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Mori M, Villa S, Chiarelli LR, Meneghetti F, Bellinzoni M. Structural Study of a New MbtI-Inhibitor Complex: Towards an Optimized Model for Structure-Based Drug Discovery. Pharmaceuticals (Basel) 2023; 16:1559. [PMID: 38004425 PMCID: PMC10675255 DOI: 10.3390/ph16111559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
MbtI from Mycobacterium tuberculosis (Mtb) is a Mg2+-dependent salicylate synthase, belonging to the chorismate-utilizing enzyme (CUE) family. As a fundamental player in iron acquisition, MbtI promotes the survival and pathogenicity of Mtb in the infected host. Hence, it has emerged in the last decade as an innovative, potential target for the anti-virulence therapy of tuberculosis. In this context, 5-phenylfuran-2-carboxylic acids have been identified as potent MbtI inhibitors. The first co-crystal structure of MbtI in complex with a member of this class was described in 2020, showing the enzyme adopting an open configuration. Due to the high mobility of the loop adjacent to the binding pocket, large portions of the amino acid chain were not defined in the electron density map, hindering computational efforts aimed at structure-driven ligand optimization. Herein, we report a new, high-resolution co-crystal structure of MbtI with a furan-based derivative, in which the closed configuration of the enzyme allowed tracing the entirety of the active site pocket in the presence of the bound inhibitor. Moreover, we describe a new crystal structure of MbtI in open conformation and in complex with the known inhibitor methyl-AMT, suggesting that in vitro potency is not related to the observed enzyme conformation. These findings will prove fundamental to enhance the potency of this series via rational structure-based drug-design approaches.
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Affiliation(s)
- Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata 9, 27100 Pavia, Italy;
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015 Paris, France
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2
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Kumar G, Adhikrao PA. Targeting Mycobacterium tuberculosis iron-scavenging tools: a recent update on siderophores inhibitors. RSC Med Chem 2023; 14:1885-1913. [PMID: 37859726 PMCID: PMC10583813 DOI: 10.1039/d3md00201b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/22/2023] [Indexed: 10/21/2023] Open
Abstract
Among the various bacterial infections, tuberculosis (TB) remains a life-threatening infectious disease responsible as the most significant cause of mortality and morbidity worldwide. The co-infection of human immunodeficiency virus (HIV) in association with TB burdens the healthcare system substantially. Notably, M.tb possesses defence against most antitubercular antibiotic drugs, and the efficacy of existing frontline anti-TB drugs is waning. Also, new and recurring cases of TB from resistant bacteria such as multidrug-resistant TB (MDR), extensively drug-resistant TB (XDR), and totally drug-resistant TB (TDR) strains are increasing. Hence, TB begs the scientific community to explore the new therapeutic class of compounds with their novel mechanism. M.tb requires iron from host cells to sustain, grow, and carry out several biological processes. M.tb has developed strategic methods of acquiring iron from the surrounding environment. In this communication, we discuss an overview of M.tb iron-scavenging tools. Also, we have summarized recently identified MbtA and MbtI inhibitors, which prevent M.tb from scavenging iron. These iron-scavenging tool inhibitors have the potential to be developed as anti-TB agents/drugs.
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Affiliation(s)
- Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad (NIPER-Hyderabad) Balanagar Hyderabad 500037 India
| | - Patil Amruta Adhikrao
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad (NIPER-Hyderabad) Balanagar Hyderabad 500037 India
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3
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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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4
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Perveen S, Sharma R. Screening approaches and therapeutic targets: The two driving wheels of tuberculosis drug discovery. Biochem Pharmacol 2022; 197:114906. [PMID: 34990594 DOI: 10.1016/j.bcp.2021.114906] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) is an infectious disease, infecting a quarter of world's population. Drug resistant TB further exacerbates the grim scenario of the drying TB drug discovery pipeline. The limited arsenal to fight TB presses the need for thorough efforts for identifying promising hits to combat the disease. The review highlights the efforts in the field of tuberculosis drug discovery, with an emphasis on massive drug screening campaigns for identifying novel hits against Mtb in both industry and academia. As an intracellular pathogen, mycobacteria reside in a complicated intracellular environment with multiple factors at play. Here, we outline various strategies employed in an effort to mimic the intracellular milieu for bringing the screening models closer to the actual settings. The review also focuses on the novel targets and pathways that could aid in target-based drug discovery in TB. The recent high throughput screening efforts resulting in the identification of potent hits against Mtb has been summarized in this article. There is a pressing need for effective screening strategies and approaches employing innovative tools and recent technologies; including nanotechnology, gene-editing tools such as CRISPR-cas system, host-directed bacterial killing and high content screening to augment the TB drug discovery pipeline with safer and shorter drug regimens.
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Affiliation(s)
- Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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5
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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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Amann M, Fritz P, Krupp A, Heuser S. Establishment of salicylic acid derived silylation reagents for protection of alcohols. RESULTS IN CHEMISTRY 2021. [DOI: 10.1016/j.rechem.2021.100139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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7
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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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8
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Currie MF, Persaud DM, Rana NK, Platt AJ, Beld J, Jaremko KL. Synthesis of an acyl-acyl carrier protein synthetase inhibitor to study fatty acid recycling. Sci Rep 2020; 10:17776. [PMID: 33082446 PMCID: PMC7575536 DOI: 10.1038/s41598-020-74731-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/06/2020] [Indexed: 11/18/2022] Open
Abstract
Fatty acids are essential to most organisms and are made endogenously by the fatty acid synthase (FAS). FAS is an attractive target for antibiotics and many inhibitors are in clinical development. However, some gram-negative bacteria harbor an enzyme known as the acyl-acyl carrier protein synthetase (AasS), which allows them to scavenge fatty acids from the environment and shuttle them into FAS and ultimately lipids. The ability of AasS to recycle fatty acids may help pathogenic gram-negative bacteria circumvent FAS inhibition. We therefore set out to design and synthesize an inhibitor of AasS and test its effectiveness on an AasS enzyme from Vibrio harveyi, the most well studied AasS to date, and from Vibrio cholerae, a pathogenic model. The inhibitor C10-AMS [5′-O-(N-decanylsulfamoyl)adenosine], which mimics the tightly bound acyl-AMP reaction intermediate, was able to effectively inhibit AasS catalytic activity in vitro. Additionally, C10-AMS stopped the ability of Vibrio cholerae to recycle fatty acids from media and survive when its endogenous FAS was inhibited with cerulenin. C10-AMS can be used to study fatty acid recycling in other bacteria as more AasS enzymes continue to be annotated and provides a platform for potential antibiotic development.
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Affiliation(s)
- Madeline F Currie
- Department of Chemistry, Hofstra University, Hempstead, NY, 11549, USA
| | - Dylan M Persaud
- Department of Chemistry, Hofstra University, Hempstead, NY, 11549, USA
| | - Niralee K Rana
- Department of Chemistry, Hofstra University, Hempstead, NY, 11549, USA
| | - Amanda J Platt
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
| | - Kara L Jaremko
- Department of Chemistry, Hofstra University, Hempstead, NY, 11549, USA.
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9
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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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10
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El-Hashash MA, Ali AT, Hussein RA, El-Sayed WM. Synthesis and Reactivity of 6,8-Dibromo-2-ethyl-4H-benzo[d][1,3]oxazin-4-one Towards Nucleophiles and Electrophiles and Their Anticancer Activity. Anticancer Agents Med Chem 2020; 19:538-545. [PMID: 30714530 DOI: 10.2174/1871520619666190201145221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/14/2019] [Accepted: 01/19/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The genetic heterogeneity of tumor cells and the development of therapy-resistant cancer cells in addition to the high cost necessitate the continuous development of novel targeted therapies. METHODS In this regard, 14 novel benzoxazinone derivatives were synthesized and examined for anticancer activity against two human epithelial cancer cell lines; breast MCF-7 and liver HepG2 cells. 6,8-Dibromo-2- ethyl-4H-benzo[d][1,3]oxazin-4-one was subjected to react with nitrogen nucleophiles to afford quinazolinone derivatives and other related moieties (3-12). Benzoxazinone 2 responds to attack with oxygen nucleophile such as ethanol to give ethyl benzoate derivative 13. The reaction of benzoxazinone 2 with carbon electrophile such as benzaldehyde derivatives afforded benzoxazinone derivatives 14a and 14b.The structure of the prepared compounds was confirmed with spectroscopic tools including IR, 1H-NMR, and 13C-NMR. RESULTS Derivatives 3, 9, 12, 13, and 14b exhibited high antiproliferative activity and were selective against cancer cells showing no toxicity in normal fibroblasts. Derivative 3 with NH-CO group in quinazolinone ring was effective only against breast cells, while derivative 12 with NH-CO group in imidazole moiety was only effective against liver cells probably through arresting cell cycle and enabling repair mechanisms. The other derivatives (9, 13, and 14b) had broader antiproliferative activity against both cell lines. These derivatives enhance the expression of the p53 and caspases 9 and 3 to varying degrees in both cell lines. Derivative 14b caused the highest induction in the investigated genes and was the only derivative to inhibit the EGFR activity. CONCLUSIONS The unique features about derivative 14b could be attributed to its high lipophilicity, high carbon content, or its extended conjugation through planar aromatic system. More investigations are required to identify the lead compound(s) in animal models.
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Affiliation(s)
- Maher A El-Hashash
- University of Ain Shams, Faculty of Science, Department of Chemistry, Abbassia 11566, Cairo, Egypt
| | - Amira T Ali
- University of Ain Shams, Faculty of Science, Department of Chemistry, Abbassia 11566, Cairo, Egypt
| | - Rasha A Hussein
- Hormonal Evaluation Department, National Organization for Drug Control & Research (NODCAR), Cairo, Egypt
| | - Wael M El-Sayed
- University of Ain Shams, Faculty of Science, Department of Zoology, Abbassia 11566, Cairo, Egypt
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11
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Vickery CR, McCulloch IP, Sonnenschein EC, Beld J, Noel JP, Burkart MD. Dissecting modular synthases through inhibition: A complementary chemical and genetic approach. Bioorg Med Chem Lett 2020; 30:126820. [PMID: 31812466 DOI: 10.1016/j.bmcl.2019.126820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 01/23/2023]
Abstract
Modular synthases, such as fatty acid, polyketide, and non-ribosomal peptide synthases (NRPSs), are sophisticated machineries essential in both primary and secondary metabolism. Various techniques have been developed to understand their genetic background and enzymatic abilities. However, uncovering the actual biosynthetic pathways remains challenging. Herein, we demonstrate a pipeline to study an assembly line synthase by interrogating the enzymatic function of each individual enzymatic domain of BpsA, a NRPS that produces the blue 3,3'-bipyridyl pigment indigoidine. Specific inhibitors for each biosynthetic domain of BpsA were obtained or synthesized, and the enzymatic performance of BpsA upon addition of each inhibitor was monitored by pigment development in vitro and in living bacteria. The results were verified using genetic mutants to inactivate each domain. Finally, the results complemented the currently proposed biosynthetic pathway of BpsA.
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Affiliation(s)
- Christopher R Vickery
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ian P McCulloch
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Eva C Sonnenschein
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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12
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Kandula V, Balakrishna C, Behera M, Nagababu U, Kumar GK, Chatterjee A. Catalytic Efficiency of Biosynthesized Silver Nanoparticles in Synthesis of Chromones and Reduction of Nitro Aromatics. ChemistrySelect 2019. [DOI: 10.1002/slct.201903001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Venu Kandula
- Department of ChemistryKoneru Laksmaiah Education Foundation Vaddeswaram, Guntur, Andhra Pradesh India 522502
- Medicinal Chemistry DepartmentGVK Biosciences Pvt. Ltd., Mallapur Hyderabad, Telangana India 500076
| | - C. Balakrishna
- Medicinal Chemistry DepartmentGVK Biosciences Pvt. Ltd., Mallapur Hyderabad, Telangana India 500076
| | - Manoranjan Behera
- Medicinal Chemistry DepartmentGVK Biosciences Pvt. Ltd., Mallapur Hyderabad, Telangana India 500076
| | - Uppu Nagababu
- Department of ChemistryKoneru Laksmaiah Education Foundation Vaddeswaram, Guntur, Andhra Pradesh India 522502
| | - G. Kiran Kumar
- Department of PhysicsRaghu Engineering College Visakhapatnam, Andhra Pradesh India - 531162
| | - Anindita Chatterjee
- Department of ChemistryKoneru Laksmaiah Education Foundation Vaddeswaram, Guntur, Andhra Pradesh India 522502
- Department of ChemistryRaghu Engineering College Visakhapatnam, Andhra Pradesh India
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13
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Cheng D, Wang M, Deng Z, Yan X, Xu X, Yan J. 2,3-Dichloro-5,6-dicyano-1,4-benzoquinone Mediated Tandem Oxidative-Coupling/Annulation of Enaminones with 1,3-Diarylpropenes for the Synthesis of 3-Allylchromones. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900793] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Dongping Cheng
- College of Pharmaceutical Science; Zhejiang University of Technology; 18 Chaowang Road 310014 Hangzhou Zhejiang P. R. China
| | - Mingliang Wang
- College of Pharmaceutical Science; Zhejiang University of Technology; 18 Chaowang Road 310014 Hangzhou Zhejiang P. R. China
| | - Zhiteng Deng
- College of Pharmaceutical Science; Zhejiang University of Technology; 18 Chaowang Road 310014 Hangzhou Zhejiang P. R. China
| | - Xianhang Yan
- College of Pharmaceutical Science; Zhejiang University of Technology; 18 Chaowang Road 310014 Hangzhou Zhejiang P. R. China
| | - Xiaoliang Xu
- College of Chemical Engineering; Zhejiang University of Technology; 18 Chaowang Road 310014 Hangzhou Zhejiang P. R. China
| | - Jizhong Yan
- College of Pharmaceutical Science; Zhejiang University of Technology; 18 Chaowang Road 310014 Hangzhou Zhejiang P. R. China
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14
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Malnuit V, Smoleń S, Tichý M, Poštová Slavětínská L, Hocek M. Synthesis of Cyclic and Acyclic Nucleoside Phosphonates and Sulfonamides Derived from 6-(Thiophen-2-yl)-7-fluoro-7-deazapurine. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vincent Malnuit
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Sabina Smoleń
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Tichý
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry; Faculty of Science; Charles University in Prague; Hlavova 8 12843 Prague 2 Czech Republic
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15
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Fu L, Wan J. C3‐Functionalized Chromones Synthesis by Tandem C−H Elaboration and Chromone Annulation of Enaminones. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900196] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Leiqing Fu
- College of Chemistry and Chemical EngineeringJiangxi Normal University Nanchang 330022 P. R. China
| | - Jie‐Ping Wan
- College of Chemistry and Chemical EngineeringJiangxi Normal University Nanchang 330022 P. R. China
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16
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Lux MC, Standke LC, Tan DS. Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors. J Antibiot (Tokyo) 2019; 72:325-349. [PMID: 30982830 PMCID: PMC6594144 DOI: 10.1038/s41429-019-0171-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Adenylate-forming enzymes are a mechanistic superfamily that are involved in diverse biochemical pathways. They catalyze ATP-dependent activation of carboxylic acid substrates as reactive acyl adenylate (acyl-AMP) intermediates and subsequent coupling to various nucleophiles to generate ester, thioester, and amide products. Inspired by natural products, acyl sulfonyladenosines (acyl-AMS) that mimic the tightly bound acyl-AMP reaction intermediates have been developed as potent inhibitors of adenylate-forming enzymes. This simple yet powerful inhibitor design platform has provided a wide range of biological probes as well as several therapeutic lead compounds. Herein, we provide an overview of the nine structural classes of adenylate-forming enzymes and examples of acyl-AMS inhibitors that have been developed for each.
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Affiliation(s)
- Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Lisa C Standke
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Chemical Biology Program, Sloan Kettering Institute, and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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17
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Evans CE, Si Y, Matarlo JS, Yin Y, French JB, Tonge PJ, Tan DS. Structure-Based Design, Synthesis, and Biological Evaluation of Non-Acyl Sulfamate Inhibitors of the Adenylate-Forming Enzyme MenE. Biochemistry 2019; 58:1918-1930. [PMID: 30912442 PMCID: PMC6653581 DOI: 10.1021/acs.biochem.9b00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
N-Acyl sulfamoyladenosines (acyl-AMS) have been used
extensively to inhibit adenylate-forming enzymes that are involved in a wide
range of biological processes. These acyl-AMS inhibitors are nonhydrolyzable
mimics of the cognate acyl adenylate intermediates that are bound tightly by
adenylate-forming enzymes. However, the anionic acyl sulfamate moiety presents a
pharmacological liability that may be detrimental to cell permeability and
pharmacokinetic profiles. We have previously developed the acyl sulfamate
OSB-AMS (1) as a potent inhibitor of the adenylate-forming enzyme
MenE, an o-succinylbenzoate-CoA (OSB-CoA) synthetase that is
required for bacterial menaquinone biosynthesis. Herein, we report the use of
computational docking to develop novel, non-acyl sulfamate inhibitors of MenE. A
m-phenyl ether-linked analogue (5) was found
to be the most potent inhibitor (IC50 = 8 μM;
Kd = 244 nM), and its X-ray co-crystal structure
was determined to characterize its binding mode in comparison to the
computational prediction. This work provides a framework for the development of
potent non-acyl sulfamate inhibitors of other adenylate-forming enzymes in the
future.
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18
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Huang B, Chen W, Zhao T, Li Z, Jiang X, Ginex T, Vílchez D, Luque FJ, Kang D, Gao P, Zhang J, Tian Y, Daelemans D, De Clercq E, Pannecouque C, Zhan P, Liu X. Exploiting the Tolerant Region I of the Non-Nucleoside Reverse Transcriptase Inhibitor (NNRTI) Binding Pocket: Discovery of Potent Diarylpyrimidine-Typed HIV-1 NNRTIs against Wild-Type and E138K Mutant Virus with Significantly Improved Water Solubility and Favorable Safety Profiles. J Med Chem 2019; 62:2083-2098. [PMID: 30721060 DOI: 10.1021/acs.jmedchem.8b01729] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Wenmin Chen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Zhenyu Li
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021 Shandong, China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Tiziana Ginex
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - David Vílchez
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Francisco Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Ye Tian
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Dirk Daelemans
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
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19
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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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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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Liu K, Chen ZB, Zhang FL, Chun qian, Tao SW, Xu QM, Zhu YM. Cu-Mediated Stereoselective [4+2] Annulation between N-Hydroxybenzimidoyl Cyanide and Norbornene. J Org Chem 2018; 83:8457-8463. [DOI: 10.1021/acs.joc.8b01081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kui Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Zhen-Bang Chen
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Fang-Ling Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Chun qian
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Shou-Wei Tao
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Qiong-Ming Xu
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Yong-Ming Zhu
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
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22
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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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23
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Cincinelli R, Beretta G, Dallavalle S. Total synthesis of tetracyclic kynurenic acid analogues isolated from chestnut honey. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2017.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Yao Q, Kong L, Zhang F, Tao X, Li Y. Base-Promoted Tandem Reaction towards Conjugated Dienone or Chromone Derivatives with a Cyano Group: Insertion of Alkynes into C-C σ-Bonds of 3-Oxopropanenitriles. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700565] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Qiyi Yao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 People's Republic of China
| | - Lingkai Kong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 People's Republic of China
| | - Fangfang Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 People's Republic of China
| | - Xianghua Tao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 People's Republic of China
| | - Yanzhong Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 People's Republic of China
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25
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Yi H, Zhang G, Wang H, Huang Z, Wang J, Singh AK, Lei A. Recent Advances in Radical C-H Activation/Radical Cross-Coupling. Chem Rev 2017. [PMID: 28639787 DOI: 10.1021/acs.chemrev.6b00620] [Citation(s) in RCA: 863] [Impact Index Per Article: 123.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Research and industrial interest in radical C-H activation/radical cross-coupling chemistry has continuously grown over the past few decades. These reactions offer fascinating and unconventional approaches toward connecting molecular fragments with high atom- and step-economy that are often complementary to traditional methods. Success in this area of research was made possible through the development of photocatalysis and first-row transition metal catalysis along with the use of peroxides as radical initiators. This Review provides a brief and concise overview of the current status and latest methodologies using radicals or radical cations as key intermediates produced via radical C-H activation. This Review includes radical addition, radical cascade cyclization, radical/radical cross-coupling, coupling of radicals with M-R groups, and coupling of radical cations with nucleophiles (Nu).
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Affiliation(s)
- Hong Yi
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies (IAS), Wuhan University , Wuhan, Hubei 430072, China
| | - Guoting Zhang
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies (IAS), Wuhan University , Wuhan, Hubei 430072, China
| | - Huamin Wang
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies (IAS), Wuhan University , Wuhan, Hubei 430072, China
| | - Zhiyuan Huang
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies (IAS), Wuhan University , Wuhan, Hubei 430072, China
| | - Jue Wang
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies (IAS), Wuhan University , Wuhan, Hubei 430072, China
| | - Atul K Singh
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies (IAS), Wuhan University , Wuhan, Hubei 430072, China
| | - Aiwen Lei
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies (IAS), Wuhan University , Wuhan, Hubei 430072, China.,National Research Center for Carbohydrate Synthesis, Jiangxi Normal University , Nanchang 330022, China
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26
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Cheng X, Zhou Y, Zhang F, Zhu K, Liu Y, Li Y. Base-Promoted Tandem Reaction Involving Insertion into Carbon-Carbon σ-Bonds: Synthesis of Xanthone and Chromone Derivatives. Chemistry 2016; 22:12655-9. [DOI: 10.1002/chem.201602064] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Xingcan Cheng
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Yuanyuan Zhou
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Fangfang Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Kai Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Yuanyuan Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
| | - Yanzhong Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; School of Chemistry and Molecular Engineering; East China Normal University; 500 Dongchuan Road Shanghai 200241 China
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27
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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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28
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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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29
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Yang XH, Song RJ, Li JH. Metal-Free [4+2] Annulation of Arylalkynes withtert-Butyl Nitrite through C(sp2)H Oxidation to Assemble Benzo[e][1,2]oxazin-4-ones. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500656] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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30
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Parker KS, Wilson JD, Marschall J, Mucha PJ, Henderson JP. Network Analysis Reveals Sex- and Antibiotic Resistance-Associated Antivirulence Targets in Clinical Uropathogens. ACS Infect Dis 2015; 1:523-532. [PMID: 26985454 PMCID: PMC4788272 DOI: 10.1021/acsinfecdis.5b00022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Indexed: 01/29/2023]
Abstract
Increasing antibiotic resistance among uropathogenic Escherichia coli (UPEC) is driving interest in therapeutic targeting of nonconserved virulence factor (VF) genes. The ability to formulate efficacious combinations of antivirulence agents requires an improved understanding of how UPEC deploy these genes. To identify clinically relevant VF combinations, we applied contemporary network analysis and biclustering algorithms to VF profiles from a large, previously characterized inpatient clinical cohort. These mathematical approaches identified four stereotypical VF combinations with distinctive relationships to antibiotic resistance and patient sex that are independent of traditional phylogenetic grouping. Targeting resistance- or sex-associated VFs based upon these contemporary mathematical approaches may facilitate individualized anti-infective therapies and identify synergistic VF combinations in bacterial pathogens.
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Affiliation(s)
| | | | - Jonas Marschall
- Department
of Infectious Diseases, Bern University Hospital and University of Bern, 3010 Bern, Switzerland
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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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Acyl peptidic siderophores: structures, biosyntheses and post-assembly modifications. Biometals 2015; 28:445-59. [PMID: 25677460 DOI: 10.1007/s10534-015-9827-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/28/2015] [Indexed: 10/24/2022]
Abstract
Acyl peptidic siderophores are produced by a variety of bacteria and possess unique amphiphilic properties. Amphiphilic siderophores are generally produced in a suite where the iron(III)-binding headgroup remains constant while the fatty acid appendage varies by length and functionality. Acyl peptidic siderophores are commonly synthesized by non-ribosomal peptide synthetases; however, the method of peptide acylation during biosynthesis can vary between siderophores. Following biosynthesis, acyl siderophores can be further modified enzymatically to produce a more hydrophilic compound, which retains its ferric chelating abilities as demonstrated by pyoverdine from Pseudomonas aeruginosa and the marinobactins from certain Marinobacter species. Siderophore hydrophobicity can also be altered through photolysis of the ferric complex of certain β-hydroxyaspartic acid-containing acyl peptidic siderophores.
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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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Wang P, Li Z, Cao S, Rao H. Metal-free catalytic cascade to chromones: direct coupling of salicylaldehydes and activated alkynes triggered by aryloxyl radicals. RSC Adv 2015. [DOI: 10.1039/c5ra24634b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The first intermolecular addition reaction of aryloxyl radicals to CC bonds was disclosed, which can afford biologically important chromonsviaa PhNMe3I-catalyzed direct coupling of salicylaldehydes and activated internal alkynes in only one step.
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Affiliation(s)
- Ping Wang
- Department of Chemistry
- Capital Normal University
- Beijing 100048
- P. R. China
- School of Chemical Engineering
| | - Zhongfeng Li
- Department of Chemistry
- Capital Normal University
- Beijing 100048
- P. R. China
| | - Shengli Cao
- Department of Chemistry
- Capital Normal University
- Beijing 100048
- P. R. China
| | - Honghua Rao
- Department of Chemistry
- Capital Normal University
- Beijing 100048
- P. R. China
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35
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X-ray diffraction and VT-NMR studies of (E)-3-(piperidinyl)-1-(2′-hydroxyphenyl)-prop-2-en-1-one. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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36
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Zhao Y, Wang ZT, Cheng Y. N-Heterocyclic Carbene/Brønsted Base Cascade Catalysis: Base-Controlled Selective Synthesis of Multifunctional Benzofuran-3-ones or Flavone Derivatives from the Reaction of 3-(2-Formylphenoxy)propenoates with Imines. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400331] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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37
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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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Narayan R, Antonchick AP. Hypervalent Iodine-Mediated Selective Oxidative Functionalization of (Thio)chromones with Alkanes. Chemistry 2014; 20:4568-72. [DOI: 10.1002/chem.201400186] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Indexed: 11/11/2022]
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