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Lefrançois LH, Nitschke J, Wu H, Panis G, Prados J, Butler RE, Mendum TA, Hanna N, Stewart GR, Soldati T. Temporal genome-wide fitness analysis of Mycobacterium marinum during infection reveals the genetic requirement for virulence and survival in amoebae and microglial cells. mSystems 2024; 9:e0132623. [PMID: 38270456 PMCID: PMC10878075 DOI: 10.1128/msystems.01326-23] [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: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Tuberculosis remains the most pervasive infectious disease and the recent emergence of drug-resistant strains emphasizes the need for more efficient drug treatments. A key feature of pathogenesis, conserved between the human pathogen Mycobacterium tuberculosis and the model pathogen Mycobacterium marinum, is the metabolic switch to lipid catabolism and altered expression of virulence genes at different stages of infection. This study aims to identify genes involved in sustaining viable intracellular infection. We applied transposon sequencing (Tn-Seq) to M. marinum, an unbiased genome-wide strategy combining saturation insertional mutagenesis and high-throughput sequencing. This approach allowed us to identify the localization and relative abundance of insertions in pools of transposon mutants. Gene essentiality and fitness cost of mutations were quantitatively compared between in vitro growth and different stages of infection in two evolutionary distinct phagocytes, the amoeba Dictyostelium discoideum and the murine BV2 microglial cells. In the M. marinum genome, 57% of TA sites were disrupted and 568 genes (10.2%) were essential, which is comparable to previous Tn-Seq studies on M. tuberculosis and M. bovis. Major pathways involved in the survival of M. marinum during infection of D. discoideum are related to DNA damage repair, lipid and vitamin metabolism, the type VII secretion system (T7SS) ESX-1, and the Mce1 lipid transport system. These pathways, except Mce1 and some glycolytic enzymes, were similarly affected in BV2 cells. These differences suggest subtly distinct nutrient availability or requirement in different host cells despite the known predominant use of lipids in both amoeba and microglial cells.IMPORTANCEThe emergence of biochemically and genetically tractable host model organisms for infection studies holds the promise to accelerate the pace of discoveries related to the evolution of innate immunity and the dissection of conserved mechanisms of cell-autonomous defenses. Here, we have used the genetically and biochemically tractable infection model system Dictyostelium discoideum/Mycobacterium marinum to apply a genome-wide transposon-sequencing experimental strategy to reveal comprehensively which mutations confer a fitness advantage or disadvantage during infection and compare these to a similar experiment performed using the murine microglial BV2 cells as host for M. marinum to identify conservation of virulence pathways between hosts.
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Affiliation(s)
- Louise H. Lefrançois
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
| | - Jahn Nitschke
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
| | - Huihai Wu
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/CMU, University of Geneva, Institute of Genetics and Genomics in Geneva (iGE3), Genève, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/CMU, University of Geneva, Institute of Genetics and Genomics in Geneva (iGE3), Genève, Switzerland
- Bioinformatics Support Platform for data analysis, Geneva University, Medicine Faculty, Geneva, Switzerland
| | - Rachel E. Butler
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Tom A. Mendum
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Nabil Hanna
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
| | - Graham R. Stewart
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Science, University of Geneva, Science II, Geneva, Switzerland
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2
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Duysak T, Jeong JH, Kim K, Kim JS, Choy HE. Analysis of random mutations in Salmonella Gallinarum dihydropteroate synthase conferring sulfonamide resistance. Arch Microbiol 2023; 205:363. [PMID: 37906281 DOI: 10.1007/s00203-023-03696-5] [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: 08/29/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 11/02/2023]
Abstract
In bacteria and primitive eukaryotes, sulfonamide antibiotics block the folate pathway by inhibiting dihydropteroate synthase (FolP) that combines para-aminobenzoic acid (pABA) and dihydropterin pyrophosphate (DHPP) to form dihydropteroic acid (DHP), a precursor for tetrahydrofolate synthesis. However, the emergence of resistant strains has severely compromised the use of pABA mimetics as sulfonamide drugs. Salmonella enterica serovar Gallinarum (S. Gallinarum) is a significant source of antibiotic-resistant infections in poultry. Here, a sulfonamide-resistant FolP mutant library of S. Gallinarum was generated through random mutagenesis. Among resistant strains, substitution of amino acid Arginine 171 with Proline (R171P) in the FolP protein conferred the highest resistance against sulfonamide. Substitution of Phe28 with Leu or Ile (F28L/I) led to modest sulfonamide resistance. Structural modeling indicates that R171P and Phenylalanine 28 with leucine or isoleucine (F28L/I) substitution mutations are located far from the substrate-binding site and cause insignificant conformational changes in the FolP protein. Rather, in silico studies suggest that the mutations altered the stability of the protein, potentially resulting in sulfonamide resistance. Identification of specific mutations in FolP that confer resistance to sulfonamide would contribute to our understanding of the molecular mechanisms of antibiotic resistance.
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Affiliation(s)
- Taner Duysak
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61468, Korea
- Basic Medical Research Building, Odysseus Bio, Chonnam National University Medical College, 322 Seoyang-ro, Hwasun, 58128, Jeonnam, Korea
| | - Jae-Ho Jeong
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61468, Korea
| | - Kwangsoo Kim
- Basic Medical Research Building, Odysseus Bio, Chonnam National University Medical College, 322 Seoyang-ro, Hwasun, 58128, Jeonnam, Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Korea.
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, Gwangju, 61468, Korea.
- Basic Medical Research Building, Odysseus Bio, Chonnam National University Medical College, 322 Seoyang-ro, Hwasun, 58128, Jeonnam, Korea.
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Venkatesan M, Fruci M, Verellen LA, Skarina T, Mesa N, Flick R, Pham C, Mahadevan R, Stogios PJ, Savchenko A. Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics. Nat Commun 2023; 14:4031. [PMID: 37419898 PMCID: PMC10328974 DOI: 10.1038/s41467-023-39778-7] [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: 01/16/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
The sulfonamides (sulfas) are the oldest class of antibacterial drugs and inhibit the bacterial dihydropteroate synthase (DHPS, encoded by folP), through chemical mimicry of its co-substrate p-aminobenzoic acid (pABA). Resistance to sulfa drugs is mediated either by mutations in folP or acquisition of sul genes, which code for sulfa-insensitive, divergent DHPS enzymes. While the molecular basis of resistance through folP mutations is well understood, the mechanisms mediating sul-based resistance have not been investigated in detail. Here, we determine crystal structures of the most common Sul enzyme types (Sul1, Sul2 and Sul3) in multiple ligand-bound states, revealing a substantial reorganization of their pABA-interaction region relative to the corresponding region of DHPS. We use biochemical and biophysical assays, mutational analysis, and in trans complementation of E. coli ΔfolP to show that a Phe-Gly sequence enables the Sul enzymes to discriminate against sulfas while retaining pABA binding and is necessary for broad resistance to sulfonamides. Experimental evolution of E. coli results in a strain harboring a sulfa-resistant DHPS variant that carries a Phe-Gly insertion in its active site, recapitulating this molecular mechanism. We also show that Sul enzymes possess increased active site conformational dynamics relative to DHPS, which could contribute to substrate discrimination. Our results reveal the molecular foundation for Sul-mediated drug resistance and facilitate the potential development of new sulfas less prone to resistance.
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Affiliation(s)
- Meenakshi Venkatesan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Michael Fruci
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V 4T3, Canada
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Lou Ann Verellen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V 4T3, Canada
- Department of Microbiology and Immunology, Western University, London, ON, N6A 3K7, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Nathalie Mesa
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3E2, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.
- Center for Structural Biology of Infectious Diseases (CSBID), Calgary, AB, Canada.
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 1A4, Canada.
- Center for Structural Biology of Infectious Diseases (CSBID), Calgary, AB, Canada.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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Das BK, Chakraborty D. Deciphering the competitive inhibition of dihydropteroate synthase by 8 marcaptoguanine analogs: enhanced potency in phenylsulfonyl fragments. J Biomol Struct Dyn 2022; 40:13083-13102. [PMID: 34581241 DOI: 10.1080/07391102.2021.1981452] [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: 12/27/2022]
Abstract
The emergence of sulfa-drug resistance and reduced efficacy of pterin-based analogs towards Dihydropteroate synthase (DHPS) inhibition dictate a pressing need of developing novel antimicrobial agents for immune-compromised patients. Recently, a series of 8-Marcaptoguanin (8-MG) derivatives synthesized for 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (experimental KD ∼ 100-.0.36) showed remarkable homology with the pteroic-acid and serve as a template for product antagonism in DHPS. The present work integrates ligand-based drug discovery techniques with structure-based docking, enhanced MD simulation, and MM/PBSA techniques to demonstrate the essential features of 8-MG analogs which make it a potent inhibitor for DHPS. The delicate balance in hydrophilic, hydrophobic substitutions on the 8-MG core is the crucial signature for DHPS inhibition. It is found that the dynamic interactions of active compounds are mainly dominated by consistent hydrogen bonding network with Asp 96, Asn 115, Asp 185, Ser 222, Arg 255 and π-π stacking, π-cation interactions with Phe 190, Lys 221. Further, two new 8-MG compounds containing N-phenylacetamide (compound S1, ΔGbind-eff = -62.03 kJ/mol) and phenylsulfonyl (compound S3, ΔGbind-eff = -71.29 kJ/mol) fragments were found to be the most potent inhibitor of DHPS, which stabilize the flexible pABA binding loop, thereby increasing their binding affinity. MM/PBSA calculation shows electrostatic energy contribution to be the principal component in stabilizing the inhibitors in the binding pocket. This fact is further confirmed by the higher energy barrier obtained in umbrella sampling for this class of inhibitors.
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Affiliation(s)
- Bratin Kumar Das
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Mangalore, India
| | - Debashree Chakraborty
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Mangalore, India
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Yadav A, Kaushik CP. Synthesis and antibacterial evaluation of sulfonamide bridged disubstituted 1,2,3-triazoles. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2141126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Archna Yadav
- Department of Chemistry, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - C. P. Kaushik
- Department of Chemistry, Guru Jambheshwar University of Science and Technology, Hisar, India
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In Silico Drug Discovery Strategies Identified ADMET Properties of Decoquinate RMB041 and Its Potential Drug Targets against Mycobacterium tuberculosis. Microbiol Spectr 2022; 10:e0231521. [PMID: 35352998 PMCID: PMC9045315 DOI: 10.1128/spectrum.02315-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The highly adaptive cellular response of Mycobacterium tuberculosis to various antibiotics and the high costs for clinical trials, hampers the development of novel antimicrobial agents with improved efficacy and safety. Subsequently, in silico drug screening methods are more commonly being used for the discovery and development of drugs, and have been proven useful for predicting the pharmacokinetics, toxicities, and targets, of prospective new antimicrobial agents. In this investigation we used a reversed target fishing approach to determine potential hit targets and their possible interactions between M. tuberculosis and decoquinate RMB041, a propitious new antituberculosis compound. Two of the 13 identified targets, Cyp130 and BlaI, were strongly proposed as optimal drug-targets for dormant M. tuberculosis, of which the first showed the highest comparative binding affinity to decoquinate RMB041. The metabolic pathways associated with the selected target proteins were compared to previously published molecular mechanisms of decoquinate RMB041 against M. tuberculosis, whereby we confirmed disrupted metabolism of proteins, cell wall components, and DNA. We also described the steps within these pathways that are inhibited and elaborated on decoquinate RMB041’s activity against dormant M. tuberculosis. This compound has previously showed promising in vitro safety and good oral bioavailability, which were both supported by this in silico study. The pharmacokinetic properties and toxicity of this compound were predicted and investigated using the online tools pkCSM and SwissADME, and Discovery Studio software, which furthermore supports previous safety and bioavailability characteristics of decoquinate RMB041 for use as an antimycobacterial medication. IMPORTANCE This article elaborates on the mechanism of action of a novel antibiotic compound against both, active and dormant Mycobacterium tuberculosis and describes its pharmacokinetics (including oral bioavailability and toxicity). Information provided in this article serves useful during the search for drugs that shorten the treatment regimen for Tuberculosis and cause minimal adverse effects.
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7
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Daraji DG, Rajani DP, Jayanthi S, Patel HD. Design, synthesis, and biological evaluations of (
E
)‐2‐(1‐[2‐mercapto‐4‐methyl‐1‐phenyl‐1
H
‐imidazol‐5‐yl]ethylidene)hydrazinecarbothioamide derivatives as antimicrobial agents. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Drashti G. Daraji
- Department of Chemistry, School of Sciences Gujarat University Navarangpura India
| | | | - Sivaraman Jayanthi
- School of Bio Sciences and Technology Vellore Institute of Technology Vellore India
| | - Hitesh D. Patel
- Department of Chemistry, School of Sciences Gujarat University Navarangpura India
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8
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He T, Liu J, Wang JP. Development of a Dihydropteroate Synthase-Based Fluorescence Polarization Assay for Detection of Sulfonamides and Studying Its Recognition Mechanism. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13953-13963. [PMID: 34783550 DOI: 10.1021/acs.jafc.1c05674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this study, the dihydropteroate synthase of Staphylococcus aureus was obtained, and its recognition mechanisms for 31 sulfonamide drugs were studied. Results showed that their core structure matched well with the binding pocket of para-aminobenzoic acid, and all the sulfonamide side chains were out of the binding pocket. Hydrogen bonds and hydrophobic interactions were the main intermolecular forces, and the key amino acids were Gly171 and Lys203. The binding sites in sulfonamide molecules were mainly around the para-aminobenzenesulfonamide part. This enzyme was used to develop a fluorescence polarization assay for detection of these drugs in chicken muscles. The change trends of half of inhibition concentrations and cross-reactivities for the 31 drugs were identical with the receptor-ligand affinities. The limits of detection were in the range of 2.0-38.5 ng/g, and one assay could be finished within several minutes. Therefore, this method could be used for multiscreening of sulfonamide residues in meat samples.
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Affiliation(s)
- Tong He
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Jing Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Jian Ping Wang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, Hebei 071000, China
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9
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Madugula SS, Nagamani S, Jamir E, Priyadarsinee L, Sastry GN. Drug repositioning for anti-tuberculosis drugs: an in silico polypharmacology approach. Mol Divers 2021; 26:1675-1695. [PMID: 34468898 DOI: 10.1007/s11030-021-10296-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/10/2021] [Indexed: 01/20/2023]
Abstract
Development of potential antitubercular molecules is a challenging task due to the rapidly emerging drug-resistant strains of Mycobacterium tuberculosis (M.tb). Structure-based approaches hold greater benefit in identifying compounds/drugs with desired polypharmacological profiles. These methods can be employed based on the knowledge of protein binding sites to identify the complementary ligands. In this study, polypharmacology guided computational drug repurposing approach was applied to identify potential antitubercular drugs. 20 important druggable protein targets in M.tb were considered from the target library of Molecular Property Diagnostic Suite-Tuberculosis (MPDSTB- http://mpds.neist.res.in:8084 ) for virtual screening. FDA approved drugs were collected, preprocessed and docked in the active sites of the 20 M.tb targets. The top 300 drug molecules from each target (20 × 300) were filtered-in and subsequently screened for possible antitubercular and antimycobacterial activity using PASS tool. Using this approach, 34 drugs with predicted antitubercular and anti-mycobacterial activity were identified along with good binding affinity against multiple M.tb targets. Interestingly, 21 out of the 34 identified drugs are antibiotics while 4 drug molecules (nitrofural, stavudine, quinine and quinidine) are non-antibiotics showing promising predicted antitubercular activity. Most of these molecules have the similar privileged antimycobacterial drugs scaffold. Further drug likeness properties were calculated to get deeper insights to M.tb lead molecules. Interestingly, it was also observed that the drugs identified from the study are under different stages of drug discovery (i.e., in vitro, clinical trials) for the effective treatment of various diseases including cancer, degenerative diseases, dengue virus infection, tuberculosis, etc. Krasavin et al., 2017 synthesized nitrofuran analogues with appreciable MICs (22-23 µM) against M.tb H37Rv. These experiments further add to the credibility of the drugs identified in this study (TB).
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Affiliation(s)
- Sita Sirisha Madugula
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India
| | - Esther Jamir
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India
| | - Lipsa Priyadarsinee
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India
| | - G Narahari Sastry
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. .,Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, 785 006, India.
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10
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Nagamani S, Sastry GN. Mycobacterium tuberculosis Cell Wall Permeability Model Generation Using Chemoinformatics and Machine Learning Approaches. ACS OMEGA 2021; 6:17472-17482. [PMID: 34278133 PMCID: PMC8280707 DOI: 10.1021/acsomega.1c01865] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/28/2021] [Indexed: 05/21/2023]
Abstract
The drug-resistant strains of Mycobacterium tuberculosis (M.tb) are evolving at an alarming rate, and this indicates the urgent need for the development of novel antitubercular drugs. However, genetic mutations, complex cell wall system of M.tb, and influx-efflux transporter systems are the major permeability barriers that significantly affect the M.tb drugs activity. Thus, most of the small molecules are ineffective to arrest the M.tb cell growth, even though they are effective at the cellular level. To address the permeability issue, different machine learning models that effectively distinguish permeable and impermeable compounds were developed. The enzyme-based (IC50) and cell-based (minimal inhibitory concentration) data were considered for the classification of M.tb permeable and impermeable compounds. It was assumed that the compounds that have high activity in both enzyme-based and cell-based assays possess the required M.tb cell wall permeability. The XGBoost model was outperformed when compared to the other models generated from different algorithms such as random forest, support vector machine, and naïve Bayes. The XGBoost model was further validated using the validation data set (21 permeable and 19 impermeable compounds). The obtained machine learning models suggested that various descriptors such as molecular weight, atom type, electrotopological state, hydrogen bond donor/acceptor counts, and extended topochemical atoms of molecules are the major determining factors for both M.tb cell permeability and inhibitory activity. Furthermore, potential antimycobacterial drugs were identified using computational drug repurposing. All the approved drugs from DrugBank were collected and screened using the developed permeability model. The screened compounds were given as input in the PASS server for the identification of possible antimycobacterial compounds. The drugs that were retained after two filters were docked to the active site of 10 different potential antimycobacterial drug targets. The results obtained from this study may improve the understanding of M.tb permeability and activity that may aid in the development of novel antimycobacterial drugs.
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Affiliation(s)
- Selvaraman Nagamani
- Advanced
Computation and Data Sciences Division, CSIR − North East Institute of Science and Technology, Jorhat, Assam 785 006, India
| | - G. Narahari Sastry
- Advanced
Computation and Data Sciences Division, CSIR − North East Institute of Science and Technology, Jorhat, Assam 785 006, India
- ;
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Zhang A, Li W, Liu X, Wu M, Xuan G. Synthesis, Biological Evaluation and in Silico Studies of Several Substituted Benzene Sulfonamides as Potential Antibacterial Agents. ACTA ACUST UNITED AC 2020. [DOI: 10.1088/1742-6596/1624/2/022058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Computer-aided synthesis of dapsone-phytochemical conjugates against dapsone-resistant Mycobacterium leprae. Sci Rep 2020; 10:6839. [PMID: 32322091 PMCID: PMC7176699 DOI: 10.1038/s41598-020-63913-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 01/23/2020] [Indexed: 11/09/2022] Open
Abstract
Leprosy continues to be the belligerent public health hazard for the causation of high disability and eventual morbidity cases with stable prevalence rates, even with treatment by the on-going multidrug therapy (MDT). Today, dapsone (DDS) resistance has led to fear of leprosy in more unfortunate people of certain developing countries. Herein, DDS was chemically conjugated with five phytochemicals independently as dapsone-phytochemical conjugates (DPCs) based on azo-coupling reaction. Possible biological activities were verified with computational chemistry and quantum mechanics by molecular dynamics simulation program before chemical synthesis and spectral characterizations viz., proton-HNMR, FTIR, UV and LC-MS. The in vivo antileprosy activity was monitored using the 'mouse-foot-pad propagation method', with WHO recommended concentration 0.01% mg/kg each DPC for 12 weeks, and the host-toxicity testing of the active DPC4 was seen in cultured-human-lymphocytes in vitro. One-log bacilli cells in DDS-resistant infected mice footpads decreased by the DPC4, and no bacilli were found in the DDS-sensitive mice hind pads. Additionally, the in vitro host toxicity study also confirmed that the DCP4 up to 5,000 mg/L level was safety for oral administration, since a minor number of dead cells were found in red color under a fluorescent microscope. Several advanced bioinformatics tools could help locate the potential chemical entity, thereby reducing the time and resources required for in vitro and in vitro tests. DPC4 could be used in place of DDS in MDT, evidenced from in vivo antileprosy activity and in vitro host toxicity study.
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13
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Potshangbam AM, Rathore RS, Nongdam P. Discovery of sulfone-resistant dihydropteroate synthase (DHPS) as a target enzyme for kaempferol, a natural flavanoid. Heliyon 2020; 6:e03378. [PMID: 32083215 PMCID: PMC7016458 DOI: 10.1016/j.heliyon.2020.e03378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/27/2019] [Accepted: 02/04/2020] [Indexed: 11/17/2022] Open
Abstract
Kaempferol is a ubiquitous flavonoid, found in various plants having a wide range of known pharmacological activities, including antioxidant, antiinflammatory, anticancer, antiallergic, antidiabetic, neuroprotective, cardioprotective and antimicrobial activities. Nonetheless various evidence suggest that kaempferol is also able to interact with many unknown therapeutic targets modulating signalling pathways, thus providing an opportunity to explore the potential target space of kaempferol. In this study, we have employed various ligand-based approaches to identify the potential targets of kaempferol, followed by validations using modelling and docking studies. Molecular dynamics, free energy calculations, volume and residue contact map analyses were made to delineate the cause of drug-resistance among mutants. We have discovered dihydropteroate synthase (DHPS) as a novel potential therapeutic target for kaempferol. Further studies employing molecular dynamics simulations and binding free energies indicate that kaempferol has potential to inhibit even the sulfone-resistant DHPS mutants, which makes it a very attractive antibiotic agent. The identification of natural-product based kaempferol opens up the door for the design of antibiotics in a quick and high throughput fashion for identifying antibiotic leads.
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Affiliation(s)
| | - Ravindranath Singh Rathore
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, India
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Bechard ME, Farahani P, Greene D, Pham A, Orry A, Rasche ME. Purification, kinetic characterization, and site-directed mutagenesis of Methanothermobacter thermautotrophicus RFAP Synthase Produced in Escherichia coli. AIMS Microbiol 2019; 5:186-204. [PMID: 31663056 PMCID: PMC6787355 DOI: 10.3934/microbiol.2019.3.186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/15/2019] [Indexed: 11/18/2022] Open
Abstract
Methane-producing archaea are among a select group of microorganisms that utilize tetrahydromethanopterin (H4MPT) as a one-carbon carrier instead of tetrahydrofolate. In H4MPT biosynthesis, β-ribofuranosylaminobenzene 5'-phosphate (RFAP) synthase catalyzes the production of RFAP, CO2, and pyrophosphate from p-aminobenzoic acid (pABA) and phosphoribosyl-pyrophosphate (PRPP). In this work, to gain insight into amino acid residues required for substrate binding, RFAP synthase from Methanothermobacter thermautotrophicus was produced in Escherichia coli, and site-directed mutagenesis was used to alter arginine 26 (R26) and aspartic acid 19 (D19), located in a conserved sequence of amino acids resembling the pABA binding site of dihydropteroate synthase. Replacement of R26 with lysine increased the KM for pABA by an order of magnitude relative to wild-type enzyme without substantially altering the KM for PRPP. Although replacement of D19 with alanine produced inactive enzyme, asparagine substitution allowed retention of some activity, and the K M for pABA increased about threefold relative to wild-type enzyme. A molecular model developed by threading RFAP synthase onto the crystal structure of homoserine kinase places R26 in the proposed active site. In the static model, D19 is located close to the active site, yet appears too far away to influence ligand binding directly. This may be indicative of the protein conformational change predicted previously in the Bi-Ter kinetic mechanism and/or formation of the active site at the interface of two subunits. Due to the vital role of RFAP synthase in H4MPT biosynthesis, insights into the mode of substrate binding and mechanism could be beneficial for developing RFAP synthase inhibitors designed to reduce the production of methane as a greenhouse gas.
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Affiliation(s)
- Matthew E Bechard
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Payam Farahani
- Chemistry and Biochemistry Department, California State University at Fullerton, 800 North State College Blvd., Fullerton, CA 92834
| | - Dina Greene
- Northern California Regional Laboratories, The Permanente Medical Group, Berkeley, CA 94710
| | - Anna Pham
- Chemistry and Biochemistry Department, California State University at Fullerton, 800 North State College Blvd., Fullerton, CA 92834
| | - Andrew Orry
- Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, CA 92121
| | - Madeline E Rasche
- Chemistry and Biochemistry Department, California State University at Fullerton, 800 North State College Blvd., Fullerton, CA 92834
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15
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Kordus SL, Baughn AD. Revitalizing antifolates through understanding mechanisms that govern susceptibility and resistance. MEDCHEMCOMM 2019; 10:880-895. [PMID: 31303985 PMCID: PMC6595967 DOI: 10.1039/c9md00078j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022]
Abstract
In prokaryotes and eukaryotes, folate (vitamin B9) is an essential metabolic cofactor required for all actively growing cells. Specifically, folate serves as a one-carbon carrier in the synthesis of amino acids (such as methionine, serine, and glycine), N-formylmethionyl-tRNA, coenzyme A, purines and thymidine. Many microbes are unable to acquire folates from their environment and rely on de novo folate biosynthesis. In contrast, mammals lack the de novo folate biosynthesis pathway and must obtain folate from commensal microbiota or the environment using proton-coupled folate transporters. The essentiality and dichotomy between mammalian and bacterial folate biosynthesis and utilization pathways make it an ideal drug target for the development of antimicrobial agents and cancer chemotherapeutics. In this minireview, we discuss general aspects of folate biosynthesis and the underlying mechanisms that govern susceptibility and resistance of organisms to antifolate drugs.
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Affiliation(s)
- Shannon Lynn Kordus
- Department of Microbiology and Immunology , University of Minnesota , Minneapolis , MN , USA .
| | - Anthony David Baughn
- Department of Microbiology and Immunology , University of Minnesota , Minneapolis , MN , USA .
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16
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Sánchez-Osuna M, Cortés P, Barbé J, Erill I. Origin of the Mobile Di-Hydro-Pteroate Synthase Gene Determining Sulfonamide Resistance in Clinical Isolates. Front Microbiol 2019; 9:3332. [PMID: 30687297 PMCID: PMC6335563 DOI: 10.3389/fmicb.2018.03332] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/21/2018] [Indexed: 12/25/2022] Open
Abstract
Sulfonamides are synthetic chemotherapeutic agents that work as competitive inhibitors of the di-hydro-pteroate synthase (DHPS) enzyme, encoded by the folP gene. Resistance to sulfonamides is widespread in the clinical setting and predominantly mediated by plasmid- and integron-borne sul1-3 genes encoding mutant DHPS enzymes that do not bind sulfonamides. In spite of their clinical importance, the genetic origin of sul1-3 genes remains unknown. Here we analyze sul genes and their genetic neighborhoods to uncover sul signature elements that enable the elucidation of their genetic origin. We identify a protein sequence Sul motif associated with sul-encoded proteins, as well as consistent association of a phosphoglucosamine mutase gene (glmM) with the sul2 gene. We identify chromosomal folP genes bearing these genetic markers in two bacterial families: the Rhodobiaceae and the Leptospiraceae. Bayesian phylogenetic inference of FolP/Sul and GlmM protein sequences clearly establishes that sul1-2 and sul3 genes originated as a mobilization of folP genes present in, respectively, the Rhodobiaceae and the Leptospiraceae, and indicate that the Rhodobiaceae folP gene was transferred from the Leptospiraceae. Analysis of %GC content in folP/sul gene sequences supports the phylogenetic inference results and indicates that the emergence of the Sul motif in chromosomally encoded FolP proteins is ancient and considerably predates the clinical introduction of sulfonamides. In vitro assays reveal that both the Rhodobiaceae and the Leptospiraceae, but not other related chromosomally encoded FolP proteins confer resistance in a sulfonamide-sensitive Escherichia coli background, indicating that the Sul motif is associated with sulfonamide resistance. Given the absence of any known natural sulfonamides targeting DHPS, these results provide a novel perspective on the emergence of resistance to synthetic chemotherapeutic agents, whereby preexisting resistant variants in the vast bacterial pangenome may be rapidly selected for and disseminated upon the clinical introduction of novel chemotherapeuticals.
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Affiliation(s)
- Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jordi Barbé
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, United States
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17
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Swain SS, Paidesetty SK, Dehury B, Sahoo J, Vedithi SC, Mahapatra N, Hussain T, Padhy RN. Molecular docking and simulation study for synthesis of alternative dapsone derivative as a newer antileprosy drug in multidrug therapy. J Cell Biochem 2018; 119:9838-9852. [DOI: 10.1002/jcb.27304] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/28/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Shasank S. Swain
- Central Research Laboratory, Institute of Medical Sciences and Sum Hospital, Siksha “O” Anusandhan (Deemed to be University) Bhubaneswar Odisha India
- NCDs Division ICMR‐Regional Medical Research Centre Bhubaneswar Odisha India
| | - Sudhir K. Paidesetty
- Department of Pharmaceutical Chemistry School of Pharmaceutical Sciences, Siksha “O” Anusandhan (Deemed to be University) Bhubaneswar Odisha India
| | - Budheswar Dehury
- Biomedical Informatics Centre, ICMR‐Regional Medical Research Centre Bhubaneswar Odisha India
| | - Jyotirmaya Sahoo
- Department of Pharmaceutical Chemistry School of Pharmaceutical Sciences, Siksha “O” Anusandhan (Deemed to be University) Bhubaneswar Odisha India
| | - Sundeep Chaitanya Vedithi
- Schieffelin Institute of Health‐Research and Leprosy Centre (SIH R & LC), Karigiri Vellore Tamil Nadu India
- Department of Biochemistry University of Cambridge Cambridge UK
| | - Namita Mahapatra
- Biomedical Informatics Centre, ICMR‐Regional Medical Research Centre Bhubaneswar Odisha India
| | - Tahziba Hussain
- NCDs Division ICMR‐Regional Medical Research Centre Bhubaneswar Odisha India
| | - Rabindra N. Padhy
- Central Research Laboratory, Institute of Medical Sciences and Sum Hospital, Siksha “O” Anusandhan (Deemed to be University) Bhubaneswar Odisha India
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18
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Yogavel M, Nettleship JE, Sharma A, Harlos K, Jamwal A, Chaturvedi R, Sharma M, Jain V, Chhibber-Goel J, Sharma A. Structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase-dihydropteroate synthase from Plasmodium vivax sheds light on drug resistance. J Biol Chem 2018; 293:14962-14972. [PMID: 30104413 DOI: 10.1074/jbc.ra118.004558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/08/2018] [Indexed: 11/06/2022] Open
Abstract
The genomes of the malaria-causing Plasmodium parasites encode a protein fused of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS) domains that catalyze sequential reactions in the folate biosynthetic pathway. Whereas higher organisms derive folate from their diet and lack the enzymes for its synthesis, most eubacteria and a number of lower eukaryotes including malaria parasites synthesize tetrahydrofolate via DHPS. Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) HPPK-DHPSs are currently targets of drugs like sulfadoxine (SDX). The SDX effectiveness as an antimalarial drug is increasingly diminished by the rise and spread of drug-resistant mutations. Here, we present the crystal structure of PvHPPK-DHPS in complex with four substrates/analogs, revealing the bifunctional PvHPPK-DHPS architecture in an unprecedented state of enzymatic activation. SDX's effect on HPPK-DHPS is due to 4-amino benzoic acid (pABA) mimicry, and the PvHPPK-DHPS structure sheds light on the SDX-binding cavity, as well as on mutations that effect SDX potency. We mapped five dominant drug resistance mutations in PvHPPK-DHPS: S382A, A383G, K512E/D, A553G, and V585A, most of which occur individually or in clusters proximal to the pABA-binding site. We found that these resistance mutations subtly alter the intricate enzyme/pABA/SDX interactions such that DHPS affinity for pABA is diminished only moderately, but its affinity for SDX is changed substantially. In conclusion, the PvHPPK-DHPS structure rationalizes and unravels the structural bases for SDX resistance mutations and highlights architectural features in HPPK-DHPSs from malaria parasites that can form the basis for developing next-generation anti-folate agents to combat malaria parasites.
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Affiliation(s)
- Manickam Yogavel
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India,
| | - Joanne E Nettleship
- the Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom, and.,the Oxford Protein Production Facility, United Kingdom Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, United Kingdom
| | - Akansha Sharma
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Karl Harlos
- the Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom, and
| | - Abhishek Jamwal
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Rini Chaturvedi
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Manmohan Sharma
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Vitul Jain
- the Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom, and
| | - Jyoti Chhibber-Goel
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Amit Sharma
- From the Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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19
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Sarkar R, Mdladla C, Macingwana L, Pietersen RD, Ngwane A, Tabb D, van Helden P, Wiid I, Baker B. Proteomic analysis reveals that sulfamethoxazole induces oxidative stress in M. tuberculosis. Tuberculosis (Edinb) 2018; 111:78-85. [DOI: 10.1016/j.tube.2018.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/27/2018] [Accepted: 05/15/2018] [Indexed: 02/04/2023]
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20
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Pathogenic Nocardia cyriacigeorgica and Nocardia nova Evolve To Resist Trimethoprim-Sulfamethoxazole by both Expected and Unexpected Pathways. Antimicrob Agents Chemother 2018; 62:AAC.00364-18. [PMID: 29686152 DOI: 10.1128/aac.00364-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/15/2018] [Indexed: 12/12/2022] Open
Abstract
Nocardia spp. are Gram-positive opportunistic pathogens that affect largely immunocompromised patients, leading to serious pulmonary or systemic infections. Combination therapy using the folate biosynthesis pathway inhibitors trimethoprim (TMP) and sulfamethoxazole (SMX) is commonly used as an antimicrobial therapy. Not surprisingly, as antibiotic therapies for nocardiosis can extend for many months, resistance to TMP-SMX has emerged. Using experimental evolution, we surveyed the genetic basis of adaptation to TMP-SMX across 8 strains of Nocardia nova and 2 strains of Nocardia cyriacigeorgica By employing both continuous experimental evolution to provide longitudinal information on the order of changes and characterization of resistant endpoint isolates, we observe changes that are consistent with modifications of two enzymes of the folate biosynthesis pathway: dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) (FolP), with the mutations often being clustered near the active site of the enzymes. While changes to DHFR and DHPS might be expected, we also noted that mutations in a previously undescribed homolog of DHPS (DHPS2 or FolP2) that was annotated as being "nonfunctional" were also sufficient to generate TMP-SMX resistance, which serves as a cautionary tale for the use of automated annotation by investigators and for the future discovery of drugs against this genus. Additionally, folP2 overlapped glucosyl-3-phosphoglycerate synthase. Remarkably, an adaptive frameshift mutation within the overlapping region resulted in a new in-frame fusion to the downstream gene to produce a potentially new bifunctional enzyme. How a single potentially bifunctional DHPS2 enzyme might confer resistance is unclear. However, it highlights the unexpected ways in which adaptive evolution finds novel solutions for selection.
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21
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Passi A, Rajput NK, Wild DJ, Bhardwaj A. RepTB: a gene ontology based drug repurposing approach for tuberculosis. J Cheminform 2018; 10:24. [PMID: 29785561 PMCID: PMC5962481 DOI: 10.1186/s13321-018-0276-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/23/2018] [Indexed: 11/12/2022] Open
Abstract
Tuberculosis (TB) is the world’s leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function correlations among known drug-target pairs to predict novel drug-target interactions. In this study, we have created a Gene Ontology based network containing 26,404 edges, 6630 drug and 4083 target nodes. The network, enriched with molecular function ontology, was analyzed using Network Based Inference (NBI). The association scores computed from NBI are used to identify novel drug-target interactions. These interactions are further evaluated based on a combined evidence approach for identification of potential drug repurposing candidates. In this approach, targets which have no known variation in clinical isolates, no human homologs, and are essential for Mtb’s survival and or virulence are prioritized. We analyzed predicted DTIs to identify target pairs whose predicted drugs may have synergistic bactericidal effect. From the list of predicted DTIs from RepTB, four TB targets, namely, FolP1 (Dihydropteroate synthase), Tmk (Thymidylate kinase), Dut (Deoxyuridine 5′-triphosphate nucleotidohydrolase) and MenB (1,4-dihydroxy-2-naphthoyl-CoA synthase) may be selected for further validation. In addition, we observed that in some cases there is significant chemical structure similarity between predicted and reported drugs of prioritized targets, lending credence to our approach. We also report new chemical space for prioritized targets that may be tested further. We believe that with increasing drug-target interaction dataset RepTB will be able to offer better predictive value and is amenable for identification of drug-repurposing candidates for other disease indications too.
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Affiliation(s)
- Anurag Passi
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India.,Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, Tamil Nadu, 600113, India
| | - Neeraj Kumar Rajput
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India
| | - David J Wild
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47405, USA.
| | - Anshu Bhardwaj
- Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India. .,Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai, Tamil Nadu, 600113, India.
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22
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Dhiman R, Singh R. Recent advances for identification of new scaffolds and drug targets for Mycobacterium tuberculosis. IUBMB Life 2018; 70:905-916. [PMID: 29761628 DOI: 10.1002/iub.1863] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/07/2018] [Indexed: 02/06/2023]
Abstract
Tuberculosis (TB) is a leading cause of mortality and morbidity with an estimated 1.7 billion people latently infected with the pathogen worldwide. Clinically, TB infection presents itself as an asymptomatic infection, which gradually manifests to life threatening disease. The emergence of various drug resistant strains of Mycobacterium tuberculosis and lengthy duration of chemotherapy are major challenges in the field of TB drug development. Hence, there is an urgent need to develop scaffolds that possess a novel mechanism of action, can shorten the duration of therapy, and are active against both drug resistant and susceptible strains. In this review, we will discuss recent progress made in the field of TB drug development with emphasis on screening methods and drug targets from M. tuberculosis. The current review provides insights into mechanism of action of new scaffolds that are being evaluated in various stages of clinical trials. © 2018 IUBMB Life, 70(9):905-916, 2018.
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Affiliation(s)
- Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana, India
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23
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Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases. Future Med Chem 2018; 10:935-959. [PMID: 29629843 DOI: 10.4155/fmc-2017-0168] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Folate pathway is a key target for the development of new drugs against infectious diseases since the discovery of sulfa drugs and trimethoprim. The knowledge about this pathway has increased in the last years and the catalytic mechanism and structures of all enzymes of the pathway are fairly understood. In addition, differences among enzymes from prokaryotes and eukaryotes could be used for the design of specific inhibitors. In this review, we show a panorama of progress that has been achieved within the folate pathway obtained in the last years. We explored the structure and mechanism of enzymes, several genetic features, strategies, and approaches used in the design of new inhibitors that have been used as targets in pathogen chemotherapy.
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24
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Chotpatiwetchkul W, Boonyarattanakalin K, Gleeson D, Gleeson MP. Exploring the catalytic mechanism of dihydropteroate synthase: elucidating the differences between the substrate and inhibitor. Org Biomol Chem 2018. [PMID: 28639657 DOI: 10.1039/c7ob01272a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Dihydropteroate synthase (DHPS) catalyzes the condensation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) with p-aminobenzoic acid (pABA) and is a well validated target for anti-malarial and anti-bacterial drugs. However, in recent years its utility as a therapeutic target has diminished considerably due to multiple mutations. As such, considerable structural biology and medicinal chemistry effort has been expended to understand and overcome this issue. To date no detailed computational analysis of the protein mechanism has been made despite the detailed crystal structures and multiple mechanistic proposals being made. In this study the mechanistic proposals for DHPS have been systematically investigated using a hybrid QM/MM method. We aimed to compare the energetics associated with SN1 and SN2 processes, whether the SN1 process involves a carbocation or neutral DHP intermediate, uncover the identity of the general base in the catalytic mechanism, and understand the differences in substrate vs. inhibitor reactivity. Our results suggest a reaction that follows an SN1 process with the rate determining step being C-O bond breaking to give a carbocation intermediate. Comparative studies on the inhibitor STZ confirm the experimental observations that it is also a DHPS substrate.
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Affiliation(s)
- Warot Chotpatiwetchkul
- Faculty of Pharmacy, Siam University, 38 Petkasem Rd., Phasicharoen, Bangkok, 10160, Thailand
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25
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Dennis ML, Lee MD, Harjani JR, Ahmed M, DeBono AJ, Pitcher NP, Wang ZC, Chhabra S, Barlow N, Rahmani R, Cleary B, Dolezal O, Hattarki M, Aurelio L, Shonberg J, Graham B, Peat TS, Baell JB, Swarbrick JD. 8-Mercaptoguanine Derivatives as Inhibitors of Dihydropteroate Synthase. Chemistry 2018; 24:1922-1930. [PMID: 29171692 DOI: 10.1002/chem.201704730] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Indexed: 01/26/2023]
Abstract
Dihydropteroate synthase (DHPS) is an enzyme of the folate biosynthesis pathway, which catalyzes the formation of 7,8-dihydropteroate (DHPt) from 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) and para-aminobenzoic acid (pABA). DHPS is the long-standing target of the sulfonamide class of antibiotics that compete with pABA. In the wake of sulfa drug resistance, targeting the structurally rigid (and more conserved) pterin site has been proposed as an alternate strategy to inhibit DHPS in wild-type and sulfa drug resistant strains. Following the work on developing pterin-site inhibitors of the adjacent enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), we now present derivatives of 8-mercaptoguanine, a fragment that binds weakly within both enzymes, and quantify sub-μm binding using surface plasmon resonance (SPR) to Escherichia coli DHPS (EcDHPS). Eleven ligand-bound EcDHPS crystal structures delineate the structure-activity relationship observed providing a structural framework for the rational development of novel, substrate-envelope-compliant DHPS inhibitors.
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Affiliation(s)
- Matthew L Dennis
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia.,CSIRO Biomedical Program, Manufacturing, Parkville, 3052, Victoria, Australia
| | - Michael D Lee
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia.,CSIRO Biomedical Program, Manufacturing, Parkville, 3052, Victoria, Australia
| | - Jitendra R Harjani
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Mohamed Ahmed
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia.,School of Pharmacy, University College London, Bloomsbury, London, WC1N 1AX, UK
| | - Aaron J DeBono
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Noel P Pitcher
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Zhong-Chang Wang
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, P. R. China
| | - Sandeep Chhabra
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Nicholas Barlow
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Raphaël Rahmani
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Ben Cleary
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Olan Dolezal
- CSIRO Biomedical Program, Manufacturing, Parkville, 3052, Victoria, Australia
| | - Meghan Hattarki
- CSIRO Biomedical Program, Manufacturing, Parkville, 3052, Victoria, Australia
| | - Luigi Aurelio
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Jeremy Shonberg
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
| | - Thomas S Peat
- CSIRO Biomedical Program, Manufacturing, Parkville, 3052, Victoria, Australia
| | - Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia.,School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - James D Swarbrick
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052, Victoria, Australia
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26
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Detection of virulence-related genes in Lactococcus garvieae and their expression in response to different conditions. Folia Microbiol (Praha) 2017; 63:291-298. [DOI: 10.1007/s12223-017-0566-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
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Pornthanakasem W, Riangrungroj P, Chitnumsub P, Ittarat W, Kongkasuriyachai D, Uthaipibull C, Yuthavong Y, Leartsakulpanich U. Role of Plasmodium vivax Dihydropteroate Synthase Polymorphisms in Sulfa Drug Resistance. Antimicrob Agents Chemother 2016; 60:4453-63. [PMID: 27161627 PMCID: PMC4958149 DOI: 10.1128/aac.01835-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 04/19/2016] [Indexed: 11/20/2022] Open
Abstract
Dihydropteroate synthase (DHPS) is a known sulfa drug target in malaria treatment, existing as a bifunctional enzyme together with hydroxymethyldihydropterin pyrophosphokinase (HPPK). Polymorphisms in key residues of Plasmodium falciparum DHPS (PfDHPS) have been characterized and linked to sulfa drug resistance in malaria. Genetic sequencing of P. vivax dhps (Pvdhps) from clinical isolates has shown several polymorphisms at the positions equivalent to those in the Pfdhps genes conferring sulfa drug resistance, suggesting a mechanism for sulfa drug resistance in P. vivax similar to that seen in P. falciparum To characterize the role of polymorphisms in the PvDHPS in sulfa drug resistance, various mutants of recombinant PvHPPK-DHPS enzymes were expressed and characterized. Moreover, due to the lack of a continuous in vitro culture system for P. vivax parasites, a surrogate P. berghei model expressing Pvhppk-dhps genes was established to demonstrate the relationship between sequence polymorphisms and sulfa drug susceptibility and to test the activities of PvDHPS inhibitors on the transgenic parasites. Both enzyme activity and transgenic parasite growth were sensitive to sulfadoxine to different degrees, depending on the number of mutations that accumulated in DHPS. Ki values and 50% effective doses were higher for mutant PvDHPS enzymes than the wild-type enzymes. Altogether, the study provides the first evidence of sulfa drug resistance at the molecular level in P. vivax Furthermore, the enzyme inhibition assay and the in vivo screening system can be useful tools for screening new compounds for their activities against PvDHPS.
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Affiliation(s)
| | | | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Wanwipa Ittarat
- National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | | | - Chairat Uthaipibull
- National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
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Estrada A, Wright DL, Anderson AC. Antibacterial Antifolates: From Development through Resistance to the Next Generation. Cold Spring Harb Perspect Med 2016; 6:a028324. [PMID: 27352799 PMCID: PMC4968165 DOI: 10.1101/cshperspect.a028324] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The folate cycle is one of the key metabolic pathways used by bacteria to synthesize vital building blocks required for proliferation. Therapeutic agents targeting enzymes in this cycle, such as trimethoprim and sulfamethoxazole, are among some of the most important and continually used antibacterials to treat both Gram-positive and Gram-negative pathogens. As with all antibacterial agents, the emergence of resistance threatens the continued clinical use of these life-saving drugs. In this article, we describe and analyze resistance mechanisms that have been clinically observed and review newer generations of preclinical compounds designed to overcome the molecular basis of the resistance.
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Affiliation(s)
- Alexavier Estrada
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
| | - Dennis L Wright
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
| | - Amy C Anderson
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
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Nisha J, Ramanathan K, Nawaz Khan F, Dhanasekaran D, Shanthi V. Discovery of a potential lead compound for treating leprosy with dapsone resistance mutation in M. leprae folP1. MOLECULAR BIOSYSTEMS 2016; 12:2178-88. [DOI: 10.1039/c6mb00225k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A potential lead compound to overcome dapsone resistance in M. leprae folP1 was identified by a virtual screening strategy.
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Affiliation(s)
- J. Nisha
- Department of Biotechnology
- School of BioSciences and Technology
- VIT University
- Vellore
- India
| | - K. Ramanathan
- Department of Biotechnology
- School of BioSciences and Technology
- VIT University
- Vellore
- India
| | - F. Nawaz Khan
- Department of Chemistry
- School of Advanced Sciences
- VIT University
- Vellore
- India
| | - D. Dhanasekaran
- Department of Microbiology
- Bharathidasan University
- Tiruchirappalli
- India
| | - V. Shanthi
- Department of Biotechnology
- School of BioSciences and Technology
- VIT University
- Vellore
- India
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30
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References. Antibiotics (Basel) 2015. [DOI: 10.1128/9781555819316.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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31
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Minato Y, Thiede JM, Kordus SL, McKlveen EJ, Turman BJ, Baughn AD. Mycobacterium tuberculosis folate metabolism and the mechanistic basis for para-aminosalicylic acid susceptibility and resistance. Antimicrob Agents Chemother 2015; 59:5097-106. [PMID: 26033719 PMCID: PMC4538520 DOI: 10.1128/aac.00647-15] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
para-Aminosalicylic acid (PAS) entered clinical use in 1946 as the second exclusive drug for the treatment of tuberculosis (TB). While PAS was initially a first-line TB drug, the introduction of more potent antitubercular agents relegated PAS to the second-line tier of agents used for the treatment of drug-resistant Mycobacterium tuberculosis infections. Despite the long history of PAS usage, an understanding of the molecular and biochemical mechanisms governing the susceptibility and resistance of M. tuberculosis to this drug has lagged behind that of most other TB drugs. Herein, we discuss previous studies that demonstrate PAS-mediated disruption of iron acquisition, as well as recent genetic, biochemical, and metabolomic studies that have revealed that PAS is a prodrug that ultimately corrupts one-carbon metabolism through inhibition of the formation of reduced folate species. We also discuss findings from laboratory and clinical isolates that link alterations in folate metabolism to PAS resistance. These advancements in our understanding of the basis of the susceptibility and resistance of M. tuberculosis to PAS will enable the development of novel strategies to revitalize this and other antimicrobial agents for use in the global effort to eradicate TB.
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Affiliation(s)
- Yusuke Minato
- Department of Microbiology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Joshua M Thiede
- Department of Microbiology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Shannon Lynn Kordus
- Department of Microbiology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Edward J McKlveen
- Department of Chemistry, Harvard University, Cambridge, Massachusetts, USA
| | - Breanna J Turman
- Department of Microbiology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Anthony D Baughn
- Department of Microbiology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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Chaitanya S, Das M, Bhat P, Ebenezer M. Computational Modelling of Dapsone Interaction With Dihydropteroate Synthase inMycobacterium leprae; Insights Into Molecular Basis of Dapsone Resistance in Leprosy. J Cell Biochem 2015; 116:2293-303. [DOI: 10.1002/jcb.25180] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 03/31/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Sundeep Chaitanya
- Research Officer; Department of Laboratories; Molecular Biology and Immunology Division; The Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC); Karigiri; Vellore Tamil Nadu 632106 India
| | - Madhusmita Das
- Research Officer; Department of Laboratories; Molecular Biology and Immunology Division; The Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC); Karigiri; Vellore Tamil Nadu 632106 India
| | - Pritesh Bhat
- Applications Scientist; Schrodinger, Inc.; Near KMWA Vidya Niketan; Mahalakshmipuram; Bangalore 560 086 India
| | - Mannam Ebenezer
- The Schieffelin Institute of Health-Research and Leprosy Center (SIH-R&LC); Karigiri; Vellore Tamil Nadu 632106 India
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Abstract
More research effort needs to be invested in antimicrobial drug development to address the increasing threat of multidrug-resistant organisms. The enzyme DHPS has been a validated drug target for over 70 years as the target for the highly successful sulfa drugs. The use of sulfa drugs has been compromised by the widespread presence of resistant organisms and the adverse side effects associated with their use. Despite the large amount of structural information available for DHPS, few recent publications address the possibility of using this knowledge for novel drug design. This article reviews the relevant papers and patents that report promising new small-molecule inhibitors of DHPS, and discuss these data in light of new insights into the DHPS catalytic mechanism and recently determined crystal structures of DHPS bound to potent small-molecule inhibitors. This new functional understanding confirms that DHPS deserves further consideration as an antimicrobial drug target.
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Sousa FL, Martin WF. Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:964-81. [PMID: 24513196 DOI: 10.1016/j.bbabio.2014.02.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/31/2014] [Accepted: 02/03/2014] [Indexed: 12/27/2022]
Abstract
The deep dichotomy of archaea and bacteria is evident in many basic traits including ribosomal protein composition, membrane lipid synthesis, cell wall constituents, and flagellar composition. Here we explore that deep dichotomy further by examining the distribution of genes for the synthesis of the central carriers of one carbon units, tetrahydrofolate (H4F) and tetrahydromethanopterin (H4MPT), in bacteria and archaea. The enzymes underlying those distinct biosynthetic routes are broadly unrelated across the bacterial-archaeal divide, indicating that the corresponding pathways arose independently. That deep divergence in one carbon metabolism is mirrored in the structurally unrelated enzymes and different organic cofactors that methanogens (archaea) and acetogens (bacteria) use to perform methyl synthesis in their H4F- and H4MPT-dependent versions, respectively, of the acetyl-CoA pathway. By contrast, acetyl synthesis in the acetyl-CoA pathway - from a methyl group, CO2 and reduced ferredoxin - is simpler, uniform and conserved across acetogens and methanogens, and involves only transition metals as catalysts. The data suggest that the acetyl-CoA pathway, while being the most ancient of known CO2 assimilation pathways, reflects two phases in early evolution: an ancient phase in a geochemically confined and non-free-living universal common ancestor, in which acetyl thioester synthesis proceeded spontaneously with the help of geochemically supplied methyl groups, and a later phase that reflects the primordial divergence of the bacterial and archaeal stem groups, which independently invented genetically-encoded means to synthesize methyl groups via enzymatic reactions. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Filipa L Sousa
- Institute for Molecular Evolution,University of Düsseldorf, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute for Molecular Evolution,University of Düsseldorf, 40225 Düsseldorf, Germany.
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Utility of the Biosynthetic Folate Pathway for Targets in Antimicrobial Discovery. Antibiotics (Basel) 2014; 3:1-28. [PMID: 27025730 PMCID: PMC4790348 DOI: 10.3390/antibiotics3010001] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 01/07/2023] Open
Abstract
The need for new antimicrobials is great in face of a growing pool of resistant pathogenic organisms. This review will address the potential for antimicrobial therapy based on polypharmacological activities within the currently utilized bacterial biosynthetic folate pathway. The folate metabolic pathway leads to synthesis of required precursors for cellular function and contains a critical node, dihydrofolate reductase (DHFR), which is shared between prokaryotes and eukaryotes. The DHFR enzyme is currently targeted by methotrexate in anti-cancer therapies, by trimethoprim for antibacterial uses, and by pyrimethamine for anti-protozoal applications. An additional anti-folate target is dihyropteroate synthase (DHPS), which is unique to prokaryotes as they cannot acquire folate through dietary means. It has been demonstrated as a primary target for the longest standing antibiotic class, the sulfonamides, which act synergistically with DHFR inhibitors. Investigations have revealed most DHPS enzymes possess the ability to utilize sulfa drugs metabolically, producing alternate products that presumably inhibit downstream enzymes requiring the produced dihydropteroate. Recent work has established an off-target effect of sulfonamide antibiotics on a eukaryotic enzyme, sepiapterin reductase, causing alterations in neurotransmitter synthesis. Given that inhibitors of both DHFR and DHPS are designed to mimic their cognate substrate, which contain shared substructures, it is reasonable to expect such “off-target” effects. These inhibitors are also likely to interact with the enzymatic neighbors in the folate pathway that bind products of the DHFR or DHPS enzymes and/or substrates of similar substructure. Computational studies designed to assess polypharmacology reiterate these conclusions. This leads to hypotheses exploring the vast utility of multiple members of the folate pathway for modulating cellular metabolism, and includes an appealing capacity for prokaryotic-specific polypharmacology for antimicrobial applications.
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Gotthard G, Muhammed Ameen S, Drancourt M, Chabriere E. Long-range DHPS mutations unexpectedly increase Mycobacterium chimaera susceptibility to sulfonamides. J Glob Antimicrob Resist 2013; 1:181-188. [DOI: 10.1016/j.jgar.2013.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/24/2013] [Indexed: 02/01/2023] Open
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Liang X, Wang Z, Wang C, Wen K, Mi T, Zhang J, Zhang S. A proof-of-concept receptor-based assay for sulfonamides. Anal Biochem 2013; 438:110-6. [DOI: 10.1016/j.ab.2013.03.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 10/27/2022]
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Chu WT, Zhang JL, Zheng QC, Chen L, Xue Q, Zhang HX. Insights into the drug resistance induced by the BaDHPS mutations: molecular dynamic simulations and MM/GBSA studies. J Biomol Struct Dyn 2012; 31:1127-36. [PMID: 23030549 DOI: 10.1080/07391102.2012.726529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dihydropteroate synthase (DHPS) is essential for the folic acid biosynthetic pathway in prokaryotes; the mutation forms for DHPS are found to be relative to the urgent drug resistance problems. In our study, the Bacillus anthracis DHPS (BaDHPS) was selected for molecular dynamics and binding free energy studies to investigate the biochemistry behaviors of the wild-type and mutation form BaDHPS proteins (D184N and K220Q). It is found that the conformational change of the ligand dihydropteroate sulfathiazole binding site in mutation D184N and K220Q systems is mainly attributed from the Loop 1, Loop 2, and Loop 7 regions, and the binding free energy of these mutation systems is lower than that of the wild-type system. Additionally, some important hydrogen bonds of the mutation systems are disrupted during the simulations. But the shortening of the distance between residue Thr67 and the ligand would cause significant change of the binding pose in the K220Q system. These studies of DHPS family will be helpful for further drug resistance investigations. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:24.
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Affiliation(s)
- Wen-Ting Chu
- a State Key Laboratory of Theoretical and Computational Chemistry , Institute of Theoretical Chemistry, Jilin University , Changchun , 130023 , China
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Wolff KA, Nguyen L. Strategies for potentiation of ethionamide and folate antagonists against Mycobacterium tuberculosis. Expert Rev Anti Infect Ther 2012; 10:971-81. [PMID: 23106273 PMCID: PMC3971469 DOI: 10.1586/eri.12.87] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Antifolates inhibit de novo folate biosynthesis, whereas ethionamide targets the mycolate synthetic pathway in Mycobacterium tuberculosis. These antibiotics are effective against M. tuberculosis but their use has been hampered by concerns over toxicity and low therapeutic indexes. With the increasing spread of drug-resistant forms, interest in using old drugs for tuberculosis treatment has been renewed. Specific inhibitors targeting resistance mechanisms could sensitize M. tuberculosis to these available, clinically approved drugs. This review discusses recently developed strategies to boost the antituberculous activity of ethionamide and antifolates. These approaches might help broaden the currently limited chemotherapeutic options of not only drug-resistant but also drug-susceptible tuberculosis, which still remains one of the most common infectious diseases in the developing world.
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Affiliation(s)
- Kerstin A Wolff
- Case Western Reserve University School of Medicine, Department of Molecular Biology and Microbiology, Cleveland, OH 44106, USA
| | - Liem Nguyen
- Case Western Reserve University School of Medicine, Department of Molecular Biology and Microbiology, Cleveland, OH 44106, USA
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40
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Zhao Y, Hammoudeh D, Yun MK, Qi J, White SW, Lee RE. Structure-based design of novel pyrimido[4,5-c]pyridazine derivatives as dihydropteroate synthase inhibitors with increased affinity. ChemMedChem 2012; 7:861-70. [PMID: 22416048 DOI: 10.1002/cmdc.201200049] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 02/27/2012] [Indexed: 11/12/2022]
Abstract
Dihydropteroate synthase (DHPS) is the validated drug target for sulfonamide antimicrobial therapy. However, due to widespread drug resistance and poor tolerance, the use of sulfonamide antibiotics is now limited. The pterin binding pocket in DHPS is highly conserved and is distinct from the sulfonamide binding site. It therefore represents an attractive alternative target for the design of novel antibacterial agents. We previously carried out the structural characterization of a known pyridazine inhibitor in the Bacillus anthracis DHPS pterin site and identified a number of unfavorable interactions that appear to compromise binding. With this structural information, a series of 4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazines were designed to improve binding affinity. Most importantly, the N-methyl ring substitution was removed to improve binding within the pterin pocket, and the length of the side chain carboxylic acid was optimized to fully engage the pyrophosphate binding site. These inhibitors were synthesized and evaluated by an enzyme activity assay, X-ray crystallography, isothermal calorimetry, and surface plasmon resonance to obtain a comprehensive understanding of the binding interactions from structural, kinetic, and thermodynamic perspectives. This study clearly demonstrates that compounds lacking the N-methyl substitution exhibit increased inhibition of DHPS, but the beneficial effects of optimizing the side chain length are less apparent.
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Affiliation(s)
- Ying Zhao
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Yun MK, Wu Y, Li Z, Zhao Y, Waddell MB, Ferreira AM, Lee RE, Bashford D, White SW. Catalysis and sulfa drug resistance in dihydropteroate synthase. Science 2012; 335:1110-4. [PMID: 22383850 PMCID: PMC3531234 DOI: 10.1126/science.1214641] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The sulfonamide antibiotics inhibit dihydropteroate synthase (DHPS), a key enzyme in the folate pathway of bacteria and primitive eukaryotes. However, resistance mutations have severely compromised the usefulness of these drugs. We report structural, computational, and mutagenesis studies on the catalytic and resistance mechanisms of DHPS. By performing the enzyme-catalyzed reaction in crystalline DHPS, we have structurally characterized key intermediates along the reaction pathway. Results support an S(N)1 reaction mechanism via formation of a novel cationic pterin intermediate. We also show that two conserved loops generate a substructure during catalysis that creates a specific binding pocket for p-aminobenzoic acid, one of the two DHPS substrates. This substructure, together with the pterin-binding pocket, explains the roles of the conserved active-site residues and reveals how sulfonamide resistance arises.
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Affiliation(s)
- Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yinan Wu
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Zhenmei Li
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ying Zhao
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - M. Brett Waddell
- The Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Antonio M. Ferreira
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Information Sciences, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Donald Bashford
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Stephen W. White
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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Zhao Y, Hammoudeh D, Lin W, Das S, Yun MK, Li Z, Griffith E, Chen T, White SW, Lee RE. Development of a pterin-based fluorescent probe for screening dihydropteroate synthase. Bioconjug Chem 2011; 22:2110-7. [PMID: 21916405 DOI: 10.1021/bc200346e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydropteroate synthase (DHPS) is the classical target of the sulfonamide class of antimicrobial agents, whose use has been limited by widespread resistance and pharmacological side effects. We have initiated a structure-based drug design approach for the development of novel DHPS inhibitors that bind to the highly conserved and structured pterin subsite rather than to the adjacent p-aminobenzoic acid binding pocket that is targeted by the sulfonamide class of antibiotics. To facilitate these studies, a robust pterin site-specific fluorescence polarization (FP) assay has been developed and is discussed herein. These studies include the design, synthesis, and characterization of two fluorescent probes, and the development and validation of a rapid DHPS FP assay. This assay has excellent DMSO tolerance and is highly reproducible as evidenced by a high Z' factor. This assay offers significant advantages over traditional radiometric or phosphate release assays against this target, and is suitable for site-specific high-throughput and fragment-based screening studies.
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Affiliation(s)
- Ying Zhao
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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Morgan RE, Batot GO, Dement JM, Rao VA, Eadsforth TC, Hunter WN. Crystal structures of Burkholderia cenocepacia dihydropteroate synthase in the apo-form and complexed with the product 7,8-dihydropteroate. BMC STRUCTURAL BIOLOGY 2011; 11:21. [PMID: 21554707 PMCID: PMC3098144 DOI: 10.1186/1472-6807-11-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 05/09/2011] [Indexed: 11/22/2022]
Abstract
Background The enzyme dihydropteroate synthase (DHPS) participates in the de novo synthesis of folate cofactors by catalyzing the formation of 7,8-dihydropteroate from condensation of p-aminobenzoic acid with 6-hydroxymethyl-7,8-dihydropteroate pyrophosphate. DHPS is absent from humans, who acquire folates from diet, and has been validated as an antimicrobial therapeutic target by chemical and genetic means. The bacterium Burkholderia cenocepacia is an opportunistic pathogen and an infective agent of cystic fibrosis patients. The organism is highly resistant to antibiotics and there is a recognized need for the identification of new drugs against Burkholderia and related Gram-negative pathogens. Our characterization of the DHPS active site and interactions with the enzyme product are designed to underpin early stage drug discovery. Results An efficient recombinant protein expression system for DHPS from B. cenocepacia (BcDHPS) was prepared, the dimeric enzyme purified in high yield and crystallized. The structure of the apo-enzyme and the complex with the product 7,8-dihydropteroate have been determined to 2.35 Å and 1.95 Å resolution respectively in distinct orthorhombic crystal forms. The latter represents the first crystal structure of the DHPS-pterin product complex, reveals key interactions involved in ligand binding, and reinforces data generated by other structural studies. Comparisons with orthologues identify plasticity near the substrate-binding pocket and in particular a range of loop conformations that contribute to the architecture of the DHPS active site. These structural data provide a foundation for hit discovery. An intriguing observation, an artifact of the analysis, that of a potential sulfenamide bond within the ligand complex structure is mentioned. Conclusion Structural similarities between BcDHPS and orthologues from other Gram-negative species are evident as expected on the basis of a high level of sequence identity. The presence of 7,8-dihydropteroate in the binding site provides details about ligand recognition by the enzyme and the different states of the enzyme allow us to visualize distinct conformational states of loops adjacent to the active site. Improved drugs to combat infections by Burkholderia sp. and related Gram-negative bacteria are sought and our study now provides templates to assist that process and allow us to discuss new ways of inhibiting DHPS.
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Affiliation(s)
- Rachel E Morgan
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
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Role of mutations in dihydrofolate reductase DfrA (Rv2763c) and thymidylate synthase ThyA (Rv2764c) in Mycobacterium tuberculosis drug resistance. Antimicrob Agents Chemother 2011; 54:4522-3; author reply 5423-5. [PMID: 20852189 DOI: 10.1128/aac.00422-10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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45
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Qi J, Virga KG, Das S, Zhao Y, Yun MK, White SW, Lee RE. Synthesis of bi-substrate state mimics of dihydropteroate synthase as potential inhibitors and molecular probes. Bioorg Med Chem 2010; 19:1298-305. [PMID: 21216602 DOI: 10.1016/j.bmc.2010.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/25/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
Abstract
The increasing emergence of resistant bacteria drives us to design and develop new antimicrobial agents. Pursuant to that goal, a new targeting approach of the dihydropteroate synthase enzyme, which serves as the site of action for the sulfonamide class of antimicrobial agents, is being explored. Using structural information, a new class of transition state mimics has been designed and synthesized that have the capacity to bind to the pterin, phosphate and para-amino binding sites. The design, synthesis and evaluation of these compounds as inhibitors of Bacillusanthracis dihydropteroate synthase is described herein. Outcomes from this work have identified the first trivalent inhibitors of dihydropteroate synthase whose activity displayed slow binding inhibition. The most active compounds in this series contained an oxidized pterin ring. The binding of these inhibitors was modeled into the dihydropteroate synthase active site and demonstrated a good correlation with the observed bioassay data, as well as provided important insight for the future design of higher affinity transition state mimics.
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Affiliation(s)
- Jianjun Qi
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Ave., Rm327, Memphis, TN 38613, USA
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Pemble CW, Mehta PK, Mehra S, Li Z, Nourse A, Lee RE, White SW. Crystal structure of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase•dihydropteroate synthase bifunctional enzyme from Francisella tularensis. PLoS One 2010; 5:e14165. [PMID: 21152407 PMCID: PMC2994781 DOI: 10.1371/journal.pone.0014165] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/09/2010] [Indexed: 11/30/2022] Open
Abstract
The 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS) enzymes catalyze sequential metabolic reactions in the folate biosynthetic pathway of bacteria and lower eukaryotes. Both enzymes represent validated targets for the development of novel anti-microbial therapies. We report herein that the genes which encode FtHPPK and FtDHPS from the biowarfare agent Francisella tularensis are fused into a single polypeptide. The potential of simultaneously targeting both modules with pterin binding inhibitors prompted us to characterize the molecular details of the multifunctional complex. Our high resolution crystallographic analyses reveal the structural organization between FtHPPK and FtDHPS which are tethered together by a short linker. Additional structural analyses of substrate complexes reveal that the active sites of each module are virtually indistinguishable from those of the monofunctional enzymes. The fused bifunctional enzyme therefore represents an excellent vehicle for finding inhibitors that engage the pterin binding pockets of both modules that have entirely different architectures. To demonstrate that this approach has the potential of producing novel two-hit inhibitors of the folate pathway, we identify and structurally characterize a fragment-like molecule that simultaneously engages both active sites. Our study provides a molecular framework to study the enzyme mechanisms of HPPK and DHPS, and to design novel and much needed therapeutic compounds to treat infectious diseases.
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Affiliation(s)
- Charles W. Pemble
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Perdeep K. Mehta
- Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Smriti Mehra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Zhenmei Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Amanda Nourse
- The Hartwell Center, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Richard E. Lee
- Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- * E-mail: (SWW); (REL)
| | - Stephen W. White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail: (SWW); (REL)
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Mutation analysis of the Mycobacterium leprae folP1 gene and dapsone resistance. Antimicrob Agents Chemother 2010; 55:762-6. [PMID: 21115799 DOI: 10.1128/aac.01212-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diaminodiphenylsulfone (dapsone) has long been used as a first-line drug worldwide for the treatment of leprosy. Diagnosis for dapsone resistance of Mycobacterium leprae by DNA tests would be of great clinical value, but the relationship between the nucleotide substitutions and susceptibility to dapsone must be clarified before use. In this study, we constructed recombinant strains of cultivable Mycobacterium smegmatis carrying the M. leprae folP1 gene with or without a point mutation, disrupting their own folP gene on the chromosome. Dapsone susceptibilities of the recombinant bacteria were measured to examine influence of the mutations. Dapsone MICs for most of the strains with mutations at codon 53 or 55 of M. leprae folP1 were 2 to 16 times as high as the MIC for the strain with the wild-type folP1 sequence, but mutations that changed Thr to Ser at codon 53 showed somewhat lower MIC values than the wild-type sequence. Strains with mutations at codon 48 or 54 showed levels of susceptibility to dapsone comparable to the susceptibility of the strain with the wild-type sequence. This study confirmed that point mutations at codon 53 or 55 of the M. leprae folP1 gene result in dapsone resistance.
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Computational quantum chemistry and adaptive ligand modeling in mechanistic QSAR. Drug Discov Today 2010; 15:859-66. [DOI: 10.1016/j.drudis.2010.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Revised: 06/25/2010] [Accepted: 08/06/2010] [Indexed: 01/18/2023]
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Hevener KE, Yun MK, Qi J, Kerr ID, Babaoglu K, Hurdle JG, Balakrishna K, White SW, Lee RE. Structural studies of pterin-based inhibitors of dihydropteroate synthase. J Med Chem 2010; 53:166-77. [PMID: 19899766 DOI: 10.1021/jm900861d] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dihydropteroate synthase (DHPS) is a key enzyme in bacterial folate synthesis and the target of the sulfonamide class of antibacterials. Resistance and toxicities associated with sulfonamides have led to a decrease in their clinical use. Compounds that bind to the pterin binding site of DHPS, as opposed to the p-amino benzoic acid (pABA) binding site targeted by the sulfonamide agents, are anticipated to bypass sulfonamide resistance. To identify such inhibitors and map the pterin binding pocket, we have performed virtual screening, synthetic, and structural studies using Bacillus anthracis DHPS. Several compounds with inhibitory activity have been identified, and crystal structures have been determined that show how the compounds engage the pterin site. The structural studies identify the key binding elements and have been used to generate a structure-activity based pharmacophore map that will facilitate the development of the next generation of DHPS inhibitors which specifically target the pterin site.
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Affiliation(s)
- Kirk E Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Avenue, Room 327 Johnson Building, Memphis, Tennessee 38163, USA
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Probing the roles of non-homologous insertions in the N-terminal domain of Plasmodium falciparum hydroxymethylpterin pyrophosphokinase–dihydropteroate synthase. Mol Biochem Parasitol 2009; 168:135-42. [DOI: 10.1016/j.molbiopara.2009.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 06/29/2009] [Accepted: 07/09/2009] [Indexed: 11/19/2022]
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