1
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Sheikhi N, Bahraminejad M, Saeedi M, Mirfazli SS. A review: FDA-approved fluorine-containing small molecules from 2015 to 2022. Eur J Med Chem 2023; 260:115758. [PMID: 37657268 DOI: 10.1016/j.ejmech.2023.115758] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
Fluorine-containing small molecules have occupied a special position in drug discovery research. The successful clinical use of fluorinated corticosteroids in the 1950s and fluoroquinolones in the 1980s led to an ever-increasing number of approved fluorinated compounds over the last 50 years. They have shown various biological properties such as antitumor, antimicrobial, and anti-inflammatory activities. Fluoro-pharmaceuticals have been considered a strong and practical tool in the rational drug design approach due to their benefits from potency and ADME (absorption, distribution, metabolism, and excretion) points of view. Herein, approved fluorinated drugs from 2015 to 2022 were reviewed.
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Affiliation(s)
- Negar Sheikhi
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Bahraminejad
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
| | - Mina Saeedi
- Medicinal Plants Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Seyedeh Sara Mirfazli
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran.
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2
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Fernandes GFS, Manieri KF, Bonjorno AF, Campos DL, Ribeiro CM, Demarqui FM, Ruiz DAG, Nascimento-Junior NM, Denny WA, Thompson AM, Pavan FR, Dos Santos JL. Synthesis and Anti-Mycobacterium tuberculosis Activity of Imidazo[2,1-b][1,3]oxazine Derivatives against Multidrug-Resistant Strains. ChemMedChem 2023; 18:e202300015. [PMID: 37002895 DOI: 10.1002/cmdc.202300015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/09/2023] [Accepted: 03/31/2023] [Indexed: 04/04/2023]
Abstract
The emergence of multidrug-resistant strains of M. tuberculosis has raised concerns due to the greater difficulties in patient treatment and higher mortality rates. Herein, we revisited the 2-nitro-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine scaffold and identified potent new carbamate derivatives having MIC90 values of 0.18-1.63 μM against Mtb H37Rv. Compounds 47-49, 51-53, and 55 exhibited remarkable activity against a panel of clinical isolates, displaying MIC90 values below 0.5 μM. In Mtb-infected macrophages, several compounds demonstrated a 1-log greater reduction in mycobacterial burden than rifampicin and pretomanid. The compounds tested did not exhibit significant cytotoxicity against three cell lines or any toxicity to Galleria mellonella. Furthermore, the imidazo[2,1-b][1,3]oxazine derivatives did not show substantial activity against other bacteria or fungi. Finally, molecular docking studies revealed that the new compounds could interact with the deazaflavin-dependent nitroreductase (Ddn) in a similar manner to pretomanid. Collectively, our findings highlight the chemical universe of imidazo[2,1-b][1,3]oxazines and their promising potential against MDR-TB.
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Affiliation(s)
- Guilherme F S Fernandes
- School of Pharmaceutical Sciences, São Paulo State University, Rod. Araraquara-Jaú, Araraquara, 14800903, Brazil
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Present address: Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Karyn F Manieri
- School of Pharmaceutical Sciences, São Paulo State University, Rod. Araraquara-Jaú, Araraquara, 14800903, Brazil
| | - Andressa F Bonjorno
- School of Pharmaceutical Sciences, São Paulo State University, Rod. Araraquara-Jaú, Araraquara, 14800903, Brazil
| | - Debora L Campos
- School of Pharmaceutical Sciences, São Paulo State University, Rod. Araraquara-Jaú, Araraquara, 14800903, Brazil
| | - Camila M Ribeiro
- School of Pharmaceutical Sciences, São Paulo State University, Rod. Araraquara-Jaú, Araraquara, 14800903, Brazil
| | - Fernanda M Demarqui
- School of Pharmaceutical Sciences, São Paulo State University, Rod. Araraquara-Jaú, Araraquara, 14800903, Brazil
| | - Daniel A G Ruiz
- Institute of Chemistry, São Paulo State University, Rua Professor Francisco Degni, 55, Araraquara, 14800060, Brazil
| | - Nailton M Nascimento-Junior
- Institute of Chemistry, São Paulo State University, Rua Professor Francisco Degni, 55, Araraquara, 14800060, Brazil
| | - William A Denny
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Andrew M Thompson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Fernando R Pavan
- School of Pharmaceutical Sciences, São Paulo State University, Rod. Araraquara-Jaú, Araraquara, 14800903, Brazil
| | - Jean L Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University, Rod. Araraquara-Jaú, Araraquara, 14800903, Brazil
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3
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Kang SW, Antoney J, Frkic RL, Lupton DW, Speight R, Scott C, Jackson CJ. Asymmetric Ene-Reduction of α,β-Unsaturated Compounds by F 420-Dependent Oxidoreductases A Enzymes from Mycobacterium smegmatis. Biochemistry 2023; 62:873-891. [PMID: 36637210 DOI: 10.1021/acs.biochem.2c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
The stereoselective reduction of alkenes conjugated to electron-withdrawing groups by ene-reductases has been extensively applied to the commercial preparation of fine chemicals. Although several different enzyme families are known to possess ene-reductase activity, the old yellow enzyme (OYE) family has been the most thoroughly investigated. Recently, it was shown that a subset of ene-reductases belonging to the flavin/deazaflavin oxidoreductase (FDOR) superfamily exhibit enantioselectivity that is generally complementary to that seen in the OYE family. These enzymes belong to one of several FDOR subgroups that use the unusual deazaflavin cofactor F420. Here, we explore several enzymes of the FDOR-A subgroup, characterizing their substrate range and enantioselectivity with 20 different compounds, identifying enzymes (MSMEG_2027 and MSMEG_2850) that could reduce a wide range of compounds stereoselectively. For example, MSMEG_2027 catalyzed the complete conversion of both isomers of citral to (R)-citronellal with 99% ee, while MSMEG_2850 catalyzed complete conversion of ketoisophorone to (S)-levodione with 99% ee. Protein crystallography combined with computational docking has allowed the observed stereoselectivity to be mechanistically rationalized for two enzymes. These findings add further support for the FDOR and OYE families of ene-reductases displaying general stereocomplementarity to each other and highlight their potential value in asymmetric ene-reduction.
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Affiliation(s)
- Suk Woo Kang
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,Natural Products Research Center, Korea Institute of Science and Technology (KIST), Gangneung25451, Republic of Korea
| | - James Antoney
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, Queensland4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland4000, Australia
| | - Rebecca L Frkic
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia
| | - David W Lupton
- School of Chemistry, Monash University, Melbourne, Victoria3800, Australia
| | - Robert Speight
- School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, Queensland4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland4000, Australia
| | - Colin Scott
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria3168, Australia.,CSIRO Synthetic Biology Future Science Platform, GPO Box 1700, Canberra, Australian Capital Territory2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,ARC Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia.,ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory2601, Australia
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4
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Kang SW, Antoney J, Lupton DW, Speight R, Scott C, Jackson CJ. Asymmetric Ene-Reduction by F 420 -Dependent Oxidoreductases B (FDOR-B) from Mycobacterium smegmatis. Chembiochem 2023; 24:e202200797. [PMID: 36716144 DOI: 10.1002/cbic.202200797] [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: 12/29/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 01/31/2023]
Abstract
Asymmetric reduction by ene-reductases has received considerable attention in recent decades. While several enzyme families possess ene-reductase activity, the Old Yellow Enzyme (OYE) family has received the most scientific and industrial attention. However, there is a limited substrate range and few stereocomplementary pairs of current ene-reductases, necessitating the development of a complementary class. Flavin/deazaflavin oxidoreductases (FDORs) that use the uncommon cofactor F420 have recently gained attention as ene-reductases for use in biocatalysis due to their stereocomplementarity with OYEs. Although the enzymes of the FDOR-As sub-group have been characterized in this context and reported to catalyse ene-reductions enantioselectively, enzymes from the similarly large, but more diverse, FDOR-B sub-group have not been investigated in this context. In this study, we investigated the activity of eight FDOR-B enzymes distributed across this sub-group, evaluating their specific activity, kinetic properties, and stereoselectivity against α,β-unsaturated compounds. The stereochemical outcomes of the FDOR-Bs are compared with enzymes of the FDOR-A sub-group and OYE family. Computational modelling and induced-fit docking are used to rationalize the observed catalytic behaviour and proposed a catalytic mechanism.
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Affiliation(s)
- Suk Woo Kang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Natural Products Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451 (Republic of, Korea
| | - James Antoney
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - David W Lupton
- School of Chemistry, Monash University, Melbourne, Victoria, 3800, Australia
| | - Robert Speight
- School of Biology and Environmental Sciences, Queensland University of Technology, Brisbane, QLD 4000, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | - Colin Scott
- Environment, Commonwealth Scientific and Industrial Research Organization, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence in Synthetic Biology, Australian National University, Canberra, ACT 2601, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
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5
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Singh R, Shaheer M, Sobhia ME. Molecular dynamic assisted investigation on impact of mutations in deazaflavin dependent nitroreductase against pretomanid: a computational study. J Biomol Struct Dyn 2022:1-23. [PMID: 35574601 DOI: 10.1080/07391102.2022.2069156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the past decade, TB drugs belonging to the nitroimidazole class, pretomanid and delamanid, have been authorised to treat MDR-TB and XDR-TB. With a novel inhibition mechanism and a reduction in the span of treatment, it is now being administered in various combinations. This approach is not the ultimate remedy since the target protein Deazaflavin dependent nitroreductase (Ddn) has a high mutation frequency, and already pretomanid resistant clinical isolates are reported in various studies. Ddn is essential for M.tuberculosis to emerge from hypoxia, and point mutations in critical residues confer resistance to Nitro-imidazoles. Among the pool of available mutants, we have selected seven mutants viz DdnL49P, DdnY65S, DdnS78Y, DdnK79Q, DdnW88R, DdnY133C, and DdnY136S, all of which exhibited resistance to pretomanid. To address this issue, through computational study primarily by MD simulation, we attempted to elucidate these point mutations' impact and investigate the resistance mechanism. Hence, the DdnWT and mutant (MT) complexes were subjected to all-atom molecular dynamics (MD) simulations for 100 ns. Interestingly, we observed the escalation of the distance between cofactor and ligand in some mutants, along with a significant change in ligand conformation relative to the DdnWT. Moreover, we confirmed that mutations rendered ligand instability and were ejected from the binding pocket as a result. In conclusion, the results obtained provide a new structural insight and vital clues for designing novel inhibitors to combat nitroimidazole resistanceCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Singh
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Punjab, India
| | - Muhammed Shaheer
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Punjab, India
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6
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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7
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Potency boost of a Mycobacterium tuberculosis dihydrofolate reductase inhibitor by multienzyme F 420H 2-dependent reduction. Proc Natl Acad Sci U S A 2021; 118:2025172118. [PMID: 34161270 PMCID: PMC8237569 DOI: 10.1073/pnas.2025172118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial metabolism can cause intrinsic drug resistance but can also convert inactive parent drugs into bioactive derivatives, as is the case for several antimycobacterial prodrugs. Here, we show that the intrabacterial metabolism of a Mtb dihydrofolate reductase (DHFR) inhibitor with moderate affinity for its target boosts its on-target activity by two orders of magnitude. This is a “prodrug-like” antimycobacterial that possesses baseline activity in the absence of intracellular bioactivation. By elucidating the metabolic enhancement mechanism, we have provided the basis for the rational optimization of a class of DHFR inhibitors and uncovered an antibacterial drug discovery concept. Triaza-coumarin (TA-C) is a Mycobacterium tuberculosis (Mtb) dihydrofolate reductase (DHFR) inhibitor with an IC50 (half maximal inhibitory concentration) of ∼1 µM against the enzyme. Despite this moderate target inhibition, TA-C shows exquisite antimycobacterial activity (MIC50, concentration inhibiting growth by 50% = 10 to 20 nM). Here, we investigated the mechanism underlying this potency disconnect. To confirm that TA-C targets DHFR and investigate its unusual potency pattern, we focused on resistance mechanisms. In Mtb, resistance to DHFR inhibitors is frequently associated with mutations in thymidylate synthase thyA, which sensitizes Mtb to DHFR inhibition, rather than in DHFR itself. We observed thyA mutations, consistent with TA-C interfering with the folate pathway. A second resistance mechanism involved biosynthesis of the redox coenzyme F420. Thus, we hypothesized that TA-C may be metabolized by Mtb F420–dependent oxidoreductases (FDORs). By chemically blocking the putative site of FDOR-mediated reduction in TA-C, we reproduced the F420-dependent resistance phenotype, suggesting that F420H2-dependent reduction is required for TA-C to exert its potent antibacterial activity. Indeed, chemically synthesized TA-C-Acid, the putative product of TA-C reduction, displayed a 100-fold lower IC50 against DHFR. Screening seven recombinant Mtb FDORs revealed that at least two of these enzymes reduce TA-C. This redundancy in activation explains why no mutations in the activating enzymes were identified in the resistance screen. Analysis of the reaction products confirmed that FDORs reduce TA-C at the predicted site, yielding TA-C-Acid. This work demonstrates that intrabacterial metabolism converts TA-C, a moderately active “prodrug,” into a 100-fold-more-potent DHFR inhibitor, thus explaining the disconnect between enzymatic and whole-cell activity.
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8
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Lee BM, Harold LK, Almeida DV, Afriat-Jurnou L, Aung HL, Forde BM, Hards K, Pidot SJ, Ahmed FH, Mohamed AE, Taylor MC, West NP, Stinear TP, Greening C, Beatson SA, Nuermberger EL, Cook GM, Jackson CJ. Predicting nitroimidazole antibiotic resistance mutations in Mycobacterium tuberculosis with protein engineering. PLoS Pathog 2020; 16:e1008287. [PMID: 32032366 PMCID: PMC7032734 DOI: 10.1371/journal.ppat.1008287] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 02/20/2020] [Accepted: 12/16/2019] [Indexed: 12/21/2022] Open
Abstract
Our inability to predict which mutations could result in antibiotic resistance has made it difficult to rapidly identify the emergence of resistance, identify pre-existing resistant populations, and manage our use of antibiotics to effectively treat patients and prevent or slow the spread of resistance. Here we investigated the potential for resistance against the new antitubercular nitroimidazole prodrugs pretomanid and delamanid to emerge in Mycobacterium tuberculosis, the causative agent of tuberculosis (TB). Deazaflavin-dependent nitroreductase (Ddn) is the only identified enzyme within M. tuberculosis that activates these prodrugs, via an F420H2-dependent reaction. We show that the native menaquinone-reductase activity of Ddn is essential for emergence from hypoxia, which suggests that for resistance to spread and pose a threat to human health, the native activity of Ddn must be at least partially retained. We tested 75 unique mutations, including all known sequence polymorphisms identified among ~15,000 sequenced M. tuberculosis genomes. Several mutations abolished pretomanid and delamanid activation in vitro, without causing complete loss of the native activity. We confirmed that a transmissible M. tuberculosis isolate from the hypervirulent Beijing family already possesses one such mutation and is resistant to pretomanid, before being exposed to the drug. Notably, delamanid was still effective against this strain, which is consistent with structural analysis that indicates delamanid and pretomanid bind to Ddn differently. We suggest that the mutations identified in this work be monitored for informed use of delamanid and pretomanid treatment and to slow the emergence of resistance.
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Affiliation(s)
- Brendon M. Lee
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Liam K. Harold
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Deepak V. Almeida
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Livnat Afriat-Jurnou
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
- MIGAL, Galilee Research Institute, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, Israel
| | - Htin Lin Aung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Brian M. Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kiel Hards
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - F. Hafna Ahmed
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - A. Elaaf Mohamed
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C. Taylor
- Land and Water Flagship, The Commonwealth Scientific and Industrial Organisation, Canberra, Australian Capital Territory, Australia
| | - Nicholas P. West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chris Greening
- Land and Water Flagship, The Commonwealth Scientific and Industrial Organisation, Canberra, Australian Capital Territory, Australia
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Eric L. Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
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9
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Nothling MD, Xiao Z, Bhaskaran A, Blyth MT, Bennett CW, Coote ML, Connal LA. Synthetic Catalysts Inspired by Hydrolytic Enzymes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03326] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mitchell D. Nothling
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zeyun Xiao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
| | - Ayana Bhaskaran
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Mitchell T. Blyth
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christopher W. Bennett
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michelle L. Coote
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A. Connal
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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10
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Ney B, Carere CR, Sparling R, Jirapanjawat T, Stott MB, Jackson CJ, Oakeshott JG, Warden AC, Greening C. Cofactor Tail Length Modulates Catalysis of Bacterial F 420-Dependent Oxidoreductases. Front Microbiol 2017; 8:1902. [PMID: 29021791 PMCID: PMC5623714 DOI: 10.3389/fmicb.2017.01902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/15/2017] [Indexed: 11/13/2022] Open
Abstract
F420 is a microbial cofactor that mediates a wide range of physiologically important and industrially relevant redox reactions, including in methanogenesis and tetracycline biosynthesis. This deazaflavin comprises a redox-active isoalloxazine headgroup conjugated to a lactyloligoglutamyl tail. Here we studied the catalytic significance of the oligoglutamate chain, which differs in length between bacteria and archaea. We purified short-chain F420 (two glutamates) from a methanogen isolate and long-chain F420 (five to eight glutamates) from a recombinant mycobacterium, confirming their different chain lengths by HPLC and LC/MS analysis. F420 purified from both sources was catalytically compatible with purified enzymes from the three major bacterial families of F420-dependent oxidoreductases. However, long-chain F420 bound to these enzymes with a six- to ten-fold higher affinity than short-chain F420. The cofactor side chain also significantly modulated the kinetics of the enzymes, with long-chain F420 increasing the substrate affinity (lower Km) but reducing the turnover rate (lower kcat) of the enzymes. Molecular dynamics simulations and comparative structural analysis suggest that the oligoglutamate chain of F420 makes dynamic electrostatic interactions with conserved surface residues of the oxidoreductases while the headgroup binds the catalytic site. In conjunction with the kinetic data, this suggests that electrostatic interactions made by the oligoglutamate tail result in higher-affinity, lower-turnover catalysis. Physiologically, we propose that bacteria have selected for long-chain F420 to better control cellular redox reactions despite tradeoffs in catalytic rate. Conversely, this suggests that industrial use of shorter-length F420 will greatly increase the rates of bioremediation and biocatalysis processes relying on purified F420-dependent oxidoreductases.
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Affiliation(s)
- Blair Ney
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Carlo R Carere
- GNS Science, Wairakei Research Centre, Lower Hutt, New Zealand
| | - Richard Sparling
- GNS Science, Wairakei Research Centre, Lower Hutt, New Zealand.,Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | | | - Matthew B Stott
- GNS Science, Wairakei Research Centre, Lower Hutt, New Zealand
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - John G Oakeshott
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Andrew C Warden
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
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11
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Greening C, Jirapanjawat T, Afroze S, Ney B, Scott C, Pandey G, Lee BM, Russell RJ, Jackson CJ, Oakeshott JG, Taylor MC, Warden AC. Mycobacterial F 420H 2-Dependent Reductases Promiscuously Reduce Diverse Compounds through a Common Mechanism. Front Microbiol 2017; 8:1000. [PMID: 28620367 PMCID: PMC5449967 DOI: 10.3389/fmicb.2017.01000] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/18/2017] [Indexed: 01/24/2023] Open
Abstract
An unusual aspect of actinobacterial metabolism is the use of the redox cofactor F420. Studies have shown that actinobacterial F420H2-dependent reductases promiscuously hydrogenate diverse organic compounds in biodegradative and biosynthetic processes. These enzymes therefore represent promising candidates for next-generation industrial biocatalysts. In this work, we undertook the first broad survey of these enzymes as potential industrial biocatalysts by exploring the extent, as well as mechanistic and structural bases, of their substrate promiscuity. We expressed and purified 11 enzymes from seven subgroups of the flavin/deazaflavin oxidoreductase (FDOR) superfamily (A1, A2, A3, B1, B2, B3, B4) from the model soil actinobacterium Mycobacterium smegmatis. These enzymes reduced compounds from six chemical classes, including fundamental monocycles such as a cyclohexenone, a dihydropyran, and pyrones, as well as more complex quinone, coumarin, and arylmethane compounds. Substrate range and reduction rates varied between the enzymes, with the A1, A3, and B1 groups exhibiting greatest promiscuity. Molecular docking studies suggested that structurally diverse compounds are accommodated in the large substrate-binding pocket of the most promiscuous FDOR through hydrophobic interactions with conserved aromatic residues and the isoalloxazine headgroup of F420H2. Liquid chromatography-mass spectrometry (LC/MS) and gas chromatography-mass spectrometry (GC/MS) analysis of derivatized reaction products showed reduction occurred through a common mechanism involving hydride transfer from F420H- to the electron-deficient alkene groups of substrates. Reduction occurs when the hydride donor (C5 of F420H-) is proximal to the acceptor (electrophilic alkene of the substrate). These findings suggest that engineered actinobacterial F420H2-dependent reductases are promising novel biocatalysts for the facile transformation of a wide range of α,β-unsaturated compounds.
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Affiliation(s)
- Chris Greening
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Thanavit Jirapanjawat
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,School of Biological Sciences, Monash University, ClaytonVIC, Australia.,Research School of Chemistry, Australian National University, ActonACT, Australia
| | - Shahana Afroze
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,Research School of Chemistry, Australian National University, ActonACT, Australia
| | - Blair Ney
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,School of Biological Sciences, Monash University, ClaytonVIC, Australia.,Research School of Chemistry, Australian National University, ActonACT, Australia
| | - Colin Scott
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Gunjan Pandey
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Brendon M Lee
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia.,Research School of Chemistry, Australian National University, ActonACT, Australia
| | - Robyn J Russell
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, ActonACT, Australia
| | - John G Oakeshott
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Matthew C Taylor
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
| | - Andrew C Warden
- Land and Water Flagship, The Commonwealth Scientific and Industrial Research Organisation, ActonACT, Australia
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