1
|
Nonato MC, van Raaij MJ, Agirre J. Beyond publishing: introducing Interviews with authors. Acta Crystallogr F Struct Biol Commun 2024; 80:73. [PMID: 38656225 PMCID: PMC11058510 DOI: 10.1107/s2053230x24003339] [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] [Indexed: 04/26/2024] Open
Abstract
To find out what lies behind the articles published in Acta Cryst. F - Structural Biology Communications the journal now publishes interviews with its authors.
Collapse
Affiliation(s)
- Maria Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Mark J. van Raaij
- Centro Nacional de Biotecnologia – CSIC, calle Darwin 3, 28049, Madrid, Spain
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, North Yorkshire YO10 5DD, United Kingdom
| |
Collapse
|
2
|
Nonato MC. Shaping the future of Acta Crystallographica F: unveiling our vision. Acta Crystallogr F Struct Biol Commun 2023; 79:294. [PMID: 38108884 PMCID: PMC10833121 DOI: 10.1107/s2053230x2301052x] [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] [Indexed: 12/19/2023] Open
Abstract
One of the Editors of Acta Cryst. F - Structural Biology Communications describes what the future holds for the journal.
Collapse
Affiliation(s)
- Maria Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
3
|
Menozzi CAC, França RRF, Luccas PH, Baptista MDS, Fernandes TVA, Hoelz LVB, Sales Junior PA, Murta SMF, Romanha A, Galvão BVD, Macedo MDO, Goldstein ADC, Araujo-Lima CF, Felzenszwalb I, Nonato MC, Castelo-Branco FS, Boechat N. Anti- Trypanosoma cruzi Activity, Mutagenicity, Hepatocytotoxicity and Nitroreductase Enzyme Evaluation of 3-Nitrotriazole, 2-Nitroimidazole and Triazole Derivatives. Molecules 2023; 28:7461. [PMID: 38005183 PMCID: PMC10672842 DOI: 10.3390/molecules28227461] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Chagas disease (CD), which is caused by Trypanosoma cruzi and was discovered more than 100 years ago, remains the leading cause of death from parasitic diseases in the Americas. As a curative treatment is only available for the acute phase of CD, the search for new therapeutic options is urgent. In this study, nitroazole and azole compounds were synthesized and underwent molecular modeling, anti-T. cruzi evaluations and nitroreductase enzymatic assays. The compounds were designed as possible inhibitors of ergosterol biosynthesis and/or as substrates of nitroreductase enzymes. The in vitro evaluation against T. cruzi clearly showed that nitrotriazole compounds are significantly more potent than nitroimidazoles and triazoles. When their carbonyls were reduced to hydroxyl groups, the compounds showed a significant increase in activity. In addition, these substances showed potential for action via nitroreductase activation, as the substances were metabolized at higher rates than benznidazole (BZN), a reference drug against CD. Among the compounds, 1-(2,4-difluorophenyl)-2-(3-nitro-1H-1,2,4-triazol-1-yl)ethanol (8) is the most potent and selective of the series, with an IC50 of 0.39 µM and selectivity index of 3077; compared to BZN, 8 is 4-fold more potent and 2-fold more selective. Moreover, this compound was not mutagenic at any of the concentrations evaluated, exhibited a favorable in silico ADMET profile and showed a low potential for hepatotoxicity, as evidenced by the high values of CC50 in HepG2 cells. Furthermore, compared to BZN, derivative 8 showed a higher rate of conversion by nitroreductase and was metabolized three times more quickly when both compounds were tested at a concentration of 50 µM. The results obtained by the enzymatic evaluation and molecular docking studies suggest that, as planned, nitroazole derivatives may utilize the nitroreductase metabolism pathway as their main mechanism of action against Trypanosoma cruzi. In summary, we have successfully identified and characterized new nitrotriazole analogs, demonstrating their potential as promising candidates for the development of Chagas disease drug candidates that function via nitroreductase activation, are considerably selective and show no mutagenic potential.
Collapse
Affiliation(s)
- Cheyene Almeida Celestino Menozzi
- Programa de Pós-Graduação em Farmacologia e Química Medicinal—PPGFQM-Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Bloco J, Ilha do Fundão, Rio de Janeiro 21941-902, Brazil (R.R.F.F.)
- Laboratório de Síntese de Fármacos—LASFAR, Instituto de Tecnologia em Fármacos, Fundação Oswaldo Cruz, Farmanguinhos—Fiocruz, Manguinhos, Rio de Janeiro 21041-250, Brazil
| | - Rodolfo Rodrigo Florido França
- Programa de Pós-Graduação em Farmacologia e Química Medicinal—PPGFQM-Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Bloco J, Ilha do Fundão, Rio de Janeiro 21941-902, Brazil (R.R.F.F.)
- Laboratório de Síntese de Fármacos—LASFAR, Instituto de Tecnologia em Fármacos, Fundação Oswaldo Cruz, Farmanguinhos—Fiocruz, Manguinhos, Rio de Janeiro 21041-250, Brazil
| | - Pedro Henrique Luccas
- Laboratório de Cristalografia de Proteínas—LCP-RP, Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo FCFRP-USP, Monte Alegre, Ribeirão Preto 14040-903, Brazil
| | - Mayara dos Santos Baptista
- Laboratório de Síntese de Fármacos—LASFAR, Instituto de Tecnologia em Fármacos, Fundação Oswaldo Cruz, Farmanguinhos—Fiocruz, Manguinhos, Rio de Janeiro 21041-250, Brazil
| | - Tácio Vinício Amorim Fernandes
- Laboratório de Síntese de Fármacos—LASFAR, Instituto de Tecnologia em Fármacos, Fundação Oswaldo Cruz, Farmanguinhos—Fiocruz, Manguinhos, Rio de Janeiro 21041-250, Brazil
| | - Lucas Villas Bôas Hoelz
- Laboratório de Síntese de Fármacos—LASFAR, Instituto de Tecnologia em Fármacos, Fundação Oswaldo Cruz, Farmanguinhos—Fiocruz, Manguinhos, Rio de Janeiro 21041-250, Brazil
| | | | | | - Alvaro Romanha
- Centro de Pesquisas René Rachou/CPqRR—Fiocruz, Belo Horizonte 30190-009, Brazil
| | - Bárbara Verena Dias Galvão
- Laboratório de Mutagênese Ambiental, Programa de Pós-Graduação em Biociências—PPGB—Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20551-030, Brazil
| | - Marcela de Oliveira Macedo
- Programa de Pós-Graduação em Biologia Molecular e Celular—PPGBMC—Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-010, Brazil
| | - Alana da Cunha Goldstein
- Laboratório de Mutagênese Ambiental, Programa de Pós-Graduação em Biociências—PPGB—Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20551-030, Brazil
| | - Carlos Fernando Araujo-Lima
- Laboratório de Mutagênese Ambiental, Programa de Pós-Graduação em Biociências—PPGB—Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20551-030, Brazil
- Programa de Pós-Graduação em Biologia Molecular e Celular—PPGBMC—Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-010, Brazil
| | - Israel Felzenszwalb
- Laboratório de Mutagênese Ambiental, Programa de Pós-Graduação em Biociências—PPGB—Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro 20551-030, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas—LCP-RP, Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo FCFRP-USP, Monte Alegre, Ribeirão Preto 14040-903, Brazil
| | - Frederico Silva Castelo-Branco
- Laboratório de Síntese de Fármacos—LASFAR, Instituto de Tecnologia em Fármacos, Fundação Oswaldo Cruz, Farmanguinhos—Fiocruz, Manguinhos, Rio de Janeiro 21041-250, Brazil
| | - Nubia Boechat
- Laboratório de Síntese de Fármacos—LASFAR, Instituto de Tecnologia em Fármacos, Fundação Oswaldo Cruz, Farmanguinhos—Fiocruz, Manguinhos, Rio de Janeiro 21041-250, Brazil
| |
Collapse
|
4
|
Teixeira O, Martins IBS, Froes TQ, de Araújo AS, Nonato MC. Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition. Biochim Biophys Acta Gen Subj 2023; 1867:130378. [PMID: 37150227 DOI: 10.1016/j.bbagen.2023.130378] [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: 01/27/2023] [Revised: 04/06/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Tuberculosis (TB) is a leading cause of death worldwide. TB represents a serious public health threat, and it is characterized by high transmission rates, prevalence in impoverished regions, and high co-infection rates with HIV. Moreover, the serious side effects of long-term treatment that decrease patient adherence, and the emergence of multi-resistant strains of Mycobacterium tuberculosis, the causing agent of TBs, pose several challenges for its eradication. The search for a new TB treatment is necessary and urgent. Dihydroorotate dehydrogenase (DHODH) is responsible for the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway. DHODH has been considered an attractive target against infectious diseases. As a first step towards exploiting DHODH as a drug target against TB, we performed a full kinetic characterization of both bacterial MtDHODH and its human ortholog (HsDHDOH) using both substrates coenzyme Q0 (Q0) and vitamin K3 (K3). MtDHODH follows a ping-pong mechanism of catalysis and shares similar catalytic parameters with the human enzyme. Serendipitously, Q0 was found to inhibit MtDHODH (KI (Q0) = 138 ± 31 μM). To the best of our knowledge, Q0 is the first non-orotate like dihydroorotate-competitive inhibitor for class 2 DHODHs ever described. Molecular dynamics simulations along with in silico solvent mapping allowed us to successfully probe protein flexibility and correlate it with the druggability of binding sites. Together, our results provide the starting point for the design of a new generation of potent and selective inhibitors against MtDHODH.
Collapse
Affiliation(s)
- Olívia Teixeira
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil; Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil
| | - Ingrid Bernardes Santana Martins
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto de Biociências, Letras e Ciências Exatas, Departamento de Física, UNESP, 15054-000 São José do Rio Preto, SP, Brazil
| | - Thamires Quadros Froes
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil; Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil
| | - Alexandre Suman de Araújo
- Instituto de Biociências, Letras e Ciências Exatas, Departamento de Física, UNESP, 15054-000 São José do Rio Preto, SP, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil; Center for the Research and Advancement in Fragments and molecular Targets (CRAFT), Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil.
| |
Collapse
|
5
|
Hicks KG, Cluntun AA, Schubert HL, Hackett SR, Berg JA, Leonard PG, Ajalla Aleixo MA, Zhou Y, Bott AJ, Salvatore SR, Chang F, Blevins A, Barta P, Tilley S, Leifer A, Guzman A, Arok A, Fogarty S, Winter JM, Ahn HC, Allen KN, Block S, Cardoso IA, Ding J, Dreveny I, Gasper WC, Ho Q, Matsuura A, Palladino MJ, Prajapati S, Sun P, Tittmann K, Tolan DR, Unterlass J, VanDemark AP, Vander Heiden MG, Webb BA, Yun CH, Zhao P, Wang B, Schopfer FJ, Hill CP, Nonato MC, Muller FL, Cox JE, Rutter J. Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase. Science 2023; 379:996-1003. [PMID: 36893255 PMCID: PMC10262665 DOI: 10.1126/science.abm3452] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/07/2023] [Indexed: 03/11/2023]
Abstract
Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.
Collapse
Affiliation(s)
- Kevin G Hicks
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ahmad A Cluntun
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Jordan A Berg
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul G Leonard
- Core for Biomolecular Structure and Function, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Applied Cancer Sciences, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mariana A Ajalla Aleixo
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Youjia Zhou
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Alex J Bott
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sonia R Salvatore
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fei Chang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Aubrie Blevins
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paige Barta
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Samantha Tilley
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aaron Leifer
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrea Guzman
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ajak Arok
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Sarah Fogarty
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jacob M Winter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hee-Chul Ahn
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Samuel Block
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Iara A Cardoso
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | - Quinn Ho
- Department of Biology, Boston University, Boston, MA, USA
| | - Atsushi Matsuura
- Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, The Republic of Korea
| | - Michael J Palladino
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pengkai Sun
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dean R Tolan
- Department of Biology, Boston University, Boston, MA, USA
| | - Judith Unterlass
- Department of Oncology and Pathology, Karolinska Institute, Stockholm, Sweden
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew G Vander Heiden
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bradley A Webb
- Department of Biochemistry, West Virginia University, Morgantown, WV, USA
| | - Cai-Hong Yun
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Pengkai Zhao
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Bei Wang
- School of Computing, University of Utah, Salt Lake City, UT, USA
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA
| | - Francisco J Schopfer
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, Pittsburgh, PA, USA
- Center for Metabolism and Mitochondrial Medicine, Pittsburgh, PA, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteinas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Florian L Muller
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James E Cox
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| |
Collapse
|
6
|
Lesbon JCC, Poleti MD, de Mattos Oliveira EC, Patané JSL, Clemente LG, Viala VL, Ribeiro G, Giovanetti M, de Alcantara LCJ, Teixeira O, Nonato MC, de Lima LPO, Martins AJ, dos Santos Barros CR, Marqueze EC, de Souza Todão Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Slavov SN, dos Santos RB, Rodrigues ES, Santos EV, Borges JS, de La Roque DGL, Kitajima JP, Santos B, Assato PA, da Silva da Costa FA, Banho CA, Sacchetto L, Moraes MM, Palmieri M, da Silva FEV, Grotto RMT, Souza-Neto JA, Nogueira ML, Coutinho LL, Calado RT, Neto RM, Covas DT, Kashima S, Elias MC, Sampaio SC, Fukumasu H. Correction: Lesbon et al. Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results. Viruses 2021, 13, 2474. Viruses 2022; 14:v14091967. [PMID: 36146888 PMCID: PMC9506407 DOI: 10.3390/v14091967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
The authors hereby request the inclusion of two authors (Olivia Teixeira and Maria Cristina Nonato) in the recently published article in Viruses entitled “Nucleocapsid (N) gene mutations of SARS-CoV-2 can affect real-time RT-PCR diagnostic and impact false-negative results” [...]
Collapse
Affiliation(s)
- Jéssika Cristina Chagas Lesbon
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, São Paulo, Brazil
| | - Mirele Daiana Poleti
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, São Paulo, Brazil
| | - Elisângela Chicaroni de Mattos Oliveira
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, São Paulo, Brazil
| | | | - Luan Gaspar Clemente
- Functional Genomic Center, Department of Animal Science, Luiz de Queiroz School of Agriculture, University of Sao Paulo, Piracicaba 13418-900, São Paulo, Brazil
| | | | | | - Marta Giovanetti
- Fundação Oswaldo Cruz, FIOCRUZ, Manguinhos 21040-900, Rio de Janeiro, Brazil
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | | | - Olivia Teixeira
- Ribeirao Preto Protein Crystallography Laboratory, School of Pharmaceutical Sciences, University of São Paulo, Ribeirao Preto 14040-903, São Paulo, Brazil
| | - Maria Cristina Nonato
- Ribeirao Preto Protein Crystallography Laboratory, School of Pharmaceutical Sciences, University of São Paulo, Ribeirao Preto 14040-903, São Paulo, Brazil
| | | | | | | | | | | | | | - Ricardo Augusto Brassaloti
- Functional Genomic Center, Department of Animal Science, Luiz de Queiroz School of Agriculture, University of Sao Paulo, Piracicaba 13418-900, São Paulo, Brazil
| | - Raquel de Lello Rocha Campos Cassano
- Functional Genomic Center, Department of Animal Science, Luiz de Queiroz School of Agriculture, University of Sao Paulo, Piracicaba 13418-900, São Paulo, Brazil
| | | | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil
| | - Rafael Bezerra dos Santos
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil
| | - Evandra Strazza Rodrigues
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil
| | - Elaine Vieira Santos
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil
| | - Josiane Serrano Borges
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil
| | - Debora Glenda Lima de La Roque
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil
| | | | - Bibiana Santos
- Mendelics Genomic Analysis, São Paulo 02511-000, São Paulo, Brazil
| | - Patricia Akemi Assato
- School of Agricultural Sciences, São Paulo State University, Botucatu 18618-970, São Paulo, Brazil
| | | | - Cecilia Artico Banho
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, São Paulo, Brazil
| | - Livia Sacchetto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, São Paulo, Brazil
| | - Marilia Mazzi Moraes
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, São Paulo, Brazil
| | - Melissa Palmieri
- Coordenação de Vigilância em Saúde—Secretaria Municipal da Saúde, São Paulo 01223-906, São Paulo, Brazil
| | | | | | - Jayme A. Souza-Neto
- School of Agricultural Sciences, São Paulo State University, Botucatu 18618-970, São Paulo, Brazil
| | - Mauricio Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, São Paulo, Brazil
| | - Luiz Lehman Coutinho
- Functional Genomic Center, Department of Animal Science, Luiz de Queiroz School of Agriculture, University of Sao Paulo, Piracicaba 13418-900, São Paulo, Brazil
| | - Rodrigo Tocantins Calado
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil
| | | | - Dimas Tadeu Covas
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil
| | | | | | - Heidge Fukumasu
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, São Paulo, Brazil
- Correspondence: ; Tel.: +55-19-35656864
| |
Collapse
|
7
|
Lesbon JCC, Poleti MD, de Mattos Oliveira EC, Patané JSL, Clemente LG, Viala VL, Ribeiro G, Giovanetti M, de Alcantara LCJ, Teixeira O, Nonato MC, de Lima LPO, Martins AJ, dos Santos Barros CR, Marqueze EC, de Souza Todão Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Slavov SN, dos Santos RB, Rodrigues ES, Santos EV, Borges JS, de La Roque DGL, Kitajima JP, Santos B, Assato PA, da Silva da Costa FA, Banho CA, Sacchetto L, Moraes MM, Palmieri M, da Silva FEV, Grotto RMT, Souza-Neto JA, Nogueira ML, Coutinho LL, Calado RT, Neto RM, Covas DT, Kashima S, Elias MC, Sampaio SC, Fukumasu H. Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results. Viruses 2021; 13:v13122474. [PMID: 34960743 PMCID: PMC8707239 DOI: 10.3390/v13122474] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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] [Received: 10/27/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 01/17/2023] Open
Abstract
The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.
Collapse
Affiliation(s)
- Jéssika Cristina Chagas Lesbon
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, São Paulo, Brazil; (J.C.C.L.); (M.D.P.); (E.C.d.M.O.)
| | - Mirele Daiana Poleti
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, São Paulo, Brazil; (J.C.C.L.); (M.D.P.); (E.C.d.M.O.)
| | - Elisângela Chicaroni de Mattos Oliveira
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, São Paulo, Brazil; (J.C.C.L.); (M.D.P.); (E.C.d.M.O.)
| | - José Salvatore Leister Patané
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Luan Gaspar Clemente
- Functional Genomic Center, Department of Animal Science, Luiz de Queiroz School of Agriculture, University of Sao Paulo, Piracicaba 13418-900, São Paulo, Brazil; (L.G.C.); (R.A.B.); (R.d.L.R.C.C.); (L.L.C.)
| | - Vincent Louis Viala
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Gabriela Ribeiro
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Marta Giovanetti
- Fundação Oswaldo Cruz, FIOCRUZ, Manguinhos 21040-900, Rio de Janeiro, Brazil; (M.G.); (L.C.J.d.A.)
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | | | - Olivia Teixeira
- Ribeirao Preto Protein Crystallography Laboratory, School of Pharmaceutical Sciences, University of São Paulo, Ribeirao Preto 14040-903, São Paulo, Brazil; (O.T.); (M.C.N.)
| | - Maria Cristina Nonato
- Ribeirao Preto Protein Crystallography Laboratory, School of Pharmaceutical Sciences, University of São Paulo, Ribeirao Preto 14040-903, São Paulo, Brazil; (O.T.); (M.C.N.)
| | - Loyze Paola Oliveira de Lima
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Antonio Jorge Martins
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Claudia Renata dos Santos Barros
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Elaine Cristina Marqueze
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Jardelina de Souza Todão Bernardino
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Debora Botequio Moretti
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Ricardo Augusto Brassaloti
- Functional Genomic Center, Department of Animal Science, Luiz de Queiroz School of Agriculture, University of Sao Paulo, Piracicaba 13418-900, São Paulo, Brazil; (L.G.C.); (R.A.B.); (R.d.L.R.C.C.); (L.L.C.)
| | - Raquel de Lello Rocha Campos Cassano
- Functional Genomic Center, Department of Animal Science, Luiz de Queiroz School of Agriculture, University of Sao Paulo, Piracicaba 13418-900, São Paulo, Brazil; (L.G.C.); (R.A.B.); (R.d.L.R.C.C.); (L.L.C.)
| | | | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil; (S.N.S.); (R.B.d.S.); (E.S.R.); (E.V.S.); (J.S.B.); (D.G.L.d.L.R.); (R.T.C.); (S.K.)
| | - Rafael Bezerra dos Santos
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil; (S.N.S.); (R.B.d.S.); (E.S.R.); (E.V.S.); (J.S.B.); (D.G.L.d.L.R.); (R.T.C.); (S.K.)
| | - Evandra Strazza Rodrigues
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil; (S.N.S.); (R.B.d.S.); (E.S.R.); (E.V.S.); (J.S.B.); (D.G.L.d.L.R.); (R.T.C.); (S.K.)
| | - Elaine Vieira Santos
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil; (S.N.S.); (R.B.d.S.); (E.S.R.); (E.V.S.); (J.S.B.); (D.G.L.d.L.R.); (R.T.C.); (S.K.)
| | - Josiane Serrano Borges
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil; (S.N.S.); (R.B.d.S.); (E.S.R.); (E.V.S.); (J.S.B.); (D.G.L.d.L.R.); (R.T.C.); (S.K.)
| | - Debora Glenda Lima de La Roque
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil; (S.N.S.); (R.B.d.S.); (E.S.R.); (E.V.S.); (J.S.B.); (D.G.L.d.L.R.); (R.T.C.); (S.K.)
| | - Joao Paulo Kitajima
- Mendelics Genomic Analysis, São Paulo 02511-000, São Paulo, Brazil; (J.P.K.); (B.S.)
| | - Bibiana Santos
- Mendelics Genomic Analysis, São Paulo 02511-000, São Paulo, Brazil; (J.P.K.); (B.S.)
| | - Patricia Akemi Assato
- School of Agricultural Sciences, São Paulo State University, Botucatu 18618-970, São Paulo, Brazil; (P.A.A.); (F.A.d.S.d.C.); (R.M.T.G.); (J.A.S.-N.)
| | - Felipe Allan da Silva da Costa
- School of Agricultural Sciences, São Paulo State University, Botucatu 18618-970, São Paulo, Brazil; (P.A.A.); (F.A.d.S.d.C.); (R.M.T.G.); (J.A.S.-N.)
| | - Cecilia Artico Banho
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, São Paulo, Brazil; (C.A.B.); (L.S.); (M.M.M.); (M.L.N.)
| | - Livia Sacchetto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, São Paulo, Brazil; (C.A.B.); (L.S.); (M.M.M.); (M.L.N.)
| | - Marilia Mazzi Moraes
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, São Paulo, Brazil; (C.A.B.); (L.S.); (M.M.M.); (M.L.N.)
| | - Melissa Palmieri
- Coordenação de Vigilância em Saúde—Secretaria Municipal da Saúde, São Paulo 01223-906, São Paulo, Brazil;
| | | | - Rejane Maria Tommasini Grotto
- School of Agricultural Sciences, São Paulo State University, Botucatu 18618-970, São Paulo, Brazil; (P.A.A.); (F.A.d.S.d.C.); (R.M.T.G.); (J.A.S.-N.)
| | - Jayme A. Souza-Neto
- School of Agricultural Sciences, São Paulo State University, Botucatu 18618-970, São Paulo, Brazil; (P.A.A.); (F.A.d.S.d.C.); (R.M.T.G.); (J.A.S.-N.)
| | - Mauricio Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, São Paulo, Brazil; (C.A.B.); (L.S.); (M.M.M.); (M.L.N.)
| | - Luiz Lehman Coutinho
- Functional Genomic Center, Department of Animal Science, Luiz de Queiroz School of Agriculture, University of Sao Paulo, Piracicaba 13418-900, São Paulo, Brazil; (L.G.C.); (R.A.B.); (R.d.L.R.C.C.); (L.L.C.)
| | - Rodrigo Tocantins Calado
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil; (S.N.S.); (R.B.d.S.); (E.S.R.); (E.V.S.); (J.S.B.); (D.G.L.d.L.R.); (R.T.C.); (S.K.)
| | - Raul Machado Neto
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Dimas Tadeu Covas
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil; (S.N.S.); (R.B.d.S.); (E.S.R.); (E.V.S.); (J.S.B.); (D.G.L.d.L.R.); (R.T.C.); (S.K.)
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-060, São Paulo, Brazil; (S.N.S.); (R.B.d.S.); (E.S.R.); (E.V.S.); (J.S.B.); (D.G.L.d.L.R.); (R.T.C.); (S.K.)
| | - Maria Carolina Elias
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Sandra Coccuzzo Sampaio
- Butantan Institute, São Paulo 05503-000, São Paulo, Brazil; (J.S.L.P.); (V.L.V.); (G.R.); (L.P.O.d.L.); (A.J.M.); (C.R.d.S.B.); (E.C.M.); (J.d.S.T.B.); (D.B.M.); (R.M.N.); (D.T.C.); (M.C.E.); (S.C.S.)
| | - Heidge Fukumasu
- Laboratory of Comparative and Translational Oncology, Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 13635-900, São Paulo, Brazil; (J.C.C.L.); (M.D.P.); (E.C.d.M.O.)
- Correspondence: ; Tel.: +55-19-35656864
| |
Collapse
|
8
|
|
9
|
Venancio-Brochi JC, Pereira LM, Calil FA, Teixeira O, Baroni L, Abreu-Filho PG, Braga GÚL, Nonato MC, Yatsuda AP. Glutathione reductase: A cytoplasmic antioxidant enzyme and a potential target for phenothiazinium dyes in Neospora caninum. Int J Biol Macromol 2021; 187:964-975. [PMID: 34310993 DOI: 10.1016/j.ijbiomac.2021.07.108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/04/2020] [Revised: 05/21/2021] [Accepted: 07/15/2021] [Indexed: 11/21/2022]
Abstract
Neospora caninum causes heavy losses related to abortions in bovine cattle. This parasite developed a complex defense redox system, composed of enzymes as glutathione reductase (GR). Methylene blue (MB) impairs the activity of recombinant form of Plasmodium GR and inhibits the parasite proliferation in vivo and in vitro. Likewise, MB and its derivatives inhibits Neospora caninum proliferation, however, whether the MB mechanism of action is correlated to GR function remains unclear. Therefore, here, N. caninum GR (NcGR) was characterized and its potential inhibitors were determined. NcGR was found in the tachyzoite cytosol and has a similar structure and sequence compared to its homologs. We verified the in vitro activity of rNcGR (875 nM) following NADPH absorbance at 340 nM (100 mM KH2PO4, pH 7.5, 1 mM EDTA, ionic strength: 600 mM, 25 °C). rNcGR exhibited a Michaelian behavior (Km(GSSG):0.10 ± 0.02 mM; kcat(GSSG):0.076 ± 0.003 s-1; Km(NADPH):0.006 ± 0.001 mM; kcat(NADPH): 0.080 ± 0.003 s-1). The IC50 of MB,1,9-dimethyl methylene blue, new methylene blue, and toluidine blue O on rNcGR activity were 2.1 ± 0.2 μM, 11 ± 2 μM, 0.7 ± 0.1 μM, and 0.9 ± 0.2 μM, respectively. Our results suggest the importance of NcGR in N. caninum biology and antioxidant mechanisms. Moreover, data presented here strongly suggest that NcGR is an important target of phenothiazinium dyes in N. caninum proliferation inhibition.
Collapse
Affiliation(s)
- Jade Cabestre Venancio-Brochi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, Brazil
| | - Luiz Miguel Pereira
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, Brazil
| | - Felipe Antunes Calil
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto, Brazil; Ludwig Institute for Cancer Research, University of California, School of Medicine, 92093-0669 La Jolla, CA, USA
| | - Olívia Teixeira
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto, Brazil
| | - Luciana Baroni
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, Brazil
| | - Péricles Gama Abreu-Filho
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, Brazil
| | - Gilberto Úbida Leite Braga
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, 14040-903 Ribeirão Preto, Brazil
| | - Ana Patrícia Yatsuda
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, Brazil.
| |
Collapse
|
10
|
Froes TQ, Nonato MC, Castilho MS, Zapata LCC, Akamine JS. DHODH hot spots: an underexplored source to guide drug development efforts. Curr Top Med Chem 2021; 21:2134-2154. [PMID: 34348625 DOI: 10.2174/1568026621666210804122320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/20/2021] [Revised: 07/06/2021] [Accepted: 07/15/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Dihydroorotate dehydrogenase (DHODH) has long been recognized as an important drug target for proliferative and parasitic diseases, including compounds that exhibit trypanocidal action and broad-spectrum antiviral activity. Despite numerous and successful efforts in structural and functional characterization of DHODHs, as well as in the development of inhibitors, DHODH hot spots remain largely unmapped and underexplored. OBJECTIVE This review describes the tools that are currently available for the identification and characterization of hot spots in protein structures and how freely available webservers can be exploited to predict DHODH hot spots. Moreover, it provides for the first time a review of the antiviral properties of DHODH inhibitors. <P> Method: X-ray structures from human (HsDHODH) and Trypanosoma cruzi DHODH (TcDHODH) had their hot spots predicted by both FTMap and Fragment Hotspot Maps web servers. <P> Results: FTMap showed that hot spot occupancy in HsDHODH is correlated with the ligand efficiency (LE) of its known inhibitors, and Fragment Hotspot Maps pointed out the contribution of selected moieties to the overall LE. The conformational flexibility of the active site loop in TcDHODH was found to have a major impact on the druggability of the orotate binding site. In addition, both FTMap and Fragment Hotspot Maps servers predict a novel pocket in TcDHODH dimer interface (S6 site). <P> Conclusion: This review reports how hot spots can be exploited during hit-to-lead steps, docking studies or even to improve inhibitor binding profile and by doing so using DHODH as a model, points to new drug development opportunities.
Collapse
Affiliation(s)
- Thamires Quadros Froes
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Address Av. do Café, s/n - Vila Monte Alegre, Ribeirão Preto - SP, 14040-900. Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Address Av. do Café, s/n - Vila Monte Alegre, Ribeirão Preto - SP, 14040-900. Brazil
| | - Marcelo Santos Castilho
- Faculdade de Farmácia da Universidade Federal da Bahia, Av. Barão de Jeremoabo s/n Ondina, Salvador-BA, Brasil, 40170-115. Brazil
| | - Luana Carlos Campisano Zapata
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Address Av. do Café, s/n - Vila Monte Alegre, Ribeirão Preto - SP, 14040-900. Brazil
| | - Juliana Sayuri Akamine
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Address Av. do Café, s/n - Vila Monte Alegre, Ribeirão Preto - SP, 14040-900. Brazil
| |
Collapse
|
11
|
Uth JF, Börgel F, Lehmkuhl K, Schepmann D, Kaiser M, Jabor VAP, Nonato MC, Krauth-Siegel RL, Schmidt TJ, Wünsch B. Synthesis and Biological Evaluation of Natural-Product-Inspired, Aminoalkyl-Substituted 1-Benzopyrans as Novel Antiplasmodial Agents. J Med Chem 2021; 64:6397-6409. [PMID: 33901399 DOI: 10.1021/acs.jmedchem.1c00483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Herein, relationships between the structures of 1-aminoethyl-substituted chromenes and their antimalarial activities were thoroughly investigated. At first, the methyl moiety in the side chain was removed to eliminate chirality. The hydrogenation state of the benzopyran system, the position of the phenolic OH moiety, and the distance of the basic amino moiety toward both aromatic rings were varied systematically. 1-Benzopyran-5-ol 8b (IC50 = 10 nM), 1-benzopyran-7-ol 9c (IC50 = 38 nM), and the aminoalcohol 19c (IC50 = 17 nM) displayed antiplasmodial activity with IC50 values below 50 nM. To identify the mechanism of action, inhibition of three key enzymes by 9c was investigated. 9c was not able to reduce the number of Plasmodia in erythrocytes of mice. This low in vivo activity was explained by fast clearance from blood plasma combined with rapid biotransformation of 9c. Three main metabolites of 9c were identified by liquid chromatography-mass spectrometry (LC-MS) methods.
Collapse
Affiliation(s)
- Jan-Frederik Uth
- Institut für Pharmazeutische und Medizinische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Frederik Börgel
- Institut für Pharmazeutische und Medizinische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Kirstin Lehmkuhl
- Institut für Pharmazeutische und Medizinische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Dirk Schepmann
- Institut für Pharmazeutische und Medizinische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute (Swiss TPH), Socinstraße 57, CH-4002 Basel, Switzerland
| | - Valquiria A P Jabor
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - R Luise Krauth-Siegel
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Thomas J Schmidt
- Institut für Pharmazeutische Biologie und Phytochemie der Westfälischen Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany
| | - Bernhard Wünsch
- Institut für Pharmazeutische und Medizinische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany.,GRK 2515, Chemical Biology of Ion Channels (Chembion), Westfälische Wilhelms-Universität, 48149 Münster, Germany
| |
Collapse
|
12
|
Oliveira ISD, Pucca MB, Wiezel GA, Cardoso IA, Bordon KDCF, Sartim MA, Kalogeropoulos K, Ahmadi S, Baiwir D, Nonato MC, Sampaio SV, Laustsen AH, Auf dem Keller U, Quinton L, Arantes EC. Unraveling the structure and function of CdcPDE: A novel phosphodiesterase from Crotalus durissus collilineatus snake venom. Int J Biol Macromol 2021; 178:180-192. [PMID: 33636276 DOI: 10.1016/j.ijbiomac.2021.02.120] [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] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/20/2023]
Abstract
This study reports the isolation, structural, biochemical, and functional characterization of a novel phosphodiesterase from Crotalus durissus collilineatus venom (CdcPDE). CdcPDE was successfully isolated from whole venom using three chromatographic steps and represented 0.7% of total protein content. CdcPDE was inhibited by EDTA and reducing agents, demonstrating that metal ions and disulfide bonds are necessary for its enzymatic activity. The highest enzymatic activity was observed at pH 8-8.5 and 37 °C. Kinetic parameters indicated a higher affinity for the substrate bis(p-nitrophenyl) phosphate compared to others snake venom PDEs. Its structural characterization was done by the determination of the protein primary sequence by Edman degradation and mass spectrometry, and completed by the building of molecular and docking-based models. Functional in vitro assays showed that CdcPDE is capable of inhibiting platelet aggregation induced by adenosine diphosphate in a dose-dependent manner and demonstrated that CdcPDE is cytotoxic to human keratinocytes. CdcPDE was recognized by the crotalid antivenom produced by the Instituto Butantan. These findings demonstrate that the study of snake venom toxins can reveal new molecules that may be relevant in cases of snakebite envenoming, and that can be used as molecular tools to study pathophysiological processes due to their specific biological activities.
Collapse
Affiliation(s)
- Isadora Sousa de Oliveira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Gisele Adriano Wiezel
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Iara Aimê Cardoso
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Karla de Castro Figueiredo Bordon
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Marco Aurélio Sartim
- Institute of Biological Sciences, Federal University of Amazonas, Manaus, AM, Brazil; Department of Teaching and Research, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, AM, Brazil
| | | | - Shirin Ahmadi
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dominique Baiwir
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Liège, Belgium; GIGA Proteomics Facility, University of Liège, Liège, Belgium
| | - Maria Cristina Nonato
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Suely Vilela Sampaio
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Andreas Hougaard Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Liège, Belgium
| | - Eliane Candiani Arantes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.
| |
Collapse
|
13
|
Cardoso IA, de Souza AKL, Burgess AMG, Chalmers IW, Hoffmann KF, Nonato MC. Characterization of class II fumarase from Schistosoma mansoni provides the molecular basis for selective inhibition. Int J Biol Macromol 2021; 175:406-421. [PMID: 33549669 DOI: 10.1016/j.ijbiomac.2021.01.180] [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] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/20/2021] [Accepted: 01/28/2021] [Indexed: 01/01/2023]
Abstract
Schistosomiasis is a neglected tropical disease that affects more than 250 million people worldwide. The only drug available for its treatment undergoes first-pass hepatic metabolism and is not capable of preventing reinfection, which makes the search of new therapies urgently needed. Due to the essential role of fumarases in metabolism, these enzymes represent potential targets for developing novel schistosomiasis treatments. Here, we evaluate the expression profiles for class I and class II fumarases from Schistosoma mansoni (SmFHI and SmFHII, respectively), and report the complete characterization of SmFHII. The first SmFHII structure in complex with L-malate was determined at 1.85 Å resolution. The significant thermoshift observed for SmFHII in the presence of identified ligands makes the differential scanning fluorimetry an adequate technique for ligand screening. A complete kinetic characterization of SmFHII was performed, and comparison with the human fumarase (HsFH) revealed differences regarding the turnover number (kcat). Structural characterization allowed us to identify differences between SmFHII and HsFH that could be explored to design new selective inhibitors. This work represents the very first step towards validate the fumarases as drug targets to treat schistosomiasis. Our results provide the structural basis to rational search for selective ligands.
Collapse
Affiliation(s)
- Iara Aimê Cardoso
- Laboratório de Cristalografia de Proteínas, Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Aline Kusumota Luiz de Souza
- Laboratório de Cristalografia de Proteínas, Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Adam Muslem George Burgess
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Wales, United Kingdom
| | - Iain Wyllie Chalmers
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Wales, United Kingdom
| | - Karl Francis Hoffmann
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Wales, United Kingdom
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| |
Collapse
|
14
|
Reidenbach AG, Mesleh MF, Casalena D, Vallabh SM, Dahlin JL, Leed AJ, Chan AI, Usanov DL, Yehl JB, Lemke CT, Campbell AJ, Shah RN, Shrestha OK, Sacher JR, Rangel VL, Moroco JA, Sathappa M, Nonato MC, Nguyen KT, Wright SK, Liu DR, Wagner FF, Kaushik VK, Auld DS, Schreiber SL, Minikel EV. Multimodal small-molecule screening for human prion protein binders. J Biol Chem 2020; 295:13516-13531. [PMID: 32723867 PMCID: PMC7521658 DOI: 10.1074/jbc.ra120.014905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Prion disease is a rapidly progressive neurodegenerative disorder caused by misfolding and aggregation of the prion protein (PrP), and there are currently no therapeutic options. PrP ligands could theoretically antagonize prion formation by protecting the native protein from misfolding or by targeting it for degradation, but no validated small-molecule binders have been discovered to date. We deployed a variety of screening methods in an effort to discover binders of PrP, including 19F-observed and saturation transfer difference (STD) NMR spectroscopy, differential scanning fluorimetry (DSF), DNA-encoded library selection, and in silico screening. A single benzimidazole compound was confirmed in concentration-response, but affinity was very weak (Kd > 1 mm), and it could not be advanced further. The exceptionally low hit rate observed here suggests that PrP is a difficult target for small-molecule binders. Whereas orthogonal binder discovery methods could yield high-affinity compounds, non-small-molecule modalities may offer independent paths forward against prion disease.
Collapse
Affiliation(s)
- Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael F Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dominick Casalena
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Sonia M Vallabh
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Prion Alliance, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Jayme L Dahlin
- Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Alison J Leed
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alix I Chan
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Dmitry L Usanov
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jenna B Yehl
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Christopher T Lemke
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Arthur J Campbell
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rishi N Shah
- Undergraduate Research Opportunities Program (UROP), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Om K Shrestha
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Joshua R Sacher
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Victor L Rangel
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jamie A Moroco
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Murugappan Sathappa
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Maria Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Kong T Nguyen
- Artificial Intelligence Molecular Screen (AIMS) Awards Program, Atomwise, San Francisco, California, USA
| | - S Kirk Wright
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - David R Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Florence F Wagner
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Virendar K Kaushik
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Douglas S Auld
- Facilitated Access to Screening Technologies (FAST) Lab, Novartis Institutes for Biomedical Research (NIBR), Cambridge, Massachusetts, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Eric Vallabh Minikel
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Prion Alliance, Cambridge, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
15
|
Chibli LA, Rosa AL, Nonato MC, Da Costa FB. Untargeted LC-MS metabolomic studies of Asteraceae species to discover inhibitors of Leishmania major dihydroorotate dehydrogenase. Metabolomics 2019; 15:59. [PMID: 30949823 DOI: 10.1007/s11306-019-1520-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 03/25/2019] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Interesting data about the family Asteraceae as a new source of Leishmania major dihydroorotate dehydrogenase (LmDHODH) inhibitors are presented. This key macromolecular target for parasites causing neglected diseases catalyzes the fourth reaction of the de novo pyrimidine biosynthetic pathway, which takes part in major cell functions, including DNA and RNA biosynthesis. OBJECTIVES We aimed to (1) determine LmDHODH inhibitor candidates, revealing the type of chemistry underlying such bioactivity, and (2) predict the inhibitory potential of extracts from new untested plant species, classifying them as active or inactive based on their LC-MS based metabolic fingerprints. METHODS Extracts from 150 species were screened for the inhibition of LmDHODH, and untargeted UHPLC-(ESI)-HRMS metabolomic studies were carried out in combination with in silico approaches. RESULTS The IC50 values determined for a subset of 59 species ranged from 148 µg mL-1 to 9.4 mg mL-1. Dereplication of the metabolic fingerprints allowed the identification of 48 metabolites. A reliable OPLS-DA model (R2 > 0.9, Q2 > 0.7, RMSECV < 0.3) indicated the inhibitor candidates; nine of these metabolites were identified using data from isolated chemical standards, one of which-4,5-di-O-E-caffeoylquinic acid (IC50 73 µM)-was capable of inhibiting LmDHODH. The predictive OPLS model was also effective, with 60% correct predictions for the test set. CONCLUSION Our approach was validated for (1) the discovery of LmDHODH inhibitors or interesting starting points for the optimization of new leishmanicides from Asteraceae species and (2) the prediction of extracts from untested species, classifying them as active or inactive.
Collapse
Affiliation(s)
- Lucas A Chibli
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Annylory L Rosa
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Maria Cristina Nonato
- Laboratory of Protein Crystallography, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil
| | - Fernando B Da Costa
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Ribeirão Preto, SP, 14040-903, Brazil.
| |
Collapse
|
16
|
Ajalla Aleixo MA, Rangel VL, Rustiguel JK, de Pádua RAP, Nonato MC. Structural, biochemical and biophysical characterization of recombinant human fumarate hydratase. FEBS J 2019; 286:1925-1940. [DOI: 10.1111/febs.14782] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/09/2019] [Accepted: 02/12/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Mariana A. Ajalla Aleixo
- Laboratório de Cristalografia de Proteínas Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo Ribeirão Preto Brazil
| | - Victor L. Rangel
- Laboratório de Cristalografia de Proteínas Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo Ribeirão Preto Brazil
| | - Joane K. Rustiguel
- Laboratório de Cristalografia de Proteínas Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo Ribeirão Preto Brazil
| | - Ricardo A. P. de Pádua
- Laboratório de Cristalografia de Proteínas Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo Ribeirão Preto Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo Ribeirão Preto Brazil
| |
Collapse
|
17
|
Abstract
![]()
Leishmaniases
affect the poorest people on earth and have no effective
drug therapy. Here, we present the crystal structure of the mitochondrial
isoform of class I fumarate hydratase (FH) from Leishmania
major and compare it to the previously determined cytosolic Leishmania major isoform. We further describe the mechanism
of action of the first class-specific FH inhibitor, 2-thiomalate,
through X-ray crystallography and inhibition assays. Our crystal structures
of both FH isoforms with inhibitor bound at 2.05 Å resolution
and 1.60 Å resolution show high structural similarity. These
structures further reveal that the selectivity of 2-thiomalate for
class I FHs is due to direct coordination of the inhibitor to the
unique Fe of the catalytic [4Fe-4S] cluster that is found in class
I parasitic FHs but is absent from class II human FH. These studies
provide the structural scaffold in order to exploit class I FHs as
potential drug targets against leishmaniases as well as Chagas diseases,
sleeping sickness, and malaria.
Collapse
Affiliation(s)
- Patricia R. Feliciano
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo 14040-903, Brazil
| | - Catherine L. Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo 14040-903, Brazil
| |
Collapse
|
18
|
Maetani M, Kato N, Jabor VAP, Calil FA, Nonato MC, Scherer CA, Schreiber SL. Discovery of Antimalarial Azetidine-2-carbonitriles That Inhibit P. falciparum Dihydroorotate Dehydrogenase. ACS Med Chem Lett 2017; 8:438-442. [PMID: 28435533 PMCID: PMC5392761 DOI: 10.1021/acsmedchemlett.7b00030] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/27/2017] [Indexed: 12/15/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is an enzyme necessary for pyrimidine biosynthesis in protozoan parasites of the genus Plasmodium, the causative agents of malaria. We recently reported the identification of novel compounds derived from diversity-oriented synthesis with activity in multiple stages of the malaria parasite life cycle. Here, we report the optimization of a potent series of antimalarial inhibitors consisting of azetidine-2-carbonitriles, which we had previously shown to target P. falciparum DHODH in a biochemical assay. Optimized compound BRD9185 (27) has in vitro activity against multidrug-resistant blood-stage parasites (EC50 = 0.016 μM) and is curative after just three doses in a P. berghei mouse model. BRD9185 has a long half-life (15 h) and low clearance in mice and represents a new structural class of DHODH inhibitors with potential as antimalarial drugs.
Collapse
Affiliation(s)
- Micah Maetani
- Department of Chemistry
and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Nobutaka Kato
- Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Valquiria A. P. Jabor
- School of Pharmaceutical Sciences of Ribeirão
Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Felipe A. Calil
- School of Pharmaceutical Sciences of Ribeirão
Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Maria Cristina Nonato
- School of Pharmaceutical Sciences of Ribeirão
Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | | | - Stuart L. Schreiber
- Department of Chemistry
and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Broad Institute, Cambridge, Massachusetts 02142, United States
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
19
|
Pelá FP, Rustiguel JK, Rodrigues LC, Mendonça JN, Andrade CDC, Lopes NP, Rosa JC, Nonato MC, Favier B, Donadi EA, Dias-Baruffi M. A soluble recombinant form of human leucocyte antigen-G 6 (srHLA-G6). Biochem Biophys Res Commun 2017; 487:28-33. [PMID: 28365155 DOI: 10.1016/j.bbrc.2017.03.149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 10/19/2022]
Abstract
Human Leucocyte Antigen-G (HLA-G) is a non classical major histocompatibility complex (MHC) molecule that through RNA splicing can encode seven isoforms which are membrane bound (-G1, -G2, -G3 and -G4) and soluble (-G5, -G6 and -G7). HLA-G is described as important immune suppressor endogenous molecule to favor maternal-fetal tolerance, transplant survival and tumor immune scape. HLA-G shows low protein variability and a unique structural complexity that is related with the expression of different isoforms followed by biochemical processes, such as, proteolytic cleavage, molecular interactions, and protein ubiquitination. Studies with HLA-G have shown difficult to assess the role of the individual isoforms. Thus, the aim of this work was to obtain a HLA-G6 recombinant form. The results indicated the production of high homogeneous preparations of soluble recombinant HLA-G6 (srHLA-G6) with molecular mass 23,603.76 Da, determined by MALD-TOF/TOF. In addition, native and denatured srHLA-G6 were detected by ELISA, using commercial monoclonal antibodies. Finally, we developed a suitable methodology to express srHLA-G6 that could contribute in structural and functional studies involving specific isoforms.
Collapse
Affiliation(s)
- Flávia Porto Pelá
- Laboratório de Glicoimunologia, Universidade de São Paulo, Av. Café, s/n 14040-903, Ribeirão Preto, SP, Brazil
| | - Joane Kathelen Rustiguel
- Laboratório de Cristalografia de Proteínas, Universidade de São Paulo, Av. Café, s/n 14040-903, Ribeirão Preto, SP, Brazil
| | - Lilian Cataldi Rodrigues
- Laboratório de Glicoimunologia, Universidade de São Paulo, Av. Café, s/n 14040-903, Ribeirão Preto, SP, Brazil
| | - Jacqueline Nakau Mendonça
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Camillo Del Cistia Andrade
- Laboratório de Glicoimunologia, Universidade de São Paulo, Av. Café, s/n 14040-903, Ribeirão Preto, SP, Brazil
| | - Norberto Peporine Lopes
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - José Cesar Rosa
- Centro de Química de Proteínas, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Rua Tenente Catão Roxo, 2501, 14051-140, Ribeirão Preto, SP, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Universidade de São Paulo, Av. Café, s/n 14040-903, Ribeirão Preto, SP, Brazil
| | - Benoit Favier
- CEA/DRF/IDMIT-Université Paris Sud-INSERM U1184/IMVA, 92265, Fontenay-aux-Roses, France
| | - Eduardo Antônio Donadi
- Divisão de Imunologia Clínica, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900 - Monte Alegre, 14049-900, Ribeirão Preto, SP, Brazil
| | - Marcelo Dias-Baruffi
- Laboratório de Glicoimunologia, Universidade de São Paulo, Av. Café, s/n 14040-903, Ribeirão Preto, SP, Brazil.
| |
Collapse
|
20
|
Lewis TA, Sykes DB, Law JM, Muñoz B, Rustiguel JK, Nonato MC, Scadden DT, Schreiber SL. Development of ML390: A Human DHODH Inhibitor That Induces Differentiation in Acute Myeloid Leukemia. ACS Med Chem Lett 2016; 7:1112-1117. [PMID: 27994748 DOI: 10.1021/acsmedchemlett.6b00316] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [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: 08/11/2016] [Accepted: 09/28/2016] [Indexed: 11/29/2022] Open
Abstract
Homeobox transcription factor A9 (HoxA9) is overexpressed in 70% of patients diagnosed with acute myeloid leukemia (AML), whereas only a small subset of AML patients respond to current differentiation therapies. A cell line overexpressing HoxA9 was derived from the bone marrow of a lysozyme-GFP mouse. In this fashion, GFP served as an endogenous reporter of differentiation, permitting a high-throughput phenotypic screen against the MLPCN library. Two chemical scaffolds were optimized for activity yielding compound ML390, and genetic resistance and sequencing efforts identified dihydroorotate dehydrogenase (DHODH) as the target enzyme. The DHODH inhibitor brequinar works against these leukemic cells as well. The X-ray crystal structure of ML390 bound to DHODH elucidates ML390s binding interactions.
Collapse
Affiliation(s)
- Timothy A. Lewis
- Center
for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, United States
| | - David B. Sykes
- Center
for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Cancer
Center, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jason M. Law
- Center
for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, United States
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Benito Muñoz
- Center
for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Joane K. Rustiguel
- School
of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Maria Cristina Nonato
- School
of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - David T. Scadden
- Center
for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Cancer
Center, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Stem Cell
and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, United States
| | - Stuart L. Schreiber
- Center
for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, United States
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
21
|
Rustiguel JK, Soares ROS, Meisburger SP, Davis KM, Malzbender KL, Ando N, Dias-Baruffi M, Nonato MC. Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication. Sci Rep 2016; 6:33633. [PMID: 27642006 PMCID: PMC5027518 DOI: 10.1038/srep33633] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 05/26/2016] [Accepted: 08/31/2016] [Indexed: 12/19/2022] Open
Abstract
Galectins are proteins involved in diverse cellular contexts due to their capacity to decipher and respond to the information encoded by β-galactoside sugars. In particular, human galectin-4, normally expressed in the healthy gastrointestinal tract, displays differential expression in cancerous tissues and is considered a potential drug target for liver and lung cancer. Galectin-4 is a tandem-repeat galectin characterized by two carbohydrate recognition domains connected by a linker-peptide. Despite their relevance to cell function and pathogenesis, structural characterization of full-length tandem-repeat galectins has remained elusive. Here, we investigate galectin-4 using X-ray crystallography, small- and wide-angle X-ray scattering, molecular modelling, molecular dynamics simulations, and differential scanning fluorimetry assays and describe for the first time a structural model for human galectin-4. Our results provide insight into the structural role of the linker-peptide and shed light on the dynamic characteristics of the mechanism of carbohydrate recognition among tandem-repeat galectins.
Collapse
Affiliation(s)
- Joane K. Rustiguel
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, SP, Brazil
| | - Ricardo O. S. Soares
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, SP, Brazil
| | | | | | | | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Marcelo Dias-Baruffi
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, SP, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, SP, Brazil
| |
Collapse
|
22
|
Rustiguel JK, Kumagai PS, Dias-Baruffi M, Costa-Filho AJ, Nonato MC. Recombinant expression, purification and preliminary biophysical and structural studies of C-terminal carbohydrate recognition domain from human galectin-4. Protein Expr Purif 2015; 118:39-48. [PMID: 26432949 DOI: 10.1016/j.pep.2015.09.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 07/02/2015] [Revised: 09/26/2015] [Accepted: 09/26/2015] [Indexed: 01/16/2023]
Abstract
Galectin-4 (Gal4), a tandem-repeat type galectin, is expressed in healthy epithelium of the gastrointestinal tract. Altered levels of Gal4 expression are associated with different types of cancer, suggesting its usage as a diagnostic marker as well as target for drug development. The functional data available for this class of proteins suggest that the wide spectrum of cellular activities reported for Gal4 relies on distinct glycan specificity and structural characteristics of its two carbohydrate recognition domains. In the present work, two independent constructs for recombinant expression of the C-terminal domain of human galectin-4 (hGal4-CRD2) were developed. His6-tagged and untagged recombinant proteins were overexpressed in Escherichia coli, and purified by affinity chromatography followed by gel filtration. Correct folding and activity of hGal4-CRD2 were assessed by circular dichroism and fluorescence spectroscopies, respectively. Diffraction quality crystals were obtained by vapor-diffusion sitting drop setup and the crystal structure of CRD2 was solved by molecular replacement techniques at 1.78 Å resolution. Our work describes the development of important experimental tools that will allow further studies in order to correlate structure and binding properties of hGal4-CRD2 and human galectin-4 functional activities.
Collapse
Affiliation(s)
- Joane K Rustiguel
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café, s/n, 14040-903 Ribeirão Preto-SP, Brazil
| | - Patricia S Kumagai
- Grupo de Biofísica Molecular Sérgio Mascarenhas, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone, 1100, 13563-120 São Carlos-SP, Brazil
| | - Marcelo Dias-Baruffi
- Laboratório de Glicoimunologia, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café, s/n, 14040-903 Ribeirão Preto-SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, 14040-901 Ribeirão Preto-SP, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café, s/n, 14040-903 Ribeirão Preto-SP, Brazil.
| |
Collapse
|
23
|
Reis RAG, Lorenzato E, Silva VC, Nonato MC. Recombinant production, crystallization and crystal structure determination of dihydroorotate dehydrogenase from Leishmania (Viannia) braziliensis. Acta Crystallogr F Struct Biol Commun 2015; 71:547-52. [PMID: 25945707 DOI: 10.1107/s2053230x15000886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/15/2015] [Indexed: 11/11/2022]
Abstract
The enzyme dihydroorotate dehydrogenase (DHODH) is a flavoenzyme that catalyses the oxidation of dihydroorotate to orotate in the de novo pyrimidine-biosynthesis pathway. In this study, a reproducible protocol for the heterologous expression of active dihydroorotate dehydrogenase from Leishmania (Viannia) braziliensis (LbDHODH) was developed and its crystal structure was determined at 2.12 Å resolution. L. (V.) braziliensis is the species responsible for the mucosal form of leishmaniasis, a neglected disease for which no cure or effective therapy is available. Analyses of sequence, structural and kinetic features classify LbDHODH as a member of the class 1A DHODHs and reveal a very high degree of structural conservation with the previously reported structures of orthologous trypanosomatid enzymes. The relevance of nucleotide-biosynthetic pathways for cell metabolism together with structural and functional differences from the respective host enzyme suggests that inhibition of LbDHODH could be exploited for antileishmanicidal drug development. The present work provides the framework for further integrated in vitro, in silico and in vivo studies as a new tool to evaluate DHODH as a drug target against trypanosomatid-related diseases.
Collapse
Affiliation(s)
- Renata Almeida Garcia Reis
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Avenida Café S/N, 14040-903 Ribeirão Preto-SP, Brazil
| | - Eder Lorenzato
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Avenida Café S/N, 14040-903 Ribeirão Preto-SP, Brazil
| | - Valeria Cristina Silva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Avenida Café S/N, 14040-903 Ribeirão Preto-SP, Brazil
| | - Maria Cristina Nonato
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Avenida Café S/N, 14040-903 Ribeirão Preto-SP, Brazil
| |
Collapse
|
24
|
Pádua RAP, Tomaleri GP, Reis RAG, David JS, Silva VC, Pinheiro MP, Nonato MC. ThermoFMN - A Thermofluor Assay Developed for Ligand-Screening as an Alternative Strategy for Drug Discovery. J BRAZIL CHEM SOC 2014. [DOI: 10.5935/0103-5053.20140157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
25
|
Pereira de Pádua RA, Nonato MC. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of recombinant human fumarase. Acta Crystallogr F Struct Biol Commun 2013; 70:120-2. [PMID: 24419633 DOI: 10.1107/s2053230x13033955] [Citation(s) in RCA: 11] [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] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 12/16/2013] [Indexed: 11/10/2022]
Abstract
Human fumarase (HsFH) is a well-known citric acid cycle enzyme and is therefore a key component in energy metabolism. Genetic studies on human patients have shown that polymorphisms in the fumarase gene are responsible for diseases such as hereditary leiomyomatosis and renal cell cancer. As a first step in unravelling the molecular basis of the mechanism of fumarase deficiency in genetic disorders, the HsFH gene was cloned in pET-28a, heterologously expressed in Escherichia coli, purified by nickel-affinity chromatography and crystallized using the vapour-diffusion technique. X-ray diffraction experiments were performed at a synchrotron source and the structure was solved at 2.1 Å resolution by molecular replacement.
Collapse
Affiliation(s)
- Ricardo Augusto Pereira de Pádua
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - Universidade de São Paulo, Avenida do Café s/n, 14040-903 Ribeirão Preto-SP, Brazil
| | - Maria Cristina Nonato
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto - Universidade de São Paulo, Avenida do Café s/n, 14040-903 Ribeirão Preto-SP, Brazil
| |
Collapse
|
26
|
Rustiguel JK, Pinheiro MP, Araújo APU, Nonato MC. Crystallization and preliminary X-ray diffraction analysis of recombinant chlorocatechol 1,2-dioxygenase from Pseudomonas putida. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:507-9. [PMID: 21505253 PMCID: PMC3080162 DOI: 10.1107/s174430911100635x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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: 01/21/2011] [Accepted: 02/19/2011] [Indexed: 11/10/2022]
Abstract
Chlorocatechol 1,2-dioxygenase from the Gram-negative bacterium Pseudomonas putida (Pp 1,2-CCD) is considered to be an important biotechnological tool owing to its ability to process a broad spectrum of organic pollutants. In the current work, the crystallization, crystallographic characterization and phasing of the recombinant Pp 1,2-CCD enzyme are described. Reddish-brown crystals were obtained in the presence of polyethylene glycol and magnesium acetate by utilizing the vapour-diffusion technique in sitting drops. Crystal dehydration was the key step in obtaining data sets, which were collected on the D03B-MX2 beamline at the CNPEM/MCT - LNLS using a MAR CCD detector. Pp 1,2-CCD crystals belonged to space group P6(1)22 and the crystallographic structure of Pp 1,2-CCD has been solved by the MR-SAD technique using Fe atoms as scattering centres and the coordinates of 3-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus (PDB entry 2boy) as the search model. The initial model, which contains three molecules in the asymmetric unit, has been refined to 3.4 Å resolution.
Collapse
Affiliation(s)
- Joane Kathelen Rustiguel
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto – USP, Avenida do Café, Ribeirão Preto, 14040-903 São Paulo, Brazil
| | - Matheus Pinto Pinheiro
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto – USP, Avenida do Café, Ribeirão Preto, 14040-903 São Paulo, Brazil
| | - Ana Paula Ulian Araújo
- Grupo de Biofísica Molecular, Instituto de Física de São Carlos – USP, Avenida do Trabalhador Sãocarlense, São Carlos, 13560-970 São Paulo, Brazil
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto – USP, Avenida do Café, Ribeirão Preto, 14040-903 São Paulo, Brazil
| |
Collapse
|
27
|
Alves RM, Feliciano PR, Sampaio SV, Nonato MC. A rational protocol for the successful crystallization of L-amino-acid oxidase from Bothrops atrox. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:475-8. [PMID: 21505245 DOI: 10.1107/s1744309111003770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 01/29/2011] [Indexed: 11/10/2022]
Abstract
Despite the valuable contributions of robotics and high-throughput approaches to protein crystallization, the role of an experienced crystallographer in the evaluation and rationalization of a crystallization process is still crucial to obtaining crystals suitable for X-ray diffraction measurements. In this work, the difficult task of crystallizing the flavoenzyme L-amino-acid oxidase purified from Bothrops atrox snake venom was overcome by the development of a protocol that first required the identification of a non-amorphous precipitate as a promising crystallization condition followed by the implementation of a methodology that combined crystallization in the presence of oil and seeding techniques. Crystals were obtained and a complete data set was collected to 2.3 Å resolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 73.64, b = 123.92, c = 105.08 Å, β = 96.03°. There were four protein subunits in the asymmetric unit, which gave a Matthews coefficient V(M) of 2.12 Å(3) Da(-1), corresponding to 42% solvent content. The structure has been solved by molecular-replacement techniques.
Collapse
Affiliation(s)
- Raquel Melo Alves
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirao Preto-FCFRP-USP, Avenida do Café s/n, Ribeirão Preto, 14040-903 São Paulo, Brazil
| | | | | | | |
Collapse
|
28
|
Kriminski S, Caylor CL, Nonato MC, Finkelstein KD, Thorne RE. Flash-cooling and annealing of protein crystals. Acta Crystallogr D Biol Crystallogr 2002; 58:459-71. [PMID: 11856832 DOI: 10.1107/s0907444902000112] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2001] [Accepted: 01/02/2002] [Indexed: 11/10/2022]
Abstract
Flash-cooling and annealing of macromolecular crystals have been investigated using in situ X-ray imaging, diffraction-peak lineshape measurements and conventional crystallographic diffraction. The dominant mechanisms by which flash-cooling creates disorder are suggested and a fixed-temperature annealing protocol for reducing this disorder is demonstrated that should be more reliable and flexible than existing protocols. Flash-cooling tetragonal lysozyme crystals degrades diffraction resolution and broadens the distributions of lattice orientations (mosaicity) and lattice spacings. The diffraction resolution strongly correlates with the width of the lattice-spacing distribution. Annealing at fixed temperatures of 253 and 233 K consistently reduces the lattice-spacing spread and improves the resolution for annealing times up to approximately 30s. X-ray images show that this improvement arises from the formation of well ordered domains with characteristic sizes >10 microm and narrower mosaicities than the crystal as a whole. Flash-cooled triclinic crystals of lysozyme, which have a smaller water content than the tetragonal form, diffract to higher resolution with smaller mosaicities and exhibit pronounced ordered domain structure even before annealing. It is suggested that differential thermal expansion of the protein lattice and solvent may be the primary cause of flash-cooling-induced disorder. Mechanisms by which annealing at T << 273 K reduce this disorder are discussed.
Collapse
Affiliation(s)
- S Kriminski
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY 14853, USA
| | | | | | | | | |
Collapse
|
29
|
Batista IF, Nonato MC, Bonfadini MR, Beltramini LM, Oliva ML, Sampaio MU, Sampaio CA, Garratt RC. Preliminary crystallographic studies of EcTI, a serine proteinase inhibitor from Enterolobium contortisiliquum seeds. Acta Crystallogr D Biol Crystallogr 2001; 57:602-4. [PMID: 11264595 DOI: 10.1107/s0907444901001810] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2000] [Accepted: 01/23/2001] [Indexed: 11/10/2022]
Abstract
Enterolobium contortisiliquum trypsin inhibitor (EcTI) belongs to the Kunitz family of plant inhibitors, which are widely distributed in nature, especially in plant seeds. EcTI is composed of two polypeptide chains with a total of 174 residues, homologous to other inhibitors from the same family. EcTI crystals, which were obtained with the acupuncture-gel technique, diffract to 2.0 A resolution and belong to space group P2(1), with unit-cell parameters a = 37.12, b = 38.42, c = 54.08 A, beta = 98.08 degrees. Molecular-replacement techniques using Erythrina caffra trypsin inhibitor (PDB code 1tie) as the search model indicate one monomer in the asymmetric unit. The secondary-structure content of EcTI was determined by circular dichroism spectroscopy, yielding values compatible with the expected topology.
Collapse
Affiliation(s)
- I F Batista
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP/EPM), Rua Três de Maio 100, CEP 04044-020 Sao Paulo SP, Brazil.
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Nonato MC, Garratt RC, Mascarenhas YP, Jesus WD, Assakura MT, Serrano SM, Oliva G. Crystallization and preliminary crystallographic studies of a phospholipase A2 from the venom of the Brazilian snake Bothrops moojeni. Acta Crystallogr D Biol Crystallogr 2001; 57:599-601. [PMID: 11264594 DOI: 10.1107/s0907444901001639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2000] [Accepted: 01/23/2001] [Indexed: 11/10/2022]
Abstract
A phospholipase A(2) purified from the venom of the snake Bothrops moojeni has been crystallized by vapour-diffusion techniques in hanging drops at 291 K. The crystals, which were grown in the absence of Ca(2+), belong to the cubic system, space group P432, with unit-cell parameters a = b = c = 91.86 A, and contain one molecule in the asymmetric unit (V(M) = 2.71 A(3) Da(-1)). X-ray diffraction experiments provide data to 2.35 A resolution collected on a rotating-anode home source at cryogenic temperatures. The structure has been solved via molecular-replacement techniques using a single monomer of the crystallographic structure of the phospholipase from the Western diamondback rattlesnake (Crotalus atrox) as a search model.
Collapse
Affiliation(s)
- M C Nonato
- Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos SP, Brazil.
| | | | | | | | | | | | | |
Collapse
|
31
|
Silva GDDF, Duarte LP, Paes HCDS, Sousa JRD, Nonato MC, Portezani PJ, Mascarenhas YP. 3-Epiabruslactone A, a New Triterpene Lactone Isolated from Austroplenckia populnea. J BRAZIL CHEM SOC 1998. [DOI: 10.1590/s0103-50531998000500009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
32
|
Nonato MC, Garratt RC, Schleicher CH, Santomé JA, Oliva G. Crystallization and preliminary crystallographic studies of calgranulin C, an S100-like calcium-binding protein from pig granulocytes. Acta Crystallogr D Biol Crystallogr 1997; 53:200-2. [PMID: 15299956 DOI: 10.1107/s0907444996012577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Calgranulin C (CAGC) from pig granulocytes has been crystallized and X-ray diffraction data have been collected to 2.6 A resolution. The crystals belong to the trigonal system, space group P3(1)21 or P3(2)21, cell parameters a = b = 54.35 (2), c = 141.32 (5) A and probably contain two molecules in the asymmetric unit. CAGC is amongst the first reported typical S100-1ike calcium-binding protein to be crystallized and studied by X-ray crystallography.
Collapse
Affiliation(s)
- M C Nonato
- Instituto de Física de São Carlos, Universidade de São Paulo, Brazil
| | | | | | | | | |
Collapse
|