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Kwak SH, Lim WY, Hao A, Mashalidis EH, Kwon DY, Jeong P, Kim MJ, Lee SY, Hong J. Synthesis and evaluation of cyclopentane-based muraymycin analogs targeting MraY. Eur J Med Chem 2021; 215:113272. [PMID: 33607457 DOI: 10.1016/j.ejmech.2021.113272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 11/27/2022]
Abstract
Antibiotic resistance is one of the most challenging global health issues and presents an urgent need for the development of new antibiotics. In this regard, phospho-MurNAc-pentapeptide translocase (MraY), an essential enzyme in the early stages of peptidoglycan biosynthesis, has emerged as a promising new antibiotic target. We recently reported the crystal structures of MraY in complex with representative members of naturally occurring nucleoside antibiotics, including muraymycin D2. However, these nucleoside antibiotics are synthetically challenging targets, which limits the scope of medicinal chemistry efforts on this class of compounds. To gain access to active muraymycin analogs with reduced structural complexity and improved synthetic tractability, we prepared and evaluated cyclopentane-based muraymycin analogs for targeting MraY. For the installation of the 1,2-syn-amino alcohol group of analogs, the diastereoselective isocyanoacetate aldol reaction was explored. The structure-activity relationship analysis of the synthesized analogs suggested that a lipophilic side chain is essential for MraY inhibition. Importantly, the analog 20 (JH-MR-23) showed antibacterial efficacy against Staphylococcus aureus. These findings provide insights into designing new muraymycin-based MraY inhibitors with improved chemical tractability.
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Affiliation(s)
- Seung-Hwa Kwak
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Won Young Lim
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Aili Hao
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States
| | - Ellene H Mashalidis
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States
| | - Do-Yeon Kwon
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Pyeonghwa Jeong
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Mi Jung Kim
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States.
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC, 27708, United States.
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2
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Colasurdo DD, Pila MN, Iglesias DA, Laurella SL, Ruiz DL. Tautomerism of uracil and related compounds: A mass spectrometry study. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2018; 24:214-224. [PMID: 29232994 DOI: 10.1177/1469066717712461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
It has been demonstrated that uracil has a preponderant tautomeric form, but it is also known that different tautomers co-exist in this equilibrium. In this work, mass spectrometry is used as a helpful tool to analyse the equilibria, using derivative compounds to forbid the presence of some tautomers and ion trap mass spectrometry to follow relevant fragmentation pathways. Theoretical calculations were performed to confirm tautomers abundance by energy minimization in gas phase. Analysis of mass spectra of uracil, three methyl-substituted uracils, 2-thiouracil and three benzouracils suggest that uracil exists mainly as three tautomers in gas phase: one major structure that corresponds to the classical structure of uracil (pyrimidine-2,4(1H,3H)-dione) bearing two carbonyls and two NH moieties, and two minor enolic forms (4-hydroxypyrimidin-2(1H)-one and 2-hydroxypyrimidin-4(1H)-one). Such tautomeric distribution is supported by theoretical calculations, which show that they are the three most stable tautomers.
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Affiliation(s)
- Diego D Colasurdo
- 1 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Matías N Pila
- 1 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Dacio A Iglesias
- 1 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CONICET, Universidad Nacional de La Plata, La Plata, Argentina
| | - Sergio L Laurella
- 2 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CIC, Universidad Nacional de La Plata, La Plata, Argentina
| | - Danila L Ruiz
- 1 Facultad de Ciencias Exactas, CEDECOR, Departamento de Química, CONICET, Universidad Nacional de La Plata, La Plata, Argentina
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4
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Song L, Risseeuw MDP, Froeyen M, Karalic I, Goeman J, Cappoen D, Van der Eycken J, Cos P, Munier-Lehmann H, Van Calenbergh S. Elaboration of a proprietary thymidylate kinase inhibitor motif towards anti-tuberculosis agents. Bioorg Med Chem 2016; 24:5172-5182. [PMID: 27614917 DOI: 10.1016/j.bmc.2016.08.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 02/02/2023]
Abstract
We report the design and synthesis of a series of non-nucleoside MtbTMPK inhibitors (1-14) based on the gram-positive bacterial TMPK inhibitor hit compound 1. A practical synthesis was developed to access these analogues. Several compounds show promising MtbTMPK inhibitory potency and allow the establishment of a structure-activity relationship, which is helpful for further optimization.
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Affiliation(s)
- Lijun Song
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium
| | - Matheus Froeyen
- Medicinal Chemistry (Rega Institute), Department of Pharmaceutical and Pharmacological Sciences, KU LEUVEN, Minderbroedersstraat 10 blok x-box 1030, 3000 Leuven, Belgium
| | - Izet Karalic
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium
| | - Jan Goeman
- Laboratory for Organic and Bioorganic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, B-9000 Ghent, Belgium
| | - Davie Cappoen
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B-2610 Antwerpen,. Belgium
| | - Johan Van der Eycken
- Laboratory for Organic and Bioorganic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, B-9000 Ghent, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B-2610 Antwerpen,. Belgium
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523, Paris, France
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium.
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5
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Rygielska-Tokarska D, Andrei G, Schols D, Snoeck R, Głowacka IE. Synthesis, antiviral, cytotoxic and cytostatic evaluation of N 1-(phosphonoalkyl)uracil derivatives. MONATSHEFTE FUR CHEMIE 2016; 147:1081-1090. [PMID: 32214481 PMCID: PMC7087680 DOI: 10.1007/s00706-016-1701-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/09/2016] [Indexed: 11/20/2022]
Abstract
Abstract A series of N1-(phosphonoalkyl)uracils was prepared in a two-step reaction sequence from ω-aminoalkylphosphonates and (E)-3-ethoxyacryloyl isocyanate followed by the uracil ring closure. Under standard conditions (NCS; NBS; I2/CAN) all N1-(phosphonoalkyl)uracils were transformed into the respective 5-halogeno derivatives to be later benzoylated at N3. All compounds were evaluated in vitro for activity against a broad variety of DNA and RNA viruses. One compound was slightly active against human cytomegalovirus in HEL cell cultures (EC50 = 45 μM) while another showed weak activity against varicella-zoster virus (TK+ VZV strain OKA and TK− VZV strain 07-1) with EC50 = 43 and 53 µM, respectively. In addition, several compounds exhibited noticeable inhibitory effects on the proliferation of human cervical carcinoma cells (HeLa) at a concentration lower than 200 μM. Graphical abstract ![]()
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Affiliation(s)
- Dorota Rygielska-Tokarska
- 1Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland
| | - Graciela Andrei
- 2Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Louvain, Belgium
| | - Dominique Schols
- 2Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Louvain, Belgium
| | - Robert Snoeck
- 2Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Louvain, Belgium
| | - Iwona E Głowacka
- 1Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland
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Pohl R, Poštová Slavětínská L, Eng WS, Keough DT, Guddat LW, Rejman D. Synthesis, conformational studies, and biological properties of phosphonomethoxyethyl derivatives of nucleobases with a locked conformation via a pyrrolidine ring. Org Biomol Chem 2015; 13:4693-705. [PMID: 25798893 DOI: 10.1039/c5ob00097a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Systematic structure-activity studies on a diverse family of nucleoside phosphonic acids has led to the development of potent antiviral drugs such as HPMPC (CidofovirTM), PMEA (AdefovirTM), and PMPA (TenofovirTM), which are used in the treatment of CMV-induced retinitis, hepatitis B, and HIV, respectively. Here, we present the synthesis of a novel class of acyclic phosphonate nucleotides that have a locked conformation via a pyrrolidine ring. NMR analysis of these compounds revealed that the pyrrolidine ring has a constrained conformation when in the cis-form at pD < 10 via hydrogen bonding. Four of these compounds were tested as inhibitors of the human and Plasmodium falciparum 6-oxopurine phosphoribosyltransferases. The most potent has a Ki of 0.6 μM for Plasmodium falciparum HGXPRT.
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Affiliation(s)
- Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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7
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Páv O, Zborníková E, Buděšínský M, Rosenberg I. A new class of phosphanucleosides containing a 3-hydroxy-1-hydroxymethylphospholane 1-oxide ring. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Senger NA, Bowler JT, Mercado RS, Lin S, Wu W. Improved synthesis of N1-substituted orotic acid derivatives. Tetrahedron Lett 2013; 54:4245-4246. [PMID: 23935222 DOI: 10.1016/j.tetlet.2013.05.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
An improved method for the synthesis of N1-substituted orotic acid derivatives is reported. The method involves sequential incorporation of nitrogen atoms to the pyrimidine structure from simple starting materials and thus allows the synthesis of N1-substituted orotic acid derivatives with single 15N label at either N-1 or N-3.
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Affiliation(s)
- Nicholas A Senger
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132 USA
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9
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Raghuraman A, Xin D, Perez LM, Burgess K. Expanding the scope of oligo-pyrrolinone-pyrrolidines as protein-protein interface mimics. J Org Chem 2013; 78:4823-33. [PMID: 23654284 PMCID: PMC3702049 DOI: 10.1021/jo400323k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligo-pyrrolinone-pyrrolidines (generic structure 1) have the potential to interfere with protein-protein interactions (PPIs), but to reduce this to practice it is necessary to be able to synthesize these structures with a variety of different side chains corresponding to genetically encoded proteins. This paper describes expansion of the synthetic scope of 1, the difficulties encountered in this process, particularly issues with epimerization and slow coupling rates, and methods to overcome them. Finally, spectroscopic and physicochemical properties as well as proteolytic stabilities of molecules in this series were measured; these data highlight the suitability of oligo-pyrrolinone-pyrrolidines for the development of pharmacological probes or pharmaceutical leads.
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Affiliation(s)
- Arjun Raghuraman
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX 77841
| | - Dongyue Xin
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX 77841
| | - Lisa M. Perez
- Laboratory for Molecular Simulation, Texas A&M University, Box 30012, College Station, Texas 77842, United States
| | - Kevin Burgess
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX 77841
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Rejman D, Pohl R, Dračínský M. The Synthesis and Conformation of Dihydroxypiperidinyl Derivates of Nucleobases as Novel Iminosugar Nucleoside Analogs. European J Org Chem 2011. [DOI: 10.1002/ejoc.201001610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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11
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Kovačková S, Dračínský M, Rejman D. The synthesis of piperidine nucleoside analogs—a comparison of several methods to access the introduction of nucleobases. Tetrahedron 2011. [DOI: 10.1016/j.tet.2010.12.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Chen L, Lou T, Yu C, Kang Q, Chen L. N-1-(2-Mercaptoethyl)thymine modification of gold nanoparticles: a highly selective and sensitive colorimetric chemosensor for Hg2+. Analyst 2011; 136:4770-3. [DOI: 10.1039/c1an15585g] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Pohl R, Rulíšek L, Rejman D. The stability and reactivity of activated acryloylcarbamates as reagents for the synthesis of N-1 substituted thymine and uracil - an NMR and DFT study. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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