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Andrade CH, Nonato MC, da Silva Emery F. Introducing CRAFT: The Center for Research and Advancement in Fragments and molecular Targets. ACS Med Chem Lett 2024; 15:1174-1177. [PMID: 39140068 PMCID: PMC11318094 DOI: 10.1021/acsmedchemlett.4c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024] Open
Abstract
We introduce the Center for Research and Advancement in Fragments and Molecular Targets (CRAFT), a pioneering research center established in 2021 through a collaboration between the University of São Paulo (USP) and the Federal University of Goiás (UFG). CRAFT integrates fragment-based drug discovery (FBDD), artificial intelligence (AI), and structural biology to develop novel therapeutic strategies. We have created fragment and target libraries and utilize AI models to streamline the drug discovery process. We invite the global scientific community to collaborate with us in addressing neglected diseases, with the goal of enhancing research capabilities and fostering scientific innovation across Latin America.
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Affiliation(s)
- Carolina Horta Andrade
- Center
for Research and Advancement in Fragments and Molecular Targets (CRAFT),
School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, São Paulo 05508-060, Brazil
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, Goiás 74605-170, Brazil
- Center
for Excellence in Artificial Intelligence (CEIA), Institute of Informatics, Universidade Federal de Goiás, Goiânia, Goiás 74605-170, Brazil
| | - Maria Cristina Nonato
- Center
for Research and Advancement in Fragments and Molecular Targets (CRAFT),
School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, São Paulo 05508-060, Brazil
- Protein
Crystallography Laboratory, Department of Biomolecular Sciences, School
of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, São Paulo 05508-060, Brazil
| | - Flavio da Silva Emery
- Center
for Research and Advancement in Fragments and Molecular Targets (CRAFT),
School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, São Paulo 05508-060, Brazil
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2
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Purificação A, Silva-Mendonça S, Cruz LV, Sacramento CQ, Temerozo JR, Fintelman-Rodrigues N, de Freitas CS, Godoi BF, Vaidergorn MM, Leite JA, Salazar Alvarez LC, Freitas MV, Silvac MFB, Martin BA, Lopez RFV, Neves BJ, Costa FTM, Souza TML, da Silva Emery F, Andrade CH, Nonato MC. Unveiling the Antiviral Capabilities of Targeting Human Dihydroorotate Dehydrogenase against SARS-CoV-2. ACS OMEGA 2024; 9:11418-11430. [PMID: 38496952 PMCID: PMC10938441 DOI: 10.1021/acsomega.3c07845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 03/19/2024]
Abstract
The urgent need for effective treatments against emerging viral diseases, driven by drug-resistant strains and new viral variants, remains critical. We focus on inhibiting the human dihydroorotate dehydrogenase (HsDHODH), one of the main enzymes responsible for pyrimidine nucleotide synthesis. This strategy could impede viral replication without provoking resistance. We evaluated naphthoquinone fragments, discovering potent HsDHODH inhibition with IC50 ranging from 48 to 684 nM, and promising in vitro anti-SARS-CoV-2 activity with EC50 ranging from 1.2 to 2.3 μM. These compounds exhibited low toxicity, indicating potential for further development. Additionally, we employed computational tools such as molecular docking and quantitative structure-activity relationship (QSAR) models to analyze protein-ligand interactions, revealing that these naphthoquinones exhibit a protein binding pattern similar to brequinar, a potent HsDHODH inhibitor. These findings represent a significant step forward in the search for effective antiviral treatments and have great potential to impact the development of new broad-spectrum antiviral drugs.
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Affiliation(s)
- Aline
D. Purificação
- Protein
Crystallography Laboratory, Department of Biomolecular Sciences, School
of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
- Center
for the Research and Advancement in Fragments and molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
| | - Sabrina Silva-Mendonça
- Center
for the Research and Advancement in Fragments and molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
| | - Luiza V. Cruz
- Center
for the Research and Advancement in Fragments and molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
| | - Carolina Q. Sacramento
- Laboratory
of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de
Janeiro 21040-900, RJ, Brazil
- National
Institute for Science and Technology on Innovation in Diseases of
Neglected Populations (INCT/IDPN), Center for Technological Development
in Health (CDTS), Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Jairo R. Temerozo
- Laboratory
of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de
Janeiro 21040-900, RJ, Brazil
- National
Institute for Science and Technology on Innovation in Diseases of
Neglected Populations (INCT/IDPN), Center for Technological Development
in Health (CDTS), Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
- National
Institute for Science and Technology on Neuroimmunomodulation, Oswaldo
Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratory
of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de
Janeiro 21040-900, RJ, Brazil
- National
Institute for Science and Technology on Innovation in Diseases of
Neglected Populations (INCT/IDPN), Center for Technological Development
in Health (CDTS), Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Caroline Souza de Freitas
- Laboratory
of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de
Janeiro 21040-900, RJ, Brazil
- National
Institute for Science and Technology on Innovation in Diseases of
Neglected Populations (INCT/IDPN), Center for Technological Development
in Health (CDTS), Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Bruna Fleck Godoi
- Center
for the Research and Advancement in Fragments and molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
- Laboratory
of Heterocyclic and Medicinal Chemistry (QHeteM), Department of Pharmaceutical
Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirao Preto 05508-060, SP, Brazil
| | - Miguel Menezes Vaidergorn
- Center
for the Research and Advancement in Fragments and molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
- Laboratory
of Heterocyclic and Medicinal Chemistry (QHeteM), Department of Pharmaceutical
Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirao Preto 05508-060, SP, Brazil
| | - Juliana Almeida Leite
- Laboratory
of Tropical Diseases, Department of Genetics, Evolution, Microbiology
and Immunology, Institute of Biology, Unicamp, Campinas 13.083-857, SP, Brazil
| | - Luis Carlos Salazar Alvarez
- Laboratory
of Tropical Diseases, Department of Genetics, Evolution, Microbiology
and Immunology, Institute of Biology, Unicamp, Campinas 13.083-857, SP, Brazil
| | - Murillo V. Freitas
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
| | - Meryck F. B. Silvac
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
- Laboratory
of Cheminformatics, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
| | - Bianca A. Martin
- Innovation
Center in Nanostructured Systems and Topical Administration (NanoTop),
School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
| | - Renata F. V. Lopez
- Innovation
Center in Nanostructured Systems and Topical Administration (NanoTop),
School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
| | - Bruno J. Neves
- Laboratory
of Cheminformatics, Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
| | - Fabio T. M. Costa
- Laboratory
of Tropical Diseases, Department of Genetics, Evolution, Microbiology
and Immunology, Institute of Biology, Unicamp, Campinas 13.083-857, SP, Brazil
| | - Thiago M. L. Souza
- Laboratory
of Immunopharmacology, Oswaldo Cruz Institute, Fiocruz, Rio de
Janeiro 21040-900, RJ, Brazil
- National
Institute for Science and Technology on Innovation in Diseases of
Neglected Populations (INCT/IDPN), Center for Technological Development
in Health (CDTS), Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Flavio da Silva Emery
- Center
for the Research and Advancement in Fragments and molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
- Laboratory
of Heterocyclic and Medicinal Chemistry (QHeteM), Department of Pharmaceutical
Sciences, School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirao Preto 05508-060, SP, Brazil
| | - Carolina Horta Andrade
- Center
for the Research and Advancement in Fragments and molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
- Center
for Excellence in Artificial Intelligence (CEIA), Institute of Informatics, Universidade Federal de Goiás, Goiânia 74605-170, GO, Brazil
| | - M. Cristina Nonato
- Protein
Crystallography Laboratory, Department of Biomolecular Sciences, School
of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
- Center
for the Research and Advancement in Fragments and molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto 05508-060, SP, Brazil
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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] [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.
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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.
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4
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Sousa FM, Pires P, Barreto A, Refojo PN, Silva MS, Fernandes PB, Carapeto AP, Robalo TT, Rodrigues MS, Pinho MG, Cabrita EJ, Pereira MM. Unveiling the membrane bound dihydroorotate: Quinone oxidoreductase from Staphylococcus aureus. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148948. [PMID: 36481274 DOI: 10.1016/j.bbabio.2022.148948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Staphylococcus aureus is an opportunistic pathogen and one of the most frequent causes for community acquired and nosocomial bacterial infections. Even so, its energy metabolism is still under explored and its respiratory enzymes have been vastly overlooked. In this work, we unveil the dihydroorotate:quinone oxidoreductase (DHOQO) from S. aureus, the first example of a DHOQO from a Gram-positive organism. This protein was shown to be a FMN containing menaquinone reducing enzyme, presenting a Michaelis-Menten behaviour towards the two substrates, which was inhibited by Brequinar, Leflunomide, Lapachol, HQNO, Atovaquone and TFFA with different degrees of effectiveness. Deletion of the DHOQO coding gene (Δdhoqo) led to lower bacterial growth rates, and effected in cell morphology and metabolism, most importantly in the pyrimidine biosynthesis, here systematized for S. aureus MW2 for the first time. This work unveils the existence of a functional DHOQO in the respiratory chain of the pathogenic bacterium S. aureus, enlarging the understanding of its energy metabolism.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia Pires
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Andreia Barreto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Patrícia N Refojo
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Micael S Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Pedro B Fernandes
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Ana P Carapeto
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago T Robalo
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mário S Rodrigues
- University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal; Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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5
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Li J, Li YA, Wu G, Zhang X. Metal-Free Aminohalogenation of Quinones With Alkylamines and NXS at Room Temperature. Front Chem 2022; 10:917371. [PMID: 35707457 PMCID: PMC9189915 DOI: 10.3389/fchem.2022.917371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
A simple and practical strategy for intermolecular aminohalogenation of quinone with alkyl amines and NXS was developed, in which haloamines generated in situ were employed as bifunctional reagents. The reaction system is reliable, efficient and wide in substrate range, which is suitable for the two-fold aminochlorination of 1, 4-benzoquinones, large-scale reaction and late-stage modification of pharmaceuticals.
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Affiliation(s)
- Jia Li
- Department of Neurology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yu-An Li
- Department of Orthopaedics Surgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Yu-An Li, ; Ge Wu,
| | - Ge Wu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Yu-An Li, ; Ge Wu,
| | - Xu Zhang
- Department of Neurology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Egu SA, Onoabedje EA, Okoro UC, Khan KM, Hameed A, Ali I, Iftekhar S, Odin EM, Shamim S. The Synthesis and Chemistry of Quinolinediones and their Carbocyclic Analogs. MINI-REV ORG CHEM 2021. [DOI: 10.2174/1570193x18666211007120708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Quinoline-5,8-dione and naphthoquinone nuclei are very important substructures in industrial chemicals and pharmaceuticals. These compounds exhibit a wide variety of activities, including activity as antifungal, antibacterial, antimalarial, antineoplastic, anticoagulant, anticancer, antiviral, radical scavenging, antiplatelet, trypanocidal, cytotoxic and antineoplastic agents. Currently, several research articles about the importance of many natural and synthetic drugs containing quinolinequinone have been reported. This review covers the progress in quinolinequinone and naphthoquinone chemistry over the last five decades.
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Affiliation(s)
- Samuel Attah Egu
- Department of Pure and Industrial Chemistry, Kogi State University, Anyigba, Kogi State, Nigeria
| | | | - Uchechukwu Chris Okoro
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Abdul Hameed
- Department of Chemistry, University of Sahiwal, Sahiwal 57000, Pakistan
| | - Irfan Ali
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Shafia Iftekhar
- 5 Department of Chemistry, University of Sahiwal, Sahiwal 57000, Pakistan
| | - Eboh Monday Odin
- Department of Pure and Industrial Chemistry, Kogi State University, Anyigba, Kogi State, Nigeria
| | - Shahbaz Shamim
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
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7
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Zhang L, Zhang G, Xu S, Song Y. Recent advances of quinones as a privileged structure in drug discovery. Eur J Med Chem 2021; 223:113632. [PMID: 34153576 DOI: 10.1016/j.ejmech.2021.113632] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/03/2021] [Accepted: 06/06/2021] [Indexed: 01/08/2023]
Abstract
Privileged structures are conductive to discover novel bioactive substances because they can bind to multiple targets with high affinity. Quinones are considered to be a privileged structure and useful template for the design of new compounds with potential pharmacological activity. This article presents the recent developments (2014-2021 update) of quinones in the fields of antitumor, antibacterial, antifungal, antiviral, anti-Alzheimer's disease (AD) and antimalarial, mainly focusing on biological activities, structural modification and mechanism of action.
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Affiliation(s)
- Li Zhang
- Department of Pharmacy, Jinan Second People's Hospital, 250001, 148 Jingyi Road, Jinan, PR China
| | - Guiying Zhang
- Department of Pharmacy, Rizhao People's Hospital, 276800, 126 Tai'an Road, Rizhao, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, 250012, Jinan, PR China.
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8
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Zhou Y, Tao L, Zhou X, Zuo Z, Gong J, Liu X, Zhou Y, Liu C, Sang N, Liu H, Zou J, Gou K, Yang X, Zhao Y. DHODH and cancer: promising prospects to be explored. Cancer Metab 2021; 9:22. [PMID: 33971967 PMCID: PMC8107416 DOI: 10.1186/s40170-021-00250-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/10/2021] [Indexed: 02/08/2023] Open
Abstract
Human dihydroorotate dehydrogenase (DHODH) is a flavin-dependent mitochondrial enzyme catalyzing the fourth step in the de novo pyrimidine synthesis pathway. It is originally a target for the treatment of the non-neoplastic diseases involving in rheumatoid arthritis and multiple sclerosis, and is re-emerging as a validated therapeutic target for cancer therapy. In this review, we mainly unravel the biological function of DHODH in tumor progression, including its crucial role in de novo pyrimidine synthesis and mitochondrial respiratory chain in cancer cells. Moreover, various DHODH inhibitors developing in the past decades are also been displayed, and the specific mechanism between DHODH and its additional effects are illustrated. Collectively, we detailly discuss the association between DHODH and tumors in recent years here, and believe it will provide significant evidences and potential strategies for utilizing DHODH as a potential target in preclinical and clinical cancer therapies.
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Affiliation(s)
- Yue Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Lei Tao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Xia Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Zeping Zuo
- The Laboratory of Anesthesiology and Critical Care Medicine, Translational Neuroscience Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jin Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Xiaocong Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Yang Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Chunqi Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Na Sang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Huan Liu
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Jiao Zou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Kun Gou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Xiaowei Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Yinglan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China. .,West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
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Yu P, Li DD, Wang L, Zhang LH, Cao FL, Fang XY, Zhao LG. Identification of dihydroorotate dehydrogenase as a protein target of ginkgolic acid by molecular docking and dynamics. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Investigating the amino acid sequences of membrane bound dihydroorotate:quinone oxidoreductases (DHOQOs): Structural and functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148321. [PMID: 32991846 DOI: 10.1016/j.bbabio.2020.148321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/26/2022]
Abstract
Dihydroorotate:quinone oxidoreductases (DHOQOs) are membrane bound enzymes responsible for oxidizing dihydroorotate (DHO) to orotate with concomitant reduction of quinone to quinol. They have FMN as prosthetic group and are part of the monotopic quinone reductase superfamily. These enzymes are also members of the dihydroorotate dehydrogenases (DHODHs) family, which besides membrane bound DHOQOs, class 2, includes soluble enzymes which reduce either NAD+ or fumarate, class 1. As key enzymes in both the de novo pyrimidine biosynthetic pathway as well as in the energetic metabolism, inhibitors of DHOQOs have been investigated as leads for therapeutics in cancer, immunological disorders and bacterial/viral infections. This work is a thorough bioinformatic approach on the structural conservation and taxonomic distribution of DHOQOs. We explored previously established structural/functional hallmarks of these enzymes, while searching for uncharacterized common elements. We also discuss the cellular role of DHOQOs and organize the identified protein sequences within six sub-classes 2A to 2F, according to their taxonomic origin and sequence traits. We concluded that DHOQOs are present in Archaea, Eukarya and Bacteria, including the first recognition in Gram-positive organisms. DHOQOs can be the single dihydroorotate dehydrogenase encoded in the genome of a species, or they can coexist with other DHODHs, as the NAD+ or fumarate reducing enzymes. Furthermore, we show that the type of catalytic base present in the active site is not an absolute criterium to distinguish between class 1 and class 2 enzymes. We propose the existence of a quinone binding motif ("ExAH") adjacent to a hydrophobic cavity present in the membrane interacting N-terminal domain.
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de Mori RM, Aleixo MAA, Zapata LCC, Calil FA, Emery FS, Nonato MC. Structural basis for the function and inhibition of dihydroorotate dehydrogenase from Schistosoma mansoni. FEBS J 2020; 288:930-944. [PMID: 32428996 DOI: 10.1111/febs.15367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/06/2020] [Accepted: 05/14/2020] [Indexed: 12/13/2022]
Abstract
Schistosomiasis is a serious public health problem, prevalent in tropical and subtropical areas, especially in poor communities without access to safe drinking water and adequate sanitation. Transmission has been reported in 78 countries, and its control depends on a single drug, praziquantel, which has been used over the past 30 years. Our work is focused on exploiting target-based drug discovery strategies to develop new therapeutics to treat schistosomiasis. In particular, we are interested in evaluating the enzyme dihydroorotate dehydrogenase (DHODH) as a drug target. DHODH is a flavoenzyme that catalyzes the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway. Previously, we identified atovaquone, used in the treatment of malaria, and its analogues, as potent and selective inhibitors against Schistosoma mansoni DHODH (SmDHODH). In the present article, we report the first crystal structure of SmDHODH in complex with the atovaquone analogue inhibitor 2-((4-fluorophenyl)amino)-3-hydroxynaphthalene-1,4-dione (QLA). We discuss three major findings: (a) the open conformation of the active site loop and the unveiling of a novel transient druggable pocket for class 2 DHODHs; (b) the presence of a protuberant domain, only present in Schistosoma spp DHODHs, that was found to control and modulate the dynamics of the inhibitor binding site; (c) a detailed description of an unexpected binding mode for the atovaquone analogue to SmDHODH. Our findings contribute to the understanding of the catalytic mechanism performed by class 2 DHODHs and provide the molecular basis for structure-guided design of SmDHODH inhibitors. DATABASE: The structural data are available in Protein Data Bank (PDB) database under the accession code number 6UY4.
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Affiliation(s)
- Renan M de Mori
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Mariana A A Aleixo
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Luana C C Zapata
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Felipe A Calil
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Flávio S Emery
- Laboratório de Química Heterocíclica e Medicinal, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - M Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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Ribeiro LMBC, Fumagalli F, Mello RB, Froes TQ, da Silva MVS, Villamizar Gómez SM, Barros TF, Emery FS, Castilho MS. Structure-activity relationships and mechanism of action of tetragomycin derivatives as inhibitors of Staphylococcus aureus staphyloxanthin biosynthesis. Microb Pathog 2020; 144:104127. [PMID: 32169485 DOI: 10.1016/j.micpath.2020.104127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/13/2020] [Accepted: 03/06/2020] [Indexed: 12/31/2022]
Abstract
Despite the main strategy to overcome bacterial resistance has focused on the development of more potent antimicrobial agents, the evolutionary pressure caused by such drugs makes this strategy limited. Molecules that interfere with virulence factors appear as a promising alternative though, as they cause reduced selective pressure. As a matter of fact, staphyloxanthin biosynthesis inhibition (STXBI) has been pursued as promising strategy to reduce S. aureus virulence. Herein, we report the inhibitory profile of 27 tetrangomycin derivatives over staphyloxanthin production. The experimental result showed that naphthoquinone dehydro-α-lapachone (25 - EC50 = 57.29 ± 1.15 μM) and 2-Isopropylnaphtho[2,3-b]furan-4,9-dione (26 EC50 = 82.10 ± 1.09 μM) are the most potent compounds and suggest that hydrogen acceptor groups and lipophilic moieties decorating the naphthoquinone ring are crucial for STXBI. In addition, we present an in situ analysis, through RAMAN spectroscopy, that is inexpensive and might be employed to probe the mechanism of action of staphyloxanthin biosynthesis inhibitors. Therefore, our molecular simplification strategies afforded promising lead compounds for the development of drugs that modulate S. aureus staphyloxanthin biosynthesis.
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Affiliation(s)
- L M B C Ribeiro
- Programa de Pós-graduação Em Biotecnologia, Universidade Estadual de Feira de Santana, Brazil
| | - F Fumagalli
- Centro de Ciências da Saúde da Universidade Federal de Santa Maria, Brazil
| | - R B Mello
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Brazil
| | - T Q Froes
- Programa de Pós-graduação Em Biotecnologia, Universidade Estadual de Feira de Santana, Brazil
| | - M V S da Silva
- Instituto de Física da Universidade Federal da Bahia, Brazil
| | | | - T F Barros
- Faculdade de Farmácia da Universidade Federal da Bahia, Brazil
| | - F S Emery
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Brazil
| | - M S Castilho
- Programa de Pós-graduação Em Biotecnologia, Universidade Estadual de Feira de Santana, Brazil; Faculdade de Farmácia da Universidade Federal da Bahia, Brazil.
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