1
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Shankar G, Akhter Y. Stealing survival: Iron acquisition strategies of Mycobacteriumtuberculosis. Biochimie 2024:S0300-9084(24)00142-1. [PMID: 38901792 DOI: 10.1016/j.biochi.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), faces iron scarcity within the host due to immune defenses. This review explores the importance of iron for Mtb and its strategies to overcome iron restriction. We discuss how the host limits iron as an innate immune response and how Mtb utilizes various iron acquisition systems, particularly the siderophore-mediated pathway. The review illustrates the structure and biosynthesis of mycobactin, a key siderophore in Mtb, and the regulation of its production. We explore the potential of targeting siderophore biosynthesis and uptake as a novel therapeutic approach for TB. Finally, we summarize current knowledge on Mtb's iron acquisition and highlight promising directions for future research to exploit this pathway for developing new TB interventions.
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Affiliation(s)
- Gauri Shankar
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226 025, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226 025, India.
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2
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Correia C, Leite AC, Fraga AG, Proença MF, Pedrosa J, Carvalho MA. Discovery of 2,9-diaryl-6-carbamoylpurines as a novel class of antitubercular agents. Eur J Med Chem 2024; 268:116297. [PMID: 38458108 DOI: 10.1016/j.ejmech.2024.116297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
Abstract
A series of novel 9-alkyl/aryl-2-aryl-6-carbamoylpurines were synthesized, and their activity against Mycobacterium tuberculosis strain H37Rv was assessed. The SAR analysis on the first set of derivatives, with an alkyl or aryl unit at N-9 and a phenolic unit at C-2, showed that the activity depends on the purine ring substituents at N-9 and C-2. A phenyl group at N-9 combined with a 3-hydroxyphenyl or 4-hydroxyphenyl at C-2 improve the activity. The most active compound of this set has a phenyl group at N-9 and a 4-hydroxyphenyl group at C-2, displaying an IC90 = 1.2 μg/mL and a selectivity index higher than 25.5. This compound served as a Hit to design the second set of derivatives. A phenyl group at N-9 was maintained, and the group at C-2 was diversified. The SAR analysis showed that the aryl unit at C-2 must have an oxygen or nitrogen atom bonded in the para position. A proton, a small alkyl or a substituted aryl group may also be bonded to the oxygen. The compound with the 4-methoxyphenyl group at C-2, 1Bd, exhibits the highest activity with an IC90 < 0.19 μg/mL. This compound is highly potent against M. tuberculosis strain H37Rv and non-toxic for VERO mammalian cells with an SI > 153.8. Compound 1Bd was also non-cytotoxic against primary macrophage cultures at IC90, 2xIC90, and 10xIC90 and significantly reduced the bacterial load in M. tuberculosis-infected macrophages at the same concentrations. Compound 1Bd showed a favorable pharmacokinetic profile when administered orally, with major lung and liver accumulation. In vivo antimycobacterial efficacy of 1Bd was tested at 25 mg/kg. At the tested regimen, a decrease in bacterial burden was observed in the liver. Optimization of the treatment regimen should be performed to fully potentiate the in vivo efficacy of our lead molecule, particularly in the lung, the main target organ of M. tuberculosis.
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Affiliation(s)
- Carla Correia
- CQUM - Centre of Chemistry, Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ana Claúdia Leite
- CQUM - Centre of Chemistry, Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; PT Government Associate Laboratory ICVS/3B's, Portugal
| | - Alexandra G Fraga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; PT Government Associate Laboratory ICVS/3B's, Portugal
| | - M Fernanda Proença
- CQUM - Centre of Chemistry, Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Jorge Pedrosa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; PT Government Associate Laboratory ICVS/3B's, Portugal
| | - M Alice Carvalho
- CQUM - Centre of Chemistry, Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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3
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Ishikawa F, Konno S, Kakeya H, Tanabe G. Development of a chemical scaffold for inhibiting nonribosomal peptide synthetases in live bacterial cells. Beilstein J Org Chem 2024; 20:445-451. [PMID: 38440174 PMCID: PMC10910458 DOI: 10.3762/bjoc.20.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
The adenylation (A) domain is essential for non-ribosomal peptide synthetases (NRPSs), which synthesize various peptide-based natural products, including virulence factors, such as siderophores and genotoxins. Hence, the inhibition of A-domains could attenuate the virulence of pathogens. 5'-O-N-(Aminoacyl or arylacyl)sulfamoyladenosine (AA-AMS) is a bisubstrate small-molecule inhibitor of the A-domains of NRPSs. However, the bacterial cell permeability of AA-AMS is typically a problem owing to its high hydrophilicity. In this study, we investigated the influence of a modification of 2'-OH in the AMS scaffold with different functional groups on binding to target enzymes and bacterial cell penetration. The inhibitor 7 with a cyanomethyl group at 2'-OH showed desirable inhibitory activity against both recombinant and intracellular gramicidin S synthetase A (GrsA) in the gramicidin S-producer Aneurinibacillus migulanus ATCC 9999, providing an alternative scaffold to develop novel A-domain inhibitors.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Sho Konno
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
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4
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Novakova Z, Tehrani ZA, Jurok R, Motlova L, Kutil Z, Pavlicek J, Shukla S, Choy CJ, Havlinova B, Baranova P, Berkman CE, Kuchar M, Cerny J, Barinka C. Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. J Chem Inf Model 2024; 64:1030-1042. [PMID: 38224368 PMCID: PMC10865363 DOI: 10.1021/acs.jcim.3c01542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/16/2024]
Abstract
The sulfonamide function is used extensively as a general building block in various inhibitory scaffolds and, more specifically, as a zinc-binding group (ZBG) of metalloenzyme inhibitors. Here, we provide biochemical, structural, and computational characterization of a metallopeptidase in complex with inhibitors, where the mono- and bisubstituted sulfamide functions are designed to directly engage zinc ions of a bimetallic enzyme site. Structural data showed that while monosubstituted sulfamides coordinate active-site zinc ions via the free negatively charged amino group in a canonical manner, their bisubstituted counterparts adopt an atypical binding pattern divergent from expected positioning of corresponding tetrahedral reaction intermediates. Accompanying quantum mechanics calculations revealed that electroneutrality of the sulfamide function is a major factor contributing to the markedly lower potency of bisubstituted compounds by considerably lowering their interaction energy with the enzyme. Overall, while bisubstituted uncharged sulfamide functions can bolster favorable pharmacological properties of a given inhibitor, their use as ZBGs in metalloenzyme inhibitors might be less advantageous due to their suboptimal metal-ligand properties.
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Affiliation(s)
- Zora Novakova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Zahra Aliakbar Tehrani
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Radek Jurok
- Forensic
Laboratory of Biologically Active Substances, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic
| | - Lucia Motlova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Zsofia Kutil
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Jiri Pavlicek
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Shivam Shukla
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Cindy J. Choy
- Department
of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Barbora Havlinova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Petra Baranova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Clifford E. Berkman
- Department
of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Martin Kuchar
- Forensic
Laboratory of Biologically Active Substances, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic
| | - Jiri Cerny
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Cyril Barinka
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
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5
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Zhao S, Maceren J, Chung M, Stone S, Geißen R, Boby ML, Sherborne BS, Tan DS. Design and synthesis of a library of C2-substituted sulfamidoadenosines to probe bacterial permeability. Bioorg Med Chem Lett 2024; 97:129486. [PMID: 37734424 PMCID: PMC10842738 DOI: 10.1016/j.bmcl.2023.129486] [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: 09/04/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
Antibiotic resistance is a major threat to public health, and Gram-negative bacteria pose a particular challenge due to their combination of a low permeability cell envelope and efflux pumps. Our limited understanding of the chemical rules for overcoming these barriers represents a major obstacle in antibacterial drug discovery. Several recent efforts to address this problem have involved screening compound libraries for accumulation in bacteria in order to understand the structural properties required for Gram-negative permeability. Toward this end, we used cheminformatic analysis to design a library of sulfamidoadenosines (AMSN) having diverse substituents at the adenine C2 position. An efficient synthetic route was developed with installation of a uniform cross-coupling reagent set using Sonogashira and Suzuki reactions of a C2-iodide. The potential utility of these compounds was demonstrated by pilot analysis of selected analogues for accumulation in Escherichia coli.
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Affiliation(s)
- Shibin Zhao
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Julian Maceren
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Mia Chung
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Samantha Stone
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Raphael Geißen
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA; Doctoral Program, Faculty of Biology, Albert-Ludwigs-Universität Freiburg,79104 Freiburg im Breisgau, Germany
| | - Melissa L Boby
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA; Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | | | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA; Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA; Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.
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6
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Hegde P, Orimoloye MO, Sharma S, Engelhart CA, Schnappinger D, Aldrich CC. Polyfluorinated salicylic acid analogs do not interfere with siderophore biosynthesis. Tuberculosis (Edinb) 2023; 140:102346. [PMID: 37119793 PMCID: PMC10247463 DOI: 10.1016/j.tube.2023.102346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/01/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) is a leading cause of infectious disease mortality. The salicylic acid derived small molecule siderophores known as mycobactins are essential in vivo for iron acquisition of Mtb where iron is restricted in the host. Herein, we synthesize and explore the mechanism of action of polyfluorinated salicylic acid derivates, which were previously reported to possess potent antimycobacterial activity. We hypothesized fluorinated salicylic acid derivates may inhibit mycobactin biosynthesis through initial bioactivation and conversion to downstream metabolites that block late steps in assembly of the mycobactins. Enzymatic studies demonstrated that some of the fluorinated salicylic acid derivatives compounds were readily activated by the bifunctional adenylating enzyme MbtA, responsible for incorporation of salicylic acid into the mycobactin biosynthetic pathway; however, they did not inhibit mycobactin biosynthesis as confirmed by LS-MS/MS using an authentic synthetic mycobactin standard. Further mechanistic analysis of the most active derivative (Sal-4) using an MbtA-overexpressing Mtb strain as well as complementation studies with iron and salicylic acid revealed Sal-4 cannot be antagonized by overexpression of MbtA or through supplementation with iron or salicylic acid. Taken together, our results indicate the observed antimycobacterial activity of polyfluorinated salicylic acid derivative is independent of mycobactin biosynthesis.
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Affiliation(s)
- Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Moyosore O Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA.
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7
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Stelitano G, Cocorullo M, Mori M, Villa S, Meneghetti F, Chiarelli LR. Iron Acquisition and Metabolism as a Promising Target for Antimicrobials (Bottlenecks and Opportunities): Where Do We Stand? Int J Mol Sci 2023; 24:ijms24076181. [PMID: 37047161 PMCID: PMC10094389 DOI: 10.3390/ijms24076181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) infections is one of the most crucial challenges currently faced by the scientific community. Developments in the fundamental understanding of their underlying mechanisms may open new perspectives in drug discovery. In this review, we conducted a systematic literature search in PubMed, Web of Science, and Scopus, to collect information on innovative strategies to hinder iron acquisition in bacteria. In detail, we discussed the most interesting targets from iron uptake and metabolism pathways, and examined the main chemical entities that exhibit anti-infective activities by interfering with their function. The mechanism of action of each drug candidate was also reviewed, together with its pharmacodynamic, pharmacokinetic, and toxicological properties. The comprehensive knowledge of such an impactful area of research will hopefully reflect in the discovery of newer antibiotics able to effectively tackle the antimicrobial resistance issue.
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8
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Shelton CL, Meneely KM, Ronnebaum TA, Chilton AS, Riley AP, Prisinzano TE, Lamb AL. Rational inhibitor design for Pseudomonas aeruginosa salicylate adenylation enzyme PchD. J Biol Inorg Chem 2022; 27:541-551. [PMID: 35513576 PMCID: PMC9470617 DOI: 10.1007/s00775-022-01941-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/21/2022] [Indexed: 12/04/2022]
Abstract
Pseudomonas aeruginosa is an increasingly antibiotic-resistant pathogen that causes severe lung infections, burn wound infections, and diabetic foot infections. P. aeruginosa produces the siderophore pyochelin through the use of a non-ribosomal peptide synthetase (NRPS) biosynthetic pathway. Targeting members of siderophore NRPS proteins is one avenue currently under investigation for the development of new antibiotics against antibiotic-resistant organisms. Here, the crystal structure of the pyochelin adenylation domain PchD is reported. The structure was solved to 2.11 Å when co-crystallized with the adenylation inhibitor 5'-O-(N-salicylsulfamoyl)adenosine (salicyl-AMS) and to 1.69 Å with a modified version of salicyl-AMS designed to target an active site cysteine (4-cyano-salicyl-AMS). In the structures, PchD adopts the adenylation conformation, similar to that reported for AB3403 from Acinetobacter baumannii.
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Affiliation(s)
- Catherine L. Shelton
- grid.266515.30000 0001 2106 0692Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA ,grid.261132.50000 0001 2180 142XPresent Address: Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, Kentucky 41099 USA
| | - Kathleen M. Meneely
- grid.266515.30000 0001 2106 0692Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA ,grid.215352.20000000121845633Present Address: Department of Chemistry, University of Texas San Antonio, San Antonio, TX 78249 USA
| | - Trey A. Ronnebaum
- grid.266515.30000 0001 2106 0692Department of Chemistry, University of Kansas, Lawrence, KS 66045 USA ,grid.25879.310000 0004 1936 8972Present Address: Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323 USA
| | - Annemarie S. Chilton
- grid.266515.30000 0001 2106 0692Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA
| | - Andrew P. Riley
- grid.185648.60000 0001 2175 0319Present Address: Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612 USA ,grid.266515.30000 0001 2106 0692Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66045 USA
| | - Thomas E. Prisinzano
- grid.266515.30000 0001 2106 0692Department of Medicinal Chemistry, School of Pharmacy, University of Kansas, Lawrence, KS 66045 USA ,grid.266539.d0000 0004 1936 8438Present Address: Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596 USA
| | - Audrey L. Lamb
- grid.266515.30000 0001 2106 0692Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045 USA ,grid.215352.20000000121845633Present Address: Department of Chemistry, University of Texas San Antonio, San Antonio, TX 78249 USA
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9
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Hinotani N, Saito-Tarashima N, Minakawa N. Convenient Synthesis of 3-Deazapurine Nucleosides (3-Deazainosine, 3-Deazaadenosine and 3-Deazaguanosine) Using Inosine as a Starting Material. Curr Protoc 2021; 1:e297. [PMID: 34837670 DOI: 10.1002/cpz1.297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A convenient synthetic method for preparing 3-deazapurine nucleosides (3-deazainosine, 3-deazaadenosine, and 3-deazaguanosine) from inosine via a 5-ethynyl-1-β-D-ribofuranosylimidazole-4-carboxamide (EICAR) derivative, which is a key intermediate, is described. A large-scale synthesis of an EICAR derivative starting from inosine was achieved in six steps via dinitrophenylation at the N1 position followed by ring opening, iodination of the resulting 5-amino group, and a palladium-catalyzed cross-coupling reaction. The resulting EICAR derivative was then converted into 3-deazainosine, 3-deazaadenosine, and 3-deazaguanosine. This route enabled us to synthesize 3-deazapurine nucleosides conveniently in good yields. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 5-ethynyl-1-β-D-ribofuranosylimidazole-4-carboxamide (EICAR) derivative 6 Basic Protocol 2: Preparation of 3-deazapurine nucleosides 8, 11, and 14.
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Affiliation(s)
- Naoto Hinotani
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima, Japan
| | | | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima, Japan
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10
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Zampieri D, Mamolo MG. Hybridization Approach to Drug Discovery Inhibiting Mycobacterium tuberculosis-An Overview. Curr Top Med Chem 2021; 21:777-788. [PMID: 32814528 DOI: 10.2174/1568026620666200819151342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 11/22/2022]
Abstract
Tuberculosis is one of the top 10 causes of death worldwide and the leading cause of death from a single infectious agent, mainly due to Mycobacterium tuberculosis (MTB). Recently, clinical prognoses have worsened due to the emergence of multi-drug resistant (MDR) and extensive-drug resistant (XDR) tuberculosis, which lead to the need for new, efficient and safe drugs. Among the several strategies, polypharmacology could be considered one of the best solutions, in particular, the multitarget directed ligands strategy (MTDLs), based on the synthesis of hybrid ligands acting against two targets of the pathogen. The framework strategy comprises linking, fusing and merging approaches to develop new chemical entities. With these premises, this review aims to provide an overview of the recent hybridization approach, in medicinal chemistry, of the most recent and promising multitargeting antimycobacterial candidates.
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Affiliation(s)
- Daniele Zampieri
- Department of Chemical and Pharmaceutical Sciences, P.le Europa 1, University of Trieste, Trieste 34127, Italy
| | - Maria G Mamolo
- Department of Chemical and Pharmaceutical Sciences, P.le Europa 1, University of Trieste, Trieste 34127, Italy
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11
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Can natural products stop the SARS-CoV-2 virus? A docking and molecular dynamics study of a natural product database. Future Med Chem 2021; 13:363-378. [PMID: 33415989 PMCID: PMC7798421 DOI: 10.4155/fmc-2020-0248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background: The SARS-CoV-2 3CLpro is one of the primary targets for designing new and repurposing known drugs. Methodology: A virtual screening of molecules from the Natural Product Atlas was performed, followed by molecular dynamics simulations of the most potent inhibitor bound to two conformations of the protease and into two binding sites. Conclusion: Eight molecules with appropriate ADMET properties are suggested as potential inhibitors. The greatest benefit of this study is the demonstration that these ligands can bind in the catalytic site but also to the groove between domains II and III, where they interact with a series of residues which have an important role in the dimerization and the maturation process of the enzyme.
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12
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Shyam M, Shilkar D, Verma H, Dev A, Sinha BN, Brucoli F, Bhakta S, Jayaprakash V. The Mycobactin Biosynthesis Pathway: A Prospective Therapeutic Target in the Battle against Tuberculosis. J Med Chem 2020; 64:71-100. [PMID: 33372516 DOI: 10.1021/acs.jmedchem.0c01176] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The alarming rise in drug-resistant clinical cases of tuberculosis (TB) has necessitated the rapid development of newer chemotherapeutic agents with novel mechanisms of action. The mycobactin biosynthesis pathway, conserved only among the mycolata family of actinobacteria, a group of intracellularly surviving bacterial pathogens that includes Mycobacterium tuberculosis, generates a salicyl-capped peptide mycobactin under iron-stress conditions in host macrophages to support the iron demands of the pathogen. This in vivo essentiality makes this less explored mycobactin biosynthesis pathway a promising endogenous target for novel lead-compounds discovery. In this Perspective, we have provided an up-to-date account of drug discovery efforts targeting selected enzymes (MbtI, MbtA, MbtM, and PPTase) from the mbt gene cluster (mbtA-mbtN). Furthermore, a succinct discussion on non-specific mycobactin biosynthesis inhibitors and the Trojan horse approach adopted to impair iron metabolism in mycobacteria has also been included in this Perspective.
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Affiliation(s)
- Mousumi Shyam
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India.,Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Harshita Verma
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Abhimanyu Dev
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Barij Nayan Sinha
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Federico Brucoli
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, U.K
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
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13
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Gram-scale preparation of the antibiotic lead compound salicyl-AMS, a potent inhibitor of bacterial salicylate adenylation enzymes. Methods Enzymol 2020. [PMID: 32416922 DOI: 10.1016/bs.mie.2020.04.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Salicyl-AMS (1) is a potent inhibitor of salicylate adenylation enzymes used in bacterial siderophore biosynthesis and a promising lead compound for the treatment of tuberculosis. An optimized, multigram synthesis is presented, which provides salicyl-AMS as its sodium salt (1·Na) in three synthetic steps followed by a two-step salt formation process. The synthesis proceeds in 11.6% overall yield from commercially available adenosine 2',3'-acetonide and provides highly purified material.
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14
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Marchetti M, De Bei O, Bettati S, Campanini B, Kovachka S, Gianquinto E, Spyrakis F, Ronda L. Iron Metabolism at the Interface between Host and Pathogen: From Nutritional Immunity to Antibacterial Development. Int J Mol Sci 2020; 21:E2145. [PMID: 32245010 PMCID: PMC7139808 DOI: 10.3390/ijms21062145] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 02/08/2023] Open
Abstract
Nutritional immunity is a form of innate immunity widespread in both vertebrates and invertebrates. The term refers to a rich repertoire of mechanisms set up by the host to inhibit bacterial proliferation by sequestering trace minerals (mainly iron, but also zinc and manganese). This strategy, selected by evolution, represents an effective front-line defense against pathogens and has thus inspired the exploitation of iron restriction in the development of innovative antimicrobials or enhancers of antimicrobial therapy. This review focuses on the mechanisms of nutritional immunity, the strategies adopted by opportunistic human pathogen Staphylococcus aureus to circumvent it, and the impact of deletion mutants on the fitness, infectivity, and persistence inside the host. This information finally converges in an overview of the current development of inhibitors targeting the different stages of iron uptake, an as-yet unexploited target in the field of antistaphylococcal drug discovery.
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Affiliation(s)
- Marialaura Marchetti
- Interdepartmental Center Biopharmanet-TEC, University of Parma, 43124 Parma, Italy; (M.M.); (S.B.)
| | - Omar De Bei
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (O.D.B.); (B.C.)
| | - Stefano Bettati
- Interdepartmental Center Biopharmanet-TEC, University of Parma, 43124 Parma, Italy; (M.M.); (S.B.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Institute of Biophysics, National Research Council, 56124 Pisa, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124 Parma, Italy; (O.D.B.); (B.C.)
| | - Sandra Kovachka
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (S.K.); (E.G.); (F.S.)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (S.K.); (E.G.); (F.S.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, 10125 Turin, Italy; (S.K.); (E.G.); (F.S.)
| | - Luca Ronda
- Interdepartmental Center Biopharmanet-TEC, University of Parma, 43124 Parma, Italy; (M.M.); (S.B.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Institute of Biophysics, National Research Council, 56124 Pisa, Italy
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15
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Khandazhinskaya AL, Matyugina ES, Alexandrova LA, Kezin VA, Chernousova LN, Smirnova TG, Andreevskaya SN, Popenko VI, Leonova OG, Kochetkov SN. Interaction of 5-substituted pyrimidine nucleoside analogues and M.Tuberculosis: A view through an electron microscope. Biochimie 2020; 171-172:170-177. [PMID: 32147512 DOI: 10.1016/j.biochi.2020.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/03/2020] [Indexed: 01/17/2023]
Abstract
The data of transmission electron microscopy (TEM) on morphology of M. tuberculosis H37Rv bacterial cells treated with four analogues of pyrimidine nucleosides with different substituents at 5 position of base are presented. We showed that the growth of M. tuberculosis H37Rv cells effectively inhibited by each of these compounds. This process is accompanied with the accumulation of lipid intracellular vacuole-like inclusions in the cells, appearance of deep protrusions and indentations on the surface, partial and/or complete destruction of the three-layered cell envelope. The exact molecular mechanism of action of 5-substituted pyrimidine nucleosides on M. tuberculosis cells remains to be proved. However, one can suggest that mechanism of action for these compounds is related either to their direct interactions with bacteria cell walls or to interactions with enzymes participating in the process of cell wall formation.
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Affiliation(s)
- Anastasia L Khandazhinskaya
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Elena S Matyugina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Liudmila A Alexandrova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Vasiliy A Kezin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia
| | - Larisa N Chernousova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow, 107564, Russia.
| | - Tatiana G Smirnova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow, 107564, Russia.
| | - Sofya N Andreevskaya
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow, 107564, Russia.
| | - Vladimir I Popenko
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Olga G Leonova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
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16
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Veale CGL. Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease. ChemMedChem 2019; 14:386-453. [PMID: 30614200 DOI: 10.1002/cmdc.201800755] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 12/13/2022]
Abstract
The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
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17
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Bythrow GV, Mohandas P, Guney T, Standke LC, Germain GA, Lu X, Ji C, Levendosky K, Chavadi SS, Tan DS, Quadri LEN. Kinetic Analyses of the Siderophore Biosynthesis Inhibitor Salicyl-AMS and Analogues as MbtA Inhibitors and Antimycobacterial Agents. Biochemistry 2019; 58:833-847. [PMID: 30582694 DOI: 10.1021/acs.biochem.8b01153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
There is a paramount need for expanding the drug armamentarium to counter the growing problem of drug-resistant tuberculosis. Salicyl-AMS, an inhibitor of salicylic acid adenylation enzymes, is a first-in-class antibacterial lead compound for the development of tuberculosis drugs targeting the biosynthesis of salicylic-acid-derived siderophores. In this study, we determined the Ki of salicyl-AMS for inhibition of the salicylic acid adenylation enzyme MbtA from Mycobacterium tuberculosis (MbtAtb), designed and synthesized two new salicyl-AMS analogues to probe structure-activity relationships (SAR), and characterized these two analogues alongside salicyl-AMS and six previously reported analogues in biochemical and cell-based studies. The biochemical studies included determination of kinetic parameters ( Kiapp, konapp, koff, and tR) and analysis of the mechanism of inhibition. For these studies, we optimized production and purification of recombinant MbtAtb, for which Km and kcat values were determined, and used the enzyme in conjunction with an MbtAtb-optimized, continuous, spectrophotometric assay for MbtA activity and inhibition. The cell-based studies provided an assessment of the antimycobacterial activity and postantibiotic effect of the nine MbtAtb inhibitors. The antimycobacterial properties were evaluated using a strain of nonpathogenic, fast-growing Mycobacterium smegmatis that was genetically engineered for MbtAtb-dependent susceptibility to MbtA inhibitors. This convenient model system greatly facilitated the cell-based studies by bypassing the methodological complexities associated with the use of pathogenic, slow-growing M. tuberculosis. Collectively, these studies provide new information on the mechanism of inhibition of MbtAtb by salicyl-AMS and eight analogues, afford new SAR insights for these inhibitors, and highlight several suitable candidates for future preclinical evaluation.
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Affiliation(s)
- Glennon V Bythrow
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Poornima Mohandas
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Tezcan Guney
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Lisa C Standke
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Gabrielle A Germain
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Xuequan Lu
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Cheng Ji
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Keith Levendosky
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Sivagami Sundaram Chavadi
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States.,Pharmacology Program, Weill Cornell Graduate School of Medical Sciences , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States.,Tri-Institutional Research Program , Memorial Sloan Kettering Cancer Center , 1275 York Avenue , New York , New York 10065 , United States
| | - Luis E N Quadri
- Department of Biology, Brooklyn College , City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Biology Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States.,Biochemistry Program, Graduate Center , City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
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18
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Tuning the Anti(myco)bacterial Activity of 3-Hydroxy-4-pyridinone Chelators through Fluorophores. Pharmaceuticals (Basel) 2018; 11:ph11040110. [PMID: 30347802 PMCID: PMC6316862 DOI: 10.3390/ph11040110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 02/08/2023] Open
Abstract
Controlling the sources of Fe available to pathogens is one of the possible strategies that can be successfully used by novel antibacterial drugs. We focused our interest on the design of chelators to address Mycobacterium avium infections. Taking into account the molecular structure of mycobacterial siderophores and considering that new chelators must be able to compete for Fe(III), we selected ligands of the 3-hydroxy-4-pyridinone class to achieve our purpose. After choosing the type of chelating unit it was also our objective to design chelators that could be monitored inside the cell and for that reason we designed chelators that could be functionalized with fluorophores. We didn’t realize at the time that the incorporation a fluorophore, to allow spectroscopic detection, would be so relevant for the antimycobacterial effect or to determine the affinity of the chelators towards biological membranes. From a biophysical perspective, this is a fascinating illustration of the fact that functionalization of a molecule with a particular label may lead to a change in its membrane permeation properties and result in a dramatic change in biological activity. For that reason we believe it is interesting to give a critical account of our entire work in this area and justify the statement “to label means to change”. New perspectives regarding combined therapeutic approaches and the use of rhodamine B conjugates to target closely related problems such as bacterial resistance and biofilm production are also discussed.
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19
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Mishra A, Surolia A. Mycobacterium tuberculosis: Surviving and Indulging in an Unwelcoming Host. IUBMB Life 2018; 70:917-925. [DOI: 10.1002/iub.1882] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Archita Mishra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India 560012
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India 560012
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20
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Patel K, Butala S, Khan T, Suvarna V, Sherje A, Dravyakar B. Mycobacterial siderophore: A review on chemistry and biology of siderophore and its potential as a target for tuberculosis. Eur J Med Chem 2018; 157:783-790. [PMID: 30142615 DOI: 10.1016/j.ejmech.2018.08.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022]
Abstract
Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis is known to secrete low molecular mass compounds called siderophores especially under low iron conditions to chelate iron from host environment. Iron is essential for growth and other essential processes to sustain life of the bacterium in the host. Hence targeting siderophore is considered to be an alternative approach to prevent further virulence of bacterium into the host. This review article presents classification of siderophores, their role in transporting iron into the tubercular cell, biosynthesis of mycobactins, viability of siderophore as a therapeutic target and also focuses on overview on various approaches to target siderophore. The approaches encompass mutation effect on genes involved in siderophore recycling, synthetic as well as natural compounds that can inhibit further spread of bacterium by targeting siderophore.
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Affiliation(s)
- Kavitkumar Patel
- Department of Pharmaceutical Chemistry, SVKM'S Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, 400 056, India.
| | - Sahil Butala
- Department of Pharmaceutical Chemistry, SVKM'S Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, 400 056, India
| | - Tabassum Khan
- Department of Pharmaceutical Chemistry, SVKM'S Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, 400 056, India
| | - Vasanti Suvarna
- Department of Pharmaceutical Chemistry, SVKM'S Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, 400 056, India
| | - Atul Sherje
- Department of Pharmaceutical Chemistry, SVKM'S Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, 400 056, India
| | - Bhushan Dravyakar
- Department of Pharmaceutical Chemistry, SVKM'S Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, 400 056, India
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21
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Gruzdev DA, Musiyak VV, Levit GL, Krasnov VP, Charushin VN. Purine derivatives with antituberculosis activity. RUSSIAN CHEMICAL REVIEWS 2018. [DOI: 10.1070/rcr4772] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review summarizes the data published over the last 10 – 15 years concerning the key groups of purine derivatives with antituberculosis activity. The structures of purines containing heteroatoms (S, O, N), fragments of heterocycles, amino acids and peptides, in the 6-position, as well as of purine nucleosides are presented. The possible targets for the action of such compounds and structure – activity relationship are discussed. Particular attention is paid to the most active compounds, which are of considerable interest as a basis for the development of efficient antituberculosis drugs.
The bibliography includes 99 references.
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22
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Abstract
After decades of relative inactivity, a large increase in efforts to discover antitubercular therapeutics has brought insights into the biology of Mycobacterium tuberculosis (Mtb) and promising new drugs such as bedaquiline, which inhibits ATP synthase, and the nitroimidazoles delamanid and pretomanid, which inhibit both mycolic acid synthesis and energy production. Despite these advances, the drug discovery pipeline remains underpopulated. The field desperately needs compounds with novel mechanisms of action capable of inhibiting multi- and extensively drug -resistant Mtb (M/XDR-TB) and, potentially, nonreplicating Mtb with the hope of shortening the duration of required therapy. New knowledge about Mtb, along with new methods and technologies, has driven exploration into novel target areas, such as energy production and central metabolism, that diverge from the classical targets in macromolecular synthesis. Here, we review new small molecule drug candidates that act on these novel targets to highlight the methods and perspectives advancing the field. These new targets bring with them the aspiration of shortening treatment duration as well as a pipeline of effective regimens against XDR-TB, positioning Mtb drug discovery to become a model for anti-infective discovery.
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Affiliation(s)
- Samantha Wellington
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Deborah T. Hung
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
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23
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Dawadi S, Boshoff HIM, Park SW, Schnappinger D, Aldrich CC. Conformationally Constrained Cinnolinone Nucleoside Analogues as Siderophore Biosynthesis Inhibitors for Tuberculosis. ACS Med Chem Lett 2018; 9:386-391. [PMID: 29670706 DOI: 10.1021/acsmedchemlett.8b00090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 03/16/2018] [Indexed: 12/25/2022] Open
Abstract
5'-O-[N-(Salicyl)sulfamoyl]adenosine (Sal-AMS, 1) is a nucleoside antibiotic that inhibits incorporation of salicylate into siderophores required for bacterial iron acquisition and has potent activity against Mycobacterium tuberculosis (Mtb). Cinnolone analogues exemplified by 5 were designed to replace the acidic acyl-sulfamate functional group of 1 (pKa = 3) by a more stable sulfonamide linkage (pKa = 6.0) in an attempt to address potential metabolic liabilities and improve membrane permeability. We showed 5 potently inhibited the mycobacterial salicylate ligase MbtA (apparent Ki = 12 nM), blocked production of the salicylate-capped siderophores in whole-cell Mtb, and exhibited excellent antimycobacterial activity under iron-deficient conditions (minimum inhibitor concentration, MIC = 2.3 μM). To provide additional confirmation of the mechanism of action, we demonstrated the whole-cell activity of 5 could be fully antagonized by the addition of exogenous salicylate to the growth medium. Although the total polar surface area (tPSA) of 5 still exceeds the nominal threshold value (140 Å) typically required for oral bioavailability, we were pleasantly surprised to observe introduction of the less acidic and conformationally constrained cinnolone moiety conferred improved drug disposition properties as evidenced by the 7-fold increase in volume of distribution in Sprague-Dawley rats.
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Affiliation(s)
- Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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24
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Wang X, Dowd CS. The Methylerythritol Phosphate Pathway: Promising Drug Targets in the Fight against Tuberculosis. ACS Infect Dis 2018; 4:278-290. [PMID: 29390176 DOI: 10.1021/acsinfecdis.7b00176] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a severe infectious disease in need of new chemotherapies especially for drug-resistant cases. To meet the urgent requirement of new TB drugs with novel modes of action, the TB research community has been validating numerous targets from several biosynthetic pathways. The methylerythritol phosphate (MEP) pathway is utilized by Mtb for the biosynthesis of isopentenyl pyrophosphate (IPP) and its isomer dimethylallyl pyrophosphate (DMAPP), the universal five-carbon building blocks of isoprenoids. While being a common biosynthetic pathway in pathogens, the MEP pathway is completely absent in humans. Due to its unique presence in pathogens as well as the essentiality of the MEP pathway in Mtb, the enzymes in this pathway are promising targets for the development of new drugs against tuberculosis. In this Review, we discuss three enzymes in the MEP pathway: 1-deoxy-d-xylulose-5-phosphate synthase (DXS), 1-deoxy-d-xylulose-5-phosphate reductoisomerase (IspC/DXR), and 2 C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF), which appear to be the most promising antitubercular drug targets. Structural and mechanistic features of these enzymes are reviewed, as well as selected inhibitors that show promise as antitubercular agents.
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Affiliation(s)
- Xu Wang
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington, D.C. 20052, United States
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25
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Steele AD, Ernouf G, Lee YE, Wuest WM. Diverted Total Synthesis of the Baulamycins and Analogues Reveals an Alternate Mechanism of Action. Org Lett 2018; 20:1126-1129. [PMID: 29388431 PMCID: PMC5869691 DOI: 10.1021/acs.orglett.8b00054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The baulamycins were identified as in vitro siderophore biosynthesis inhibitors. Diverted total synthesis was used to construct the natural products and eight strategic analogues, three of which had improved inhibitory activity. Biological testing then revealed that membrane damage is the predominant mode of action in Staphylococcus aureus cells.
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Affiliation(s)
- Andrew D. Steele
- Department of Chemistry, Emory University, 1515 Dickey Drive Atlanta, Georgia 30322, United States
| | - Guillaume Ernouf
- Department of Chemistry, Emory University, 1515 Dickey Drive Atlanta, Georgia 30322, United States
| | - Young Eun Lee
- Department of Chemistry, Temple University, 1901 North 13th Street Philadelphia, Pennsylvania 19122, United States
| | - William M. Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive Atlanta, Georgia 30322, United States
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26
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Ishikawa F, Tanabe G, Kakeya H. Activity-Based Protein Profiling of Non-ribosomal Peptide Synthetases. Curr Top Microbiol Immunol 2018; 420:321-349. [PMID: 30178264 DOI: 10.1007/82_2018_133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-ribosomal peptide (NRP) natural products are one of the most promising resources for drug discovery and development because of their wide-ranging of therapeutic potential, and their behavior as virulence factors and signaling molecules. The NRPs are biosynthesized independently of the ribosome by enzyme assembly lines known as the non-ribosomal peptide synthetase (NRPS) machinery. Genetic, biochemical, and bioinformatics analyses have provided a detailed understanding of the mechanism of NRPS catalysis. However, proteomic techniques for natural product biosynthesis remain a developing field. New strategies are needed to investigate the proteomes of diverse producer organisms and directly analyze the endogenous NRPS machinery. Advanced platforms should verify protein expression, protein folding, and activities and also enable the profiling of the NRPS machinery in biological samples from wild-type, heterologous, and engineered bacterial systems. Here, we focus on activity-based protein profiling strategies that have been recently developed for studies aimed at visualizing and monitoring the NRPS machinery and also for rapid labeling, identification, and biochemical analysis of NRPS enzyme family members as required for proteomic chemistry in natural product sciences.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan.
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka, 577-8502, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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27
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Paladugu S, Mainkar PS, Chandrasekhar S. Synthesis of complete carbon framework of baulamycin A. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.06.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Guchhait S, Chatterjee S, Ampapathi RS, Goswami RK. Total Synthesis of Reported Structure of Baulamycin A and Its Congeners. J Org Chem 2017; 82:2414-2435. [DOI: 10.1021/acs.joc.6b02838] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sandip Guchhait
- Department
of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Shamba Chatterjee
- Department
of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Rajib Kumar Goswami
- Department
of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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Singh A, Biot C, Viljoen A, Dupont C, Kremer L, Kumar K, Kumar V. 1H
-1,2,3-triazole-tethered uracil-ferrocene and uracil-ferrocenylchalcone conjugates: Synthesis and antitubercular evaluation. Chem Biol Drug Des 2016; 89:856-861. [DOI: 10.1111/cbdd.12908] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Amandeep Singh
- Department of Chemistry; Guru Nanak Dev University; Amritsar Punjab India
| | - Christophe Biot
- UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle; University of Lille; Lille France
- CNRS; UMR 8576; Lille France
| | - Albertus Viljoen
- CNRS; Centre d'étude d'agents Pathogènes et Biotechnologies pour la Santé; Université de Montpellier; Montpellier France
| | - Christian Dupont
- CNRS; Centre d'étude d'agents Pathogènes et Biotechnologies pour la Santé; Université de Montpellier; Montpellier France
| | - Laurent Kremer
- CNRS; Centre d'étude d'agents Pathogènes et Biotechnologies pour la Santé; Université de Montpellier; Montpellier France
- INSERM; CPBS; Montpellier France
| | - Kewal Kumar
- Department of Chemistry; Guru Nanak Dev University; Amritsar Punjab India
- Department of Applied Chemistry; Giani Zail Singh Campus College of Engineering and Technology; MRSPTU; Bathinda Punjab India
| | - Vipan Kumar
- Department of Chemistry; Guru Nanak Dev University; Amritsar Punjab India
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Krajczyk A, Zeidler J, Januszczyk P, Dawadi S, Boshoff HI, Barry CE, Ostrowski T, Aldrich CC. 2-Aryl-8-aza-3-deazaadenosine analogues of 5'-O-[N-(salicyl)sulfamoyl]adenosine: Nucleoside antibiotics that block siderophore biosynthesis in Mycobacterium tuberculosis. Bioorg Med Chem 2016; 24:3133-43. [PMID: 27265685 DOI: 10.1016/j.bmc.2016.05.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 11/16/2022]
Abstract
A series of 5'-O-[N-(salicyl)sulfamoyl]-2-aryl-8-aza-3-deazaadenosines were designed to block mycobactin biosynthesis in Mycobacterium tuberculosis (Mtb) through inhibition of the essential adenylating enzyme MbtA. The synthesis of the 2-aryl-8-aza-3-deazaadenosine nucleosides featured sequential copper-free palladium-catalyzed Sonogashira coupling of a precursor 4-cyano-5-iodo-1,2,3-triazolonucleoside with terminal alkynes and a Minakawa-Matsuda annulation reaction. These modified nucleosides were shown to inhibit MbtA with apparent Ki values ranging from 6.1 to 25nM and to inhibit Mtb growth under iron-deficient conditions with minimum inhibitory concentrations ranging from 12.5 to >50μM.
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Affiliation(s)
- Anna Krajczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Joanna Zeidler
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Piotr Januszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Helena I Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Clifton E Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Tomasz Ostrowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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31
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Dawadi S, Kawamura S, Rubenstein A, Remmel R, Aldrich CC. Synthesis and pharmacological evaluation of nucleoside prodrugs designed to target siderophore biosynthesis in Mycobacterium tuberculosis. Bioorg Med Chem 2016; 24:1314-21. [PMID: 26875934 PMCID: PMC4769951 DOI: 10.1016/j.bmc.2016.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 11/22/2022]
Abstract
The nucleoside antibiotic, 5'-O-[N-(salicyl)sulfamoyl]adenosine (1), possesses potent whole-cell activity against Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis (TB). This compound is also active in vivo, but suffers from poor drug disposition properties that result in poor bioavailability and rapid clearance. The synthesis and evaluation of a systematic series of lipophilic ester prodrugs containing linear and α-branched alkanoyl groups from two to twelve carbons at the 3'-position of a 2'-fluorinated analog of 1 is reported with the goal to improve oral bioavailability. The prodrugs were stable in simulated gastric fluid (pH 1.2) and under physiological conditions (pH 7.4). The prodrugs were also remarkably stable in mouse, rat, and human serum (relative serum stability: human∼rat≫mouse) displaying a parabolic trend in the SAR with hydrolysis rates increasing with chain length up to eight carbons (t1/2=1.6 h for octanoyl prodrug 7 in mouse serum) and then decreasing again with higher chain lengths. The permeability of the prodrugs was also assessed in a Caco-2 cell transwell model. All of the prodrugs were found to have reduced permeation in the apical-to-basolateral direction and enhanced permeation in the basolateral-to-apical direction relative to the parent compound 2, resulting in efflux ratios 5-28 times greater than 2. Additionally, Caco-2 cells were found to hydrolyze the prodrugs with SAR mirroring the serum stability results and a preference for hydrolysis on the apical side. Taken together, these results suggest that the described prodrug strategy will lead to lower than expected oral bioavailability of 2 and highlight the contribution of intestinal esterases for prodrug hydrolysis.
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Affiliation(s)
- Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Shuhei Kawamura
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Anja Rubenstein
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Rory Remmel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
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Njogu PM, Guantai EM, Pavadai E, Chibale K. Computer-Aided Drug Discovery Approaches against the Tropical Infectious Diseases Malaria, Tuberculosis, Trypanosomiasis, and Leishmaniasis. ACS Infect Dis 2016; 2:8-31. [PMID: 27622945 DOI: 10.1021/acsinfecdis.5b00093] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Despite the tremendous improvement in overall global health heralded by the adoption of the Millennium Declaration in the year 2000, tropical infections remain a major health problem in the developing world. Recent estimates indicate that the major tropical infectious diseases, namely, malaria, tuberculosis, trypanosomiasis, and leishmaniasis, account for more than 2.2 million deaths and a loss of approximately 85 million disability-adjusted life years annually. The crucial role of chemotherapy in curtailing the deleterious health and economic impacts of these infections has invigorated the search for new drugs against tropical infectious diseases. The research efforts have involved increased application of computational technologies in mainstream drug discovery programs at the hit identification, hit-to-lead, and lead optimization stages. This review highlights various computer-aided drug discovery approaches that have been utilized in efforts to identify novel antimalarial, antitubercular, antitrypanosomal, and antileishmanial agents. The focus is largely on developments over the past 5 years (2010-2014).
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Affiliation(s)
- Peter M. Njogu
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Eric M. Guantai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Elumalai Pavadai
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Pharmaceutical Chemistry and ‡Division of Pharmacology, School of Pharmacy, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
- Department of Chemistry, ⊗Institute of Infectious
Disease and Molecular Medicine, and ΘSouth African Medical Research Council Drug
Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
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Abstract
Purine and pyrimidine nucleoside and nucleotide analogs have been extensively studied as anticancer and antiviral agents. In addition to this, they have recently shown great potential against Mycobacterium Tuberculosis, the causative agent of TB. TB ranks as the tenth most common cause of death in the world. The current treatment for TB infection is limited by side effects and cost of the drugs and most importantly by the development of resistance to the therapy. Therefore the development of novel drugs, capable of overcoming the drawbacks of the existing treatments, has become the focus of many research programs. In parallel to that, a tremendous effort has been made to elucidate the unique metabolism of this pathogen with the aim to identify new possible targets. This review presents the state of the art in nucleoside and nucleotide analogs in the treatment of TB. In particular, we report on the inhibitory activity of this class of compounds, both in enzymatic and whole-cell assays, providing a brief insight to which reported target these novel compounds are hitting.
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Ishikawa F, Miyamoto K, Konno S, Kasai S, Kakeya H. Accurate Detection of Adenylation Domain Functions in Nonribosomal Peptide Synthetases by an Enzyme-linked Immunosorbent Assay System Using Active Site-directed Probes for Adenylation Domains. ACS Chem Biol 2015; 10:2816-26. [PMID: 26474351 DOI: 10.1021/acschembio.5b00595] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A significant gap exists between protein engineering and enzymes used for the biosynthesis of natural products, largely because there is a paucity of strategies that rapidly detect active-site phenotypes of the enzymes with desired activities. Herein, we describe a proof-of-concept study of an enzyme-linked immunosorbent assay (ELISA) system for the adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) using a combination of active site-directed probes coupled to a 5'-O-N-(aminoacyl)sulfamoyladenosine scaffold with a biotin functionality that immobilizes probe molecules onto a streptavidin-coated solid support. The recombinant NRPSs have a C-terminal His-tag motif that is targeted by an anti-6×His mouse antibody as the primary antibody and a horseradish peroxidase-linked goat antimouse antibody as the secondary antibody. These probes can selectively capture the cognate A domains by ligand-directed targeting. In addition, the ELISA technique detected A domains in the crude cell-free homogenates from the Escherichia coli expression systems. When coupled with a chromogenic substrate, the antibody-based ELISA technique can visualize probe-protein binding interactions, which provides accurate readouts of the A-domain functions in NRPS enzymes. To assess the ELISA-based engineering of the A domains of NRPSs, we reprogramed 2,3-dihydroxybenzoic acid (DHB)-activating enzyme EntE toward salicylic acid (Sal)-activating enzymes and investigated a correlation between binding properties for probe molecules and enzyme catalysts. We generated a mutant of EntE that displayed negligible loss in the kcat/Km value with the noncognate substrate Sal and a corresponding 48-fold decrease in the kcat/Km value with the cognate substrate DHB. The resulting 26-fold switch in substrate specificity was achieved by the replacement of a Ser residue in the active site of EntE with a Cys toward the nonribosomal codes of Sal-activating enzymes. Bringing a laboratory ELISA technique and adenylating enzymes together using a combination of active site-directed probes for the A domains in NRPSs should accelerate both the functional characterization and manipulation of the A domains in NRPSs.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Kengo Miyamoto
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Sho Konno
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Shota Kasai
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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35
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Harder M, Schäfer E, Kümin T, Illarionov B, Bacher A, Fischer M, Diederich F, Bernet B. 8-Substituted, syn-Configured Adenosine Derivatives as Potential Inhibitors of the Enzyme IspE from the Non-Mevalonate Pathway of Isoprenoid Biosynthesis. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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36
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Pergolizzi G, Cominetti MMD, Butt JN, Field RA, Bowater RP, Wagner GK. Base-modified NAD and AMP derivatives and their activity against bacterial DNA ligases. Org Biomol Chem 2015; 13:6380-98. [PMID: 25974621 DOI: 10.1039/c5ob00294j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We report the chemical synthesis and conformational analysis of a collection of 2-, 6- and 8-substituted derivatives of β-NAD(+) and AMP, and their biochemical evaluation against NAD(+)-dependent DNA ligases from Escherichia coli and Mycobacterium tuberculosis. Bacterial DNA ligases are validated anti-microbial targets, and new strategies for their inhibition are therefore of considerable scientific and practical interest. Our study includes several pairs of β-NAD(+) and AMP derivatives with the same substitution pattern at the adenine base. This has enabled the first direct comparison of co-substrate and inhibitor behaviour against bacterial DNA ligases. Our results suggest that an additional substituent in position 6 or 8 of the adenine base in β-NAD(+) is detrimental for activity as either co-substrate or inhibitor. In contrast, substituents in position 2 are not only tolerated, but appear to give rise to a new mode of inhibition, which targets the conformational changes these DNA ligases undergo during catalysis. Using a molecular modelling approach, we highlight that these findings have important implications for our understanding of ligase mechanism and inhibition, and may provide a promising starting point for the rational design of a new class of inhibitors against NAD(+)-dependent DNA ligases.
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Affiliation(s)
- Giulia Pergolizzi
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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37
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Bockman MR, Kalinda AS, Petrelli R, De la Mora-Rey T, Tiwari D, Liu F, Dawadi S, Nandakumar M, Rhee KY, Schnappinger D, Finzel BC, Aldrich CC. Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors. J Med Chem 2015; 58:7349-7369. [PMID: 26299766 PMCID: PMC4667793 DOI: 10.1021/acs.jmedchem.5b00719] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis (Mtb), responsible for both latent and symptomatic tuberculosis (TB), remains the second leading cause of mortality among infectious diseases worldwide. Mycobacterial biotin protein ligase (MtBPL) is an essential enzyme in Mtb and regulates lipid metabolism through the post-translational biotinylation of acyl coenzyme A carboxylases. We report the synthesis and evaluation of a systematic series of potent nucleoside-based inhibitors of MtBPL that contain modifications to the ribofuranosyl ring of the nucleoside. All compounds were characterized by isothermal titration calorimetry (ITC) and shown to bind potently with K(D)s ≤ 2 nM. Additionally, we obtained high-resolution cocrystal structures for a majority of the compounds. Despite fairly uniform biochemical potency, the whole-cell Mtb activity varied greatly with minimum inhibitory concentrations (MIC) ranging from 0.78 to >100 μM. Cellular accumulation studies showed a nearly 10-fold enhancement in accumulation of a C-2'-α analogue over the corresponding C-2'-β analogue, consistent with their differential whole-cell activity.
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Affiliation(s)
- Matthew R. Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alvin S. Kalinda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Riccardo Petrelli
- Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Teresa De la Mora-Rey
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Feng Liu
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Surrendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Madhumitha Nandakumar
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kyu Y. Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA,Corresponding Author Footnote: To whom correspondence should be addressed. Phone 612-625-7956. Fax 612-626-3114.
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38
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Yu M, Wang Z, Hu J, Li S, Du H. Copper-Catalyzed Intramolecular Alkoxylation of Purine Nucleosides: One-Step Synthesis of 5′-O,8-Cyclopurine Nucleosides. J Org Chem 2015; 80:9446-53. [DOI: 10.1021/acs.joc.5b01360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mingwu Yu
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Zhiqian Wang
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Junbin Hu
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Shunlai Li
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Hongguang Du
- Faculty of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
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39
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Nelson KM, Viswanathan K, Dawadi S, Duckworth BP, Boshoff HI, Barry CE, Aldrich CC. Synthesis and Pharmacokinetic Evaluation of Siderophore Biosynthesis Inhibitors for Mycobacterium tuberculosis. J Med Chem 2015; 58:5459-75. [PMID: 26110337 DOI: 10.1021/acs.jmedchem.5b00391] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MbtA catalyzes the first committed biosynthetic step of the mycobactins, which are important virulence factors associated with iron acquisition in Mycobacterium tuberculosis. MbtA is a validated therapeutic target for antitubercular drug development. 5'-O-[N-(Salicyl)sulfamoyl]adenosine (1) is a bisubstrate inhibitor of MbtA and exhibits exceptionally potent biochemical and antitubercular activity. However, 1 suffers from suboptimal drug disposition properties resulting in a short half-life (t(1/2)), low exposure (AUC), and low bioavailability (F). Four strategies were pursued to address these liabilities including the synthesis of prodrugs, increasing the pK(a) of the acyl-sulfonyl moiety, modulation of the lipophilicity, and strategic introduction of fluorine into 1. Complete pharmacokinetic (PK) analysis of all compounds was performed. The most successful modifications involved fluorination of the nucleoside that provided substantial improvements in t(1/2) and AUC. Increasing the pK(a) of the acyl-sulfonyl linker yielded incremental enhancements, while modulation of the lipophilicity and prodrug approaches led to substantially poorer PK parameters.
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Affiliation(s)
- Kathryn M Nelson
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kishore Viswanathan
- ‡Department of Medicinal Chemistry, University of Minnesota, 8-174 WDH, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Surendra Dawadi
- ‡Department of Medicinal Chemistry, University of Minnesota, 8-174 WDH, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Benjamin P Duckworth
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Helena I Boshoff
- §Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, United States
| | - Clifton E Barry
- §Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, United States
| | - Courtney C Aldrich
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.,‡Department of Medicinal Chemistry, University of Minnesota, 8-174 WDH, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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40
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Mujumdar P, Poulsen SA. Natural Product Primary Sulfonamides and Primary Sulfamates. JOURNAL OF NATURAL PRODUCTS 2015; 78:1470-1477. [PMID: 26035239 DOI: 10.1021/np501015m] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Primary sulfonamide and primary sulfamate functional groups feature prominently in the structures of U.S. FDA-approved drugs. However, the natural product chemical space contains few examples of these well-known zinc-binding chemotypes, with just two primary sulfonamide and five primary sulfamate natural products isolated and characterized to date. One of these natural products was isolated from a marine sponge, with the remainder isolated from Streptomyces species. In this review are outlined for the first time the discovery, isolation, striking breadth of bioactivity, and total synthesis (where available) for this rare group of natural products.
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Affiliation(s)
- Prashant Mujumdar
- Eskitis Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Eskitis Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland 4111, Australia
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41
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Dawadi S, Viswanathan K, Boshoff HI, Barry CE, Aldrich CC. Investigation and conformational analysis of fluorinated nucleoside antibiotics targeting siderophore biosynthesis. J Org Chem 2015; 80:4835-50. [PMID: 25916415 PMCID: PMC4674167 DOI: 10.1021/acs.joc.5b00550] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Antibiotic resistance represents one of the greatest threats to public health. The adenylation inhibitor 5'-O-[N-(salicyl)sulfamoyl]adenosine (SAL-AMS) is the archetype for a new class of nucleoside antibiotics that target iron acquisition in pathogenic microorganisms and is especially effective against Mycobacterium tuberculosis, the causative agent of tuberculosis. Strategic incorporation of fluorine at the 2' and 3' positions of the nucleoside was performed by direct fluorination to enhance activity and improve drug disposition properties. The resulting SAL-AMS analogues were comprehensively assessed for biochemical potency, whole-cell antitubercular activity, and in vivo pharmacokinetic parameters. Conformational analysis suggested a strong preference of fluorinated sugar rings for either a 2'-endo, 3'-exo (South), or a 3'-endo,2'-exo (North) conformation. The structure-activity relationships revealed a strong conformational bias for the C3'-endo conformation to maintain potent biochemical and whole-cell activity, whereas improved pharmacokinetic properties were associated with the C2'-endo conformation.
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Affiliation(s)
- Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Kishore Viswanathan
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Helena I. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, United States
| | - Clifton E. Barry
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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42
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Lamb AL. Breaking a pathogen's iron will: Inhibiting siderophore production as an antimicrobial strategy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1054-70. [PMID: 25970810 DOI: 10.1016/j.bbapap.2015.05.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 04/29/2015] [Accepted: 05/06/2015] [Indexed: 12/24/2022]
Abstract
The rise of antibiotic resistance is a growing public health crisis. Novel antimicrobials are sought, preferably developing nontraditional chemical scaffolds that do not inhibit standard targets such as cell wall synthesis or the ribosome. Iron scavenging has been proposed as a viable target, because bacterial and fungal pathogens must overcome the nutritional immunity of the host to be virulent. This review highlights the recent work toward exploiting the biosynthetic enzymes of siderophore production for the design of next generation antimicrobials.
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Affiliation(s)
- Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
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43
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Mdluli K, Kaneko T, Upton A. The tuberculosis drug discovery and development pipeline and emerging drug targets. Cold Spring Harb Perspect Med 2015; 5:a021154. [PMID: 25635061 PMCID: PMC4448709 DOI: 10.1101/cshperspect.a021154] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent accelerated approval for use in extensively drug-resistant and multidrug-resistant-tuberculosis (MDR-TB) of two first-in-class TB drugs, bedaquiline and delamanid, has reinvigorated the TB drug discovery and development field. However, although several promising clinical development programs are ongoing to evaluate new TB drugs and regimens, the number of novel series represented is few. The global early-development pipeline is also woefully thin. To have a chance of achieving the goal of better, shorter, safer TB drug regimens with utility against drug-sensitive and drug-resistant disease, a robust and diverse global TB drug discovery pipeline is key, including innovative approaches that make use of recently acquired knowledge on the biology of TB. Fortunately, drug discovery for TB has resurged in recent years, generating compounds with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review summarizes the current TB drug development pipeline and proposes strategies for generating improved hits and leads in the discovery phase that could help achieve this goal.
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Affiliation(s)
- Khisimuzi Mdluli
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Anna Upton
- Global Alliance for TB Drug Development, New York, New York 10005
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Smithen DA, Forget SM, McCormick NE, Syvitski RT, Jakeman DL. Polyphosphate-containing bisubstrate analogues as inhibitors of a bacterial cell wall thymidylyltransferase. Org Biomol Chem 2015; 13:3347-50. [DOI: 10.1039/c4ob02583k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first synthesis and evaluation of bisubstrate analogues with a thymidylyltransferase is reported. WaterLOGSY NMR and kinetic analyses provide insight into bisubstrate analogue binding.
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Affiliation(s)
| | | | | | | | - David L. Jakeman
- Department of Chemistry
- Dalhousie University
- Halifax
- Canada
- College of Pharmacy
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45
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Abstract
Resistance of important bacterial pathogens to common antimicrobial therapies and the emergence of multidrug-resistant bacteria are increasing at an alarming rate and constitute one of our greatest challenges in the combat of bacterial infection and accompanied diseases. The current shortage of effective drugs, lack of successful prevention measures and only a few new antibiotics in the clinical pipeline demand the development of novel treatment options and alternative antimicrobial therapies. Our increasing understanding of bacterial virulence strategies and the induced molecular pathways of the infectious disease provides novel opportunities to target and interfere with crucial pathogenicity factors or virulence-associated traits of the bacteria while bypassing the evolutionary pressure on the bacterium to develop resistance. In the past decade, numerous new bacterial targets for anti-virulence therapies have been identified, and structure-based tailoring of intervention strategies and screening assays for small-molecule inhibitors of such pathways were successfully established. In this chapter, we will take a closer look at the bacterial virulence-related factors and processes that present promising targets for anti-virulence therapies, recently discovered inhibitory substances and their promises and discuss the challenges, and problems that have to be faced.
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Davis TD, Gerry CJ, Tan DS. General platform for systematic quantitative evaluation of small-molecule permeability in bacteria. ACS Chem Biol 2014; 9:2535-44. [PMID: 25198656 PMCID: PMC4245172 DOI: 10.1021/cb5003015] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical features that impact small-molecule permeability across bacterial membranes are poorly understood, and the resulting lack of tools to predict permeability presents a major obstacle to the discovery and development of novel antibiotics. Antibacterials are known to have vastly different structural and physicochemical properties compared to nonantiinfective drugs, as illustrated herein by principal component analysis (PCA). To understand how these properties influence bacterial permeability, we have developed a systematic approach to evaluate the penetration of diverse compounds into bacteria with distinct cellular envelopes. Intracellular compound accumulation is quantitated using LC-MS/MS, then PCA and Pearson pairwise correlations are used to identify structural and physicochemical parameters that correlate with accumulation. An initial study using 10 sulfonyladenosines in Escherichia coli, Bacillus subtilis, and Mycobacterium smegmatis has identified nonobvious correlations between chemical structure and permeability that differ among the various bacteria. Effects of cotreatment with efflux pump inhibitors were also investigated. This sets the stage for use of this platform in larger prospective analyses of diverse chemotypes to identify global relationships between chemical structure and bacterial permeability that would enable the development of predictive tools to accelerate antibiotic drug discovery.
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Affiliation(s)
- Tony D. Davis
- Pharmacology Program−Weill Cornell Graduate School of Medical Sciences, ‡Gerstner Sloan Kettering Summer Undergraduate Research Program, §Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, United States
| | - Christopher J. Gerry
- Pharmacology Program−Weill Cornell Graduate School of Medical Sciences, ‡Gerstner Sloan Kettering Summer Undergraduate Research Program, §Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, United States
| | - Derek S. Tan
- Pharmacology Program−Weill Cornell Graduate School of Medical Sciences, ‡Gerstner Sloan Kettering Summer Undergraduate Research Program, §Molecular Pharmacology & Chemistry Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New York 10065, United States
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47
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Moeker J, Mahon BP, Bornaghi LF, Vullo D, Supuran CT, McKenna R, Poulsen SA. Structural insights into carbonic anhydrase IX isoform specificity of carbohydrate-based sulfamates. J Med Chem 2014; 57:8635-45. [PMID: 25254302 PMCID: PMC4207533 DOI: 10.1021/jm5012935] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Carbonic anhydrase IX (CA IX) is
an extracellular transmembrane
homodimeric zinc metalloenzyme that has been validated as a prognostic
marker and therapeutic target for several types of aggressive cancers.
CA IX shares a close homology with other CA isoforms, making the design
of CA IX isoform selective inhibitors challenging. In this paper,
we describe the development of a new class of CA IX inhibitors that
comprise a sulfamate as the zinc binding group, a variable linker,
and a carbohydrate “tail” moiety. Seven compounds inhibited
CA IX with low nM Ki values of 1–2
nM and also exhibited permeability profiles to preferentially target
the binding of extracellular CA IX over cytosolic CAs. The crystal
structures of two of these compounds in complex with a CA IX-mimic
(a variant of CA II, with active site residues that mimic CA IX) and
one compound in complex with CA II have been determined to 1.7 Å
resolution or better and demonstrate a selective mechanism of binding
between the hydrophilic and hydrophobic pockets of CA IX versus CA
II. These compounds present promising candidates for anti-CA IX drugs
and the treatment for several aggressive cancer types.
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Affiliation(s)
- Janina Moeker
- Eskitis Institute for Drug Discovery, Griffith University , Nathan, Queensland 4111, Australia
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48
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Meneely KM, Luo Q, Riley AP, Taylor B, Roy A, Stein RL, Prisinzano TE, Lamb AL. Expanding the results of a high throughput screen against an isochorismate-pyruvate lyase to enzymes of a similar scaffold or mechanism. Bioorg Med Chem 2014; 22:5961-9. [PMID: 25282647 DOI: 10.1016/j.bmc.2014.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 01/31/2023]
Abstract
Antibiotic resistance is a growing health concern, and new avenues of antimicrobial drug design are being actively sought. One suggested pathway to be targeted for inhibitor design is that of iron scavenging through siderophores. Here we present a high throughput screen to the isochorismate-pyruvate lyase of Pseudomonas aeruginosa, an enzyme required for the production of the siderophore pyochelin. Compounds identified in the screen are high nanomolar to low micromolar inhibitors of the enzyme and produce growth inhibition in PAO1 P. aeruginosa in the millimolar range under iron-limiting conditions. The identified compounds were also tested for enzymatic inhibition of Escherichia coli chorismate mutase, a protein of similar fold and similar chemistry, and of Yersinia enterocolitica salicylate synthase, a protein of differing fold but catalyzing the same lyase reaction. In both cases, subsets of the inhibitors from the screen were found to be inhibitory to enzymatic activity (mutase or synthase) in the micromolar range and capable of growth inhibition in their respective organisms (E. coli or Y. enterocolitica).
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Qianyi Luo
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Andrew P Riley
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS 66045, United States
| | - Byron Taylor
- High Throughput Screening Facility, University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, United States
| | - Anuradha Roy
- High Throughput Screening Facility, University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, United States
| | - Ross L Stein
- High Throughput Screening Facility, University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, United States
| | - Thomas E Prisinzano
- Department of Medicinal Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS 66045, United States
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States.
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Maier L, Hylse O, Nečas M, Trbušek M, Ytre-Arne M, Dalhus B, Bjorås M, Paruch K. New carbocyclic nucleosides: synthesis of carbocyclic pseudoisocytidine and its analogs. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.05.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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50
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Abstract
Current tuberculosis (TB) therapies take too long and the regimens are complex and subject to adverse effects and drug-drug interactions with concomitant medications. The emergence of drug-resistant TB strains exacerbates the situation. Drug discovery for TB has resurged in recent years, generating compounds (hits) with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review proposes strategies for generating improved hits and leads that could help achieve this goal.
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