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Kagami LP, Gonçalves IL, da Silva ÁC, Silva AC, das Neves GM, Göethel G, Spillere A, Dos Santos MR, Figueiró F, Garcia SC, Ávila DS, Battastini AMO, Eifler-Lima VL. LaSOM 335, active against bladder cancer cells, interferes with Let-60 (hRas) and reduces CD73 expression/activity. Chem Biol Drug Des 2023; 102:536-546. [PMID: 37272688 DOI: 10.1111/cbdd.14273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/04/2023] [Accepted: 05/08/2023] [Indexed: 06/06/2023]
Abstract
Bladder cancer is the fourth most common malignancy in men. It can present along the entire continuum of severity, from mild to well-differentiated disease to extremely malignant tumors with low survival rates. Human RAS genes are the most frequently mutated oncogenes in human cancers, and the critical role of aberrant Ras protein function in carcinogenesis is well established. Therefore, considerable efforts have been devoted to the development of anti-Ras inhibitors for cancer treatment. This study presents the biphenyl dihydropyrimidinone LaSOM 335 with high activity against T24 bladder cancer cells (IC50 = 10.73 ± 0.53 μM) and selectivity of cytotoxicity for this cancer cell line compared to two non-cancer cell lines investigated. Furthermore, we also show that this compound reduced vulvar development in the mutant let-60 gene of Caenorhabditis elegans. Let-60 is a homolog of the mammalian Ras gene. In addition, we observed that LaSOM 335 inhibits the enzymatic activity of CD73 and decreases CD73 expression. Possibly, this expression decrease is due to downstream EGFR signaling via the Ras-Raf-ERK pathway, that directly regulates CD73 expression via ERK1/2. Evidence suggests that non-immunomodulating functions of CD73 play an equally important role for cancer cell survival, progression, and migration. Regarding we also notice that LaSOM 335 was safe in the in vivo model of C. elegans. The set of these findings makes this biphenyl dihydropyrimidinone a promising candidate for further investigations in the bladder cancer field.
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Affiliation(s)
- Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal - LaSOM®, Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Itamar Luís Gonçalves
- Laboratório de Síntese Orgânica Medicinal - LaSOM®, Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Faculdade de Medicina, Universidade Regional Integrada do Alto Uruguai e das Missões-URI, Erechim, Brazil
| | - Álisson Coldebella da Silva
- Departamento de Bioquímica, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Aline Castro Silva
- Graduation Program in Biochemistry, Laboratory of Biochemistry and Toxicology in Caenorhabditis elegans, Federal University of Pampa, Uruguaiana, Brazil
| | - Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal - LaSOM®, Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Gabriela Göethel
- Laboratório de Síntese Orgânica Medicinal - LaSOM®, Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriano Spillere
- Laboratório de Síntese Orgânica Medicinal - LaSOM®, Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maitê Roxo Dos Santos
- Laboratório de Síntese Orgânica Medicinal - LaSOM®, Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fabrício Figueiró
- Departamento de Bioquímica, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Solange Cristina Garcia
- Laboratory of Toxicology (LATOX), Department of Analyses, Programa de Pós-Graduação em Ciências Farmacêuticas, Faculty of Pharmacy, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Daiana Silva Ávila
- Graduation Program in Biochemistry, Laboratory of Biochemistry and Toxicology in Caenorhabditis elegans, Federal University of Pampa, Uruguaiana, Brazil
| | - Ana Maria Oliveira Battastini
- Departamento de Bioquímica, Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal - LaSOM®, Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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das Neves GM, Kagami LP, Battastini AMO, Figueiró F, Eifler-Lima VL. Targeting ecto-5'-nucleotidase: A comprehensive review into small molecule inhibitors and expression modulators. Eur J Med Chem 2023; 247:115052. [PMID: 36599229 DOI: 10.1016/j.ejmech.2022.115052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/11/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023]
Abstract
The purinergic signaling has drawn attention from academia and more recently from pharmaceutical industries as a potential therapeutic route for cancer treatment, since ATP may act as chemotactic agent and possess in vitro antineoplastic activity. On the other way, adenosine, produced in extracellular medium by ecto-5'-NT, acts as immunosuppressor and is related to neoangiogenesis, vasculogenesis and evasion to the immune system. Consequently, inhibitors of ecto-5'-NT may prevent tumor progression, reducing adenosine concentrations, preventing escape from the host's immune system and slowing cancer's growth. This review aims to highlight important biochemical and structural features of ecto-5'NT, highlight its expression profile in normal and cancer cell lines detailing compounds which may act as expression regulators and to review the several classes of ecto-5'NT inhibitors developed in the past 12 years, in order to build a general structure-activity relationship model to guide further compound design.
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Affiliation(s)
- Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal (LaSOM), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal (LaSOM), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana Maria Oliveira Battastini
- Laboratório de Imunobioquímica do Câncer (LIBC), Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Fabrício Figueiró
- Laboratório de Imunobioquímica do Câncer (LIBC), Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal (LaSOM), Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Gonçalves IL, das Neves GM, Kagami LP, Gonçalves GA, Davi L, Eifler-Lima VL. Exploring the N1 Position of Biginelli Compounds: New Insights and Trends for Chemical Diversity Generation of Bioactive Derivatives. Mini Rev Med Chem 2021; 22:1545-1558. [PMID: 34711161 DOI: 10.2174/1389557521666211027105534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/13/2021] [Accepted: 08/05/2021] [Indexed: 11/22/2022]
Abstract
Dihydropyrimidinones (DHPMs) are heterocycles obtained by the multicomponent Biginelli reaction. Recently, new synthetic protocols have allowed us to explore functionalisation at less explored positions of DHPMs, such as the N1 position. In this context, we have performed a full literature survey of N1-substituted DHPMs. We analysed 27 papers and identified 379 compounds with substituents at the N1 position, most of them with alkyl groups, and of 28% with aromatic substituents attached at the N1 position. N1-substituted DHPMs are explored mainly due to their effects on cancer cell proliferation via numerous targets, such as kinesin Eg5, heat shock protein 70, heat shock protein 90 and the epidermal growth factor receptor. Similarity analyses were performed using the data of 379 DHPMs from different cheminformatic approaches, i.e. chemical property correlations, principal component analysis, similarity networks and compound clustering.
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Affiliation(s)
- Itamar Luís Gonçalves
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Guilherme Arraché Gonçalves
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Leonardo Davi
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
| | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre - RS, 90610-000. Brazil
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Kagami LP, Orlando G, Raimondi D, Ancien F, Dixit B, Gavaldá-García J, Ramasamy P, Roca-Martínez J, Tzavella K, Vranken W. b2bTools: online predictions for protein biophysical features and their conservation. Nucleic Acids Res 2021; 49:W52-W59. [PMID: 34057475 PMCID: PMC8262692 DOI: 10.1093/nar/gkab425] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/21/2021] [Accepted: 05/05/2021] [Indexed: 11/13/2022] Open
Abstract
We provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches. Upload of a FASTA file or text input of a sequence provides integrated predictions from DynaMine backbone and side-chain dynamics, conformational propensities, and derived EFoldMine early folding, DisoMine disorder, and Agmata β-sheet aggregation. These predictions, several of which were previously not available online, capture 'emergent' properties of proteins, i.e. the inherent biophysical propensities encoded in their sequence, rather than context-dependent behaviour (e.g. final folded state). In addition, upload of a multiple sequence alignment (MSA) in a variety of formats enables exploration of the biophysical variation observed in homologous proteins. The associated plots indicate the biophysical limits of functionally relevant protein behaviour, with unusual residues flagged by a Gaussian mixture model analysis. The prediction results are available as JSON or CSV files and directly accessible via an API. Online visualisation is available as interactive plots, with brief explanations and tutorial pages included. The server and API employ an email-free token-based system that can be used to anonymously access previously generated results.
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Affiliation(s)
- Luciano Porto Kagami
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
| | - Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
| | - Daniele Raimondi
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
| | - Francois Ancien
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
- 3Bio, Université Libre de Bruxelles, Brussels 1050, Belgium
| | - Bhawna Dixit
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
- VIB Structural Biology Research Centre, Brussels, 1050, Belgium
| | - Jose Gavaldá-García
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
- VIB Structural Biology Research Centre, Brussels, 1050, Belgium
| | - Pathmanaban Ramasamy
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
- VIB Structural Biology Research Centre, Brussels, 1050, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9000, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, 9000, Belgium
| | - Joel Roca-Martínez
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
- VIB Structural Biology Research Centre, Brussels, 1050, Belgium
| | - Konstantina Tzavella
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
- VIB Structural Biology Research Centre, Brussels, 1050, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
- VIB Structural Biology Research Centre, Brussels, 1050, Belgium
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Gonçalves IL, Machado das Neves G, Porto Kagami L, Eifler-Lima VL, Merlo AA. Discovery, development, chemical diversity and design of isoxazoline-based insecticides. Bioorg Med Chem 2020; 30:115934. [PMID: 33360575 DOI: 10.1016/j.bmc.2020.115934] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/09/2020] [Accepted: 12/03/2020] [Indexed: 12/29/2022]
Abstract
Isoxazoline is a 5-membered heterocycle present in the active compounds of many commercial veterinary anti-ectoparasitic products. The molecular target of isoxazolines is the inhibition of GABA-gated chloride channels in insects. These facts have inspired the use of the isoxazoline scaffold in the design of novel insecticide compounds. The main strategies used for isoxazoline synthesis are either the 1,3-dipolar cycloaddition between a nitrile oxide and an alkene or the reaction between hydroxylamine and an α,β-unsaturated carbonyl compound. This review highlights the utilization of isoxazoline as insecticide: its mode of action, its commercial preparations and its consideration in the design of novel insecticides. Similarity analyses were performed with 235 isoxazoline derivatives in three different cheminformatic approaches - chemical property correlations, similarity network and compound clustering. The cheminformatic methodologies are interesting tools to use in evaluating the similarity between commercial isoxazolines and to clarify the main features explored within their derivatives.
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Affiliation(s)
- Itamar Luís Gonçalves
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre-RS 90610-000, Brazil
| | - Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre-RS 90610-000, Brazil
| | - Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre-RS 90610-000, Brazil
| | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752, Porto Alegre-RS 90610-000, Brazil
| | - Aloir Antonio Merlo
- Institute of Chemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501970 RS, Brazil.
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Gonçalves IL, Davi L, Machado das Neves G, Porto Kagami L, Garcia SC, Oliveira Battastini AM, Figueiró F, Faria Santos Canto R, Merlo AA, Eifler‐Lima VL. Atropisomerism in
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1‐aryl Substituted 3,4‐dihydropyrimidin‐2(1H)‐thiones. ChemistrySelect 2020. [DOI: 10.1002/slct.202003229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Itamar L. Gonçalves
- Laboratório de Síntese Orgânica Medicinal-LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752 Porto Alegre-RS 90610-000 Brazil
| | - Leonardo Davi
- Laboratório de Síntese Orgânica Medicinal-LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752 Porto Alegre-RS 90610-000 Brazil
| | - Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal-LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752 Porto Alegre-RS 90610-000 Brazil
| | - Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal-LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752 Porto Alegre-RS 90610-000 Brazil
| | - Solange C. Garcia
- Laboratório de Toxicologia-LATOX, Programa de Pós-Graduação em Ciências Farmacêuticas Universidade Federal do Rio Grande do Sul Rua São Luís 150, Porto Alegre-RS 90610-000 Brazil
| | - Ana M. Oliveira Battastini
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2600 Porto Alegre-RS 90610-000 Brazil
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde Universidade Federal do Rio Grande do Sul Rua Ramiro Barcelos 2600 Porto Alegre-RS, 90610–000 Brazil
| | - Fabrício Figueiró
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2600 Porto Alegre-RS 90610-000 Brazil
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde Universidade Federal do Rio Grande do Sul Rua Ramiro Barcelos 2600 Porto Alegre-RS, 90610–000 Brazil
| | - Rômulo Faria Santos Canto
- Laboratório de Síntese Orgânica Medicinal-LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752 Porto Alegre-RS 90610-000 Brazil
- Laboratório de Química Medicinal de Compostos de Selênio/QMCSe Universidade Federal de Ciências da Saúde de Porto Alegre Porto Alegre/RS Brazil
| | - Aloir A. Merlo
- Institute of Chemistry Universidade Federal do Rio Grande do Sul Porto Alegre 91501970 RS Brazil
| | - Vera L. Eifler‐Lima
- Laboratório de Síntese Orgânica Medicinal-LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752 Porto Alegre-RS 90610-000 Brazil
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Gonçalves GA, Spillere AR, das Neves GM, Kagami LP, von Poser GL, Canto RFS, Eifler-Lima V. Natural and synthetic coumarins as antileishmanial agents: A review. Eur J Med Chem 2020; 203:112514. [DOI: 10.1016/j.ejmech.2020.112514] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/18/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022]
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Orlando G, Raimondi D, Kagami LP, Vranken WF. ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values. Nucleic Acids Res 2020; 48:W36-W40. [PMID: 32459331 PMCID: PMC7319548 DOI: 10.1093/nar/gkaa391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy data provides valuable information on the behaviour of proteins in solution. The primary data to determine when studying proteins are the per-atom NMR chemical shifts, which reflect the local environment of atoms and provide insights into amino acid residue dynamics and conformation. Within an amino acid residue, chemical shifts present multi-dimensional and complexly cross-correlated information, making them difficult to analyse. The ShiftCrypt method, based on neural network auto-encoder architecture, compresses the per-amino acid chemical shift information in a single, interpretable, amino acid-type independent value that reflects the biophysical state of a residue. We here present the ShiftCrypt web server, which makes the method readily available. The server accepts chemical shifts input files in the NMR Exchange Format (NEF) or NMR-STAR format, executes ShiftCrypt and visualises the results, which are also accessible via an API. It also enables the ”biophysically-based” pairwise alignment of two proteins based on their ShiftCrypt values. This approach uses Dynamic Time Warping and can optionally include their amino acid code information, and has applications in, for example, the alignment of disordered regions. The server uses a token-based system to ensure the anonymity of the users and results. The web server is available at www.bio2byte.be/shiftcrypt.
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Affiliation(s)
- Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, Brussels 1050, Belgium.,Switch Laboratory, VIB, Leuven, Belgium
| | - Daniele Raimondi
- ESAT-STADIUS, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | - Luciano Porto Kagami
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, Brussels 1050, Belgium
| | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, Brussels 1050, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium.,VIB Structural Biology Research Centre, Pleinlaan 2, Brussels 1050, Belgium
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Vendruscolo MH, das Neves GM, Kagami LP, Rodrigues Junior LC, Nunes Diehl ML, Gnoatto SCB, de Loreto Bordignon SA, Romão PRT, Eifler-Lima VL, von Poser GL. In vitro and in silico Activity of Iridoids Against Leishmania amazonensis. Curr Drug Discov Technol 2020; 16:173-183. [PMID: 28969568 DOI: 10.2174/1570163814666171002102058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/18/2017] [Accepted: 09/18/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND Leishmaniasis reaches millions of people around the world. The control of the disease is difficult due to the restricted access to the diagnosis and medication, and low adherence to the treatment. Thus, more efficient drugs are needed and natural products are good alternatives. Iridoids, natural products with reported leishmanicidal activity, can be exploited for the development of anti- Leishmania drugs. The aim of this study was to isolate and to investigate the in vitro activity of iridoids against Leishmania amazonensis and to compare the activity in silico of these compounds with those reported as active against this parasite. METHODS Iridoids were isolated by chromatographic methods. The in vitro activity of asperuloside (1) and geniposide (2) from Escalonia bifida, galiridoside (3) from Angelonia integerrima and theveridoside (4) and ipolamiide (5) from Amphilophium crucigerum was investigated against promastigote forms of Leishmania amazonensis. Molecular modeling studies of 1-5 and iridoids cited as active against Leishmania spp. were performed. RESULTS Compounds 1-5 (5-100 µM) did not inhibit the parasite survival. Physicochemical parameters predicted for 1-5 did not show differences compared to those described in literature. The SAR and the pharmacophoric model confirmed the importance of maintaining the cyclopentane[C]pyran ring of the iridoid, of oxygen-linked substituents at the C1 and C6 positions and of bulky substituents attached to the iridoid ring to present leishmanicidal activity. CONCLUSION The results obtained in this study indicate that iridoids are a promising group of secondary metabolites and should be further investigated in the search for new anti-Leishmania drugs.
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Affiliation(s)
- Maria Helena Vendruscolo
- Post-graduate Program in Pharmaceutical Sciences, College of Pharmacy, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gustavo Machado das Neves
- Post-graduate Program in Pharmaceutical Sciences, College of Pharmacy, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciano Porto Kagami
- Post-graduate Program in Pharmaceutical Sciences, College of Pharmacy, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luiz Carlos Rodrigues Junior
- Post-Graduate Program in Health Sciences, Department of Basic Health Sciences, College of Pharmacy, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, Brazil
| | - Maria Luísa Nunes Diehl
- Post-graduate Program in Pharmaceutical Sciences, College of Pharmacy, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Simone Cristina Baggio Gnoatto
- Post-graduate Program in Pharmaceutical Sciences, College of Pharmacy, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Pedro Roosevelt Torres Romão
- Post-Graduate Program in Health Sciences, Department of Basic Health Sciences, College of Pharmacy, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, Brazil
| | - Vera Lucia Eifler-Lima
- Post-graduate Program in Pharmaceutical Sciences, College of Pharmacy, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gilsane Lino von Poser
- Post-graduate Program in Pharmaceutical Sciences, College of Pharmacy, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Kagami LP, das Neves GM, Timmers LFSM, Caceres RA, Eifler-Lima VL. Geo-Measures: A PyMOL plugin for protein structure ensembles analysis. Comput Biol Chem 2020; 87:107322. [PMID: 32604028 DOI: 10.1016/j.compbiolchem.2020.107322] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 01/15/2023]
Abstract
Although molecular dynamics encompasses several applications, studies focusing on biomolecular systems are central issues of this research area. Such simulations require the generation of trajectory files, which provide a path for the analysis and interpretation of results with biological significance. However, although several programs have been developed in Python language for the analyses of molecular dynamics (MD) trajectories, they usually require some knowledge of programming languages in order to write or run the scripts using command lines, which certainly hinders the access of MD simulations to many scientists with the necessary biological background to interpret their results. To ease the access to Python packages focusing on MD trajectory analyses, we built a user-friendly and easy-to-install graphical PyMOL interface. Geo-Measures integrates the PyMOL functionalities with MDTraj, a powerful library of trajectory analyses, allowing the users to access up to 14 different types of analyses. Two sample cases are reported here to demonstrate the use of Geo-Measures. In the first example, which involves the use a MD trajectory file of hemoglobin from the MoDEL MD bank, we exemplified the analyses of the following variables: root mean square deviation, radius of gyration, free energy landscape and principal component analysis. In the second case, we built a trajectory file for the ecto-5'-nucleotidase using the LiGRO program to study the carbon alpha pincer angles, to define the secondary structure of the proteins and to analyze the Modevectors. This user-friendly graphical PyMOL plugin, which can be used to generate several descriptive analyses for protein structures, is open source and can be downloaded at: https://pymolwiki.org/index.php/Geo_Measures_Plugin.
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Affiliation(s)
- Luciano Porto Kagami
- Laboratory of Medicinal Organic Synthesis (LaSOM), Faculty of Pharmacy, Federal University of Rio Grande do Sul, Ipiranga Avenue, n° 2752, Porto Alegre, RS, 90610-000, Brazil; Programa de Pós-gradução de Ciências da Saúde da Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Rua Sarmento Leite, n° 245, Porto Alegre, Rio Grande do Sul, 90050-170, Brazil.
| | - Gustavo Machado das Neves
- Laboratory of Medicinal Organic Synthesis (LaSOM), Faculty of Pharmacy, Federal University of Rio Grande do Sul, Ipiranga Avenue, n° 2752, Porto Alegre, RS, 90610-000, Brazil; Programa de Pós-gradução de Ciências da Saúde da Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Rua Sarmento Leite, n° 245, Porto Alegre, Rio Grande do Sul, 90050-170, Brazil
| | - Luís Fernando Saraiva Macedo Timmers
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Universidade do Vale do Taquari -Univates, Rua Avelino Talini, 171 - Bairro Universitário, Lajeado, RS, 95914-014, Brazil; Programa de Pós-gradução de Ciências da Saúde da Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Rua Sarmento Leite, n° 245, Porto Alegre, Rio Grande do Sul, 90050-170, Brazil.
| | - Rafael Andrade Caceres
- Programa de Pós-graduação de Biociências da Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Rua Sarmento Leite, n° 245, Porto Alegre, Rio Grande do Sul, 90050-170, Brazil; Programa de Pós-gradução de Ciências da Saúde da Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Rua Sarmento Leite, n° 245, Porto Alegre, Rio Grande do Sul, 90050-170, Brazil
| | - Vera Lucia Eifler-Lima
- Laboratory of Medicinal Organic Synthesis (LaSOM), Faculty of Pharmacy, Federal University of Rio Grande do Sul, Ipiranga Avenue, n° 2752, Porto Alegre, RS, 90610-000, Brazil; Programa de Pós-gradução de Ciências da Saúde da Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Rua Sarmento Leite, n° 245, Porto Alegre, Rio Grande do Sul, 90050-170, Brazil
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11
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Soares FGN, Göethel G, Kagami LP, das Neves GM, Sauer E, Birriel E, Varela J, Gonçalves IL, Von Poser G, González M, Kawano DF, Paula FR, de Melo EB, Garcia SC, Cerecetto H, Eifler-Lima VL. Novel coumarins active against Trypanosoma cruzi and toxicity assessment using the animal model Caenorhabditis elegans. BMC Pharmacol Toxicol 2019; 20:76. [PMID: 31852548 PMCID: PMC6921407 DOI: 10.1186/s40360-019-0357-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Chagas disease (CD) is a tropical parasitic disease. Although the number of people infected is very high, the only drugs available to treat CD, nifurtimox (Nfx) and benznidazole, are highly toxic, particularly in the chronic stage of the disease. Coumarins are a large class of compounds that display a wide range of interesting biological properties, such as antiparasitic. Hence, the aim of this work is to find a good antitrypanosomal drug with less toxicity. The use of simple organism models has become increasingly attractive for planning and simplifying efficient drug discovery. Within these models, Caenorhabditis elegans has emerged as a convenient and versatile tool with significant advantages for the toxicological potential identification for new compounds. METHODS Trypanocidal activity: Forty-two 4-methylamino-coumarins were assayed against the epimastigote form of Trypanosoma cruzi (Tulahuen 2 strain) by inhibitory concentration 50% (IC50). Toxicity assays: Lethal dose 50% (LD50) and Body Area were determined by Caenorhabditis elegans N2 strain (wild type) after acute exposure. Structure-activity relationship: A classificatory model was built using 3D descriptors. RESULTS Two of these coumarins demonstrated near equipotency to Nifurtimox (IC50 = 5.0 ± 1 μM), with values of: 11 h (LaSOM 266), (IC50 = 6.4 ± 1 μM) and 11 g (LaSOM 231), (IC50 = 8.2 ± 2.3 μM). In C. elegans it was possible to observe that Nfx showed greater toxicity in both the LD50 assay and the evaluation of the development of worms. It is possible to observe that the efficacy between Nfx and the synthesized compounds (11 h and 11 g) are similar. On the other hand, the toxicity of Nfx is approximately three times higher than that of the compounds. Results from the QSAR-3D study indicate that the volume and hydrophobicity of the substituents have a significant impact on the trypanocidal activities for derivatives that cause more than 50% of inhibition. These results show that the C. elegans model is efficient for screening potentially toxic compounds. CONCLUSION Two coumarins (11 h and 11 g) showed activity against T. cruzi epimastigote similar to Nifurtimox, however with lower toxicity in both LD50 and development of C. elegans assays. These two compounds may be a feasible starting point for the development of new trypanocidal drugs.
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Affiliation(s)
- Fabiana Gomes Nascimento Soares
- Laboratório de Síntese Orgânica Medicinal/LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gabriela Göethel
- Laboratório Toxicologia/LATOX, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal/LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal/LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Elisa Sauer
- Laboratório de Síntese Orgânica Medicinal/LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Estefania Birriel
- Facultad de Ciencias-Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Javier Varela
- Facultad de Ciencias-Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Itamar Luís Gonçalves
- Laboratório de Síntese Orgânica Medicinal/LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gilsane Von Poser
- Laboratório de Síntese Orgânica Medicinal/LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Mercedes González
- Facultad de Ciencias-Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Daniel Fábio Kawano
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Fávero Reisdorfer Paula
- Universidade Estadual do Oeste do Paraná, Centro de Ciências Médicas e Farmacêuticas, Cascavel, PR, Brazil
| | - Eduardo Borges de Melo
- Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Cascavel, PR, Brazil
| | - Solange Cristina Garcia
- Laboratório Toxicologia/LATOX, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Hugo Cerecetto
- Facultad de Ciencias-Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal/LaSOM, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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12
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Alves ACS, Dias RA, Kagami LP, das Neves GM, Torres FC, Eifler-Lima VL, Carvalho I, de Miranda Silva C, Kawano DF. Beyond the "Lock and Key" Paradigm: Targeting Lipid Rafts to Induce the Selective Apoptosis of Cancer Cells. Curr Med Chem 2018; 25:2082-2104. [PMID: 29332565 DOI: 10.2174/0929867325666180111100601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/28/2017] [Accepted: 01/05/2017] [Indexed: 11/22/2022]
Abstract
For more than 40 years, the fluid mosaic model of cellular membranes has supported our vision of an inert lipid bilayer containing membrane protein receptors that are randomly hit by extracellular molecules to trigger intracellular signaling events. However, the notion that compartmentalized cholesterol- and sphingomyelin-rich membrane microdomains (known as lipid rafts) spatially arrange receptors and effectors to promote kinetically favorable interactions necessary for the signal transduction sounds much more realistic. Despite their assumed importance for the dynamics of ligand-receptor interactions, lipid rafts and biomembranes as a whole remain less explored than the other classes of biomolecules because of the higher variability and complexity of their membrane phases, which rarely provide the detailed atomic-level structural data in X-ray crystallography assays necessary for molecular modeling studies. The fact that some alkylphospholipids (e.g. edelfosine: 1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine) selectively induce the apoptotic death of cancer cells by recruiting Fas death receptors and the downstream signaling molecules into clusters of lipid rafts suggests these potential drug targets deserve a more in-depth investigation. Herein, we review the structure of lipid rafts, their role in apoptotic signaling pathways and their potential role as drug targets for the treatment of cancer.
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Affiliation(s)
- Anna Carolina Schneider Alves
- Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Candido Portinari 200, 13083-871 Campinas-SP, Brazil
| | - Reinaldo Antonio Dias
- Institute of Chemistry, University of Campinas - UNICAMP, Rua Josue de Castro s/n, 13083-970 Campinas-SP, Brazil
| | - Luciano Porto Kagami
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Av. Ipiranga 2752, 90610-000 Porto Alegre-RS, Brazil
| | - Gustavo Machado das Neves
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Av. Ipiranga 2752, 90610-000 Porto Alegre-RS, Brazil
| | - Fernando Cidade Torres
- School of Pharmacy, UniRitter Laureate International Universities, Rua Orfanotrofio 55, 91849-440 Porto Alegre-RS, Brazil
| | - Vera Lucia Eifler-Lima
- Graduate Program in Pharmaceutical Sciences, Federal University of Rio Grande do Sul, Av. Ipiranga 2752, 90610-000 Porto Alegre-RS, Brazil
| | - Ivone Carvalho
- Faculty of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Av. do Cafe s/n, 14040- 903 Ribeirao Preto-SP, Brazil
| | | | - Daniel Fabio Kawano
- Faculty of Pharmaceutical Sciences, University of Campinas - UNICAMP, Rua Candido Portinari 200, 13083-871 Campinas-SP, Brazil.,Institute of Chemistry, University of Campinas - UNICAMP, Rua Josue de Castro s/n, 13083-970 Campinas-SP, Brazil
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13
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Gonçalves IL, Rockenbach L, das Neves GM, Göethel G, Nascimento F, Porto Kagami L, Figueiró F, Oliveira de Azambuja G, de Fraga Dias A, Amaro A, de Souza LM, da Rocha Pitta I, Avila DS, Kawano DF, Garcia SC, Battastini AMO, Eifler-Lima VL. Effect of N-1 arylation of monastrol on kinesin Eg5 inhibition in glioma cell lines. Medchemcomm 2018; 9:995-1010. [PMID: 30108989 DOI: 10.1039/c8md00095f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/14/2018] [Indexed: 01/08/2023]
Abstract
An original and focused library of two sets of dihydropyrimidin-2-thiones (DHPMs) substituted with N-1 aryl groups derived from monastrol was designed and synthesized in order to discover a more effective Eg5 ligand than the template. Based on molecular docking studies, four ligands were selected to perform pharmacological investigations against two glioma cell lines. The results led to the discovery of two original compounds, called 20h and 20e, with an anti-proliferative effects, achieving IC50 values of about half that of the IC50 of monastrol in both cell lines. As with monastrol, flow cytometry analyses showed that the 20e and 20h compounds induced cell cycle arrest in the G2/M phase, and immunocytochemistry essays revealed the formation of monopolar spindles due to Eg5 inhibition without any toxicity to Caenorhabditis elegans.
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Affiliation(s)
- Itamar Luís Gonçalves
- Laboratório de Síntese Orgânica Medicinal/LaSOM , Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Avenida Ipiranga , 2752 , Porto Alegre/RS , Brazil .
| | - Liliana Rockenbach
- Laboratório de Síntese Orgânica Medicinal/LaSOM , Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Avenida Ipiranga , 2752 , Porto Alegre/RS , Brazil .
| | - Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal/LaSOM , Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Avenida Ipiranga , 2752 , Porto Alegre/RS , Brazil .
| | - Gabriela Göethel
- Laboratório de Toxicologia - LATOX , Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Porto Alegre/RS , Brazil
| | - Fabiana Nascimento
- Laboratório de Síntese Orgânica Medicinal/LaSOM , Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Avenida Ipiranga , 2752 , Porto Alegre/RS , Brazil .
| | - Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal/LaSOM , Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Avenida Ipiranga , 2752 , Porto Alegre/RS , Brazil .
| | - Fabrício Figueiró
- Departamento de Bioquímica , ICBS , Universidade Federal do Rio Grande do Sul , Porto Alegre/RS , Brazil .
| | - Gabriel Oliveira de Azambuja
- Laboratório de Síntese Orgânica Medicinal/LaSOM , Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Avenida Ipiranga , 2752 , Porto Alegre/RS , Brazil .
| | - Amanda de Fraga Dias
- Departamento de Bioquímica , ICBS , Universidade Federal do Rio Grande do Sul , Porto Alegre/RS , Brazil .
| | - Andressa Amaro
- Departamento de Bioquímica , ICBS , Universidade Federal do Rio Grande do Sul , Porto Alegre/RS , Brazil .
| | - Lauro Mera de Souza
- Instituto de Pesquisa Pelé Pequeno Príncipe , Faculdades Pequeno Príncipe , Curitiba-PR , Brazil
| | - Ivan da Rocha Pitta
- Núcleo de Pesquisa em Inovação Terapêutica , Universidade Federal de Pernambuco , Recife/PE , Brazil
| | - Daiana Silva Avila
- Grupo de Pesquisa em Bioquímica e Toxicologia em Caenorhabditis elegans (GBToxCE) , Universidade Federal do Pampa-UNIPAMPA , Uruguaiana , RS , Brazil
| | - Daniel Fábio Kawano
- Faculdade de Ciências Farmacêuticas , Universidade Estadual de Campinas , Campinas-SP , Brazil
| | - Solange Cristina Garcia
- Laboratório de Toxicologia - LATOX , Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Porto Alegre/RS , Brazil
| | | | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal/LaSOM , Faculdade de Farmácia , Universidade Federal do Rio Grande do Sul , Avenida Ipiranga , 2752 , Porto Alegre/RS , Brazil .
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14
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Kagami LP, das Neves GM, da Silva AWS, Caceres RA, Kawano DF, Eifler-Lima VL. LiGRO: a graphical user interface for protein-ligand molecular dynamics. J Mol Model 2017; 23:304. [PMID: 28980073 DOI: 10.1007/s00894-017-3475-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/17/2017] [Indexed: 11/30/2022]
Abstract
To speed up the drug-discovery process, molecular dynamics (MD) calculations performed in GROMACS can be coupled to docking simulations for the post-screening analyses of large compound libraries. This requires generating the topology of the ligands in different software, some basic knowledge of Linux command lines, and a certain familiarity in handling the output files. LiGRO-the python-based graphical interface introduced here-was designed to overcome these protein-ligand parameterization challenges by allowing the graphical (non command line-based) control of GROMACS (MD and analysis), ACPYPE (ligand topology builder) and PLIP (protein-binder interactions monitor)-programs that can be used together to fully perform and analyze the outputs of complex MD simulations (including energy minimization and NVT/NPT equilibration). By allowing the calculation of linear interaction energies in a simple and quick fashion, LiGRO can be used in the drug-discovery pipeline to select compounds with a better protein-binding interaction profile. The design of LiGRO allows researchers to freely download and modify the software, with the source code being available under the terms of a GPLv3 license from http://www.ufrgs.br/lasomfarmacia/ligro/ .
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Affiliation(s)
- Luciano Porto Kagami
- Laboratory of Medicinal Organic Synthesis (LaSOM), Faculty of Pharmacy, Federal University of Rio Grande do Sul, Ipiranga Avenue, n° 2752, Porto Alegre, RS, 90610-000, Brazil.
| | - Gustavo Machado das Neves
- Laboratory of Medicinal Organic Synthesis (LaSOM), Faculty of Pharmacy, Federal University of Rio Grande do Sul, Ipiranga Avenue, n° 2752, Porto Alegre, RS, 90610-000, Brazil
| | - Alan Wilter Sousa da Silva
- Universal Protein Resource (UniProt), EMBL-EBI, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rafael Andrade Caceres
- Pharmacosciences Department of Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, Brazil.,Health Sciences Postgraduate Program of Federal University of Health Sciences of Porto Alegre (UFCSPA), Sarmento Leite Street, n° 245, 2nd Floor, room 200C, Porto Alegre City, Rio Grande do Sul State, Brazil
| | - Daniel Fábio Kawano
- Faculty of Pharmaceutical Sciences, University of Campinas (UNICAMP), Cândido Portinari Street, n° 200, Campinas, SP, 13083-871, Brazil.,Institute of Chemistry, University of Campinas (UNICAMP), Josué de Castro Street, Campinas, SP, 13083-970, Brazil
| | - Vera Lucia Eifler-Lima
- Laboratory of Medicinal Organic Synthesis (LaSOM), Faculty of Pharmacy, Federal University of Rio Grande do Sul, Ipiranga Avenue, n° 2752, Porto Alegre, RS, 90610-000, Brazil.
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15
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Kagami LP, das Neves GM, Rodrigues RP, da Silva VB, Eifler-Lima VL, Kawano DF. Identification of a novel putative inhibitor of the Plasmodium falciparum purine nucleoside phosphorylase: exploring the purine salvage pathway to design new antimalarial drugs. Mol Divers 2017; 21:677-695. [PMID: 28523625 DOI: 10.1007/s11030-017-9745-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 04/16/2017] [Indexed: 11/26/2022]
Abstract
Malaria, a tropical parasitic disease caused by Plasmodium spp., continues to place a heavy social burden, with almost 200 million cases and more than 580,000 deaths per year. Plasmodium falciparum purine nucleoside phosphorylase (PfPNP) can be targeted for antimalarial drug design since its inhibition kills malaria parasites both in vitro and in vivo. Although the currently known inhibitors of PfPNP, immucillins, are orally available and of low toxicity to animals and humans, to the best of our knowledge, none of these compounds has entered clinical trials for the treatment of malaria. Using a pharmacophore-based virtual screening coupled to a consensual molecular docking approach, we identified 59 potential PfPNP inhibitors that are predicted to be orally absorbed in a Caco-2 cell model. Although most of these compounds are predicted to have high plasma protein binding levels, poor water solubility (except for compound 25) and CYP3A4 metabolic stability (except for 4, 7 and 8), four structures (4, 7, 8 and 25) remain as potential leads because of their plausible interaction with a specific hydrophobic pocket of PfPNP, which would confer them higher selectivity for PfPNP over human PNP. Additionally, both predicted Gibbs free energies for binding and molecular dynamics suggest that compound 4 may form a more stable complex with PfPNP than 5[Formula: see text]-methylthio-immucillin-H, a potent and selective inhibitor of PfPNP.
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Affiliation(s)
- Luciano Porto Kagami
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga 2752, Porto Alegre, RS, 90610-000, Brazil
| | - Gustavo Machado das Neves
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga 2752, Porto Alegre, RS, 90610-000, Brazil
| | - Ricardo Pereira Rodrigues
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Vinicius Barreto da Silva
- Escola de Ciências Médicas, Farmacêuticas e Biomédicas, Pontifícia Universidade Católica de Goiás, Avenida Universitária no 1440, Goiânia, GO, 74605-010, Brazil
| | - Vera Lucia Eifler-Lima
- Laboratório de Síntese Orgânica Medicinal - LaSOM, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga 2752, Porto Alegre, RS, 90610-000, Brazil
| | - Daniel Fábio Kawano
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari 200, Campinas, SP, 13083-871, Brazil.
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual de Campinas, Rua Josué de Castro s/n, Campinas, SP, 13083-970, Brazil.
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