-NO}6 product has ∼10% of the RuIII-NO0 character. The SA-CASSCF/NEVPT2 calculations revealed that the uptake of NO by NAMI-A has a small energy barrier of ∼8 kcal mol-1 and, therefore a rate constant of 11.3 × 106 s-1 at 300 K. In addition, the reaction is thermodynamically favorable, with a Gibbs free energy of ∼30 kcal mol-1. These results show that the uptake of nitric oxide by the NAMI-A complex is kinetically and thermodynamically feasible in biological medium and, therefore, gives support to the anti-angiogenesis theory associated to the mode of action of NAMI-A and other related compounds.
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Affiliation(s)
- Eufrásia S Pereira
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha Belo Horizonte MG Brazil
| | - Gabriel L S Rodrigues
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha Belo Horizonte MG Brazil
| | - Willian R Rocha
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha Belo Horizonte MG Brazil
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24
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Achary PGR. Applications of Quantitative Structure-Activity Relationships (QSAR) based Virtual Screening in Drug Design: A Review. Mini Rev Med Chem 2020; 20:1375-1388. [DOI: 10.2174/1389557520666200429102334] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 12/18/2022]
Abstract
The scientists, and the researchers around the globe generate tremendous amount of information
everyday; for instance, so far more than 74 million molecules are registered in Chemical
Abstract Services. According to a recent study, at present we have around 1060 molecules, which are
classified as new drug-like molecules. The library of such molecules is now considered as ‘dark chemical
space’ or ‘dark chemistry.’ Now, in order to explore such hidden molecules scientifically, a good
number of live and updated databases (protein, cell, tissues, structure, drugs, etc.) are available today.
The synchronization of the three different sciences: ‘genomics’, proteomics and ‘in-silico simulation’
will revolutionize the process of drug discovery. The screening of a sizable number of drugs like molecules
is a challenge and it must be treated in an efficient manner. Virtual screening (VS) is an important
computational tool in the drug discovery process; however, experimental verification of the
drugs also equally important for the drug development process. The quantitative structure-activity relationship
(QSAR) analysis is one of the machine learning technique, which is extensively used in VS
techniques. QSAR is well-known for its high and fast throughput screening with a satisfactory hit rate.
The QSAR model building involves (i) chemo-genomics data collection from a database or literature
(ii) Calculation of right descriptors from molecular representation (iii) establishing a relationship
(model) between biological activity and the selected descriptors (iv) application of QSAR model to
predict the biological property for the molecules. All the hits obtained by the VS technique needs to be
experimentally verified. The present mini-review highlights: the web-based machine learning tools, the
role of QSAR in VS techniques, successful applications of QSAR based VS leading to the drug discovery
and advantages and challenges of QSAR.
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Affiliation(s)
- Patnala Ganga Raju Achary
- Department of Chemistry, Faculty of Engineering & Technology (ITER), Siksha ‘O’ Anusandhan, Deemed to be University, Khandagiri Square, Bhubaneswar- 751030, India
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López-López E, Barrientos-Salcedo C, Prieto-Martínez FD, Medina-Franco JL. In silico tools to study molecular targets of neglected diseases: inhibition of TcSir2rp3, an epigenetic enzyme of Trypanosoma cruzi. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:203-229. [PMID: 32951812 DOI: 10.1016/bs.apcsb.2020.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is a growing interest to study and address neglected tropical diseases (NTD). To this end, in silico methods can serve as the bridge that connects academy and industry, encouraging the development of future treatments against these diseases. This chapter discusses current challenges in the development of new therapies, available computational methods and successful cases in computer-aided design with particular focus on human trypanosomiasis. Novel targets are also discussed. As a case study, we identify amentoflavone as a potential inhibitor of TcSir2rp3 (sirtuine) from Trypanosoma cruzi (20.03 μM) with a workflow that integrates chemoinformatic approaches, molecular modeling, and theoretical affinity calculations, as well as in vitro assays.
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Affiliation(s)
- Edgar López-López
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico; Department of Pharmacology, Center of Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV), Mexico City, Mexico
| | | | - Fernando D Prieto-Martínez
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
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Partridge FA, Forman R, Bataille CJR, Wynne GM, Nick M, Russell AJ, Else KJ, Sattelle DB. Anthelmintic drug discovery: target identification, screening methods and the role of open science. Beilstein J Org Chem 2020; 16:1203-1224. [PMID: 32550933 PMCID: PMC7277699 DOI: 10.3762/bjoc.16.105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Helminths, including cestodes, nematodes and trematodes, are a huge global health burden, infecting hundreds of millions of people. In many cases, existing drugs such as benzimidazoles, diethylcarbamazine, ivermectin and praziquantel are insufficiently efficacious, contraindicated in some populations, or at risk of the development of resistance, thereby impeding progress towards World Health Organization goals to control or eliminate these neglected tropical diseases. However, there has been limited recent progress in developing new drugs for these diseases due to lack of commercial attractiveness, leading to the introduction of novel, more efficient models for drug innovation that attempt to reduce the cost of research and development. Open science aims to achieve this by encouraging collaboration and the sharing of data and resources between organisations. In this review we discuss how open science has been applied to anthelmintic drug discovery. Open resources, including genomic information from many parasites, are enabling the identification of targets for new antiparasitic agents. Phenotypic screening remains important, and there has been much progress in open-source systems for compound screening with parasites, including motility assays but also high content assays with more detailed investigation of helminth physiology. Distributed open science compound screening programs, such as the Medicines for Malaria Venture Pathogen Box, have been successful at facilitating screening in diverse assays against many different parasite pathogens and models. Of the compounds identified so far in these screens, tolfenpyrad, a repurposed insecticide, shows significant promise and there has been much progress in creating more potent and selective derivatives. This work exemplifies how open science approaches can catalyse drug discovery against neglected diseases.
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Affiliation(s)
- Frederick A Partridge
- Centre for Respiratory Biology, UCL Respiratory, Division of Medicine, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Ruth Forman
- The Lydia Becker Institute for Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Carole J R Bataille
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA United Kingdom
| | - Graham M Wynne
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA United Kingdom
| | - Marina Nick
- Centre for Respiratory Biology, UCL Respiratory, Division of Medicine, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Angela J Russell
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA United Kingdom
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, United Kingdom
| | - Kathryn J Else
- The Lydia Becker Institute for Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - David B Sattelle
- Centre for Respiratory Biology, UCL Respiratory, Division of Medicine, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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Machine learning prediction of the potential pesticide applicability of three dihydroquinoline derivatives: Syntheses, crystal structures and physical properties. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127732] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Dziwornu GA, Attram HD, Gachuhi S, Chibale K. Chemotherapy for human schistosomiasis: how far have we come? What's new? Where do we go from here? RSC Med Chem 2020; 11:455-490. [PMID: 33479649 PMCID: PMC7593896 DOI: 10.1039/d0md00062k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/22/2020] [Indexed: 01/11/2023] Open
Abstract
Globally, schistosomiasis threatens more than 700 million lives, mostly children, in poor localities of tropical and sub-tropical areas with morbidity due to acute and chronic pathological manifestations of the disease. After a century since the first antimonial-based drugs were introduced to treat the disease, anti-schistosomiasis drug development is again at a bottleneck with only one drug, praziquantel, available for treatment purposes. This review focuses on promising chemotypes as potential starting points in a drug discovery effort to meet the urgent need for new schistosomicides.
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Affiliation(s)
- Godwin Akpeko Dziwornu
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa . ; Tel: +27 21 6502553
| | - Henrietta Dede Attram
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa . ; Tel: +27 21 6502553
| | - Samuel Gachuhi
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa . ; Tel: +27 21 6502553
| | - Kelly Chibale
- Department of Chemistry , University of Cape Town , Rondebosch 7701 , South Africa . ; Tel: +27 21 6502553
- Drug Discovery and Development Centre (H3D) , University of Cape Town , Rondebosch 7701 , South Africa
- Institute of Infectious Disease and Molecular Medicine , University of Cape Town , Rondebosch 7701 , South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit , University of Cape Town , Rondebosch 7701 , South Africa
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Neves BJ, Braga RC, Alves VM, Lima MNN, Cassiano GC, Muratov EN, Costa FTM, Andrade CH. Deep Learning-driven research for drug discovery: Tackling Malaria. PLoS Comput Biol 2020; 16:e1007025. [PMID: 32069285 PMCID: PMC7048302 DOI: 10.1371/journal.pcbi.1007025] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 02/28/2020] [Accepted: 04/15/2019] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Bruno J. Neves
- Laboratory of Cheminformatics, University Center of Anápolis – UniEVANGÉLICA, Anápolis, Goiás, Brazil
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | | | - Vinicius M. Alves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Marília N. N. Lima
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Gustavo C. Cassiano
- Laboratory of Tropical Diseases–Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisboa, Portugal
| | - Eugene N. Muratov
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Chemical Technology, Odessa National Polytechnic University, Odessa, Ukraine
| | - Fabio T. M. Costa
- Laboratory of Tropical Diseases–Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carolina Horta Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
- Laboratory of Tropical Diseases–Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
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Efficient identification of novel anti-glioma lead compounds by machine learning models. Eur J Med Chem 2019; 189:111981. [PMID: 31978780 DOI: 10.1016/j.ejmech.2019.111981] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/18/2019] [Accepted: 12/16/2019] [Indexed: 11/22/2022]
Abstract
Glioblastoma multiforme (GBM) is the most devastating and widespread primary central nervous system tumor. Pharmacological treatment of this malignance is limited by the selective permeability of the blood-brain barrier (BBB) and relies on a single drug, temozolomide (TMZ), thus making the discovery of new compounds challenging and urgent. Therefore, aiming to discover new anti-glioma drugs, we developed robust machine learning models for predicting anti-glioma activity and BBB penetration ability of new compounds. Using these models, we prioritized 41 compounds from our in-house library of compounds, for further in vitro testing against three glioma cell lines and astrocytes. Subsequently, the most potent and selective compounds were resynthesized and tested in vivo using an orthotopic glioma model. This approach revealed two lead candidates, 4m and 4n, which efficiently decreased malignant glioma development in mice, probably by inhibiting thioredoxin reductase activity, as shown by our enzymological assays. Moreover, these two compounds did not promote body weight reduction, death of animals, or altered hematological and toxicological markers, making then good candidates for lead optimization as anti-glioma drug candidates.
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Andrade CH, Neves BJ, Melo-Filho CC, Rodrigues J, Silva DC, Braga RC, Cravo PVL. In Silico Chemogenomics Drug Repositioning Strategies for Neglected Tropical Diseases. Curr Med Chem 2019. [DOI: 10.2174/0929867325666180309114824] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Only ~1% of all drug candidates against Neglected Tropical Diseases (NTDs)
have reached clinical trials in the last decades, underscoring the need for new, safe and effective
treatments. In such context, drug repositioning, which allows finding novel indications
for approved drugs whose pharmacokinetic and safety profiles are already known,
emerging as a promising strategy for tackling NTDs. Chemogenomics is a direct descendent
of the typical drug discovery process that involves the systematic screening of chemical
compounds against drug targets in high-throughput screening (HTS) efforts, for the identification
of lead compounds. However, different to the one-drug-one-target paradigm, chemogenomics
attempts to identify all potential ligands for all possible targets and diseases. In
this review, we summarize current methodological development efforts in drug repositioning
that use state-of-the-art computational ligand- and structure-based chemogenomics approaches.
Furthermore, we highlighted the recent progress in computational drug repositioning
for some NTDs, based on curation and modeling of genomic, biological, and chemical data.
Additionally, we also present in-house and other successful examples and suggest possible solutions
to existing pitfalls.
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Affiliation(s)
- Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Bruno Junior Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Cleber Camilo Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Juliana Rodrigues
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Diego Cabral Silva
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Rodolpho Campos Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiania, GO, 74605-170, Brazil
| | - Pedro Vitor Lemos Cravo
- Laboratory of Cheminformatics, Centro Universitario de Anapolis (UniEVANGELICA), Anapolis, GO, 75083-515, Brazil
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Dantas RF, Evangelista TCS, Neves BJ, Senger MR, Andrade CH, Ferreira SB, Silva-Junior FP. Dealing with frequent hitters in drug discovery: a multidisciplinary view on the issue of filtering compounds on biological screenings. Expert Opin Drug Discov 2019; 14:1269-1282. [DOI: 10.1080/17460441.2019.1654453] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Rafael Ferreira Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Tereza Cristina Santos Evangelista
- LaSOPB – Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Junior Neves
- LabChem – Laboratory of Cheminformatics, Centro Universitário de Anápolis, UniEVANGÉLICA, Anápolis, Brazil
| | - Mario Roberto Senger
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina Horta Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Sabrina Baptista Ferreira
- LaSOPB – Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Floriano Paes Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Caffrey CR, El‐Sakkary N, Mäder P, Krieg R, Becker K, Schlitzer M, Drewry DH, Vennerstrom JL, Grevelding CG. Drug Discovery and Development for Schistosomiasis. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527808656.ch8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Hernandez HW, Soeung M, Zorn KM, Ashoura N, Mottin M, Andrade CH, Caffrey CR, de Siqueira-Neto JL, Ekins S. High Throughput and Computational Repurposing for Neglected Diseases. Pharm Res 2018; 36:27. [PMID: 30560386 PMCID: PMC6792295 DOI: 10.1007/s11095-018-2558-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/09/2018] [Indexed: 12/21/2022]
Abstract
Purpose Neglected tropical diseases (NTDs) represent are a heterogeneous group of communicable diseases that are found within the poorest populations of the world. There are 23 NTDs that have been prioritized by the World Health Organization, which are endemic in 149 countries and affect more than 1.4 billion people, costing these developing economies billions of dollars annually. The NTDs result from four different causative pathogens: protozoa, bacteria, helminth and virus. The majority of the diseases lack effective treatments. Therefore, new therapeutics for NTDs are desperately needed. Methods We describe various high throughput screening and computational approaches that have been performed in recent years. We have collated the molecules identified in these studies and calculated molecular properties. Results Numerous global repurposing efforts have yielded some promising compounds for various neglected tropical diseases. These compounds when analyzed as one would expect appear drug-like. Several large datasets are also now in the public domain and this enables machine learning models to be constructed that then facilitate the discovery of new molecules for these pathogens. Conclusions In the space of a few years many groups have either performed experimental or computational repurposing high throughput screens against neglected diseases. These have identified compounds which in many cases are already approved drugs. Such approaches perhaps offer a more efficient way to develop treatments which are generally not a focus for global pharmaceutical companies because of the economics or the lack of a viable market. Other diseases could perhaps benefit from these repurposing approaches. Electronic supplementary material The online version of this article (10.1007/s11095-018-2558-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Melinda Soeung
- MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina, 27606, USA
| | | | - Melina Mottin
- LabMol - Laboratory for Molecular Modeling and Drug Design Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO, 74605-170, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design Faculdade de Farmacia, Universidade Federal de Goias - UFG, Goiânia, GO, 74605-170, Brazil
| | - Conor R Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, 92093, USA
| | - Jair Lage de Siqueira-Neto
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, California, 92093, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina, 27606, USA.
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Melo-Filho CC, Braga RC, Muratov EN, Franco CH, Moraes CB, Freitas-Junior LH, Andrade CH. Discovery of new potent hits against intracellular Trypanosoma cruzi by QSAR-based virtual screening. Eur J Med Chem 2018; 163:649-659. [PMID: 30562700 DOI: 10.1016/j.ejmech.2018.11.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 12/17/2022]
Abstract
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.
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Affiliation(s)
- Cleber C Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goiás - UFG, Rua 240, Qd.87, Goiania, GO, 74605-510, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goiás - UFG, Rua 240, Qd.87, Goiania, GO, 74605-510, Brazil
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA; Department of Chemical Technology, Odessa National Polytechnic University, 1. Shevchenko Ave., Odessa, 65000, Ukraine
| | - Caio Haddad Franco
- National Laboratory of Biosciences (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, 13083-970, Brazil
| | - Carolina B Moraes
- National Laboratory of Biosciences (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, 13083-970, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Lucio H Freitas-Junior
- National Laboratory of Biosciences (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, 13083-970, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmacia, Universidade Federal de Goiás - UFG, Rua 240, Qd.87, Goiania, GO, 74605-510, Brazil.
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Neves BJ, Braga RC, Melo-Filho CC, Moreira-Filho JT, Muratov EN, Andrade CH. QSAR-Based Virtual Screening: Advances and Applications in Drug Discovery. Front Pharmacol 2018; 9:1275. [PMID: 30524275 PMCID: PMC6262347 DOI: 10.3389/fphar.2018.01275] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 10/18/2018] [Indexed: 02/03/2023] Open
Abstract
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.
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Affiliation(s)
- Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil.,Laboratory of Cheminformatics, Centro Universitário de Anápolis (UniEVANGÉLICA), Anápolis, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Cleber C Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - José Teófilo Moreira-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Chemical Technology, Odessa National Polytechnic University, Odessa, Ukraine
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
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Mottin M, Borba JVVB, Melo-Filho CC, Neves BJ, Muratov E, Torres PHM, Braga RC, Perryman A, Ekins S, Andrade CH. Computational drug discovery for the Zika virus. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000001002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
| | | | | | - Bruno Junior Neves
- Federal University of Goiás, Brazil; University Center of Anápolis, Brazil
| | - Eugene Muratov
- University of North Carolin, USA; Odessa National Polytechnic University, Ukraine
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38
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Chen Y, Yang H, Wu Z, Liu G, Tang Y, Li W. Prediction of Farnesoid X Receptor Disruptors with Machine Learning Methods. Chem Res Toxicol 2018; 31:1128-1137. [DOI: 10.1021/acs.chemrestox.8b00162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yue Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Hongbin Yang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. PLoS Comput Biol 2018; 14:e1006515. [PMID: 30346968 PMCID: PMC6211772 DOI: 10.1371/journal.pcbi.1006515] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/01/2018] [Accepted: 09/15/2018] [Indexed: 01/31/2023] Open
Abstract
The development of novel therapeutics is urgently required for diseases where existing treatments are failing due to the emergence of resistance. This is particularly pertinent for parasitic infections of the tropics and sub-tropics, referred to collectively as neglected tropical diseases, where the commercial incentives to develop new drugs are weak. One such disease is schistosomiasis, a highly prevalent acute and chronic condition caused by a parasitic helminth infection, with three species of the genus Schistosoma infecting humans. Currently, a single 40-year old drug, praziquantel, is available to treat all infective species, but its use in mass drug administration is leading to signs of drug-resistance emerging. To meet the challenge of developing new therapeutics against this disease, we developed an innovative computational drug repurposing pipeline supported by phenotypic screening. The approach highlighted several protein kinases as interesting new biological targets for schistosomiasis as they play an essential role in many parasite’s biological processes. Focusing on this target class, we also report the first elucidation of the kinome of Schistosoma japonicum, as well as updated kinomes of S. mansoni and S. haematobium. In comparison with the human kinome, we explored these kinomes to identify potential targets of existing inhibitors which are unique to Schistosoma species, allowing us to identify novel targets and suggest approved drugs that might inhibit them. These include previously suggested schistosomicidal agents such as bosutinib, dasatinib, and imatinib as well as new inhibitors such as vandetanib, saracatinib, tideglusib, alvocidib, dinaciclib, and 22 newly identified targets such as CHK1, CDC2, WEE, PAKA, MEK1. Additionally, the primary and secondary targets in Schistosoma of those approved drugs are also suggested, allowing for the development of novel therapeutics against this important yet neglected disease. The rise of resistance through the intensive use of drugs targeted to treat specific infectious diseases means that new therapeutics are continually required. Diseases common in the tropics and sub-tropics, classified as neglected tropical diseases, suffer from a lack of new drug treatments due to the difficulty in developing new drugs and the lack of market incentive. One such disease is schistosomiasis, a major human helminth disease caused by worms from the genus Schistosoma. It is currently treated by a 40-year old drug, praziquantel, but its widespread use has led to signs of drug-resistance emerging, with no alternative effective treatments available. To meet this challenge, we have developed an innovative computational drug repurposing pipeline supported by experimental phenotypic screening. Protein kinases emerged from our pipeline as interesting new biological targets. Given that many human kinase inhibitors have been successfully applied specially in cancer therapy and kinases have conserved structures and functions, we also undertook a detailed analysis of the kinases present in all infective Schistosoma species and human host. This allowed identification of new Schistosoma-specific kinase targets and suggest approved drugs to be used for treating schistosomiasis as well as opening new avenues to treat this neglected disease.
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40
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Eweas AF, Allam G. Targeting thioredoxin glutathione reductase as a potential antischistosomal drug target. Mol Biochem Parasitol 2018; 225:94-102. [DOI: 10.1016/j.molbiopara.2018.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/09/2018] [Accepted: 09/30/2018] [Indexed: 11/30/2022]
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41
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Siramshetty VB, Preissner R, Gohlke BO. Exploring Activity Profiles of PAINS and Their Structural Context in Target–Ligand Complexes. J Chem Inf Model 2018; 58:1847-1857. [DOI: 10.1021/acs.jcim.8b00385] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Vishal B. Siramshetty
- Structural Bioinformatics Group, Charité-Universitätsmedizin Berlin, 10115 Berlin, Germany
- BB3R - Berlin Brandenburg 3R Graduate School, Freie Universität Berlin, 14195 Berlin, Germany
| | - Robert Preissner
- Structural Bioinformatics Group, Charité-Universitätsmedizin Berlin, 10115 Berlin, Germany
- BB3R - Berlin Brandenburg 3R Graduate School, Freie Universität Berlin, 14195 Berlin, Germany
| | - Bjoern-Oliver Gohlke
- Structural Bioinformatics Group, Charité-Universitätsmedizin Berlin, 10115 Berlin, Germany
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42
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Alves VM, Golbraikh A, Capuzzi SJ, Liu K, Lam WI, Korn DR, Pozefsky D, Andrade CH, Muratov EN, Tropsha A. Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure-Activity Relationship Models. J Chem Inf Model 2018; 58:1214-1223. [PMID: 29809005 DOI: 10.1021/acs.jcim.8b00124] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Multiple approaches to quantitative structure-activity relationship (QSAR) modeling using various statistical or machine learning techniques and different types of chemical descriptors have been developed over the years. Oftentimes models are used in consensus to make more accurate predictions at the expense of model interpretation. We propose a simple, fast, and reliable method termed Multi-Descriptor Read Across (MuDRA) for developing both accurate and interpretable models. The method is conceptually related to the well-known kNN approach but uses different types of chemical descriptors simultaneously for similarity assessment. To benchmark the new method, we have built MuDRA models for six different end points (Ames mutagenicity, aquatic toxicity, hepatotoxicity, hERG liability, skin sensitization, and endocrine disruption) and compared the results with those generated with conventional consensus QSAR modeling. We find that models built with MuDRA show consistently high external accuracy similar to that of conventional QSAR models. However, MuDRA models excel in terms of transparency, interpretability, and computational efficiency. We posit that due to its methodological simplicity and reliable predictive accuracy, MuDRA provides a powerful alternative to a much more complex consensus QSAR modeling. MuDRA is implemented and freely available at the Chembench web portal ( https://chembench.mml.unc.edu/mudra ).
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Affiliation(s)
- Vinicius M Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Laboratory for Molecular Modeling and Design, Department of Pharmacy , Federal University of Goias , Goiania , GO 74605-170 , Brazil
| | - Alexander Golbraikh
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Stephen J Capuzzi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Kammy Liu
- Department of Computer Science , University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Wai In Lam
- Department of Computer Science , University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Daniel Robert Korn
- Department of Computer Science , University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Diane Pozefsky
- Department of Computer Science , University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Carolina Horta Andrade
- Laboratory for Molecular Modeling and Design, Department of Pharmacy , Federal University of Goias , Goiania , GO 74605-170 , Brazil
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Department of Chemical Technology , Odessa National Polytechnic University , Odessa , 65000 , Ukraine
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , North Carolina 27599 , United States
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43
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Biochemical and thermodynamic comparison of the selenocysteine containing and non-containing thioredoxin glutathione reductase of Fasciola gigantica. Biochim Biophys Acta Gen Subj 2018. [DOI: 10.1016/j.bbagen.2018.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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44
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Lima MNN, Melo-Filho CC, Cassiano GC, Neves BJ, Alves VM, Braga RC, Cravo PVL, Muratov EN, Calit J, Bargieri DY, Costa FTM, Andrade CH. QSAR-Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities. Front Pharmacol 2018; 9:146. [PMID: 29559909 PMCID: PMC5845645 DOI: 10.3389/fphar.2018.00146] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/12/2018] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Marilia N N Lima
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Cleber C Melo-Filho
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Gustavo C Cassiano
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil.,Laboratory of Cheminformatics, PPG-SOMA, University Center of Anápolis/UniEVANGELICA, Anápolis, Brazil
| | - Vinicius M Alves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Pedro V L Cravo
- Global Health and Tropical Medicine Centre, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Chemical Technology, Odessa National Polytechnic University, Odessa, Ukraine
| | - Juliana Calit
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniel Y Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fabio T M Costa
- Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Carolina H Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil.,Laboratory of Tropical Diseases - Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, Brazil
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45
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Simões RS, Maltarollo VG, Oliveira PR, Honorio KM. Transfer and Multi-task Learning in QSAR Modeling: Advances and Challenges. Front Pharmacol 2018; 9:74. [PMID: 29467659 PMCID: PMC5807924 DOI: 10.3389/fphar.2018.00074] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/22/2018] [Indexed: 12/11/2022] Open
Abstract
Medicinal chemistry projects involve some steps aiming to develop a new drug, such as the analysis of biological targets related to a given disease, the discovery and the development of drug candidates for these targets, performing parallel biological tests to validate the drug effectiveness and side effects. Approaches as quantitative study of activity-structure relationships (QSAR) involve the construction of predictive models that relate a set of descriptors of a chemical compound series and its biological activities with respect to one or more targets in the human body. Datasets used to perform QSAR analyses are generally characterized by a small number of samples and this makes them more complex to build accurate predictive models. In this context, transfer and multi-task learning techniques are very suitable since they take information from other QSAR models to the same biological target, reducing efforts and costs for generating new chemical compounds. Therefore, this review will present the main features of transfer and multi-task learning studies, as well as some applications and its potentiality in drug design projects.
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Affiliation(s)
- Rodolfo S Simões
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, Brazil
| | - Vinicius G Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Patricia R Oliveira
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, Brazil
| | - Kathia M Honorio
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, Brazil.,Center for Natural and Human Sciences, Federal University of ABC, Santo André, Brazil
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46
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Recent advance in oxazole-based medicinal chemistry. Eur J Med Chem 2018; 144:444-492. [DOI: 10.1016/j.ejmech.2017.12.044] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/04/2017] [Accepted: 12/13/2017] [Indexed: 01/09/2023]
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47
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Shukla R, Shukla H, Kalita P, Tripathi T. Structural insights into natural compounds as inhibitors of Fasciola gigantica thioredoxin glutathione reductase. J Cell Biochem 2017; 119:3067-3080. [PMID: 29052925 DOI: 10.1002/jcb.26444] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/18/2017] [Indexed: 01/12/2023]
Abstract
Fascioliasis is caused by the helminth parasites of genus Fasciola. Thioredoxin glutathione reductase (TGR) is an important enzyme in parasitic helminths and plays an indispensable role in its redox biology. In the present study, we conducted a structure-based virtual screening of natural compounds against the Fasciola gigantica TGR (FgTGR). The compounds were docked against FgTGR in four sequential docking modes. The screened ligands were further assessed for Lipinski and ADMET prediction so as to evaluate drug proficiency and likeness property. After refinement, three potential inhibitors were identified that were subjected to 50 ns molecular dynamics simulation and free energy binding analyses to evaluate the dynamics of protein-ligand interaction and the stability of the complexes. Key residues involved in the interaction of the selected ligands were also determined. The results suggested that three top hits had a negative binding energy greater than GSSG (-91.479 KJ · mol-1 ), having -152.657, -141.219, and -92.931 kJ · mol-1 for compounds with IDs ZINC85878789, ZINC85879991, and ZINC36369921, respectively. Further analysis showed that the compound ZINC85878789 and ZINC85879991 displayed substantial pharmacological and structural properties to be a drug candidate. Thus, the present study might prove useful for the future design of new derivatives with higher potency and specificity.
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Affiliation(s)
- Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Parismita Kalita
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
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48
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Azevedo LD, Bastos MM, Vasconcelos FC, Hoelz LVB, Junior FPS, Dantas RF, de Almeida ACM, de Oliveira AP, Gomes LC, Maia RC, Boechat N. Imatinib derivatives as inhibitors of K562 cells in chronic myeloid leukemia. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1993-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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49
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Gomes MN, Muratov EN, Pereira M, Peixoto JC, Rosseto LP, Cravo PVL, Andrade CH, Neves BJ. Chalcone Derivatives: Promising Starting Points for Drug Design. Molecules 2017; 22:E1210. [PMID: 28757583 PMCID: PMC6152227 DOI: 10.3390/molecules22081210] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 12/20/2022] Open
Abstract
Medicinal chemists continue to be fascinated by chalcone derivatives because of their simple chemistry, ease of hydrogen atom manipulation, straightforward synthesis, and a variety of promising biological activities. However, chalcones have still not garnered deserved attention, especially considering their high potential as chemical sources for designing and developing new effective drugs. In this review, we summarize current methodological developments towards the design and synthesis of new chalcone derivatives and state-of-the-art medicinal chemistry strategies (bioisosterism, molecular hybridization, and pro-drug design). We also highlight the applicability of computer-assisted drug design approaches to chalcones and address how this may contribute to optimizing research outputs and lead to more successful and cost-effective drug discovery endeavors. Lastly, we present successful examples of the use of chalcones and suggest possible solutions to existing limitations.
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Affiliation(s)
- Marcelo N Gomes
- Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Universidade Federal de Goiás, Setor Leste Universitário, Goiânia 74605-510, Brazil.
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27955-7568, USA.
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia 74001-970, Brazil.
| | - Josana C Peixoto
- Programa de Pós-Graduação em Sociedade, Tecnologia e Meio Ambiente, Centro Universitário de Anápolis-UniEVANGÉLICA, Anápolis 75083-515, Brazil.
| | - Lucimar P Rosseto
- Programa de Pós-Graduação em Sociedade, Tecnologia e Meio Ambiente, Centro Universitário de Anápolis-UniEVANGÉLICA, Anápolis 75083-515, Brazil.
| | - Pedro V L Cravo
- Programa de Pós-Graduação em Sociedade, Tecnologia e Meio Ambiente, Centro Universitário de Anápolis-UniEVANGÉLICA, Anápolis 75083-515, Brazil.
- GHTM/Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal.
| | - Carolina H Andrade
- Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Universidade Federal de Goiás, Setor Leste Universitário, Goiânia 74605-510, Brazil.
| | - Bruno J Neves
- Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Universidade Federal de Goiás, Setor Leste Universitário, Goiânia 74605-510, Brazil.
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia 74001-970, Brazil.
- Programa de Pós-Graduação em Sociedade, Tecnologia e Meio Ambiente, Centro Universitário de Anápolis-UniEVANGÉLICA, Anápolis 75083-515, Brazil.
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50
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Gomes MN, Braga RC, Grzelak EM, Neves BJ, Muratov E, Ma R, Klein LL, Cho S, Oliveira GR, Franzblau SG, Andrade CH. QSAR-driven design, synthesis and discovery of potent chalcone derivatives with antitubercular activity. Eur J Med Chem 2017; 137:126-138. [PMID: 28582669 DOI: 10.1016/j.ejmech.2017.05.026] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 10/19/2022]
Abstract
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.
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Affiliation(s)
- Marcelo N Gomes
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil
| | - Rodolpho C Braga
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil
| | - Edyta M Grzelak
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Bruno J Neves
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil; Postgraduate Program of Society, Technology and Environment, University Center of Anápolis/UniEVANGELICA, Anápolis, Goiás, 75083-515, Brazil
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27955-7568, United States; Department of Chemical Technology, Odessa National Polytechnic University, Odessa, 65000, Ukraine
| | - Rui Ma
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Larry L Klein
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | - Sanghyun Cho
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States
| | | | - Scott G Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612, United States.
| | - Carolina Horta Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia, Goiás 74605-510, Brazil.
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