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Diaz-Martinez J, Kotzker W, Mendoza-Hernandez MA, Gadh RS, Hernandez-Fuentes GA, Bañuelos A, Guzmán-Esquivel J, Hong A, Delgado-Enciso OG, Geyer-Roberts E, Martinez-Fierro ML, Rodriguez-Sanchez IP, Garza-Veloz I, Canseco-Ávila LM, Delgado-Enciso I. Analysis of Survival Modification by Furosemide Use in a Cohort of Hospitalized COVID-19 Patients with Severe or Critical Disease in Mexico: Due to Its Chemical Structure, Furosemide Is More than Just a Diuretic. Pharmaceutics 2024; 16:920. [PMID: 39065617 PMCID: PMC11280466 DOI: 10.3390/pharmaceutics16070920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
In the ongoing fight against Coronavirus Disease 2019 (COVID-19), researchers are exploring potential treatments to improve outcomes, especially in severe cases. This includes investigating the repurposing of existing medications, such as furosemide, which is widely available. This study aimed to evaluate the impact of furosemide on mortality rates among COVID-19 patients with severe or critical illness. We assessed a cohort of 515 hospitalized adults who experienced a high mortality rate of 43.9%. Using a multivariate analysis with adjusted risk ratios (AdRRs), factors like smoking (AdRR 2.48, 95% CI 1.53-4.01, p < 0.001), a high Pneumonia Severity Index (PSI) score (AdRR 7.89, 95% CI 5.82-10.70, p < 0.001), mechanical ventilation (AdRR 23.12, 95% CI 17.28-30.92, p < 0.001), neutrophilia (AdRR 2.12, 95% CI 1.52-2.95, p < 0.001), and an elevated neutrophil-to-lymphocyte ratio (NLR) (AdRR 2.39, 95% CI 1.72-3.32, p < 0.001) were found to increase mortality risk. In contrast, vaccination and furosemide use were associated with reduced mortality risk (AdRR 0.58, p = 0.001 and 0.60, p = 0.008; respectively). Furosemide showed a pronounced survival benefit in patients with less severe disease (PSI < 120) and those not on hemodialysis, with mortality rates significantly lower in furosemide users (3.7% vs. 25.7%). A Kaplan-Meier analysis confirmed longer survival and better oxygenation levels in patients treated with furosemide. Furthermore, a Structure-Activity Relationship analysis revealed that furosemide's sulfonamide groups may interact with cytokine sites such as tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6), potentially explaining its beneficial effects in COVID-19 management. These findings suggest that furosemide could be a beneficial treatment option in certain COVID-19 patient groups, enhancing survival and improving oxygenation.
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Affiliation(s)
- Janet Diaz-Martinez
- Research Center in Minority Institutions, Robert Stempel College of Public Health, Florida International University, Miami, FL 33199, USA;
| | - Wayne Kotzker
- Florida Kidney Physicians, Panoramic Health Practice, Boca Raton, FL 33431, USA;
| | - Martha A. Mendoza-Hernandez
- Department of Molecular Medicine, School of Medicine, University of Colima, Colima 28040, Mexico; (M.A.M.-H.); (G.A.H.-F.); (O.G.D.-E.)
- COVID Unit, General Hospital Number 1, Mexican Institute of Social Security, Villa de Alvarez, Colima 29883, Mexico
| | - Rajdeep S. Gadh
- Florida Kidney Physicians, Panoramic Health Practice, Coral Springs, FL 33071, USA;
| | - Gustavo A. Hernandez-Fuentes
- Department of Molecular Medicine, School of Medicine, University of Colima, Colima 28040, Mexico; (M.A.M.-H.); (G.A.H.-F.); (O.G.D.-E.)
| | - Andrew Bañuelos
- Department GME (General Medicine Education), Hospital Corporation of America Westside, Westside, FL 33324, USA; (A.B.); (A.H.)
| | - José Guzmán-Esquivel
- Clinical Epidemiology Research Unit, Mexican Institute of Social Security, Villa de Alvarez, Colima 29883, Mexico;
| | - Angelina Hong
- Department GME (General Medicine Education), Hospital Corporation of America Westside, Westside, FL 33324, USA; (A.B.); (A.H.)
| | - Osiris G. Delgado-Enciso
- Department of Molecular Medicine, School of Medicine, University of Colima, Colima 28040, Mexico; (M.A.M.-H.); (G.A.H.-F.); (O.G.D.-E.)
| | - Elizabeth Geyer-Roberts
- Department of Medicine, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova University, Fort Lauderdale, FL 33328, USA;
| | - Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico; (M.L.M.-F.); (I.G.-V.)
| | - Iram P. Rodriguez-Sanchez
- Molecular and Structural Physiology Laboratory, School of Biological Sciences, Autonomous University of Nuevo Leon, San Nicolas de los Garza 66455, Mexico;
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Academic Unit of Human Medicine and Health Sciences, Autonomous University of Zacatecas, Zacatecas 98160, Mexico; (M.L.M.-F.); (I.G.-V.)
| | - Luis M. Canseco-Ávila
- Diagnostic and Molecular Biomedicine Laboratory, Faculty of Chemistry Sciences, Campus IV, Autonomous University of Chiapas, Tapachula 30700, Mexico;
| | - Ivan Delgado-Enciso
- Department of Molecular Medicine, School of Medicine, University of Colima, Colima 28040, Mexico; (M.A.M.-H.); (G.A.H.-F.); (O.G.D.-E.)
- Department of Research, Colima Cancerology State Institute, Mexican Institute of Social Security (IMSS-Bienestar) Colima, Colima 28085, Mexico
- Department of Dietetics and Nutrition, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL 33199, USA
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Alves de Lima e Silva A, Rio-Tinto A. Ebselen: A Promising Repurposing Drug to Treat Infections Caused by Multidrug-Resistant Microorganisms. Interdiscip Perspect Infect Dis 2024; 2024:9109041. [PMID: 38586592 PMCID: PMC10998725 DOI: 10.1155/2024/9109041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/02/2024] [Indexed: 04/09/2024] Open
Abstract
Bacterial multiresistance to drugs is a rapidly growing global phenomenon. New resistance mechanisms have been described in different bacterial pathogens, threatening the effective treatment of even common infectious diseases. The problem worsens in infections associated with biofilms because, in addition to the pathogen's multiresistance, the biofilm provides a barrier that prevents antimicrobial access. Several "non-antibiotic" drugs have antimicrobial activity, even though it is not their primary therapeutic purpose. However, due to the urgent need to develop effective antimicrobials to treat diseases caused by multidrug-resistant pathogens, there has been an increase in research into "non-antibiotic" drugs to offer an alternative therapy through the so-called drug repositioning or repurposing. The prospect of new uses for existing drugs has the advantage of reducing the time and effort required to develop new compounds. Moreover, many drugs are already well characterized regarding toxicity and pharmacokinetic/pharmacodynamic properties. Ebselen has shown promise for use as a repurposing drug for antimicrobial purposes. It is a synthetic organoselenium with anti-inflammatory, antioxidant, and cytoprotective activity. A very attractive factor for using ebselen is that, in addition to potent antimicrobial activity, its minimum inhibitory concentration is very low for microbial pathogens.
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Affiliation(s)
- Agostinho Alves de Lima e Silva
- Laboratory of Biology and Physiology of Microorganisms, Biomedical Institute, DMP, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro 20211-030, Brazil
| | - André Rio-Tinto
- Laboratory of Pathogenic Cocci and Microbiota, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-853, Brazil
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3
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Andrés Libreros-Zúñiga G, Pavão E Pavão D, de Morais Barroso V, Cristina de Moraes Roso Mesquita N, Fehelberg Pinto Braga S, Oliva G, Salgado Ferreira R, Ishida K, Vinicius Bertacine Dias M. Integration of biophysical and biological approaches to validate fragment-like compounds targeting l,d-transpeptidases from Mycobacterium tuberculosis. Bioorg Chem 2024; 142:106960. [PMID: 37944368 DOI: 10.1016/j.bioorg.2023.106960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Tuberculosis is one of the major causes of death worldwide; more than a million people die every year because of this infection. The constant emergency of Mycobacterium tuberculosis resistant strains against the most used treatments also contributes to the burden caused by this disease. Consequently, the development of new alternative therapies against this disease is constantly required. In recent years, only a few molecules have reached the market as new antituberculosis agents. The mycobacterial cell wall biosynthesis is for a longstanding considered an important target for drug development. Particularly, in M. tuberculosis, the peptidoglycan cross-links are predominantly formed by nonclassical bridges between the third residues of adjacent tetrapeptides. The responsible enzymes for these reactions are ld-transpeptidases (Ldts), for which M. tuberculosis has five paralogues. Although these enzymes are distinct from the penicillin-binding proteins (PBPs), they can also be inactivated by β-lactam antibiotics, but since M. tuberculosis has a chromosomal β-lactamase, most of the antibiotics of these classes can be degraded. Thus, to identify alternative scaffolds for the development of new antimicrobials against tuberculosis, we have integrated several fragment-based drug discovery techniques. Based on that, we identified and validated a number of small molecules that could be the starting point in the synthesis of more potent inhibitors against at least two Ldts from M. tuberculosis, LdtMt2 and LdtMt3. Eight identified molecules inhibited the Ldts activity in at least 20%, and three of them have antimycobacterial activity. The cell ultrastructural analysis suggested that one of the best compounds induced severe effects on the septum and cell wall morphologies, which corroborates our target-based approach to identifying new Ldts hits.
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Affiliation(s)
- Gerardo Andrés Libreros-Zúñiga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil; IBILCE, São Paulo State University, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo 15054-000, Brazil; Department of Microbiology, Faculty of Health, University of Valle, Calle 4B # 36-00, 760043, Cali, Valle del Cauca, Colombia.
| | - Danilo Pavão E Pavão
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | - Vinicius de Morais Barroso
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | | | - Saulo Fehelberg Pinto Braga
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais. Av. Antônio Carlos, 6627 - Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Glaucius Oliva
- Institute of Physics of São Carlos, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, Brazil
| | - Rafaela Salgado Ferreira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais. Av. Antônio Carlos, 6627 - Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Kelly Ishida
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil; IBILCE, São Paulo State University, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo 15054-000, Brazil; Department of Chemistry, University of Warwick, Coventry CV4 7AL, England.
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de Munnik M, Lithgow J, Brewitz L, Christensen KE, Bates RH, Rodriguez-Miquel B, Schofield CJ. αβ,α'β'-Diepoxyketones are mechanism-based inhibitors of nucleophilic cysteine enzymes. Chem Commun (Camb) 2023; 59:12859-12862. [PMID: 37815791 PMCID: PMC10601815 DOI: 10.1039/d3cc02932h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/30/2023] [Indexed: 10/11/2023]
Abstract
Epoxides are an established class of electrophilic alkylating agents that react with nucleophilic protein residues. We report αβ,α'β'-diepoxyketones (DEKs) as a new type of mechanism-based inhibitors of nucleophilic cysteine enzymes. Studies with the L,D-transpeptidase LdtMt2 from Mycobacterium tuberculosis and the main protease from SARS-CoV-2 (Mpro) reveal that following epoxide ring opening by a nucleophilic cysteine, further reactions can occur, leading to irreversible alkylation.
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Affiliation(s)
- Mariska de Munnik
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Jasper Lithgow
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Kirsten E Christensen
- Chemical Crystallography, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Robert H Bates
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Calle Severo Ochoa 2, Tres Cantos, Madrid, Spain
| | - Beatriz Rodriguez-Miquel
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Calle Severo Ochoa 2, Tres Cantos, Madrid, Spain
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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5
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Yang J, Zhang L, Qiao W, Luo Y. Mycobacterium tuberculosis: Pathogenesis and therapeutic targets. MedComm (Beijing) 2023; 4:e353. [PMID: 37674971 PMCID: PMC10477518 DOI: 10.1002/mco2.353] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023] Open
Abstract
Tuberculosis (TB) remains a significant public health concern in the 21st century, especially due to drug resistance, coinfection with diseases like immunodeficiency syndrome (AIDS) and coronavirus disease 2019, and the lengthy and costly treatment protocols. In this review, we summarize the pathogenesis of TB infection, therapeutic targets, and corresponding modulators, including first-line medications, current clinical trial drugs and molecules in preclinical assessment. Understanding the mechanisms of Mycobacterium tuberculosis (Mtb) infection and important biological targets can lead to innovative treatments. While most antitubercular agents target pathogen-related processes, host-directed therapy (HDT) modalities addressing immune defense, survival mechanisms, and immunopathology also hold promise. Mtb's adaptation to the human host involves manipulating host cellular mechanisms, and HDT aims to disrupt this manipulation to enhance treatment effectiveness. Our review provides valuable insights for future anti-TB drug development efforts.
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Affiliation(s)
- Jiaxing Yang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Laiying Zhang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Wenliang Qiao
- Department of Thoracic Surgery, West China HospitalSichuan UniversityChengduSichuanChina
- Lung Cancer Center, West China HospitalSichuan UniversityChengduSichuanChina
| | - Youfu Luo
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
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6
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de Munnik M, Lang PA, De Dios Anton F, Cacho M, Bates RH, Brem J, Rodríguez Miquel B, Schofield CJ. High-throughput screen with the l,d-transpeptidase Ldt Mt2 of Mycobacterium tuberculosis reveals novel classes of covalently reacting inhibitors. Chem Sci 2023; 14:7262-7278. [PMID: 37416715 PMCID: PMC10321483 DOI: 10.1039/d2sc06858c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/29/2023] [Indexed: 07/08/2023] Open
Abstract
Disruption of bacterial cell wall biosynthesis in Mycobacterium tuberculosis is a promising target for treating tuberculosis. The l,d-transpeptidase LdtMt2, which is responsible for the formation of 3 → 3 cross-links in the cell wall peptidoglycan, has been identified as essential for M. tuberculosis virulence. We optimised a high-throughput assay for LdtMt2, and screened a targeted library of ∼10 000 electrophilic compounds. Potent inhibitor classes were identified, including established (e.g., β-lactams) and unexplored covalently reacting electrophilic groups (e.g., cyanamides). Protein-observed mass spectrometric studies reveal most classes to react covalently and irreversibly with the LdtMt2 catalytic cysteine (Cys354). Crystallographic analyses of seven representative inhibitors reveal induced fit involving a loop enclosing the LdtMt2 active site. Several of the identified compounds have a bactericidal effect on M. tuberculosis within macrophages, one with an MIC50 value of ∼1 μM. The results provide leads for the development of new covalently reaction inhibitors of LdtMt2 and other nucleophilic cysteine enzymes.
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Affiliation(s)
- Mariska de Munnik
- Chemistry Research Laboratory, Department of Chemistry, the Ineos Oxford Institute of Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Pauline A Lang
- Chemistry Research Laboratory, Department of Chemistry, the Ineos Oxford Institute of Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Francisco De Dios Anton
- Tres Cantos Medicines Development Campus, GlaxoSmithKline Calle Severo Ochoa 2, Tres Cantos Madrid Spain
| | - Mónica Cacho
- Tres Cantos Medicines Development Campus, GlaxoSmithKline Calle Severo Ochoa 2, Tres Cantos Madrid Spain
| | - Robert H Bates
- Tres Cantos Medicines Development Campus, GlaxoSmithKline Calle Severo Ochoa 2, Tres Cantos Madrid Spain
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry, the Ineos Oxford Institute of Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Beatriz Rodríguez Miquel
- Tres Cantos Medicines Development Campus, GlaxoSmithKline Calle Severo Ochoa 2, Tres Cantos Madrid Spain
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, the Ineos Oxford Institute of Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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Sharma K, Ahmed F, Sharma T, Grover A, Agarwal M, Grover S. Potential Repurposed Drug Candidates for Tuberculosis Treatment: Progress and Update of Drugs Identified in Over a Decade. ACS OMEGA 2023; 8:17362-17380. [PMID: 37251185 PMCID: PMC10210030 DOI: 10.1021/acsomega.2c05511] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/23/2022] [Indexed: 05/31/2023]
Abstract
The devastating impact of Tuberculosis (TB) has been a menace to mankind for decades. The World Health Organization (WHO) End TB Strategy aims to reduce TB mortality up to 95% and 90% of overall TB cases worldwide, by 2035. This incessant urge will be achieved with a breakthrough in either a new TB vaccine or novel drugs with higher efficacy. However, the development of novel drugs is a laborious process involving a timeline of almost 20-30 years with huge expenditure; on the other hand, repurposing previously approved drugs is a viable technique for overcoming current bottlenecks in the identification of new anti-TB agents. The present comprehensive review discusses the progress of almost all the repurposed drugs that have been identified to the present day (∼100) and are in the development or clinical testing phase against TB. We have also emphasized the efficacy of repurposed drugs in combination with already available frontline anti-TB medications along with the scope of future investigations. This study would provide the researchers a detailed overview of nearly all identified anti-TB repurposed drugs and may assist them in selecting the lead compounds for further in vivo/clinical research.
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Affiliation(s)
- Khushbu Sharma
- Department
of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Faraz Ahmed
- Department
of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Tarina Sharma
- New
Jersey Medical School, Rutgers, The State
University of New Jersey, Newark, New Jersey 07103, United States
| | - Abhinav Grover
- School
of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Meetu Agarwal
- Department
of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Sonam Grover
- Department
of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
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Abuhammad A, Laurieri N, Rice A, Lowe ED, Singh N, Naser SM, Ratrout SS, Churchill GC. Structural and biochemical analysis of human inositol monophosphatase-1 inhibition by ebselen. J Biomol Struct Dyn 2023; 41:14036-14048. [PMID: 36762717 DOI: 10.1080/07391102.2023.2176925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Bipolar disorder is a major psychiatric disorder associated with cognitive impairment and a high suicide rate. Frontline therapy for this condition includes lithium (Li+)-containing treatments that can exert severe side effects. One target of Li+ is inositol monophosphatase-1 (IMPase1); inhibition of IMPase1 through small-molecule compounds may provide an alternative treatment for bipolar disorder. One such compound is the anti-inflammatory drug ebselen, which is well tolerated and safe; however, ebselen's exact mechanism of action in IMPase1 inhibition is not fully understood, preventing rational design of IMPase1 inhibitors. To fill this gap, we performed crystallographic and biochemical studies to investigate how ebselen inhibits IMPase1. We obtained a structure of IMPase1 in space group P21 after treatment with ebselen that revealed three key active-site loops (residues 33-44, 70-79, and 161-165) that are either disordered or in multiple conformations, supporting a hypothesis whereby dynamic conformational changes may be important for catalysis and ebselen inhibition. Using the thermal shift assay, we confirmed that ebselen significantly destabilizes the enzyme. Molecular docking suggests that ebselen could bind in the vicinity of His217. Investigation of the role of IMPase1 residues His217 and Cys218 suggests that inhibition of IMPase1 by ebselen may not be mediated via covalent modification of the active-site cysteine (Cys218) and is not affected by the covalent modification of other cysteine residues in the structure. Our results suggest that effects previously ascribed to ebselen-dependent inhibition likely result from disruption of essential active-site architecture, preventing activation of the IMPase1-Mg2+ complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Areej Abuhammad
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Nicola Laurieri
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Alistair Rice
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Edward D Lowe
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Nisha Singh
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Saleem M Naser
- Research and Development Department, APIs Division, Hikma Pharmaceutical Co. Ltd, Amman, Jordan
| | - Samer S Ratrout
- Research and Development Department, APIs Division, Hikma Pharmaceutical Co. Ltd, Amman, Jordan
| | - Grant C Churchill
- Department of Pharmacology, University of Oxford, Oxford, United Kingdom
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9
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Antibacterial Activity of Ebselen. Int J Mol Sci 2023; 24:ijms24021610. [PMID: 36675123 PMCID: PMC9864093 DOI: 10.3390/ijms24021610] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Ebselen is a low-molecular-weight organoselenium compound that has been broadly studied for its antioxidant, anti-inflammatory, and cytoprotective properties. These advantageous properties were initially associated with mimicking the activity of selenoprotein glutathione peroxidase, but the biomedical impact of this compound appear to be far more complex. Ebselen serves as a substrate or inhibitor with multiple protein/enzyme targets, whereas inhibition typically originates from the covalent modification of cysteine residues by opening the benzisoselenazolone ring and S-Se bond formation. The inhibition of enzymes of various classes and origins has been associated with substantial antimicrobial potential among other activities. In this contribution, we summarize the current state of the art regarding the antibacterial activity of ebselen. This activity, alone and in combination with commercial pharmaceuticals, against pathogens, including those resistant to drugs, is presented, together with the molecular mechanism behind the reactivity. The specific inactivation of thioredoxin reductase, bacterial toxins, and other resistance factors is considered to have certain therapeutic implications. Synergistic action and sensitization to common antibiotics assisted with the use of ebselen appear to be promising directions in the treatment of persistent infections.
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Thun‐Hohenstein STD, Suits TF, Malla TR, Tumber A, Brewitz L, Choudhry H, Salah E, Schofield CJ. Structure-Activity Studies Reveal Scope for Optimisation of Ebselen-Type Inhibition of SARS-CoV-2 Main Protease. ChemMedChem 2022; 17:e202100582. [PMID: 34850566 PMCID: PMC9015279 DOI: 10.1002/cmdc.202100582] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Indexed: 11/08/2022]
Abstract
The reactive organoselenium compound ebselen is being investigated for treatment of coronavirus disease 2019 (COVID-19) and other diseases. We report structure-activity studies on sulfur analogues of ebselen with the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro ), employing turnover and protein-observed mass spectrometry-based assays. The results reveal scope for optimisation of ebselen/ebselen derivative- mediated inhibition of Mpro , particularly with respect to improved selectivity.
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Affiliation(s)
- Siegfried T. D. Thun‐Hohenstein
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Timothy F. Suits
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Tika R. Malla
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Anthony Tumber
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Lennart Brewitz
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Hani Choudhry
- Department of BiochemistryCenter for Artificial Intelligence in Precision MedicinesKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Eidarus Salah
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher J. Schofield
- Department of ChemistryUniversity of OxfordChemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research12 Mansfield RoadOxfordOX1 3TAUK
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11
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Mora-Ochomogo M, Lohans CT. β-Lactam antibiotic targets and resistance mechanisms: from covalent inhibitors to substrates. RSC Med Chem 2021; 12:1623-1639. [PMID: 34778765 PMCID: PMC8528271 DOI: 10.1039/d1md00200g] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/25/2021] [Indexed: 12/24/2022] Open
Abstract
The β-lactams are the most widely used antibacterial agents worldwide. These antibiotics, a group that includes the penicillins and cephalosporins, are covalent inhibitors that target bacterial penicillin-binding proteins and disrupt peptidoglycan synthesis. Bacteria can achieve resistance to β-lactams in several ways, including the production of serine β-lactamase enzymes. While β-lactams also covalently interact with serine β-lactamases, these enzymes are capable of deacylating this complex, treating the antibiotic as a substrate. In this tutorial-style review, we provide an overview of the β-lactam antibiotics, focusing on their covalent interactions with their target proteins and resistance mechanisms. We begin by describing the structurally diverse range of β-lactam antibiotics and β-lactamase inhibitors that are currently used as therapeutics. Then, we introduce the penicillin-binding proteins, describing their functions and structures, and highlighting their interactions with β-lactam antibiotics. We next describe the classes of serine β-lactamases, exploring some of the mechanisms by which they achieve the ability to degrade β-lactams. Finally, we introduce the l,d-transpeptidases, a group of bacterial enzymes involved in peptidoglycan synthesis which are also targeted by β-lactam antibiotics. Although resistance mechanisms are now prevalent for all antibiotics in this class, past successes in antibiotic development have at least delayed this onset of resistance. The β-lactams continue to be an essential tool for the treatment of infectious disease, and recent advances (e.g., β-lactamase inhibitor development) will continue to support their future use.
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Affiliation(s)
| | - Christopher T Lohans
- Department of Biomedical and Molecular Sciences, Queen's University Kingston ON K7L 3N6 Canada
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12
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Parise A, Romeo I, Russo N, Marino T. The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study. Int J Mol Sci 2021; 22:9792. [PMID: 34575955 PMCID: PMC8467846 DOI: 10.3390/ijms22189792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022] Open
Abstract
The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.
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Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Isabella Romeo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
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13
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Ebselen and Analogues: Pharmacological Properties and Synthetic Strategies for Their Preparation. Molecules 2021; 26:molecules26144230. [PMID: 34299505 PMCID: PMC8306772 DOI: 10.3390/molecules26144230] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023] Open
Abstract
Ebselen is the leader of selenorganic compounds, and starting from its identification as mimetic of the key antioxidant enzyme glutathione peroxidase, several papers have appeared in literature claiming its biological activities. It was the subject of several clinical trials and it is currently in clinical evaluation for the treatment of COVID-19 patients. Given our interest in the synthesis and pharmacological evaluation of selenorganic derivatives with this review, we aimed to collect all the papers focused on the biological evaluation of ebselen and its close analogues, covering the timeline between 2016 and most of 2021. Our analysis evidences that, even if it lacks specificity when tested in vitro, being able to bind to every reactive cysteine, it proved to be always well tolerated in vivo, exerting no sign of toxicity whatever the administered doses. Besides, looking at the literature, we realized that no review article dealing with the synthetic approaches for the construction of the benzo[d][1,2]-selenazol-3(2H)-one scaffold is available; thus, a section of the present review article is completely devoted to this specific topic.
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14
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Toxicology and pharmacology of synthetic organoselenium compounds: an update. Arch Toxicol 2021; 95:1179-1226. [PMID: 33792762 PMCID: PMC8012418 DOI: 10.1007/s00204-021-03003-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/10/2021] [Indexed: 12/17/2022]
Abstract
Here, we addressed the pharmacology and toxicology of synthetic organoselenium compounds and some naturally occurring organoselenium amino acids. The use of selenium as a tool in organic synthesis and as a pharmacological agent goes back to the middle of the nineteenth and the beginning of the twentieth centuries. The rediscovery of ebselen and its investigation in clinical trials have motivated the search for new organoselenium molecules with pharmacological properties. Although ebselen and diselenides have some overlapping pharmacological properties, their molecular targets are not identical. However, they have similar anti-inflammatory and antioxidant activities, possibly, via activation of transcription factors, regulating the expression of antioxidant genes. In short, our knowledge about the pharmacological properties of simple organoselenium compounds is still elusive. However, contrary to our early expectations that they could imitate selenoproteins, organoselenium compounds seem to have non-specific modulatory activation of antioxidant pathways and specific inhibitory effects in some thiol-containing proteins. The thiol-oxidizing properties of organoselenium compounds are considered the molecular basis of their chronic toxicity; however, the acute use of organoselenium compounds as inhibitors of specific thiol-containing enzymes can be of therapeutic significance. In summary, the outcomes of the clinical trials of ebselen as a mimetic of lithium or as an inhibitor of SARS-CoV-2 proteases will be important to the field of organoselenium synthesis. The development of computational techniques that could predict rational modifications in the structure of organoselenium compounds to increase their specificity is required to construct a library of thiol-modifying agents with selectivity toward specific target proteins.
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15
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Zhang J, Yang L, Wang Y, Cao T, Sun Z, Xu J, Liu Y, Chen G. Ebselen-Agents for Sensing, Imaging and Labeling: Facile and Full-Featured Application in Biochemical Analysis. ACS APPLIED BIO MATERIALS 2021; 4:2217-2230. [PMID: 35014346 DOI: 10.1021/acsabm.0c01561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Phenyl-1,2-benzoselenazol-3(2H)-one (ebselen) is a classical mimic of glutathione peroxidase (GPx). Thioredoxin interaction endows ebselen attractive biological functions, such as antioxidation and anti-infection, as well as versatile therapeutic usage. Accordingly, application of ebselen analogues in biosensing, chemical labeling, imaging analysis, disease pathology, drug development, clinical treatment, etc. have been widely developed, in which mercaptans, reactive oxygen species, reactive sulfur species, peptides, and proteins were involved. Herein, focusing on the application of ebselen-agents in biochemistry, we have made a systematic summary and comprehensive review. First, we summarized both the classical and the innovative methods for preparing ebselen-agents to present the synthetic strategies. Then we discussed the full functional applicability of ebselen analogues in three fields of biochemical analysis including the fluorescence sensing and bioimaging, derivatization for high throughput fluorescence analysis, and the labeling gents for proteomics. Finally, we discussed the current challenges and perspectives for ebselen-agents as analytical tools in biological research. By presenting the multifunctional applicability of ebselen, we hope this review could appeal researchers to design the ebselen-related biomaterials for biochemical analysis.
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Affiliation(s)
- Jiawei Zhang
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Lei Yang
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Yuxin Wang
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Tianyi Cao
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Zhiwei Sun
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Jie Xu
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Yuxia Liu
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Guang Chen
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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16
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Synthesis and recycling of the mycobacterial cell envelope. Curr Opin Microbiol 2021; 60:58-65. [PMID: 33610125 PMCID: PMC8035080 DOI: 10.1016/j.mib.2021.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023]
Abstract
The unique mycobacterial cell wall is a layered structure of carbohydrates and lipids. The architecture and biosynthesis of the cell wall have largely been elucidated. Increasing evidence indicates that each cell wall layer is remodelled and recycled. There are opportunities to discover new essential enzymes in cell wall metabolism. Cell wall metabolism is a validated source of targets for tuberculosis drug discovery.
Mycobacterium tuberculosis (Mtb), the causative agent of the disease tuberculosis, is a recognised global health concern. The efficacy of the current treatment regime is under threat due to the emergence of antibiotic resistance, directing an urgent requirement for the discovery of new anti-tubercular agents and drug targets. The mycobacterial cell wall is a well-validated drug target for Mtb and is composed of three adaptive macromolecular structures, peptidoglycan, arabinogalactan and mycolic acids, an array of complex lipids and carbohydrates. The majority of the enzymes involved in cell wall synthesis have been established, whilst studies directed towards the mechanisms of remodelling and recycling have been neglected. This review briefly describes mycobacterial cell wall synthesis, and focuses on aspects of remodelling and recycling, thus highlighting opportunities for future research.
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17
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Ma C, Hu Y, Townsend JA, Lagarias PI, Marty MT, Kolocouris A, Wang J. Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors. ACS Pharmacol Transl Sci 2020; 3:1265-1277. [PMID: 33330841 PMCID: PMC7571300 DOI: 10.1021/acsptsci.0c00130] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Indexed: 12/19/2022]
Abstract
![]()
Among the drug targets being investigated
for SARS-CoV-2, the viral
main protease (Mpro) is one of the most extensively studied.
Mpro is a cysteine protease that hydrolyzes the viral polyprotein
at more than 11 sites. It is highly conserved and has a unique substrate
preference for glutamine in the P1 position. Therefore, Mpro inhibitors are expected to have broad-spectrum antiviral activity
and a high selectivity index. Structurally diverse compounds have
been reported as Mpro inhibitors. In this study, we investigated
the mechanism of action of six previously reported Mpro inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin,
and PX-12, using a consortium of techniques including FRET-based enzymatic
assay, thermal shift assay, native mass spectrometry, cellular antiviral
assays, and molecular dynamics simulations. Collectively, the results
showed that the inhibition of Mpro by these six compounds
is nonspecific and that the inhibition is abolished or greatly reduced
with the addition of reducing reagent 1,4-dithiothreitol (DTT). Without
DTT, these six compounds inhibit not only Mpro but also
a panel of viral cysteine proteases including SARS-CoV-2 papain-like
protease and 2Apro and 3Cpro from enterovirus
A71 (EV-A71) and EV-D68. However, none of the compounds inhibits the
viral replication of EV-A71 or EV-D68, suggesting that the enzymatic
inhibition potency IC50 values obtained in the absence
of DTT cannot be used to faithfully predict their cellular antiviral
activity. Overall, we provide compelling evidence suggesting that
these six compounds are nonspecific SARS-CoV-2 Mpro inhibitors
and urge the scientific community to be stringent with hit validation.
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Affiliation(s)
- Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Panagiotis I Lagarias
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
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18
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Fenn GD, Waller-Evans H, Atack JR, Bax BD. Crystallization and structure of ebselen bound to Cys141 of human inositol monophosphatase. Acta Crystallogr F Struct Biol Commun 2020; 76:469-476. [PMID: 33006574 PMCID: PMC7531247 DOI: 10.1107/s2053230x20011310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 11/21/2022] Open
Abstract
Inositol monophosphatase (IMPase) is inhibited by lithium, which is the most efficacious treatment for bipolar disorder. Several therapies have been approved, or are going through clinical trials, aimed at the replacement of lithium in the treatment of bipolar disorder. One candidate small molecule is ebselen, a selenium-containing antioxidant, which has been demonstrated to produce lithium-like effects both in a murine model and in clinical trials. Here, the crystallization and the first structure of human IMPase covalently complexed with ebselen, a 1.47 Å resolution crystal structure (PDB entry 6zk0), are presented. In the complex with human IMPase, ebselen in a ring-opened conformation is covalently attached to Cys141, a residue located away from the active site. IMPase is a dimeric enzyme and in the crystal structure two adjacent dimers share four ebselen molecules, creating a tetramer with approximate 222 symmetry. In the crystal structure presented in this publication, the active site in the tetramer is still accessible, suggesting that ebselen may function as an allosteric inhibitor or may block the binding of partner proteins.
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Affiliation(s)
- Gareth D. Fenn
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Helen Waller-Evans
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - John R. Atack
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Benjamin D. Bax
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
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19
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Ma C, Hu Y, Townsend JA, Lagarias PI, Marty MT, Kolocouris A, Wang J. Ebselen, disulfiram, carmofur, PX-12, tideglusib, and shikonin are non-specific promiscuous SARS-CoV-2 main protease inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.15.299164. [PMID: 32995786 PMCID: PMC7523112 DOI: 10.1101/2020.09.15.299164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
There is an urgent need for vaccines and antiviral drugs to combat the COVID-19 pandemic. Encouraging progress has been made in developing antivirals targeting SARS-CoV-2, the etiological agent of COVID-19. Among the drug targets being investigated, the viral main protease (M pro ) is one of the most extensively studied drug targets. M pro is a cysteine protease that hydrolyzes the viral polyprotein at more than 11 sites and it is highly conserved among coronaviruses. In addition, M pro has a unique substrate preference for glutamine in the P1 position. Taken together, it appears that M pro inhibitors can achieve both broad-spectrum antiviral activity and a high selectivity index. Structurally diverse compounds have been reported as M pro inhibitors, with several of which also showed antiviral activity in cell culture. In this study, we investigated the mechanism of action of six previously reported M pro inhibitors, ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 using a consortium of techniques including FRET-based enzymatic assay, thermal shift assay, native mass spectrometry, cellular antiviral assays, and molecular dynamics simulations. Collectively, the results showed that the inhibition of M pro by these six compounds is non-specific and the inhibition is abolished or greatly reduced with the addition of reducing reagent DTT. In the absence of DTT, these six compounds not only inhibit M pro , but also a panel of viral cysteine proteases including SARS-CoV-2 papain-like protease, the 2A pro and 3C pro from enterovirus A71 (EV-A71) and EV-D68. However, none of the compounds inhibits the viral replication of EV-A71 or EV-D68, suggesting that the enzymatic inhibition potency IC 50 values obtained in the absence of DTT cannot be used to faithfully predict their cellular antiviral activity. Overall, we provide compelling evidence suggesting that ebselen, disulfiram, tideglusib, carmofur, shikonin, and PX-12 are non-specific SARS-CoV-2 M pro inhibitors, and urge the scientific community to be stringent with hit validation.
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Affiliation(s)
- Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
| | - Julia Alma Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Panagiotis I. Lagarias
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Michael Thomas Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, United States
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20
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Cochrane SA, Lohans CT. Breaking down the cell wall: Strategies for antibiotic discovery targeting bacterial transpeptidases. Eur J Med Chem 2020; 194:112262. [PMID: 32248005 DOI: 10.1016/j.ejmech.2020.112262] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022]
Abstract
The enzymes involved in bacterial cell wall synthesis are established antibiotic targets, and continue to be a central focus for antibiotic development. Bacterial penicillin-binding proteins (and, in some bacteria, l,d-transpeptidases) form essential peptide cross-links in the cell wall. Although the β-lactam class of antibiotics target these enzymes, bacterial resistance threatens their clinical use, and there is an urgent unmet need for new antibiotics. However, the search for new antibiotics targeting the bacterial cell wall is hindered by a number of obstacles associated with screening the enzymes involved in peptidoglycan synthesis. This review describes recent approaches for measuring the activity and inhibition of penicillin-binding proteins and l,d-transpeptidases, highlighting strategies that are poised to serve as valuable tools for high-throughput screening of transpeptidase inhibitors, supporting the development of new antibiotics.
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Affiliation(s)
- Stephen A Cochrane
- School of Chemistry and Chemical Engineering, David Keir Building, Stranmillis Road, Queen's University Belfast, Belfast, BT9 5AG, UK.
| | - Christopher T Lohans
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L 3N6, Canada.
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21
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An Q, Li C, Chen Y, Deng Y, Yang T, Luo Y. Repurposed drug candidates for antituberculosis therapy. Eur J Med Chem 2020; 192:112175. [PMID: 32126450 DOI: 10.1016/j.ejmech.2020.112175] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 02/06/2023]
Abstract
Antibiotics have been a key part of clinical treatments for more than 70 years. Long-term use of antimicrobial treatments has led to the development of severe bacterial resistance, which has become increasingly serious due to antibiotic abuse, resulting in the treatment of bacterial infections becoming challenging. The repurposing of approved drugs presents a promising strategy to address current bottlenecks in the development of novel antibacterial agents. Drug repurposing is a cost-effective emerging strategy, which aims to treat resistant infectious diseases by identifying known drugs with predicted efficacy for diseases other than the target disease. This strategy has potential in the treatment of tuberculosis (TB), particularly drug-resistant TB. In recent years, a panel of drugs approved for clinical use or clinical trials, such as linezolid, vancomycin and celecoxib, have been found to have anti-TB activities. However, the utility of drug repurposing is limited by the number of candidate compounds and their low activities. The low activities of repurposed drugs have slowed the development of a drug-repurposing strategy for anti-TB drugs. The present review discusses progress in the discovery of new anti-TB agents through drug repurposing since 2014. We also discuss the challenges faced and analyze the innovative ways that are being used to overcome these difficulties. This review may provide a useful guide for researchers in the field of drug repurposing.
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Affiliation(s)
- Qi An
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, China
| | - Chungen Li
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, China
| | - Yao Chen
- Key Laboratory of Drug Targeting and Drug Delivery System, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yong Deng
- Key Laboratory of Drug Targeting and Drug Delivery System, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, China.
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22
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de Munnik M, Lohans CT, Langley GW, Bon C, Brem J, Schofield CJ. A Fluorescence-Based Assay for Screening β-Lactams Targeting the Mycobacterium tuberculosis Transpeptidase Ldt Mt2. Chembiochem 2020; 21:368-372. [PMID: 31322798 PMCID: PMC7028133 DOI: 10.1002/cbic.201900379] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Indexed: 12/24/2022]
Abstract
Mycobacterium tuberculosis l,d-transpeptidases (Ldts), which are involved in cell-wall biosynthesis, have emerged as promising targets for the treatment of tuberculosis. However, an efficient method for testing inhibition of these enzymes is not currently available. We present a fluorescence-based assay for LdtMt2 , which is suitable for high-throughput screening. Two fluorogenic probes were identified that release a fluorophore upon reaction with LdtMt2 , thus making it possible to assess the availability of the catalytic site in the presence of inhibitors. The assay was applied to a panel of β-lactam antibiotics and related inhibitors; the results validate observations that the (carba)penem subclass of β-lactams are more potent Ldt inhibitors than other β-lactam classes, though unexpected variations in potency were observed. The method will enable systematic structure-activity relationship studies on Ldts, thereby facilitating the identification of new antibiotics active against M. tuberculosis.
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Affiliation(s)
- Mariska de Munnik
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher T. Lohans
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Department of Biomedical and Molecular SciencesQueen's University18 Stuart StreetKingstonONK7L 3N6Canada
| | - Gareth W. Langley
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Present address: Charles River LaboratoriesChesterford Research ParkSaffron WaldenEssexCB10 1XLUK
| | - Corentin Bon
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Present address: Department of Structural Biology and ChemistryInstitut PasteurUMR 3523 CNRSRue du Dr. Roux75015ParisFrance
| | - Jürgen Brem
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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23
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Daolio A, Scilabra P, Di Pietro ME, Resnati C, Rissanen K, Resnati G. Binding motif of ebselen in solution: chalcogen and hydrogen bonds team up. NEW J CHEM 2020. [DOI: 10.1039/d0nj04647g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ebselen, a compound active against SARS-CoV-2, forms a bifurcated supramolecular synthon thanks to chalcogen bond and hydrogen bond cooperation.
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Affiliation(s)
- Andrea Daolio
- Department of Chemistry
- Materials
- Chemical Engineering “Giulio Natta”
- Milano I-20131
- Italy
| | - Patrick Scilabra
- Department of Chemistry
- Materials
- Chemical Engineering “Giulio Natta”
- Milano I-20131
- Italy
| | | | - Chiara Resnati
- Recidency Program Clinical Pharmacology & Toxicology
- Università degli Studi della Campania “Luigi Vanvitelli”
- Napoli I-80138
- Italy
| | - Kari Rissanen
- Department Chemistry
- University of Jyväskylä
- Jyväskylä
- Finland
| | - Giuseppe Resnati
- Department of Chemistry
- Materials
- Chemical Engineering “Giulio Natta”
- Milano I-20131
- Italy
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