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Mogire RM, Miruka SA, Juma DW, McNamara CW, Andagalu B, Burrows JN, Chenu E, Duffy J, Ogutu BR, Akala HM. Protein target similarity is positive predictor of in vitro antipathogenic activity: a drug repurposing strategy for Plasmodium falciparum. J Cheminform 2024; 16:63. [PMID: 38831351 PMCID: PMC11145868 DOI: 10.1186/s13321-024-00856-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Drug discovery is an intricate and costly process. Repurposing existing drugs and active compounds offers a viable pathway to develop new therapies for various diseases. By leveraging publicly available biomedical information, it is possible to predict compounds' activity and identify their potential targets across diverse organisms. In this study, we aimed to assess the antiplasmodial activity of compounds from the Repurposing, Focused Rescue, and Accelerated Medchem (ReFRAME) library using in vitro and bioinformatics approaches. We assessed the in vitro antiplasmodial activity of the compounds using blood-stage and liver-stage drug susceptibility assays. We used protein sequences of known targets of the ReFRAME compounds with high antiplasmodial activity (EC50 < 10 uM) to conduct a protein-pairwise search to identify similar Plasmodium falciparum 3D7 proteins (from PlasmoDB) using NCBI protein BLAST. We further assessed the association between the compounds' in vitro antiplasmodial activity and level of similarity between their known and predicted P. falciparum target proteins using simple linear regression analyses. BLAST analyses revealed 735 P. falciparum proteins that were similar to the 226 known protein targets associated with the ReFRAME compounds. Antiplasmodial activity of the compounds was positively associated with the degree of similarity between the compounds' known targets and predicted P. falciparum protein targets (percentage identity, E value, and bit score), the number of the predicted P. falciparum targets, and their respective mutagenesis index and fitness scores (R2 between 0.066 and 0.92, P < 0.05). Compounds predicted to target essential P. falciparum proteins or those with a druggability index of 1 showed the highest antiplasmodial activity.
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Affiliation(s)
- Reagan M Mogire
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
| | - Silviane A Miruka
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Dennis W Juma
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya
| | - Case W McNamara
- Calibr-Skaggs Institute for Innovative Medicine, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Ben Andagalu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
| | | | - Elodie Chenu
- Medicines for Malaria Venture, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Bernhards R Ogutu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Hoseah M Akala
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya.
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Israr J, Alam S, Kumar A. Drug repurposing for respiratory infections. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:207-230. [PMID: 38942538 DOI: 10.1016/bs.pmbts.2024.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Respiratory infections such as Coronavirus disease 2019 are a substantial worldwide health challenge, frequently resulting in severe sickness and death, especially in susceptible groups. Conventional drug development for respiratory infections faces obstacles such as extended timescales, substantial expenses, and the rise of resistance to current treatments. Drug repurposing is a potential method that has evolved to quickly find and reuse existing medications for treating respiratory infections. Drug repurposing utilizes medications previously approved for different purposes, providing a cost-effective and time-efficient method to tackle pressing medical needs. This chapter summarizes current progress and obstacles in repurposing medications for respiratory infections, focusing on notable examples of repurposed pharmaceuticals and their probable modes of action. The text also explores the significance of computational approaches, high-throughput screening, and preclinical investigations in identifying potential candidates for repurposing. The text delves into the significance of regulatory factors, clinical trial structure, and actual data in confirming the effectiveness and safety of repurposed medications for respiratory infections. Drug repurposing is a valuable technique for quickly increasing the range of treatments for respiratory infections, leading to better patient outcomes and decreasing the worldwide disease burden.
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Affiliation(s)
- Juveriya Israr
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, India; Department of Biotechnology, Era University, Lucknow, Uttar Pradesh, India
| | - Shabroz Alam
- Department of Biotechnology, Era University, Lucknow, Uttar Pradesh, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Mandhana, Kanpur, Uttar Pradesh, India.
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Villamizar-Monsalve MA, López-Abán J, Vicente B, Peláez R, Muro A. Current drug strategies for the treatment and control of schistosomiasis. Expert Opin Pharmacother 2024; 25:409-420. [PMID: 38511392 DOI: 10.1080/14656566.2024.2333372] [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: 01/30/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Schistosomiasis, one of the current Neglected Tropical Diseases (NTDs) affects over 230 million people globally, with nearly 700 million at risk in more than 74 countries. Praziquantel (PZQ) has served as the primary treatment for the past four decades; however, its effectiveness is limited as it solely eliminates adult worms. In regions where infections are frequent, PZQ exhibits only temporary efficacy and has restricted potential to disrupt the prolonged transmission of the disease. AREAS COVERED A comprehensive exploration using the PubMed database was conducted to review current pharmacotherapy approaches for schistosomiasis. This review also encompasses recent research findings related to potential novel therapeutics and the repurposing of existing drugs. EXPERT OPINION Current schistosoma treatment strategies, primarily relying on PZQ, face challenges like temporary effectiveness and limited impact on disease transmission. Drug repurposing, due to economic constraints, is decisive for NTDs. Despite PZQ's efficacy, its failure to prevent reinfection highlights the need for complementary strategies, especially in regions with persistent environmental foci. Integrating therapies against diverse schistosome stages boosts efficacy and impedes resistance. Uncovering novel agents is essential to address resistance concerns in tackling this neglected tropical disease. Integrated strategies present a comprehensive approach to navigate the complex challenges.
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Affiliation(s)
- María Alejandra Villamizar-Monsalve
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Salamanca, Spain
| | - Julio López-Abán
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Salamanca, Spain
| | - Belén Vicente
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Salamanca, Spain
| | - Rafael Peláez
- Organic and Pharmaceutical Chemistry Department, Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Salamanca, Spain
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Salamanca, Spain
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Padalino G, Coghlan A, Pagliuca G, Forde-Thomas JE, Berriman M, Hoffmann KF. Using ChEMBL to Complement Schistosome Drug Discovery. Pharmaceutics 2023; 15:1359. [PMID: 37242601 PMCID: PMC10220823 DOI: 10.3390/pharmaceutics15051359] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Schistosomiasis is one of the most important neglected tropical diseases. Until an effective vaccine is registered for use, the cornerstone of schistosomiasis control remains chemotherapy with praziquantel. The sustainability of this strategy is at substantial risk due to the possibility of praziquantel insensitive/resistant schistosomes developing. Considerable time and effort could be saved in the schistosome drug discovery pipeline if available functional genomics, bioinformatics, cheminformatics and phenotypic resources are systematically leveraged. Our approach, described here, outlines how schistosome-specific resources/methodologies, coupled to the open-access drug discovery database ChEMBL, can be cooperatively used to accelerate early-stage, schistosome drug discovery efforts. Our process identified seven compounds (fimepinostat, trichostatin A, NVP-BEP800, luminespib, epoxomicin, CGP60474 and staurosporine) with ex vivo anti-schistosomula potencies in the sub-micromolar range. Three of those compounds (epoxomicin, CGP60474 and staurosporine) also demonstrated potent and fast-acting ex vivo effects on adult schistosomes and completely inhibited egg production. ChEMBL toxicity data were also leveraged to provide further support for progressing CGP60474 (as well as luminespib and TAE684) as a novel anti-schistosomal compound. As very few compounds are currently at the advanced stages of the anti-schistosomal pipeline, our approaches highlight a strategy by which new chemical matter can be identified and quickly progressed through preclinical development.
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Affiliation(s)
- Gilda Padalino
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff CF10 3NB, UK
| | - Avril Coghlan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK;
| | | | | | - Matthew Berriman
- Wellcome Centre for Integrative Parasitology, School of Infection and Immunity, University of Glasgow, 120 University Place, Glasgow G12 8TA, UK;
| | - Karl F. Hoffmann
- The Department of Life Sciences (DLS), Aberystwyth University, Aberystwyth SY23 3DA, UK;
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da Rosa TF, Serafin MB, Foletto VS, Franco LN, de Paula BR, Fuchs LB, Calegari L, Hörner R. Repositioning of Benzodiazepine Drugs and Synergistic Effect with Ciprofloxacin Against ESKAPE Pathogens. Curr Microbiol 2023; 80:160. [PMID: 37004588 DOI: 10.1007/s00284-023-03242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 02/23/2023] [Indexed: 04/04/2023]
Abstract
Infectious diseases are among the leading causes of morbidity and mortality worldwide. Combating them becomes more complex when caused by the pathogens of the ESKAPE group, which are Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. The purpose of this study was to investigate the repositioning potential of the benzodiazepines clonazepam and diazepam individually and in combination with the antibacterial ciprofloxacin against ESKAPE. The minimum inhibitory concentration and minimum bactericidal concentration against seven American Type Culture Collection (ATCC) reference standard strains and 64 ESKAPE clinical isolates were determined. In addition, the interaction with ciprofloxacin was determined by the checkerboard method and fractional inhibitory concentration index (FICI) of clonazepam against 11 ESKAPE and diazepam against five ESKAPE. We also list the results found and their clinical significance. Benzodiazepines showed similar antibacterial activity against Gram-positive and Gram-negative. The checkerboard and FICI results showed a synergistic effect of these drugs when associated with ciprofloxacin against almost all tested isolates. Viewing the clinical cases studied, benzodiazepines have potential as treatment alternatives. The results allow us to conclude that clonazepam and diazepam, when in combination with ciprofloxacin, have promising activity against ESKAPE, therefore, assuming the position of candidates for repositioning.
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Affiliation(s)
- Taciéli F da Rosa
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Marissa B Serafin
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Vitória S Foletto
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Laísa N Franco
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Bruno R de Paula
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Luana B Fuchs
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Luciano Calegari
- University Hospital of Santa Maria, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Rosmari Hörner
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.
- Bacteriology Laboratory, Department of Clinical and Toxicological Analysis (DACT)-Health Sciences Center (CCS)., Building 26, Room 1201, UFSM, Santa Maria, RS, 97105-900, Brazil.
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Santos AS, Borges Dos Anjos LR, Costa VAF, Freitas VAQ, Zara ALDSA, Costa CR, Neves BJ, Silva MDRR. In silico-chemogenomic repurposing of new chemical scaffolds for histoplasmosis treatment. J Mycol Med 2023; 33:101363. [PMID: 36842411 DOI: 10.1016/j.mycmed.2023.101363] [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: 09/27/2022] [Revised: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023]
Abstract
BACKGROUND Histoplasmosis is a systemic form of endemic mycosis to the American continent and may be lethal to people living with HIV/AIDS. The drugs available for treating histoplasmosis are limited, costly, and highly toxic. New drug development is time-consuming and costly; hence, drug repositioning is an advantageous strategy for discovering new therapeutic options. OBJECTIVE This study was conducted to identify drugs that can be repositioned for treating histoplasmosis in immunocompromised patients. METHODS Homologous proteins among Histoplasma capsulatum strains were selected and used to search for homologous targets in the DrugBank and Therapeutic Target Database. Essential genes were selected using Saccharomyces cerevisiae as a model, and functional regions of the therapeutic targets were analyzed. The antifungal activity of the selected drugs was verified, and homology modeling and molecular docking were performed to verify the interactions between the drugs with low inhibitory concentration values and their corresponding targets. RESULTS We selected 149 approved drugs with potential activity against histoplasmosis, among which eight were selected for evaluating their in vitro activity. For drugs with low minimum inhibitory concentration values, such as mebendazole, everolimus, butenafine, and bifonazole, molecular docking studies were performed. A chemogenomic framework revealed lanosterol 14-α-demethylase, squalene monooxygenase, serine/threonine-protein kinase mTOR, and the β-4B tubulin chain of H. capsulatum, respectively, as the protein targets of the drugs. CONCLUSIONS Our strategy can be used to identify promising antifungal targets, and drugs with repositioning potential for treating H. capsulatum.
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Affiliation(s)
- Andressa Santana Santos
- Institute of Tropical Pathology and Public Health (IPTSP), Federal University of Goiás, Goiânia, Brazil
| | | | | | | | | | - Carolina Rodrigues Costa
- Institute of Tropical Pathology and Public Health (IPTSP), Federal University of Goiás, Goiânia, Brazil
| | - Bruno Junior Neves
- Laboratory of Cheminformatics (LabChem), Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
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Drug Repurposing for COVID-19: A Review and a Novel Strategy to Identify New Targets and Potential Drug Candidates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092723. [PMID: 35566073 PMCID: PMC9099573 DOI: 10.3390/molecules27092723] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023]
Abstract
In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) was first identified in the province of Wuhan, China. Since then, there have been over 400 million confirmed cases and 5.8 million deaths by COVID-19 reported worldwide. The urgent need for therapies against SARS-CoV-2 led researchers to use drug repurposing approaches. This strategy allows the reduction in risks, time, and costs associated with drug development. In many cases, a repurposed drug can enter directly to preclinical testing and clinical trials, thus accelerating the whole drug discovery process. In this work, we will give a general overview of the main developments in COVID-19 treatment, focusing on the contribution of the drug repurposing paradigm to find effective drugs against this disease. Finally, we will present our findings using a new drug repurposing strategy that identified 11 compounds that may be potentially effective against COVID-19. To our knowledge, seven of these drugs have never been tested against SARS-CoV-2 and are potential candidates for in vitro and in vivo studies to evaluate their effectiveness in COVID-19 treatment.
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Alves VM, Auerbach SS, Kleinstreuer N, Rooney JP, Muratov EN, Rusyn I, Tropsha A, Schmitt C. Curated Data In - Trustworthy In Silico Models Out: The Impact of Data Quality on the Reliability of Artificial Intelligence Models as Alternatives to Animal Testing. Altern Lab Anim 2021; 49:73-82. [PMID: 34233495 PMCID: PMC8609471 DOI: 10.1177/02611929211029635] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
New Approach Methodologies (NAMs) that employ artificial intelligence (AI) for predicting adverse effects of chemicals have generated optimistic expectations as alternatives to animal testing. However, the major underappreciated challenge in developing robust and predictive AI models is the impact of the quality of the input data on the model accuracy. Indeed, poor data reproducibility and quality have been frequently cited as factors contributing to the crisis in biomedical research, as well as similar shortcomings in the fields of toxicology and chemistry. In this article, we review the most recent efforts to improve confidence in the robustness of toxicological data and investigate the impact that data curation has on the confidence in model predictions. We also present two case studies demonstrating the effect of data curation on the performance of AI models for predicting skin sensitisation and skin irritation. We show that, whereas models generated with uncurated data had a 7-24% higher correct classification rate (CCR), the perceived performance was, in fact, inflated owing to the high number of duplicates in the training set. We assert that data curation is a critical step in building computational models, to help ensure that reliable predictions of chemical toxicity are achieved through use of the models.
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Affiliation(s)
- Vinicius M. Alves
- Office of Data Science, Division of the National Toxicology Program (DNTP), National Institute of Environmental Health Sciences (NIEHS), Durham, NC, USA
| | - Scott S. Auerbach
- Toxinformatics Group, Predictive Toxicology Branch, DNTP, NIEHS, Durham, NC, USA
| | - Nicole Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, Scientific Director's Office, DNTP, NIEHS, Durham, NC, USA
| | - John P. Rooney
- Integrated Laboratory Systems, LLC, Morrisville, NC, USA
| | - Eugene N. Muratov
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, NC, USA
- Department of Pharmaceutical Sciences, Federal University of Paraiba, Joao Pessoa, Paraiba, Brazil
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, NC, USA
| | - Charles Schmitt
- Office of Data Science, Division of the National Toxicology Program (DNTP), National Institute of Environmental Health Sciences (NIEHS), Durham, NC, USA
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Seki Kioshima E, de Souza Bonfim de Mendonça P, de Melo Teixeira M, Grenier Capoci IR, Amaral A, Vilugron Rodrigues-Vendramini FA, Lauton Simões B, Rodrigues Abadio AK, Fernandes Matos L, Soares Felipe MS. One Century of Study: What We Learned about Paracoccidioides and How This Pathogen Contributed to Advances in Antifungal Therapy. J Fungi (Basel) 2021; 7:106. [PMID: 33540749 PMCID: PMC7913102 DOI: 10.3390/jof7020106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 02/08/2023] Open
Abstract
Paracoccidioidomycosis (PCM) is a notable fungal infection restricted to Latin America. Since the first description of the disease by Lutz up to the present day, Brazilian researchers have contributed to the understanding of the life cycle of this pathogen and provided the possibility of new targets for antifungal therapy based on the structural and functional genomics of Paracoccidioides. In this context, in silico approaches have selected molecules that act on specific targets, such as the thioredoxin system, with promising antifungal activity against Paracoccidioides. Some of these are already in advanced development stages. In addition, the application of nanostructured systems has addressed issues related to the high toxicity of conventional PCM therapy. Thus, the contribution of molecular biology and biotechnology to the advances achieved is unquestionable. However, it is still necessary to transcend the boundaries of synthetic chemistry, pharmaco-technics, and pharmacodynamics, aiming to turn promising molecules into newly available drugs for the treatment of fungal diseases.
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Affiliation(s)
- Erika Seki Kioshima
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - Patrícia de Souza Bonfim de Mendonça
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - Marcus de Melo Teixeira
- Faculty of Medicine, University of Brasília (UnB), Brasilia, Distrito Federal 70910-900, Brazil;
| | - Isis Regina Grenier Capoci
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - André Amaral
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia 74690-900, Brazil;
| | - Franciele Abigail Vilugron Rodrigues-Vendramini
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - Bruna Lauton Simões
- Program in Biosciences and Pathophysiology, Department of Clinical Analysis and Biomedicine, State University of Maringa (UEM), Maringa, Parana 87020-900, Brazil; (P.d.S.B.d.M.); (I.R.G.C.); (F.A.V.R.-V.); (B.L.S.)
| | - Ana Karina Rodrigues Abadio
- Faculty of Agricultural Social Sciences, Mato Grosso State University, Nova Mutum, Mato Grosso 78450-000, Brazil;
| | - Larissa Fernandes Matos
- Faculty of Ceilandia, University of Brasília (UnB), Brasília, Distrito Federal 72220-275, Brazil;
- Program in Microbial Biology, Institute of Biological Sciences, University of Brasília, Brasília 70910-900, Brazil
| | - Maria Sueli Soares Felipe
- Program of Genomic Sciences and Biotechnology, Catholic University of Brasilia, Brasília 70790-160, Brazil;
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10
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Rosa TFD, Machado CDS, Serafin MB, Bottega A, Coelho SS, Foletto VS, Rampelotto RF, Lorenzoni VV, Mainardi A, Hörner R. Repurposing of escitalopram oxalate and clonazepam in combination with ciprofloxacin and sulfamethoxazole-trimethoprim for treatment of multidrug-resistant microorganisms and evaluation of the cleavage capacity of plasmid DNA. Can J Microbiol 2021; 67:599-612. [PMID: 33481681 DOI: 10.1139/cjm-2020-0546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Bacterial resistance has become one of the most serious public health problems, globally, and drug repurposing is being investigated to speed up the identification of effective drugs. The aim of this study was to investigate the repurposing of escitalopram oxalate and clonazepam drugs individually, and in combination with the antibiotics ciprofloxacin and sulfamethoxazole-trimethoprim, to treat multidrug-resistant (MDR) microorganisms and to evaluate the potential chemical nuclease activity. The minimum inhibitory concentration, minimum bactericidal concentration, fractional inhibitory concentration index, and tolerance level were determined for each microorganism tested. In vitro antibacterial activity was evaluated against 47 multidrug-resistant clinical isolates and 11 standard bacterial strains from the American Type Culture Collection. Escitalopram oxalate was mainly active against Gram-positive bacteria, and clonazepam was active against both Gram-positive and Gram-negative bacteria. When associated with the two antibiotics mentioned, they had a significant synergistic effect. Clonazepam cleaved plasmid DNA, and the mechanisms involved were oxidative and hydrolytic. These results indicate the potential for repurposing these non-antibiotic drugs to treat bacterial infections. However, further studies on the mechanism of action of these drugs should be performed to ensure their safe use.
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Affiliation(s)
- Taciéli F da Rosa
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Catrine de S Machado
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Marissa B Serafin
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Angelita Bottega
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Silvana S Coelho
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Vitória S Foletto
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Roberta F Rampelotto
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Vinícius V Lorenzoni
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Amanda Mainardi
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Rosmari Hörner
- Laboratory of Bacteriology, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil.,Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
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11
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Borba JVVB, Silva AC, Lima MNN, Mendonca SS, Furnham N, Costa FTM, Andrade CH. Chemogenomics and bioinformatics approaches for prioritizing kinases as drug targets for neglected tropical diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 124:187-223. [PMID: 33632465 DOI: 10.1016/bs.apcsb.2020.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neglected tropical diseases (NTDs) are a group of twenty-one diseases classified by the World Health Organization that prevail in regions with tropical and subtropical climate and affect more than one billion people. There is an urgent need to develop new and safer drugs for these diseases. Protein kinases are a potential class of targets for developing new drugs against NTDs, since they play crucial role in many biological processes, such as signaling pathways, regulating cellular communication, division, metabolism and death. Bioinformatics is a field that aims to organize large amounts of biological data as well as develop and use tools for understanding and analyze them in order to produce meaningful information in a biological manner. In combination with chemogenomics, which analyzes chemical-biological interactions to screen ligands against selected targets families, these approaches can be used to stablish a rational strategy for prioritizing new drug targets for NTDs. Here, we describe how bioinformatics and chemogenomics tools can help to identify protein kinases and their potential inhibitors for the development of new drugs for NTDs. We present a review of bioinformatics tools and techniques that can be used to define an organisms kinome for drug prioritization, drug and target repurposing, multi-quinase inhibition approachs and selectivity profiling. We also present some successful examples of the application of such approaches in recent case studies.
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Affiliation(s)
- Joyce Villa Verde Bastos Borba
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil; Laboratory of Tropical Diseases-Prof. Luiz Jacintho da Silva, Department of Genetics, Evolution and Bioagents, University of Campinas, Campinas, SP, Brazil
| | - Arthur Carvalho Silva
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil
| | - Marilia Nunes Nascimento Lima
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil
| | - Sabrina Silva Mendonca
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases-Prof. Luiz Jacintho da Silva, Department of Genetics, Evolution and Bioagents, University of Campinas, Campinas, SP, Brazil
| | - Carolina Horta Andrade
- LabMol-Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goiás, Goiânia, GO, Brazil; Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom.
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12
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Computational Chemogenomics Drug Repositioning Strategy Enables the Discovery of Epirubicin as a New Repurposed Hit for Plasmodium falciparum and P. vivax. Antimicrob Agents Chemother 2020; 64:AAC.02041-19. [PMID: 32601162 PMCID: PMC7449180 DOI: 10.1128/aac.02041-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Widespread resistance against antimalarial drugs thwarts current efforts for controlling the disease and urges the discovery of new effective treatments. Drug repositioning is increasingly becoming an attractive strategy since it can reduce costs, risks, and time-to-market. Herein, we have used this strategy to identify novel antimalarial hits. We used a comparative in silico chemogenomics approach to select Plasmodium falciparum and Plasmodium vivax proteins as potential drug targets and analyzed them using a computer-assisted drug repositioning pipeline to identify approved drugs with potential antimalarial activity. Widespread resistance against antimalarial drugs thwarts current efforts for controlling the disease and urges the discovery of new effective treatments. Drug repositioning is increasingly becoming an attractive strategy since it can reduce costs, risks, and time-to-market. Herein, we have used this strategy to identify novel antimalarial hits. We used a comparative in silico chemogenomics approach to select Plasmodium falciparum and Plasmodium vivax proteins as potential drug targets and analyzed them using a computer-assisted drug repositioning pipeline to identify approved drugs with potential antimalarial activity. Among the seven drugs identified as promising antimalarial candidates, the anthracycline epirubicin was selected for further experimental validation. Epirubicin was shown to be potent in vitro against sensitive and multidrug-resistant P. falciparum strains and P. vivax field isolates in the nanomolar range, as well as being effective against an in vivo murine model of Plasmodium yoelii. Transmission-blocking activity was observed for epirubicin in vitro and in vivo. Finally, using yeast-based haploinsufficiency chemical genomic profiling, we aimed to get insights into the mechanism of action of epirubicin. Beyond the target predicted in silico (a DNA gyrase in the apicoplast), functional assays suggested a GlcNac-1-P-transferase (GPT) enzyme as a potential target. Docking calculations predicted the binding mode of epirubicin with DNA gyrase and GPT proteins. Epirubicin is originally an antitumoral agent and presents associated toxicity. However, its antiplasmodial activity against not only P. falciparum but also P. vivax in different stages of the parasite life cycle supports the use of this drug as a scaffold for hit-to-lead optimization in malaria drug discovery.
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13
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Rugel AR, Guzman MA, Taylor AB, Chevalier FD, Tarpley RS, McHardy SF, Cao X, Holloway SP, Anderson TJC, Hart PJ, LoVerde PT. Why does oxamniquine kill Schistosoma mansoni and not S. haematobium and S. japonicum? Int J Parasitol Drugs Drug Resist 2020; 13:8-15. [PMID: 32315953 PMCID: PMC7167500 DOI: 10.1016/j.ijpddr.2020.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 12/03/2022]
Abstract
Human schistosomiasis is a disease which globally affects over 229 million people. Three major species affecting humans are Schistosoma mansoni, S. haematobium and S. japonicum. Previous treatment of S. mansoni includes the use of oxamniquine (OXA), a prodrug that is enzymatically activated in S. mansoni but is ineffective against S. haematobium and S. japonicum. The OXA activating enzyme was identified and crystallized, as being a S. mansoni sulfotransferase (SmSULT). S. haematobium and S. japonicum possess homologs of SmSULT (ShSULT and SjSULT) begging the question; why does oxamniquine fail to kill S. haematobium and S. japonicum adult worms? Investigation of the molecular structures of the sulfotransferases indicates that structural differences, specifically in OXA contact residues, do not abrogate OXA binding in the active sites as previously hypothesized. Data presented argue that the ability of SULTs to sulfate and thus activate OXA and its derivatives is linked to the ability of OXA to fit in the binding pocket to allow the transfer of a sulfur group.
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Affiliation(s)
- Anastasia R Rugel
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA; Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Meghan A Guzman
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA; Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Alexander B Taylor
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA; X-ray Crystallography Core Laboratory, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Frédéric D Chevalier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78245, USA
| | - Reid S Tarpley
- Center for Innovative Drug Discovery, Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Stanton F McHardy
- Center for Innovative Drug Discovery, Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Xiaohang Cao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Stephen P Holloway
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Timothy J C Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 78245, USA
| | - P John Hart
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA; X-ray Crystallography Core Laboratory, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA; Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
| | - Philip T LoVerde
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA; Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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14
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Rodrigues L, Cravo P, Viveiros M. Efflux pump inhibitors as a promising adjunct therapy against drug resistant tuberculosis: a new strategy to revisit mycobacterial targets and repurpose old drugs. Expert Rev Anti Infect Ther 2020; 18:741-757. [PMID: 32434397 DOI: 10.1080/14787210.2020.1760845] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION In 2018, an estimated 377,000 people developed multidrug-resistant tuberculosis (MDR-TB), urging for new effective treatments. In the last years, it has been accepted that efflux pumps play an important role in the evolution of drug resistance. Strategies are required to mitigate the consequences of the activity of efflux pumps. AREAS COVERED Based upon the literature available in PubMed, up to February 2020, on the diversity of efflux pumps in Mycobacterium tuberculosis and their association with drug resistance, studies that identified efflux inhibitors and their effect on restoring the activity of antimicrobials subjected to efflux are reviewed. These support a new strategy for the development of anti-TB drugs, including efflux inhibitors, using in silico drug repurposing. EXPERT OPINION The current literature highlights the contribution of efflux pumps in drug resistance in M. tuberculosis and that efflux inhibitors may help to ensure the effectiveness of anti-TB drugs. However, despite the usefulness of efflux inhibitors in in vitro studies, in most cases their application in vivo is restricted due to toxicity. In a time when new drugs are needed to fight MDR-TB and extensively drug-resistant TB, cost-effective strategies to identify safer efflux inhibitors should be implemented in drug discovery programs.
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Affiliation(s)
- Liliana Rodrigues
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL , Lisboa, Portugal
| | - Pedro Cravo
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL , Lisboa, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL , Lisboa, Portugal
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15
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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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16
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Whatley KCL, Padalino G, Whiteland H, Geyer KK, Hulme BJ, Chalmers IW, Forde-Thomas J, Ferla S, Brancale A, Hoffmann KF. The repositioning of epigenetic probes/inhibitors identifies new anti-schistosomal lead compounds and chemotherapeutic targets. PLoS Negl Trop Dis 2019; 13:e0007693. [PMID: 31730617 PMCID: PMC6881072 DOI: 10.1371/journal.pntd.0007693] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/27/2019] [Accepted: 10/30/2019] [Indexed: 01/13/2023] Open
Abstract
Background Praziquantel represents the frontline chemotherapy used to treat schistosomiasis, a neglected tropical disease (NTD) caused by infection with macro-parasitic blood fluke schistosomes. While this drug is safe, its inability to kill all schistosome lifecycle stages within the human host often requires repeat treatments. This limitation, amongst others, has led to the search for novel anti-schistosome replacement or combinatorial chemotherapies. Here, we describe a repositioning strategy to assess the anthelmintic activity of epigenetic probes/inhibitors obtained from the Structural Genomics Consortium. Methodology/Principle findings Thirty-seven epigenetic probes/inhibitors targeting histone readers, writers and erasers were initially screened against Schistosoma mansoni schistosomula using the high-throughput Roboworm platform. At 10 μM, 14 of these 37 compounds (38%) negatively affected schistosomula motility and phenotype after 72 hours of continuous co-incubation. Subsequent dose-response titrations against schistosomula and adult worms revealed epigenetic probes targeting one reader (NVS-CECR2-1), one writer (LLY-507 and BAY-598) and one eraser (GSK-J4) to be particularly active. As LLY-507/BAY-598 (SMYD2 histone methyltransferase inhibitors) and GSK-J4 (a JMJD3 histone demethylase inhibitor) regulate an epigenetic process (protein methylation) known to be critical for schistosome development, further characterisation of these compounds/putative targets was performed. RNA interference (RNAi) of one putative LLY-507/BAY-598 S. mansoni target (Smp_000700) in adult worms replicated the compound-mediated motility and egg production defects. Furthermore, H3K36me2, a known product catalysed by SMYD2 activity, was also reduced by LLY-507 (25%), BAY-598 (23%) and siSmp_000700 (15%) treatment of adult worms. Oviposition and packaging of vitelline cells into in vitro laid eggs was also significantly affected by GSK-J4 (putative cell permeable prodrug inhibitor of Smp_034000), but not by the related structural analogue GSK-J1 (cell impermeable inhibitor). Conclusion/Significance Collectively, these results provide further support for the development of next-generation drugs targeting schistosome epigenetic pathway components. In particular, the progression of histone methylation/demethylation modulators presents a tractable strategy for anti-schistosomal control. Human schistosomiasis is caused by infection with parasitic blood fluke worms. Global control of this NTD is currently facilitated by administration of a single drug, praziquantel (PZQ). This mono-chemotherapeutic strategy of schistosomiasis control presents challenges as PZQ is not active against all human-dwelling schistosome lifecycle stages and the evolution of PZQ resistant parasites remains a threat. Therefore, new drugs to be used in combination with or in replacement of PZQ are urgently needed. Here, continuing our studies on Schistosoma mansoni epigenetic processes, we performed anthelmintic screening of 37 epigenetic probes/epigenetic inhibitors obtained from the Structural Genomics Consortium (SGC). The results of these studies highlighted that schistosome protein methylation/demethylation processes are acutely vulnerable. In particular, compounds affecting schistosome SMYD (LLY-507, BAY-598) or JMJD (GSK-J4) homologues are especially active on schistosomula and adult worms during in vitro phenotypic drug screens. The active epigenetic probes identified here as well as their corresponding S. mansoni protein targets offers new starting points for the development of next-generation anti-schistosomals.
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Affiliation(s)
- Kezia C. L. Whatley
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Gilda Padalino
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Helen Whiteland
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Kathrin K. Geyer
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Benjamin J. Hulme
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Iain W. Chalmers
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Josephine Forde-Thomas
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Salvatore Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, United Kingdom
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, United Kingdom
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail:
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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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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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19
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de Oliveira AA, Neves BJ, Silva LDC, Soares CMDA, Andrade CH, Pereira M. Drug Repurposing for Paracoccidioidomycosis Through a Computational Chemogenomics Framework. Front Microbiol 2019; 10:1301. [PMID: 31244810 PMCID: PMC6581699 DOI: 10.3389/fmicb.2019.01301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/24/2019] [Indexed: 12/25/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is the most prevalent endemic mycosis in Latin America. The disease is caused by fungi of the genus Paracoccidioides and mainly affects low-income rural workers after inhalation of fungal conidia suspended in the air. The current arsenal of chemotherapeutic agents requires long-term administration protocols. In addition, chemotherapy is related to a significantly increased frequency of disease relapse, high toxicity, and incomplete elimination of the fungus. Due to the limitations of current anti-PCM drugs, we developed a computational drug repurposing-chemogenomics approach to identify approved drugs or drug candidates in clinical trials with anti-PCM activity. In contrast to the one-drug-one-target paradigm, our chemogenomics approach attempts to predict interactions between drugs, and Paracoccidioides protein targets. To achieve this goal, we designed a workflow with the following steps: (a) compilation and preparation of Paracoccidioides spp. genome data; (b) identification of orthologous proteins among the isolates; (c) identification of homologous proteins in publicly available drug-target databases; (d) selection of Paracoccidioides essential targets using validated genes from Saccharomyces cerevisiae; (e) homology modeling and molecular docking studies; and (f) experimental validation of selected candidates. We prioritized 14 compounds. Two antineoplastic drug candidates (vistusertib and BGT-226) predicted to be inhibitors of phosphatidylinositol 3-kinase TOR2 showed antifungal activity at low micromolar concentrations (<10 μM). Four antifungal azole drugs (bifonazole, luliconazole, butoconazole, and sertaconazole) showed antifungal activity at low nanomolar concentrations, validating our methodology. The results suggest our strategy for predicting new anti-PCM drugs is useful. Finally, we could recommend hit-to-lead optimization studies to improve potency and selectivity, as well as pharmaceutical formulations to improve oral bioavailability of the antifungal azoles identified.
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Affiliation(s)
- Amanda Alves de Oliveira
- Laboratório de Biologia Molecular, Universidade Federal de Goiás, Goiânia, Brazil.,Laboratório de Cheminformática, Centro Universitário de Anápolis, UniEVANGÉLICA, Anápolis, Brazil
| | - Bruno Junior Neves
- Laboratório de Cheminformática, Centro Universitário de Anápolis, UniEVANGÉLICA, Anápolis, Brazil
| | - Lívia do Carmo Silva
- Laboratório de Biologia Molecular, Universidade Federal de Goiás, Goiânia, Brazil
| | | | - Carolina Horta Andrade
- Laboratório de Modelagem Molecular e Design de Medicamentos, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Universidade Federal de Goiás, Goiânia, Brazil
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20
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da Silva VBR, Boucherle B, El-Methni J, Hoffmann B, da Silva AL, Fortune A, de Lima MDCA, Thomas A. Could we expect new praziquantel derivatives? A meta pharmacometrics/pharmacoinformatics analysis of all antischistosomal praziquantel derivatives found in the literature. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:383-401. [PMID: 31144535 DOI: 10.1080/1062936x.2019.1607898] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Praziquantel (PZQ) is the first line drug for the treatment of human Schistosoma spp. worm infections. However, it suffers from low activity towards immature stages of the worm, and its prolonged use induces resistance/tolerance. During the last 40 years, 263 PZQ analogues have been synthesized and tested against Schistosoma spp. worms, but less than 10% of them showed significant activity. Here, we propose a rationalization of the chemical space of the PZQ derivatives by a ligand-based approach. First, we constructed an in-house database with all PZQ derivatives available in the literature. This analysis shows a high heterogeneity in the data. Fortunately, all studies include PZQ as a reference, permitting the classification of compounds into three classes according to their activities. Models involving ligand-based pharmacophore and logistic regression were performed. Five physicochemical parameters were identified as the best to explain the biological activity. In the end, we proposed new PZQ derivatives with modifications at positions 1 and 7, we analysed them with our models, and we observed that they can be more active than the previously synthesized derivatives. The main goal of this work was to conduct the most valuable meta-pharmacometrics/pharmacoinformatics analysis with all Praziquantel medicinal chemistry data available in the literature.
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Affiliation(s)
- V B Ribeiro da Silva
- a CNRS, DPM , Université Grenoble Alpes , Grenoble , France
- b Departamento de Antibióticos (DANTI) , Universidade Federal de Pernambuco (UFPE) , Recife , Brazil
| | - B Boucherle
- a CNRS, DPM , Université Grenoble Alpes , Grenoble , France
| | - J El-Methni
- c MAP5, UMR CNRS , Université Paris Descartes, Sorbonne Paris Cité , Paris , France
| | - B Hoffmann
- d UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, IMPMC , Sorbonne Universités, UPMC Univ Paris , Paris , France
| | - A L da Silva
- e Universidade Federal do Vale do São Francisco, Univasf, Campus Paulo Afonso , Paulo Afonso , Brazil
| | - A Fortune
- a CNRS, DPM , Université Grenoble Alpes , Grenoble , France
| | - M do Carmo Alves de Lima
- b Departamento de Antibióticos (DANTI) , Universidade Federal de Pernambuco (UFPE) , Recife , Brazil
| | - A Thomas
- a CNRS, DPM , Université Grenoble Alpes , Grenoble , France
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21
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Abstract
Schistosomiasis affects millions globally. There is no vaccine, and treatment depends entirely on praziquantel (PZQ). Field isolates exhibit reduced susceptibility to PZQ, and resistance has been experimentally induced, suggesting that reliance on a single treatment is particularly dangerous. The present study investigated the value of cinnarizine and griseofulvin against Schistosoma mansoni through their in vitro effects on adult worms and oviposition as well as in vivo evaluation in early and late infection, compared to PZQ, in a preliminary experimental model. In vitro, both cinnarizine and griseofulvin showed uncoupling, sluggish worm movement and complete absence of ova at 100 μg/ml. In early infection, cinnarizine showed a significant reduction in the number of porto-mesenteric couples compared to the griseofulvin and control groups, a finding similar to PZQ. Remarkably, cinnarizine significantly exceeded PZQ and griseofulvin in reducing the total worm burden. In late infection, cinnarizine and griseofulvin showed results similar to PZQ by significantly reducing the numbers of hepatic and porto-mesenteric couples and total worm burden compared to controls. Cinnarizine performed better than griseofulvin by reducing hepatic and intestinal ovum counts, and it led to complete disappearance of the first two immature stages. The current work suggests the possibility of using cinnarizine and griseofulvin, mainly in late S. mansoni infection, especially cinnarizine, which showed similar results to PZQ and surpassed it in early infection. Further studies are required to elucidate their exact mechanisms of action and particularly their synergistic effect with PZQ.
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Borba JV, Silva AC, Ramos PI, Grazzia N, Miguel DC, Muratov EN, Furnham N, Andrade CH. Unveiling the Kinomes of Leishmania infantum and L. braziliensis Empowers the Discovery of New Kinase Targets and Antileishmanial Compounds. Comput Struct Biotechnol J 2019; 17:352-361. [PMID: 30949306 PMCID: PMC6429582 DOI: 10.1016/j.csbj.2019.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/31/2023] Open
Abstract
Leishmaniasis is a neglected tropical disease caused by parasites of the genus Leishmania (NTD) endemic in 98 countries. Although some drugs are available, current treatments deal with issues such as toxicity, low efficacy, and emergence of resistance. Therefore, there is an urgent need to identify new targets for the development of new antileishmanial drugs. Protein kinases (PKs), which play an essential role in many biological processes, have become potential drug targets for many parasitic diseases. A refined bioinformatics pipeline was applied in order to define and compare the kinomes of L. infantum and L. braziliensis, species that cause cutaneous and visceral manifestations of leishmaniasis in the Americas, the latter being potentially fatal if untreated. Respectively, 224 and 221 PKs were identified in L. infantum and L. braziliensis overall. Almost all unclassified eukaryotic PKs were assigned to six of nine major kinase groups and, consequently, most have been classified into family and subfamily. Furthermore, revealing the kinomes for both Leishmania species allowed for the prioritization of potential drug targets that could be explored for discovering new drugs against leishmaniasis. Finally, we used a drug repurposing approach and prioritized seven approved drugs and investigational compounds to be experimentally tested against Leishmania. Trametinib and NMS-1286937 inhibited the growth of L. infantum and L. braziliensis promastigotes and amastigotes and therefore might be good candidates for the drug repurposing pipeline.
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Affiliation(s)
- Joyce V.B. Borba
- Labmol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás - UFG, Goiânia, GO, 74605-510, Brazil
| | - Arthur C. Silva
- Labmol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás - UFG, Goiânia, GO, 74605-510, Brazil
| | - Pablo I.P. Ramos
- Instituto Gonçalo Moniz (IGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, BA, 40296-710, Brazil
| | - Nathalia Grazzia
- LEBIL – Laboratory of Leishmania Biology Infection Studies, Department of Animal Biology, Biology Institute, State University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Danilo C. Miguel
- LEBIL – Laboratory of Leishmania Biology Infection Studies, Department of Animal Biology, Biology Institute, State University of Campinas (UNICAMP), Campinas, SP, 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, Odessa, 65000, Ukraine
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Carolina H. Andrade
- Labmol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás - UFG, Goiânia, GO, 74605-510, Brazil
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23
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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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Huson KM, Morphew RM, Allen NR, Hegarty MJ, Worgan HJ, Girdwood SE, Jones EL, Phillips HC, Vickers M, Swain M, Smith D, Kingston-Smith AH, Brophy PM. Polyomic tools for an emerging livestock parasite, the rumen fluke Calicophoron daubneyi; identifying shifts in rumen functionality. Parasit Vectors 2018; 11:617. [PMID: 30509301 PMCID: PMC6278170 DOI: 10.1186/s13071-018-3225-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/20/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diseases caused by parasitic flatworms of rumen tissues (paramphistomosis) are a significant threat to global food security as a cause of morbidity and mortality in ruminant livestock in subtropical and tropical climates. Calicophoron daubneyi is currently the only paramphistome species commonly infecting ruminant livestock in temperate European climates. However, recorded incidences of C. daubneyi infection in European livestock have been increasing over the last decade. Whilst clinical paramphistomosis caused by adult worms has not been confirmed in Europe, fatalities have been attributed to severe haemorrhagic enteritis of the small intestine resulting from the migration of immature paramphistomes. Large numbers of mature adults can reside in the rumen, yet to date, the impact on rumen fermentation, and consequently on productivity and economic management of infected livestock, have not been resolved. Limited publicly available nucleotide and protein sequences for C. daubneyi underpin this lack of biological and economic understanding. Here we present for the first time a de novo assembled transcriptome, with functional annotations, for adult C. daubneyi, which provides a reference database for protein and nucleotide sequence identification to facilitate fundamental biology, anthelmintic, vaccine and diagnostics discoveries. RESULTS This dataset identifies a number of genes potentially unique to C. daubneyi and, by comparison to an existing transcriptome for the related Paramphistomum cervi, identifies novel genes which may be unique to the paramphistome group of platyhelminthes. Additionally, we present the first coverage of the excretory/secretory and soluble somatic proteome profiles for adult C. daubneyi and identify the release of extracellular vesicles from adult C. daubneyi parasites during in vitro, ex-host culture. Finally, we have performed the first analysis of rumen fluke impacting upon rumen fermentation parameters using an in vitro gas production study resulting in a significant increase in propionate production. CONCLUSIONS The resulting data provide a discovery platform (transcriptome, proteomes, EV isolation pipeline and in vitro fermentation system) to further study C. daubneyi-host interaction. In addition, the acetate: propionate ratio has been demonstrated to decrease with rumen fluke infection suggesting that acidotic conditions in the rumen may occur.
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Affiliation(s)
- Kathryn M Huson
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Russell M Morphew
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK.
| | - Nathan R Allen
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Matthew J Hegarty
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Hillary J Worgan
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Susan E Girdwood
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Eleanor L Jones
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Helen C Phillips
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Martin Vickers
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Martin Swain
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Daniel Smith
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
| | - Peter M Brophy
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Ceredigion, Aberystwyth, SY23 3DA, UK
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25
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Stroehlein AJ, Gasser RB, Hall RS, Young ND. Interactive online application for the prediction, ranking and prioritisation of drug targets in Schistosoma haematobium. Parasit Vectors 2018; 11:605. [PMID: 30482220 PMCID: PMC6257948 DOI: 10.1186/s13071-018-3197-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/12/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Human schistosomiasis is a neglected tropical disease caused by parasitic worms of the genus Schistosoma that still affects some 200 million people. The mainstay of schistosomiasis control is a single drug, praziquantel. The reliance on this drug carries a risk of resistance emerging to this anthelmintic, such that research towards alternative anti-schistosomal drugs is warranted. In this context, a number of studies have employed computational approaches to prioritise proteins for investigation as drug targets, based on extensive genomic, transcriptomic and small-molecule data now available. METHODS Here, we established a customisable, online application for the prioritisation of drug targets and applied it, for the first time, to the entire inferred proteome of S. haematobium. This application enables selection of weighted and ranked proteins representing potential drug targets, and integrates transcriptional data, orthology and gene essentiality information as well as drug-drug target associations and chemical properties of predicted ligands. RESULTS Using this application, we defined 25 potential drug targets in S. haematobium that associated with approved drugs, and 3402 targets that (although they could not be linked to any compounds) are conserved among a range of socioeconomically important flatworm species and might represent targets for new trematocides. CONCLUSIONS The online application developed here represents an interactive, customisable, expandable and reproducible drug target ranking and prioritisation approach that should be useful for the prediction of drug targets in schistosomes and other species of parasitic worms in the future. We have demonstrated the utility of this online application by predicting potential drug targets in S. haematobium that can now be evaluated using functional genomics tools and/or small molecules, to establish whether they are indeed essential for parasite survival, and to assist in the discovery of novel anti-schistosomal compounds.
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Affiliation(s)
- Andreas J. Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010 Australia
| | - Robin B. Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010 Australia
| | - Ross S. Hall
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010 Australia
| | - Neil D. Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010 Australia
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26
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Ferreira DD, Mesquita JT, da Costa Silva TA, Romanelli MM, da Gama Jaen Batista D, da Silva CF, da Gama ANS, Neves BJ, Melo-Filho CC, Correia Soeiro MDN, Andrade CH, Tempone AG. Efficacy of sertraline against Trypanosoma cruzi: an in vitro and in silico study. J Venom Anim Toxins Incl Trop Dis 2018; 24:30. [PMID: 30450114 PMCID: PMC6208092 DOI: 10.1186/s40409-018-0165-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/05/2018] [Indexed: 01/07/2023] Open
Abstract
Background Drug repurposing has been an interesting and cost-effective approach, especially for neglected diseases, such as Chagas disease. Methods In this work, we studied the activity of the antidepressant drug sertraline against Trypanosoma cruzi trypomastigotes and intracellular amastigotes of the Y and Tulahuen strains, and investigated its action mode using cell biology and in silico approaches. Results Sertraline demonstrated in vitro efficacy against intracellular amastigotes of both T. cruzi strains inside different host cells, including cardiomyocytes, with IC50 values between 1 to 10 μM, and activity against bloodstream trypomastigotes, with IC50 of 14 μM. Considering the mammalian cytotoxicity, the drug resulted in a selectivity index of 17.8. Sertraline induced a change in the mitochondrial integrity of T. cruzi, resulting in a decrease in ATP levels, but not affecting reactive oxygen levels or plasma membrane permeability. In silico approaches using chemogenomic target fishing, homology modeling and molecular docking suggested the enzyme isocitrate dehydrogenase 2 of T. cruzi (TcIDH2) as a potential target for sertraline. Conclusions The present study demonstrated that sertraline had a lethal effect on different forms and strains of T. cruzi, by affecting the bioenergetic metabolism of the parasite. These findings provide a starting point for future experimental assays and may contribute to the development of new compounds. Electronic supplementary material The online version of this article (10.1186/s40409-018-0165-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daiane Dias Ferreira
- Instituto Adolfo Lutz, Centre for Parasitology and Mycology, Avenida Dr. Arnaldo 351, 8° andar, sala 9, CEP, São Paulo, SP 01246-000 Brazil
| | - Juliana Tonini Mesquita
- Instituto Adolfo Lutz, Centre for Parasitology and Mycology, Avenida Dr. Arnaldo 351, 8° andar, sala 9, CEP, São Paulo, SP 01246-000 Brazil
| | - Thais Alves da Costa Silva
- Instituto Adolfo Lutz, Centre for Parasitology and Mycology, Avenida Dr. Arnaldo 351, 8° andar, sala 9, CEP, São Paulo, SP 01246-000 Brazil
| | - Maiara Maria Romanelli
- Instituto Adolfo Lutz, Centre for Parasitology and Mycology, Avenida Dr. Arnaldo 351, 8° andar, sala 9, CEP, São Paulo, SP 01246-000 Brazil
| | - Denise da Gama Jaen Batista
- 2Fundação Oswaldo Cruz, Laboratório de Biologia Celular do Instituto Oswaldo Cruz, Av. Brasil, 4365 Manguinhos, CEP, Rio de Janeiro, RJ 21040-360 Brazil
| | - Cristiane França da Silva
- 2Fundação Oswaldo Cruz, Laboratório de Biologia Celular do Instituto Oswaldo Cruz, Av. Brasil, 4365 Manguinhos, CEP, Rio de Janeiro, RJ 21040-360 Brazil
| | - Aline Nefertiti Silva da Gama
- 2Fundação Oswaldo Cruz, Laboratório de Biologia Celular do Instituto Oswaldo Cruz, Av. Brasil, 4365 Manguinhos, CEP, Rio de Janeiro, RJ 21040-360 Brazil
| | - Bruno Junior Neves
- 3Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240 Setor Leste Universitário, Goiânia, GO 74605170 Brazil
| | - Cleber Camilo Melo-Filho
- 3Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240 Setor Leste Universitário, Goiânia, GO 74605170 Brazil
| | - Maria de Nazare Correia Soeiro
- 2Fundação Oswaldo Cruz, Laboratório de Biologia Celular do Instituto Oswaldo Cruz, Av. Brasil, 4365 Manguinhos, CEP, Rio de Janeiro, RJ 21040-360 Brazil
| | - Carolina Horta Andrade
- 3Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240 Setor Leste Universitário, Goiânia, GO 74605170 Brazil
| | - Andre Gustavo Tempone
- Instituto Adolfo Lutz, Centre for Parasitology and Mycology, Avenida Dr. Arnaldo 351, 8° andar, sala 9, CEP, São Paulo, SP 01246-000 Brazil
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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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Ranjan P, Athar M, Jha PC, Krishna KV. Probing the opportunities for designing anthelmintic leads by sub-structural topology-based QSAR modelling. Mol Divers 2018; 22:669-683. [PMID: 29611020 DOI: 10.1007/s11030-018-9825-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/16/2018] [Indexed: 12/30/2022]
Abstract
A quantitative structure-activity (QSAR) model has been developed for enriched tubulin inhibitors, which were retrieved from sequence similarity searches and applicability domain analysis. Using partial least square (PLS) method and leave-one-out (LOO) validation approach, the model was generated with the correlation statistics of [Formula: see text] and [Formula: see text] of 0.68 and 0.69, respectively. The present study indicates that topological descriptors, viz. BIC, CH_3_C, IC, JX and Kappa_2 correlate well with biological activity. ADME and toxicity (or ADME/T) assessment showed that out of 260 molecules, 255 molecules successfully passed the ADME/T assessment test, wherein the drug-likeness attributes were exhibited. These results showed that topological indices and the colchicine binding domain directly influence the aetiology of helminthic infections. Further, we anticipate that our model can be applied for guiding and designing potential anthelmintic inhibitors.
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Affiliation(s)
- Prabodh Ranjan
- CCG@CUG, School of Chemical Sciences, Central University of Gujarat, Sector-30, Gandhinagar, Gujarat, 382030, India
| | - Mohd Athar
- CCG@CUG, School of Chemical Sciences, Central University of Gujarat, Sector-30, Gandhinagar, Gujarat, 382030, India
| | - Prakash Chandra Jha
- CCG@CUG, Centre for Applied Chemistry, Central University of Gujarat, Sector-30, Gandhinagar, Gujarat, 382030, India.
| | - Kari Vijaya Krishna
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, Tamil Nadu, 632014, India
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Abstract
Following the elucidation of the human genome, chemogenomics emerged in the beginning of the twenty-first century as an interdisciplinary research field with the aim to accelerate target and drug discovery by making best usage of the genomic data and the data linkable to it. What started as a systematization approach within protein target families now encompasses all types of chemical compounds and gene products. A key objective of chemogenomics is the establishment, extension, analysis, and prediction of a comprehensive SAR matrix which by application will enable further systematization in drug discovery. Herein we outline future perspectives of chemogenomics including the extension to new molecular modalities, or the potential extension beyond the pharma to the agro and nutrition sectors, and the importance for environmental protection. The focus is on computational sciences with potential applications for compound library design, virtual screening, hit assessment, analysis of phenotypic screens, lead finding and optimization, and systems biology-based prediction of toxicology and translational research.
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Affiliation(s)
- Edgar Jacoby
- Janssen Research & Development, Beerse, Belgium.
| | - J B Brown
- Life Science Informatics Research Unit, Laboratory of Molecular Biosciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
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30
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Mogire RM, Akala HM, Macharia RW, Juma DW, Cheruiyot AC, Andagalu B, Brown ML, El-Shemy HA, Nyanjom SG. Target-similarity search using Plasmodium falciparum proteome identifies approved drugs with anti-malarial activity and their possible targets. PLoS One 2017; 12:e0186364. [PMID: 29088219 PMCID: PMC5663372 DOI: 10.1371/journal.pone.0186364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 10/01/2017] [Indexed: 11/23/2022] Open
Abstract
Malaria causes about half a million deaths annually, with Plasmodium falciparum being responsible for 90% of all the cases. Recent reports on artemisinin resistance in Southeast Asia warrant urgent discovery of novel drugs for the treatment of malaria. However, most bioactive compounds fail to progress to treatments due to safety concerns. Drug repositioning offers an alternative strategy where drugs that have already been approved as safe for other diseases could be used to treat malaria. This study screened approved drugs for antimalarial activity using an in silico chemogenomics approach prior to in vitro verification. All the P. falciparum proteins sequences available in NCBI RefSeq were mined and used to perform a similarity search against DrugBank, TTD and STITCH databases to identify similar putative drug targets. Druggability indices of the potential P. falciparum drug targets were obtained from TDR targets database. Functional amino acid residues of the drug targets were determined using ConSurf server which was used to fine tune the similarity search. This study predicted 133 approved drugs that could target 34 P. falciparum proteins. A literature search done at PubMed and Google Scholar showed 105 out of the 133 drugs to have been previously tested against malaria, with most showing activity. For further validation, drug susceptibility assays using SYBR Green I method were done on a representative group of 10 predicted drugs, eight of which did show activity against P. falciparum 3D7 clone. Seven had IC50 values ranging from 1 μM to 50 μM. This study also suggests drug-target association and hence possible mechanisms of action of drugs that did show antiplasmodial activity. The study results validate the use of proteome-wide target similarity approach in identifying approved drugs with activity against P. falciparum and could be adapted for other pathogens.
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Affiliation(s)
- Reagan M. Mogire
- Department of Molecular Biology and Biotechnology, Pan African University Institute of Science, Technology and Innovation, Nairobi, Kenya
| | - Hoseah M. Akala
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)—Walter Reed Project, Kisumu, Kenya
| | - Rosaline W. Macharia
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Dennis W. Juma
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)—Walter Reed Project, Kisumu, Kenya
| | - Agnes C. Cheruiyot
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)—Walter Reed Project, Kisumu, Kenya
| | - Ben Andagalu
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)—Walter Reed Project, Kisumu, Kenya
| | - Mathew L. Brown
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya (USAMRD-K), Kenya Medical Research Institute (KEMRI)—Walter Reed Project, Kisumu, Kenya
| | - Hany A. El-Shemy
- Department of Biochemistry, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Steven G. Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
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Discovery of Novel Antischistosomal Agents by Molecular Modeling Approaches. Trends Parasitol 2016; 32:874-886. [PMID: 27593339 DOI: 10.1016/j.pt.2016.08.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/20/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023]
Abstract
Schistosomiasis, a chronic neglected tropical disease caused by Schistosoma worms, is reported in nearly 80 countries. Although the disease affects approximately 260 million people, the treatment relies exclusively on praziquantel, a drug discovered in the mid-1970s that lacks efficacy against the larval stages of the parasite. In addition, the dependence on a single treatment has raised concerns about drug resistance, and reduced susceptibility has already been found in laboratory and field isolates. Therefore, novel therapies for schistosomiasis are needed, and several approaches have been used to that end. One of these strategies, molecular modeling, has been increasingly integrated with experimental techniques, resulting in the discovery of novel antischistosomal agents.
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Neves BJ, Dantas RF, Senger MR, Melo-Filho CC, Valente WCG, de Almeida ACM, Rezende-Neto JM, Lima EFC, Paveley R, Furnham N, Muratov E, Kamentsky L, Carpenter AE, Braga RC, Silva-Junior FP, Andrade CH. Discovery of New Anti-Schistosomal Hits by Integration of QSAR-Based Virtual Screening and High Content Screening. J Med Chem 2016; 59:7075-88. [PMID: 27396732 PMCID: PMC5844225 DOI: 10.1021/acs.jmedchem.5b02038] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Schistosomiasis is a debilitating neglected tropical disease, caused by flatworms of Schistosoma genus. The treatment relies on a single drug, praziquantel (PZQ), making the discovery of new compounds extremely urgent. In this work, we integrated QSAR-based virtual screening (VS) of Schistosoma mansoni thioredoxin glutathione reductase (SmTGR) inhibitors and high content screening (HCS) aiming to discover new antischistosomal agents. Initially, binary QSAR models for inhibition of SmTGR were developed and validated using the Organization for Economic Co-operation and Development (OECD) guidance. Using these models, we prioritized 29 compounds for further testing in two HCS platforms based on image analysis of assay plates. Among them, 2-[2-(3-methyl-4-nitro-5-isoxazolyl)vinyl]pyridine and 2-(benzylsulfonyl)-1,3-benzothiazole, two compounds representing new chemical scaffolds have activity against schistosomula and adult worms at low micromolar concentrations and therefore represent promising antischistosomal hits for further hit-to-lead optimization.
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Affiliation(s)
- 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 74605-510, Brazil
| | - Rafael F. Dantas
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Mario R. Senger
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Cleber C. Melo-Filho
- LabMol—Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Rua 240, Qd.87, Setor Leste Universitário, Goiânia 74605-510, Brazil
| | - Walter C. G. Valente
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Ana C. M. de Almeida
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - João M. Rezende-Neto
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Elid F. C. Lima
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - Ross Paveley
- Department of Infection and Immunity, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Nicholas Furnham
- Department of Infection and Immunity, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill North Carolina 27955-7568, United States
| | - Lee Kamentsky
- Imaging Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, United States
| | - Anne E. Carpenter
- Imaging Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, United States
| | - 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 74605-510, Brazil
| | - Floriano P. Silva-Junior
- LaBECFar—Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro 21040-900, Rio de Janeiro, Brazil
| | - 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 74605-510, Brazil
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Neves BJ, Muratov E, Machado RB, Andrade CH, Cravo PVL. Modern approaches to accelerate discovery of new antischistosomal drugs. Expert Opin Drug Discov 2016; 11:557-67. [PMID: 27073973 PMCID: PMC6534417 DOI: 10.1080/17460441.2016.1178230] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The almost exclusive use of only praziquantel for the treatment of schistosomiasis has raised concerns about the possible emergence of drug-resistant schistosomes. Consequently, there is an urgent need for new antischistosomal drugs. The identification of leads and the generation of high quality data are crucial steps in the early stages of schistosome drug discovery projects. AREAS COVERED Herein, the authors focus on the current developments in antischistosomal lead discovery, specifically referring to the use of automated in vitro target-based and whole-organism screens and virtual screening of chemical databases. They highlight the strengths and pitfalls of each of the above-mentioned approaches, and suggest possible roadmaps towards the integration of several strategies, which may contribute for optimizing research outputs and led to more successful and cost-effective drug discovery endeavors. EXPERT OPINION Increasing partnerships and access to funding for drug discovery have strengthened the battle against schistosomiasis in recent years. However, the authors believe this battle also includes innovative strategies to overcome scientific challenges. In this context, significant advances of in vitro screening as well as computer-aided drug discovery have contributed to increase the success rate and reduce the costs of drug discovery campaigns. Although some of these approaches were already used in current antischistosomal lead discovery pipelines, the integration of these strategies in a solid workflow should allow the production of new treatments for schistosomiasis in the near future.
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Affiliation(s)
- Bruno Junior Neves
- a LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia , Universidade Federal de Goiás , Goiânia , Brazil
| | - Eugene Muratov
- b Laboratory for Molecular Modeling, Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , NC , USA
| | - Renato Beilner Machado
- c GenoBio - Laboratory of Genomics and Biotechnology, Instituto de Patologia Tropical e Saúde Pública , Universidade Federal de Goiás , Goiânia , Brazil
| | - Carolina Horta Andrade
- a LabMol - Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia , Universidade Federal de Goiás , Goiânia , Brazil
| | - Pedro Vitor Lemos Cravo
- c GenoBio - Laboratory of Genomics and Biotechnology, Instituto de Patologia Tropical e Saúde Pública , Universidade Federal de Goiás , Goiânia , Brazil
- d Instituto de Higiene e Medicina Tropical , Universidade Nova de Lisboa , Lisbon , Portugal
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Ekins S, Mietchen D, Coffee M, Stratton TP, Freundlich JS, Freitas-Junior L, Muratov E, Siqueira-Neto J, Williams AJ, Andrade C. Open drug discovery for the Zika virus. F1000Res 2016; 5:150. [PMID: 27134728 PMCID: PMC4841202 DOI: 10.12688/f1000research.8013.1] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2016] [Indexed: 01/20/2023] Open
Abstract
The Zika virus (ZIKV) outbreak in the Americas has caused global concern that we may be on the brink of a healthcare crisis. The lack of research on ZIKV in the over 60 years that we have known about it has left us with little in the way of starting points for drug discovery. Our response can build on previous efforts with virus outbreaks and lean heavily on work done on other flaviviruses such as dengue virus. We provide some suggestions of what might be possible and propose an open drug discovery effort that mobilizes global science efforts and provides leadership, which thus far has been lacking. We also provide a listing of potential resources and molecules that could be prioritized for testing as
in vitro assays for ZIKV are developed. We propose also that in order to incentivize drug discovery, a neglected disease priority review voucher should be available to those who successfully develop an FDA approved treatment. Learning from the response to the ZIKV, the approaches to drug discovery used and the success and failures will be critical for future infectious disease outbreaks.
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Affiliation(s)
- Sean Ekins
- Collaborations in Chemistry Inc, Fuquay-Varina, NC, USA; Collaborations Pharmaceuticals Inc., Fuquay-Varina, NC, USA; Collaborative Drug Discovery Inc., Burlingame, CA, USA
| | | | - Megan Coffee
- The International Rescue Committee , NY, NY, USA
| | - Thomas P Stratton
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University-New Jersey Medical School, Newark, NJ, USA
| | - Joel S Freundlich
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University-New Jersey Medical School, Newark, NJ, USA; Division of Infectious Diseases, Department of Medicine, and the Ruy V. Lourenço Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ, USA
| | - Lucio Freitas-Junior
- Chemical Biology and Screening Platform, Brazilian Laboratory of Biosciences (LNBio), CNPEM, Campinas, Brazil
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Jair Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | | | - Carolina Andrade
- LabMol - Laboratory for Molecular Modeling and Drug Design, Faculty of Pharmacy, Federal University of Goias, Goiânia, Brazil
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Neves BJ, Dantas RF, Senger MR, Valente WCG, Rezende-Neto JDM, Chaves WT, Kamentsky L, Carpenter A, Silva-Junior FP, Andrade CH. The antidepressant drug paroxetine as a new lead candidate in schistosome drug discovery. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00596e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paroxetine is a new anti-schistosomal lead with potent activity against schistosomula and adult life stages of S. mansoni.
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Geary TG, Mackenzie CD. Adding "Filaricide" to the Gleevec Portfolio. J Infect Dis 2015; 212:677-80. [PMID: 25657258 DOI: 10.1093/infdis/jiv062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 11/12/2022] Open
Affiliation(s)
- Timothy G Geary
- Institute of Parasitology, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Charles D Mackenzie
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing
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Panic G, Vargas M, Scandale I, Keiser J. Activity Profile of an FDA-Approved Compound Library against Schistosoma mansoni. PLoS Negl Trop Dis 2015; 9:e0003962. [PMID: 26230921 PMCID: PMC4521867 DOI: 10.1371/journal.pntd.0003962] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND As plans to expand mass drug treatment campaigns to fight schistosomiasis form, worries about reliance on praziquantel as the sole available treatment motivate the investigation for novel antischistosomal compounds. Drug repurposing might be an inexpensive and effective source of novel antischistosomal leads. METHODOLOGY 1600 FDA approved compounds were first assayed against Schistosoma mansoni schistosomula at a concentration of 10 µM. Active compounds identified from this screen were advanced to the adult worm screen at 33.33 µM, followed by hit characterization. Leads with complementary pharmacokinetic and toxicity profiles were then selected for in vivo studies. PRINCIPAL FINDINGS The in vitro screen identified 121 and 36 compounds active against the schistosomula and adult stage, respectively. Further, in vitro characterization and comparison with already available pharmacokinetic and toxicity data identified 11 in vivo candidates. Doramectin (10 mg/kg) and clofazimine (400 mg/kg) were found to be active in vivo with worm burden reductions of 60.1% and 82.7%, respectively. CONCLUSIONS/SIGNIFICANCE The work presented here expands the knowledge of antischistosomal properties of already approved compounds and underscores variations observed between target-based and phenotypic approaches and among laboratories. The two in vivo-active drugs identified in this study, doramectin and clofazimine are widely available and present as novel drug classes as starting points for further investigation.
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Affiliation(s)
- Gordana Panic
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mireille Vargas
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ivan Scandale
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Jennifer Keiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail:
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