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Gendron T, Lanfranchi DA, Wenzel NI, Kessedjian H, Jannack B, Maes L, Cojean S, Müller TJJ, Loiseau PM, Davioud-Charvet E. Chemoselective Synthesis and Anti-Kinetoplastidal Properties of 2,6-Diaryl-4 H-tetrahydro-thiopyran-4-one S-Oxides: Their Interplay in a Cascade of Redox Reactions from Diarylideneacetones. Molecules 2024; 29:1620. [PMID: 38611899 PMCID: PMC11013284 DOI: 10.3390/molecules29071620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
2,6-Diaryl-4H-tetrahydro-thiopyran-4-ones and corresponding sulfoxide and sulfone derivatives were designed to lower the major toxicity of their parent anti-kinetoplatidal diarylideneacetones through a prodrug effect. Novel diastereoselective methodologies were developed and generalized from diarylideneacetones and 2,6-diaryl-4H-tetrahydro-thiopyran-4-ones to allow the introduction of a wide substitution profile and to prepare the related S-oxides. The in vitro biological activity and selectivity of diarylideneacetones, 2,6-diaryl-4H-tetrahydro-thiopyran-4-ones, and their S-sulfoxide and sulfone metabolites were evaluated against Trypanosoma brucei brucei, Trypanosoma cruzi, and various Leishmania species in comparison with their cytotoxicity against human fibroblasts hMRC-5. The data revealed that the sulfides, sulfoxides, and sulfones, in which the Michael acceptor sites are temporarily masked, are less toxic against mammal cells while the anti-trypanosomal potency was maintained against T. b. brucei, T. cruzi, L. infantum, and L. donovani, thus confirming the validity of the prodrug strategy. The mechanism of action is proposed to be due to the involvement of diarylideneacetones in cascades of redox reactions involving the trypanothione system. After Michael addition of the dithiol to the double bonds, resulting in an elongated polymer, the latter-upon S-oxidation, followed by syn-eliminations-fragments, under continuous release of reactive oxygen species and sulfenic/sulfonic species, causing the death of the trypanosomal parasites in the micromolar or submicromolar range with high selectivity indexes.
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Affiliation(s)
- Thibault Gendron
- UMR7042 Université de Strasbourg–CNRS–UHA, Laboratoire d’Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry, European School of Chemistry, Polymers and Materials (ECPM), 25 Rue Becquerel, F-67087 Strasbourg, France; (T.G.); (D.A.L.); (H.K.)
| | - Don Antoine Lanfranchi
- UMR7042 Université de Strasbourg–CNRS–UHA, Laboratoire d’Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry, European School of Chemistry, Polymers and Materials (ECPM), 25 Rue Becquerel, F-67087 Strasbourg, France; (T.G.); (D.A.L.); (H.K.)
| | - Nicole I. Wenzel
- Bioorganic & Medicinal Chemistry Laboratory, Biochemie-Zentrum, Heidelberg University, Im Neuenheimer Feld 504, D-69120 Heidelberg, Germany; (N.I.W.)
| | - Hripsimée Kessedjian
- UMR7042 Université de Strasbourg–CNRS–UHA, Laboratoire d’Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry, European School of Chemistry, Polymers and Materials (ECPM), 25 Rue Becquerel, F-67087 Strasbourg, France; (T.G.); (D.A.L.); (H.K.)
| | - Beate Jannack
- Bioorganic & Medicinal Chemistry Laboratory, Biochemie-Zentrum, Heidelberg University, Im Neuenheimer Feld 504, D-69120 Heidelberg, Germany; (N.I.W.)
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium;
| | - Sandrine Cojean
- Antiparasitic Chemotherapy, Faculty of Pharmacy, BioCIS, UMR 8076 Université Paris-Saclay-CNRS 17, Rue des Sciences, F-91400 Orsay, France; (S.C.); (P.M.L.)
| | - Thomas J. J. Müller
- Institut für Organische Chemie und Makromolekulare Chemie, Mathematisch-Naturwissenschaftliche FakultätFakultät, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany;
| | - Philippe M. Loiseau
- Antiparasitic Chemotherapy, Faculty of Pharmacy, BioCIS, UMR 8076 Université Paris-Saclay-CNRS 17, Rue des Sciences, F-91400 Orsay, France; (S.C.); (P.M.L.)
| | - Elisabeth Davioud-Charvet
- UMR7042 Université de Strasbourg–CNRS–UHA, Laboratoire d’Innovation Moléculaire et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry, European School of Chemistry, Polymers and Materials (ECPM), 25 Rue Becquerel, F-67087 Strasbourg, France; (T.G.); (D.A.L.); (H.K.)
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Ramli AH, Swain P, Mohd Fahmi MSA, Abas F, Leong SW, Tejo BA, Shaari K, Ali AH, Agustar HK, Awang R, Ng YL, Lau YL, Md Razali MA, Mastuki SN, Mohmad Misnan N, Mohd Faudzi SM, Kim CH. Preliminary insight on diarylpentanoids as potential antimalarials: In silico, in vitro pLDH and in vivo zebrafish toxicity assessment. Heliyon 2024; 10:e27462. [PMID: 38495201 PMCID: PMC10943399 DOI: 10.1016/j.heliyon.2024.e27462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024] Open
Abstract
Malaria remains a major public health problem worldwide, including in Southeast Asia. Chemotherapeutic agents such as chloroquine (CQ) are effective, but problems with drug resistance and toxicity have necessitated a continuous search for new effective antimalarial agents. Here we report on a virtual screening of ∼300 diarylpentanoids and derivatives, in search of potential Plasmodium falciparum lactate dehydrogenase (PfLDH) inhibitors with acceptable drug-like properties. Several molecules with binding affinities comparable to CQ were chosen for in vitro validation of antimalarial efficacy. Among them, MS33A, MS33C and MS34C are the most promising against CQ-sensitive (3D7) with EC50 values of 1.6, 2.5 and 3.1 μM, respectively. Meanwhile, MS87 (EC50 of 1.85 μM) shown the most active against the CQ-resistant Gombak A strain, and MS33A and MS33C the most effective P. knowlesi inhibitors (EC50 of 3.6 and 5.1 μM, respectively). The in vitro cytotoxicity of selected diarylpentanoids (MS33A, MS33C, MS34C and MS87) was tested on Vero mammalian cells to evaluate parasite selectivity (SI), showing moderate to low cytotoxicity (CC50 > 82 μM). In addition, MS87 exhibited a high SI and the lowest resistance index (RI), suggesting that MS87 may exert effective parasite inhibition with low resistance potential in the CQ-resistant P. falciparum strain. Furthermore, the in vivo toxicity of the molecules on early embryonic development, the cardiovascular system, heart rate, motor activity and apoptosis were assessed in a zebrafish animal model. The overall results indicate the preliminary potential of diarylpentanoids, which need further investigation for their development as new antimalarial agents.
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Affiliation(s)
- Amirah Hani Ramli
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Puspanjali Swain
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea
| | - Muhammad Syafiq Akmal Mohd Fahmi
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Faridah Abas
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
- Department of Food Science, Faculty of Food Science & Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Sze Wei Leong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Bimo Ario Tejo
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Khozirah Shaari
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Amatul Hamizah Ali
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Hani Kartini Agustar
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Rusdam Awang
- UPM - MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yee Ling Ng
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Siti Nurulhuda Mastuki
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Norazlan Mohmad Misnan
- Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, 40170, Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Siti Munirah Mohd Faudzi
- Natural Medicines and Product Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea
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Ramli AH, Mohd Faudzi SM. Diarylpentanoids, the privileged scaffolds in antimalarial and anti-infectives drug discovery: A review. Arch Pharm (Weinheim) 2023; 356:e2300391. [PMID: 37806761 DOI: 10.1002/ardp.202300391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
Abstract
Asia is a hotspot for infectious diseases, including malaria, dengue fever, tuberculosis, and the pandemic COVID-19. Emerging infectious diseases have taken a heavy toll on public health and the economy and have been recognized as a major cause of morbidity and mortality, particularly in Southeast Asia. Infectious disease control is a major challenge, but many surveillance systems and control strategies have been developed and implemented. These include vector control, combination therapies, vaccine development, and the development of new anti-infectives. Numerous newly discovered agents with pharmacological anti-infective potential are being actively and extensively studied for their bioactivity, toxicity, selectivity, and mode of action, but many molecules lose their efficacy over time due to resistance developments. These facts justify the great importance of the search for new, effective, and safe anti-infectives. Diarylpentanoids, a curcumin derivative, have been developed as an alternative with better bioavailability and metabolism as a therapeutic agent. In this review, the mechanisms of action and potential targets of antimalarial drugs as well as the classes of antimalarial drugs are presented. The bioactivity of diarylpentanoids as a potential scaffold for a new class of anti-infectives and their structure-activity relationships are also discussed in detail.
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Affiliation(s)
- Amirah H Ramli
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Siti M Mohd Faudzi
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Malaysia
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4
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Ledoux A, Hamann C, Bonnet O, Jullien K, Quetin-Leclercq J, Tchinda A, Smadja J, Gauvin-Bialecki A, Maquoi E, Frédérich M. Bioactive Clerodane Diterpenoids from the Leaves of Casearia coriacea Vent. Molecules 2023; 28:molecules28031197. [PMID: 36770864 PMCID: PMC9918898 DOI: 10.3390/molecules28031197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
Casearia coriacea Vent., an endemic plant from the Mascarene Islands, was investigated following its antiplasmodial potentialities highlighted during a previous screening. Three clerodane diterpene compounds were isolated and identified as being responsible for the antiplasmodial activity of the leaves of the plant: caseamembrin T (1), corybulosin I (2), and isocaseamembrin E (3), which exhibited half maximal inhibitory concentrations (IC50) of 0.25 to 0.51 µg/mL. These compounds were tested on two other parasites, Leishmania mexicana mexicana and Trypanosoma brucei brucei, to identify possible selectivity in one of them. Although these products possess both antileishmanial and antitrypanosomal properties, they displayed selectivity for the malaria parasite, with a selectivity index between 6 and 12 regarding antitrypanosomal activity and between 25 and 100 regarding antileishmanial activity. These compounds were tested on three cell lines, breast cancer cells MDA-MB-231, pulmonary adenocarcinoma cells A549, and pancreatic carcinoma cells PANC-1, to evaluate their selectivity towards Plasmodium. This has not enabled us to establish selectivity for Plasmodium, but has revealed the promising activity of compounds 1-3 (IC50 < 2 µg/mL), particularly against pancreatic carcinoma cells (IC50 < 1 µg/mL). The toxicity of the main compound, caseamembrin T (1), was then evaluated on zebrafish embryos to extend our cytotoxicity study to normal, non-cancerous cells. This highlighted the non-negligible toxicity of caseamembrin T (1).
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Affiliation(s)
- Allison Ledoux
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines, CIRM, University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium
- Correspondence: ; Tel.: +32-4366-43-90
| | - Carla Hamann
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines, CIRM, University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium
- Laboratory of Biology of Tumor and Development, GIGA/CIRM, University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium
| | - Olivier Bonnet
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines, CIRM, University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium
| | - Kateline Jullien
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines, CIRM, University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium
| | - Joëlle Quetin-Leclercq
- Pharmacognosy Research Group, Louvain Drug Research Institute, LDRI, Université Catholique de Louvain, UCLouvain, Avenue E. Mounier, B1 72.03, B-1200 Brussels, Belgium
| | - Alembert Tchinda
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines, CIRM, University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium
| | - Jacqueline Smadja
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments, Université de Réunion, Avenue René Cassin 15, BP 7151, 97715 Saint-Denis, La Réunion, France
| | - Anne Gauvin-Bialecki
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments, Université de Réunion, Avenue René Cassin 15, BP 7151, 97715 Saint-Denis, La Réunion, France
| | - Erik Maquoi
- Laboratory of Biology of Tumor and Development, GIGA/CIRM, University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium
| | - Michel Frédérich
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines, CIRM, University of Liège, Avenue Hippocrate 15, 4000 Liège, Belgium
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5
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Sinha K, Ghosh J, Sil PC. Machine Learning in Drug Metabolism Study. Curr Drug Metab 2022; 23:CDM-EPUB-128463. [PMID: 36578255 DOI: 10.2174/1389200224666221227094144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 12/30/2022]
Abstract
Metabolic reactions in the body transform the administered drug into metabolites. These metabolites exhibit diverse biological activities. Drug metabolism is the major underlying cause of drug overdose-related toxicity, adversative drug effects and the drug's reduced efficacy. Though metabolic reactions deactivate a drug, drug metabolites are often considered pivotal agents for off-target effects or toxicity. On the other side, in combination drug therapy, one drug may influence another drug's metabolism and clearance and is thus considered one of the primary causes of drug-drug interactions. Today with the advancement of machine learning, the metabolic fate of a drug candidate can be comprehensively studied throughout the drug development procedure. Naïve Bayes, Logistic Regression, k-Nearest Neighbours, Decision Trees, different Boosting and Ensemble methods, Support Vector Machines and Artificial Neural Network boosted Deep Learning are some machine learning algorithms which are being extensively used in such studies. Such tools are covering several attributes of drug metabolism, with an emphasis on the prediction of drug-drug interactions, drug-target-interactions, clinical drug responses, metabolite predictions, sites of metabolism, etc. These reports are crucial for evaluating metabolic stability and predicting prospective drug-drug interactions, and can help pharmaceutical companies accelerate the drug development process in a less resource-demanding manner than what in vitro studies offer. It could also help medical practitioners to use combinatorial drug therapy in a more resourceful manner. Also, with the help of the enormous growth of deep learning, traditional fields of computational drug development like molecular interaction fields, molecular docking, quantitative structure-to-activity relationship (QSAR) studies and quantum mechanical simulations are producing results which were unimaginable couple of years back. This review provides a glimpse of a few contextually relevant machine learning algorithms and then focuses on their outcomes in different studies.
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Affiliation(s)
| | | | - Parames C Sil
- Division of Molecular Medicine, Bose Institute, Kolkata-700054
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WU JN, TU QK, XIANG XL, SHI QX, CHEN GY, DAI MX, ZHANG LJ, YANG M, SONG CW, HUANG RZ, JIN SN. Changes in curcuminoids between crude and processed turmeric based on UPLC-QTOF-MS/MS combining with multivariate statistical analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Oguike OE, Ugwuishiwu CH, Asogwa CN, Nnadi CO, Obonga WO, Attama AA. Systematic review on the application of machine learning to quantitative structure-activity relationship modeling against Plasmodium falciparum. Mol Divers 2022; 26:3447-3462. [PMID: 35064444 PMCID: PMC8782692 DOI: 10.1007/s11030-022-10380-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Abstract
Malaria accounts for over two million deaths globally. To flatten this curve, there is a need to develop new and high potent drugs against Plasmodium falciparum. Some major challenges include the dearth of suitable animal models for anti-P. falciparum assays, resistance to first-line drugs, lack of vaccines and the complex life cycle of Plasmodium. Gladly, newer approaches to antimalarial drug discovery have emerged due to the release of large datasets by pharmaceutical companies. This review provides insights into these new approaches to drug discovery covering different machine learning tools, which enhance the development of new compounds. It provides a systematic review on the use and prospects of machine learning in predicting, classifying and clustering IC50 values of bioactive compounds against P. falciparum. The authors identified many machine learning tools yet to be applied for this purpose. However, Random Forest and Support Vector Machines have been extensively applied though on a limited dataset of compounds.
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Affiliation(s)
- Osondu Everestus Oguike
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Department of Computer Science, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Chikodili Helen Ugwuishiwu
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Department of Computer Science, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Caroline Ngozi Asogwa
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Department of Computer Science, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Charles Okeke Nnadi
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria. .,Deprtment of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.
| | - Wilfred Ofem Obonga
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Deprtment of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Anthony Amaechi Attama
- Machine Learning Research Group, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria.,Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
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Carracedo-Reboredo P, Liñares-Blanco J, Rodríguez-Fernández N, Cedrón F, Novoa FJ, Carballal A, Maojo V, Pazos A, Fernandez-Lozano C. A review on machine learning approaches and trends in drug discovery. Comput Struct Biotechnol J 2021; 19:4538-4558. [PMID: 34471498 PMCID: PMC8387781 DOI: 10.1016/j.csbj.2021.08.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 12/30/2022] Open
Abstract
Drug discovery aims at finding new compounds with specific chemical properties for the treatment of diseases. In the last years, the approach used in this search presents an important component in computer science with the skyrocketing of machine learning techniques due to its democratization. With the objectives set by the Precision Medicine initiative and the new challenges generated, it is necessary to establish robust, standard and reproducible computational methodologies to achieve the objectives set. Currently, predictive models based on Machine Learning have gained great importance in the step prior to preclinical studies. This stage manages to drastically reduce costs and research times in the discovery of new drugs. This review article focuses on how these new methodologies are being used in recent years of research. Analyzing the state of the art in this field will give us an idea of where cheminformatics will be developed in the short term, the limitations it presents and the positive results it has achieved. This review will focus mainly on the methods used to model the molecular data, as well as the biological problems addressed and the Machine Learning algorithms used for drug discovery in recent years.
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Key Words
- ADMET, Absorption, distribution, metabolism, elimination and toxicity
- ADR, Adverse Drug Reaction
- AI, Artificial Intelligence
- ANN, Artificial Neural Networks
- APFP, Atom Pairs 2d FingerPrint
- AUC, Area under the Curve
- BBB, Blood–Brain barrier
- CDK, Chemical Development Kit
- CNN, Convolutional Neural Networks
- CNS, Central Nervous System
- CPI, Compound-protein interaction
- CV, Cross Validation
- Cheminformatics
- DL, Deep Learning
- DNA, Deoxyribonucleic acid
- Deep Learning
- Drug Discovery
- ECFP, Extended Connectivity Fingerprints
- FDA, Food and Drug Administration
- FNN, Fully Connected Neural Networks
- FP, Fringerprints
- FS, Feature Selection
- GCN, Graph Convolutional Networks
- GEO, Gene Expression Omnibus
- GNN, Graph Neural Networks
- GO, Gene Ontology
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MACCS, Molecular ACCess System
- MCC, Matthews correlation coefficient
- MD, Molecular Descriptors
- MKL, Multiple Kernel Learning
- ML, Machine Learning
- Machine Learning
- Molecular Descriptors
- NB, Naive Bayes
- OOB, Out of Bag
- PCA, Principal Component Analyisis
- QSAR
- QSAR, Quantitative structure–activity relationship
- RF, Random Forest
- RNA, Ribonucleic Acid
- SMILES, simplified molecular-input line-entry system
- SVM, Support Vector Machines
- TCGA, The Cancer Genome Atlas
- WHO, World Health Organization
- t-SNE, t-Distributed Stochastic Neighbor Embedding
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Affiliation(s)
- Paula Carracedo-Reboredo
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Jose Liñares-Blanco
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
| | - Nereida Rodríguez-Fernández
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
- Department of Computer Science and Information Technologies, Faculty of Communication Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Francisco Cedrón
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Francisco J. Novoa
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Adrian Carballal
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
- Department of Computer Science and Information Technologies, Faculty of Communication Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
| | - Victor Maojo
- Biomedical Informatics Group, Artificial Intelligence Department, Polytechnic University of Madrid, Calle de los Ciruelos, Boadilla del Monte, Madrid 28660, Spain
| | - Alejandro Pazos
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
- Grupo de Redes de Neuronas Artificiales y Sistemas Adaptativos. Imagen Médica y Diagnóstico Radiológico (RNASA-IMEDIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
| | - Carlos Fernandez-Lozano
- Department of Computer Science and Information Technologies, Faculty of Computer Science, Universidade da Coruna, Campus Elviña s/n, A Coruña 15071, Spain
- CITIC-Research Center of Information and Communication Technologies, Universidade da Coruna, A Coruña 15071, Spain
- Grupo de Redes de Neuronas Artificiales y Sistemas Adaptativos. Imagen Médica y Diagnóstico Radiológico (RNASA-IMEDIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, Instituto de Investigación Biomédica de A Coruña (INIBIC), A Coruña, Spain
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Winkler DA. Use of Artificial Intelligence and Machine Learning for Discovery of Drugs for Neglected Tropical Diseases. Front Chem 2021; 9:614073. [PMID: 33791277 PMCID: PMC8005575 DOI: 10.3389/fchem.2021.614073] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/18/2021] [Indexed: 12/11/2022] Open
Abstract
Neglected tropical diseases continue to create high levels of morbidity and mortality in a sizeable fraction of the world’s population, despite ongoing research into new treatments. Some of the most important technological developments that have accelerated drug discovery for diseases of affluent countries have not flowed down to neglected tropical disease drug discovery. Pharmaceutical development business models, cost of developing new drug treatments and subsequent costs to patients, and accessibility of technologies to scientists in most of the affected countries are some of the reasons for this low uptake and slow development relative to that for common diseases in developed countries. Computational methods are starting to make significant inroads into discovery of drugs for neglected tropical diseases due to the increasing availability of large databases that can be used to train ML models, increasing accuracy of these methods, lower entry barrier for researchers, and widespread availability of public domain machine learning codes. Here, the application of artificial intelligence, largely the subset called machine learning, to modelling and prediction of biological activities and discovery of new drugs for neglected tropical diseases is summarized. The pathways for the development of machine learning methods in the short to medium term and the use of other artificial intelligence methods for drug discovery is discussed. The current roadblocks to, and likely impacts of, synergistic new technological developments on the use of ML methods for neglected tropical disease drug discovery in the future are also discussed.
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Affiliation(s)
- David A Winkler
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia.,Latrobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia.,School of Pharmacy, University of Nottingham, Nottingham, United Kingdom.,CSIRO Data61, Pullenvale, QLD, Australia
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10
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Al Audhah N, Suhartono E, Sardjono TW, Fitri LE. Duration of Storage Reduced Erythrocytes Profiles and Plasmodium Viability in Donor Blood. J Blood Med 2021; 12:87-99. [PMID: 33654448 PMCID: PMC7910220 DOI: 10.2147/jbm.s276069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/11/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Malaria screening for blood derived from any donors prior to transfusions is a standard procedure that should be performed; but, in fact, it is not routinely conducted. In case of the blood is infected with Plasmodium spp., the survival of parasites may be depending on, or even influencing, the profile of red blood cells (RBCs). METHODS This observational longitudinal study was conducted upon 55 bags of donor blood that randomly selected. Malaria infections were detected using Rapid Diagnostic Test/RDT with thin and thick blood smear confirmation. The changes of Plasmodium spp. viability and RBCs profiles, as well as other hematological parameters, were observed from the results of routine hematological examinations which were performed on days 1,7,14 and 21 of storage. RESULTS Among 55 blood samples, there were 17 and 38 bags, respectively, positive and negative for malaria, then used for analysis as the case and control groups. There were significant decreasing values (p<0.05) of all routine blood examination parameters of donor blood, started from days 1, 7, 14, 21, and 28. There were no differences in decreasing profiles between those infected and non-infected donor blood (p>0.05). On days 21 and 28 none of the positive samples still contained parasites. CONCLUSION Erythrocytes profiles of donor blood significantly decreased with the duration of storage, but were not influenced by the presence of Plasmodium spp.
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Affiliation(s)
- Nelly Al Audhah
- Doctoral Program of Medical Science, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
- Department of Parasitology, Faculty of Medicine, Lambung Mangkurat University, Banjarmasin, Indonesia
| | - Eko Suhartono
- Department of Chemistry/Biochemistry, Faculty of Medicine, Lambung Mangkurat University, Banjarmasin, Indonesia
| | - Teguh Wahju Sardjono
- Department of Parasitology, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
| | - Loeki Enggar Fitri
- Department of Parasitology, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
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11
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Horvath D, Orlov A, Osolodkin DI, Ishmukhametov AA, Marcou G, Varnek A. A Chemographic Audit of anti-Coronavirus Structure-activity Information from Public Databases (ChEMBL). Mol Inform 2020; 39:e2000080. [PMID: 32363750 PMCID: PMC7267182 DOI: 10.1002/minf.202000080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 04/26/2020] [Indexed: 01/30/2023]
Abstract
Discovery of drugs against newly emerged pathogenic agents like the SARS-CoV-2 coronavirus (CoV) must be based on previous research against related species. Scientists need to get acquainted with and develop a global oversight over so-far tested molecules. Chemography (herein used Generative Topographic Mapping, in particular) places structures on a human-readable 2D map (obtained by dimensionality reduction of the chemical space of molecular descriptors) and is thus well suited for such an audit. The goal is to map medicinal chemistry efforts so far targeted against CoVs. This includes comparing libraries tested against various virus species/genera, predicting their polypharmacological profiles and highlighting often encountered chemotypes. Maps are challenged to provide predictive activity landscapes against viral proteins. Definition of "anti-CoV" map zones led to selection of therein residing 380 potential anti-CoV agents, out of a vast pool of 800 M organic compounds.
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Affiliation(s)
- Dragos Horvath
- Chemoinformatics LaboratoryUMR 7140 CNRS/University of Strasbourg4, rue Blaise Pascal67000Strasbourg
| | - Alexey Orlov
- Chemoinformatics LaboratoryUMR 7140 CNRS/University of Strasbourg4, rue Blaise Pascal67000Strasbourg
- FSBSI “Chumakov FSC R&D IBP RAS”Poselok Instituta Poliomielita 8 bd. 1Poselenie MoskovskyMoscow108819Russia
| | - Dmitry I. Osolodkin
- FSBSI “Chumakov FSC R&D IBP RAS”Poselok Instituta Poliomielita 8 bd. 1Poselenie MoskovskyMoscow108819Russia
- Institute of Translational Medicine and BiotechnologySechenov First Moscow State Medical UniversityTrubetskaya ul. 8Moscow119991Russia
| | - Aydar A. Ishmukhametov
- FSBSI “Chumakov FSC R&D IBP RAS”Poselok Instituta Poliomielita 8 bd. 1Poselenie MoskovskyMoscow108819Russia
- Institute of Translational Medicine and BiotechnologySechenov First Moscow State Medical UniversityTrubetskaya ul. 8Moscow119991Russia
| | - Gilles Marcou
- Chemoinformatics LaboratoryUMR 7140 CNRS/University of Strasbourg4, rue Blaise Pascal67000Strasbourg
| | - Alexandre Varnek
- Chemoinformatics LaboratoryUMR 7140 CNRS/University of Strasbourg4, rue Blaise Pascal67000Strasbourg
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12
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Liu Q, Deng J, Liu M. Classification models for predicting the antimalarial activity against Plasmodium falciparum. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:313-324. [PMID: 32191533 DOI: 10.1080/1062936x.2020.1740890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/07/2020] [Indexed: 06/10/2023]
Abstract
Support vector machine (SVM) and general regression neural network (GRNN) were used to develop classification models for predicting the antimalarial activity against Plasmodium falciparum. Only 15 molecular descriptors were used to build the classification models for the antimalarial activities of 4750 compounds, which were divided into a training set (3887 compounds) and a test set (863 compounds). For the SVM model, its prediction accuracies are 89.5% for the training set and 87.3% for the test set. For the GRNN model, the prediction accuracies for the two sets are 99.7% and 88.9%, respectively. Both SVC and GRNN models have better prediction ability than the classification model based on binary logistic regression (BLR) analysis. Compared with previously published classification models both SVC and GRNN models are satisfactory in predicting antimalarial activities of compounds with in addition of fewer descriptors.
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Affiliation(s)
- Q Liu
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Regeneration, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, China
| | - J Deng
- Hunan Provincial Key Laboratory of Environmental Catalysis & Waste Regeneration, College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, China
| | - M Liu
- School of Chemistry and Materials Engineering, Huizhou University, Huizhou, PR China
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13
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Schaduangrat N, Prachayasittikul V, Choomwattana S, Wongchitrat P, Phopin K, Suwanjang W, Malik AA, Vincent B, Nantasenamat C. Multidisciplinary approaches for targeting the secretase protein family as a therapeutic route for Alzheimer's disease. Med Res Rev 2019; 39:1730-1778. [PMID: 30628099 DOI: 10.1002/med.21563] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/21/2018] [Accepted: 12/24/2018] [Indexed: 12/27/2022]
Abstract
The continual increase of the aging population worldwide renders Alzheimer's disease (AD) a global prime concern. Several attempts have been focused on understanding the intricate complexity of the disease's development along with the on- andgoing search for novel therapeutic strategies. Incapability of existing AD drugs to effectively modulate the pathogenesis or to delay the progression of the disease leads to a shift in the paradigm of AD drug discovery. Efforts aimed at identifying AD drugs have mostly focused on the development of disease-modifying agents in which effects are believed to be long lasting. Of particular note, the secretase enzymes, a group of proteases responsible for the metabolism of the β-amyloid precursor protein (βAPP) and β-amyloid (Aβ) peptides production, have been underlined for their promising therapeutic potential. This review article attempts to comprehensively cover aspects related to the identification and use of drugs targeting the secretase enzymes. Particularly, the roles of secretases in the pathogenesis of AD and their therapeutic modulation are provided herein. Moreover, an overview of the drug development process and the contribution of computational (in silico) approaches for facilitating successful drug discovery are also highlighted along with examples of relevant computational works. Promising chemical scaffolds, inhibitors, and modulators against each class of secretases are also summarized herein. Additionally, multitarget secretase modulators are also taken into consideration in light of the current growing interest in the polypharmacology of complex diseases. Finally, challenging issues and future outlook relevant to the discovery of drugs targeting secretases are also discussed.
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Affiliation(s)
- Nalini Schaduangrat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Veda Prachayasittikul
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Saowapak Choomwattana
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Prapimpun Wongchitrat
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Kamonrat Phopin
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Wilasinee Suwanjang
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Aijaz Ahmad Malik
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Bruno Vincent
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.,Centre National de la Recherche Scientifique, Paris, France
| | - Chanin Nantasenamat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
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14
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Sidorov P, Davioud-Charvet E, Marcou G, Horvath D, Varnek A. AntiMalarial Mode of Action (AMMA) Database: Data Selection, Verification and Chemical Space Analysis. Mol Inform 2018; 37:e1800021. [DOI: 10.1002/minf.201800021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/14/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Pavel Sidorov
- Laboratoire de Chemoinformatique; UMR 7140 CNRS-Univ. Strasbourg; 1 rue Blaise Pascal Strasbourg 67000 France
| | - Elisabeth Davioud-Charvet
- Laboratoire d'Innovation Moléculaire et Applications (LIMA); UMR7042 CNRS-Unistra-UHA; Bioorganic and Medicinal Chemistry Team, European School of Chemistry, Polymers and Materials (ECPM); 25, rue Becquerel Strasbourg F-67087 France
| | - Gilles Marcou
- Laboratoire de Chemoinformatique; UMR 7140 CNRS-Univ. Strasbourg; 1 rue Blaise Pascal Strasbourg 67000 France
| | - Dragos Horvath
- Laboratoire de Chemoinformatique; UMR 7140 CNRS-Univ. Strasbourg; 1 rue Blaise Pascal Strasbourg 67000 France
| | - Alexandre Varnek
- Laboratoire de Chemoinformatique; UMR 7140 CNRS-Univ. Strasbourg; 1 rue Blaise Pascal Strasbourg 67000 France
- Laboratory of Chemoinformatics, Butlerov Institute of Chemistry; Kazan Federal University; Kazan Russia
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15
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Álvarez G, Perdomo C, Coronel C, Aguilera E, Varela J, Aparicio G, Zolessi FR, Cabrera N, Vega C, Rolón M, Rojas de Arias A, Pérez-Montfort R, Cerecetto H, González M. Multi-Anti-Parasitic Activity of Arylidene Ketones and Thiazolidene Hydrazines against Trypanosoma cruzi and Leishmania spp. Molecules 2017; 22:molecules22050709. [PMID: 28481276 PMCID: PMC6154605 DOI: 10.3390/molecules22050709] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/23/2017] [Accepted: 04/25/2017] [Indexed: 11/16/2022] Open
Abstract
A series of fifty arylideneketones and thiazolidenehydrazines was evaluated against Leishmania infantum and Leishmania braziliensis. Furthermore, new simplified thiazolidenehydrazine derivatives were evaluated against Trypanosoma cruzi. The cytotoxicity of the active compounds on non-infected fibroblasts or macrophages was established in vitro to evaluate the selectivity of their anti-parasitic effects. Seven thiazolidenehydrazine derivatives and ten arylideneketones had good activity against the three parasites. The IC50 values for T. cruzi and Leishmania spp. ranged from 90 nM-25 µM. Eight compounds had multi-trypanocidal activity against T. cruzi and Leishmania spp. (the etiological agents of cutaneous and visceral forms). The selectivity of these active compounds was better than the three reference drugs: benznidazole, glucantime and miltefosine. They also had low toxicity when tested in vivo on zebrafish. Trying to understand the mechanism of action of these compounds, two possible molecular targets were investigated: triosephosphate isomerase and cruzipain. We also used a molecular stripping approach to elucidate the minimal structural requirements for their anti-T. cruzi activity.
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Affiliation(s)
- Guzmán Álvarez
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, Ruta 3 (km 363), Paysandú, C.P. 60000, Uruguay.
| | - Cintya Perdomo
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, Ruta 3 (km 363), Paysandú, C.P. 60000, Uruguay.
| | - Cathia Coronel
- Centro Para el Desarrollo de la Investigación Científica (CEDIC/FMB/Diaz Gill Medicina Laboratorial), Asunción, C.P. 1255, Paraguay.
| | - Elena Aguilera
- Grupo de Química Medicinal-Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, Montevideo, C.P. 11400, Uruguay.
| | - Javier Varela
- Grupo de Química Medicinal-Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, Montevideo, C.P. 11400, Uruguay.
| | - Gonzalo Aparicio
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, C.P. 11400, Uruguay.
- Cell Biology of Neural Development Laboratory, Institut Pasteur de Montevideo, Montevideo, C.P. 11400, Uruguay.
| | - Flavio R Zolessi
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, C.P. 11400, Uruguay.
- Cell Biology of Neural Development Laboratory, Institut Pasteur de Montevideo, Montevideo, C.P. 11400, Uruguay.
| | - Nallely Cabrera
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04510, Mexico.
| | - Celeste Vega
- Centro Para el Desarrollo de la Investigación Científica (CEDIC/FMB/Diaz Gill Medicina Laboratorial), Asunción, C.P. 1255, Paraguay.
| | - Miriam Rolón
- Centro Para el Desarrollo de la Investigación Científica (CEDIC/FMB/Diaz Gill Medicina Laboratorial), Asunción, C.P. 1255, Paraguay.
| | - Antonieta Rojas de Arias
- Centro Para el Desarrollo de la Investigación Científica (CEDIC/FMB/Diaz Gill Medicina Laboratorial), Asunción, C.P. 1255, Paraguay.
| | - Ruy Pérez-Montfort
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, C.P. 04510, Mexico.
| | - Hugo Cerecetto
- Grupo de Química Medicinal-Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, Montevideo, C.P. 11400, Uruguay.
| | - Mercedes González
- Grupo de Química Medicinal-Laboratorio de Química Orgánica, Facultad de Ciencias, Universidad de la República, Montevideo, C.P. 11400, Uruguay.
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16
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QSAR modeling and chemical space analysis of antimalarial compounds. J Comput Aided Mol Des 2017; 31:441-451. [PMID: 28374255 DOI: 10.1007/s10822-017-0019-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/18/2017] [Indexed: 10/19/2022]
Abstract
Generative topographic mapping (GTM) has been used to visualize and analyze the chemical space of antimalarial compounds as well as to build predictive models linking structure of molecules with their antimalarial activity. For this, a database, including ~3000 molecules tested in one or several of 17 anti-Plasmodium activity assessment protocols, has been compiled by assembling experimental data from in-house and ChEMBL databases. GTM classification models built on subsets corresponding to individual bioassays perform similarly to the earlier reported SVM models. Zones preferentially populated by active and inactive molecules, respectively, clearly emerge in the class landscapes supported by the GTM model. Their analysis resulted in identification of privileged structural motifs of potential antimalarial compounds. Projection of marketed antimalarial drugs on this map allowed us to delineate several areas in the chemical space corresponding to different mechanisms of antimalarial activity. This helped us to make a suggestion about the mode of action of the molecules populating these zones.
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