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Groenewald W, Parra-Cruz RA, Jäger CM, Croft AK. Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis. J Mol Model 2019; 25:68. [PMID: 30762132 PMCID: PMC7019640 DOI: 10.1007/s00894-019-3943-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/24/2019] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis remains a persistent pathogen, partly due to its lipid rich cell wall, of which mycolic acids (MAs) are a major component. The fluidity and conformational flexibilities of different MAs in the bacterial cell wall significantly influence its properties, function, and observed pathogenicity; thus, a proper conformational description of different MAs in different environments (e.g., in vacuum, in solution, in monolayers) can inform about their potential role in the complex setup of the bacterial cell wall. Previously, we have shown that molecular dynamics (MD) simulations of MA folding in vacuo can be used to characterize MA conformers in seven groupings relating to bending at the functional groups (W, U and Z-conformations). Providing a new OPLS-based forcefield parameterization for the critical cyclopropyl group of MAs and extensive simulations in explicit solvents (TIP4P water, hexane), we now present a more complete picture of MA folding properties together with improved simulation analysis techniques. We show that the 'WUZ' distance-based analysis can be used to pinpoint conformers with hairpin bends at the functional groups, with these conformers constituting only a fraction of accessible conformations. Applying principle component analysis (PCA) and refinement using free energy landscapes (FELs), we are able to discriminate a complete and unique set of conformational preferences for representative alpha-, methoxy- and keto-MAs, with overall preference for folded conformations. A control backbone-MA without any mero-chain functional groups showed significantly less folding in the mero-chain, confirming the role of functionalization in directing folding. Keto-MA showed the highest percentage of WUZ-type conformations and, in particular, a tendency to fold at its alpha-methyl trans-cyclopropane group, in agreement with results from Villeneuve et al. MAs demonstrate similar folding in vacuum and water, with a majority of folded conformations around the W-conformation, although the molecules are more flexible in vacuum than in water. Exchange between conformations, with a disperse distribution that includes unfolded conformers, is common in hexane for all MAs, although with more organization for Keto-MA. Globular, folded conformations are newly defined and may be specifically relevant in biofilms. Graphical abstract Through advanced simulation analysis, including principle component analysis and free energy landscapes, we reveal detailed physical insights into the solvent-dependant folding behavior of mycolic acids from M. tb.
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Affiliation(s)
- Wilma Groenewald
- School of Chemistry, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Ricardo A Parra-Cruz
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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Villeneuve M, Noguchi H. Roles of α-methyl trans-cyclopropane groups in behavior of mixed mycolic acid monolayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:441-448. [DOI: 10.1016/j.bbamem.2018.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/15/2018] [Accepted: 10/16/2018] [Indexed: 01/01/2023]
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3
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Ranchod H, Ndlandla F, Lemmer Y, Beukes M, Niebuhr J, Al-Dulayymi J, Wemmer S, Fehrsen J, Baird M, Verschoor J. The antigenicity and cholesteroid nature of mycolic acids determined by recombinant chicken antibodies. PLoS One 2018; 13:e0200298. [PMID: 30092023 PMCID: PMC6084858 DOI: 10.1371/journal.pone.0200298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/22/2018] [Indexed: 11/24/2022] Open
Abstract
Mycolic acids (MA) are major, species-specific lipid components of Mycobacteria and related genera. In Mycobacterium tuberculosis, it is made up of alpha-, methoxy- and keto-MA, each with specific biological functions and conformational characteristics. Antibodies in tuberculosis (TB) patient sera respond differently towards the three MA classes and were reported to cross-react with cholesterol. To understand the antigenicity and cholesterol cross-reactivity of MA, we generated three different chicken -derived phage-displayed single-chain variable fragments (scFv) that reacted similarly towards the natural mixture of MA, but the first recognized all three classes of chemically synthetic MAs, the second only the two oxygenated types of MAs and the third only methoxy MA. The cholesterol cross-reactivity was investigated after grafting each of the three scFv types onto two configurations of constant chain domains–CH1-4 and CH2-4. Weak but significant cross-reactivity with cholesterol was found only with CH2-4 versions, notably those two that were also able to recognize the trans-keto MA. The cholesteroid nature of mycobacterial mycolic acids therefore seems to be determined by the trans-keto MA subclass. The significantly weaker binding to cholesterol in comparison to MA confirms the potential TB diagnostic application of these antibodies.
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Affiliation(s)
- Heena Ranchod
- Polymers and Composites, Council for Scientific and Industrial Research, Pretoria, South Africa
- Department Biochemistry, University of Pretoria, Pretoria, South Africa
- * E-mail:
| | - Fortunate Ndlandla
- Polymers and Composites, Council for Scientific and Industrial Research, Pretoria, South Africa
- Department Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Yolandy Lemmer
- Polymers and Composites, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Mervyn Beukes
- Department Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Johann Niebuhr
- Department Biochemistry, University of Pretoria, Pretoria, South Africa
| | | | - Susan Wemmer
- Serology and Immunochemistry, Vaccines and Diagnostics Development Programme, Agricultural Research Council—Onderstepoort Veterinary Institute, Pretoria, South Africa
| | - Jeanni Fehrsen
- Serology and Immunochemistry, Vaccines and Diagnostics Development Programme, Agricultural Research Council—Onderstepoort Veterinary Institute, Pretoria, South Africa
| | - Mark Baird
- School of Chemistry, Bangor University, Wales, United Kingdom
| | - Jan Verschoor
- Department Biochemistry, University of Pretoria, Pretoria, South Africa
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Ali HM, Koza G, Hameed RT, Rowles R, Davies C, Al Dulayymi JR, Gwenin CD, Baird MS. The synthesis of single enantiomers of trans-alkene containing mycolic acids and related sugar esters. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.08.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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6
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Tanaka K, Matsuyama H, Watanabe M, Fujimori Y, Ishibashi K, Ozawa T, Sato T, Saikawa Y, Nakata M. Synthesis and Biological Evaluation of Kendomycin and Its Analogues. J Org Chem 2014; 79:9922-47. [DOI: 10.1021/jo5015273] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyosuke Tanaka
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Hiroshi Matsuyama
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Masahito Watanabe
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Yukiko Fujimori
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kodai Ishibashi
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Tomohiro Ozawa
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Tomoharu Sato
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Yoko Saikawa
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Masaya Nakata
- Department of Applied Chemistry,
Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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7
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Groenewald W, Baird MS, Verschoor JA, Minnikin DE, Croft AK. Differential spontaneous folding of mycolic acids from Mycobacterium tuberculosis. Chem Phys Lipids 2014; 180:15-22. [DOI: 10.1016/j.chemphyslip.2013.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/06/2013] [Accepted: 12/09/2013] [Indexed: 10/25/2022]
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Stocker BL, Timmer MS. Trehalose diesters, lipoteichoic acids and α-GalCer: using chemistry to understand immunology. Carbohydr Res 2014; 389:3-11. [DOI: 10.1016/j.carres.2013.08.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/29/2013] [Accepted: 08/31/2013] [Indexed: 10/26/2022]
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9
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Koza G, Muzael M, Schubert-Rowles RR, Theunissen C, Al Dulayymi JR, Baird MS. The synthesis of methoxy and keto mycolic acids containing methyl-trans-cyclopropanes. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.04.134] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Balogun MO, Huws EH, Sirhan MM, Saleh AD, Dulayymi JRA, Pilcher L, Verschoor JA, Baird MS. Thiol modified mycolic acids. Chem Phys Lipids 2013; 172-173:40-55. [DOI: 10.1016/j.chemphyslip.2013.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/21/2013] [Accepted: 03/23/2013] [Indexed: 11/30/2022]
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Verschoor JA, Baird MS, Grooten J. Towards understanding the functional diversity of cell wall mycolic acids of Mycobacterium tuberculosis. Prog Lipid Res 2012; 51:325-39. [PMID: 22659327 DOI: 10.1016/j.plipres.2012.05.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 03/05/2012] [Accepted: 05/23/2012] [Indexed: 01/08/2023]
Abstract
Mycolic acids constitute the waxy layer of the outer cell wall of Mycobacterium spp. and a few other genera. They are diverse in structure, providing a unique chromatographic foot-print for almost each of the more than 70 Mycobacterium species. Although mainly esterified to cell wall arabinogalactan, trehalose or glucose, some free mycolic acid is secreted during in vitro growth of Mycobacterium tuberculosis. In M. tuberculosis, α-, keto- and methoxy-mycolic acids are the main classes, each differing in their ability to attract neutrophils, induce foamy macrophages or adopt an antigenic structure for antibody recognition. Of interest is their particular relationship to cholesterol, discovered by their ability to attract cholesterol, to bind Amphotericin B or to be recognised by monoclonal antibodies that cross-react with cholesterol. The structural elements that determine this diverse functionality include the carboxylic acid in the mycolic motif, as well as the nature and stereochemistry of the two functional groups in the merochain. The functional diversity of mycolic acid classes implies that much information may be contained in the selective expression and secretion of mycolic acids to establish tuberculosis after infection of the host. Their cholesteroid nature may relate to how they utilize host cholesterol for their persistent survival.
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Affiliation(s)
- Jan A Verschoor
- Department Biochemistry, University of Pretoria, Pretoria 0002, South Africa.
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Khan AA, Stocker BL, Timmer MSM. Trehalose glycolipids--synthesis and biological activities. Carbohydr Res 2012; 356:25-36. [PMID: 22486827 DOI: 10.1016/j.carres.2012.03.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/10/2012] [Accepted: 03/10/2012] [Indexed: 02/04/2023]
Abstract
A variety of trehalose glycolipids have been isolated from natural sources, and several of these glycolipids exhibit important biological properties. These molecules also represent challenging synthetic targets due to their highly amphiphilic character, their large number of functional groups and additional chiral centres. This review highlights some of the recent advances made in the synthesis of trehalose glycolipids, and their associated biological activities.
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Affiliation(s)
- Ashna A Khan
- School of Chemical and Physical Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
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Synthesis of cis,cis-diunsaturated α-meromycolic acid by a palladium-catalysed alkyl–alkyl Negishi reaction. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2011.11.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Vander Beken S, Al Dulayymi JR, Naessens T, Koza G, Maza-Iglesias M, Rowles R, Theunissen C, De Medts J, Lanckacker E, Baird MS, Grooten J. Molecular structure of the Mycobacterium tuberculosis virulence factor, mycolic acid, determines the elicited inflammatory pattern. Eur J Immunol 2010; 41:450-60. [PMID: 21268014 DOI: 10.1002/eji.201040719] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 10/20/2010] [Accepted: 11/17/2010] [Indexed: 11/12/2022]
Abstract
Mycolic acids (MAs) occur in the cell wall of Mycobacterium tuberculosis as variable mixtures of different classes and chain lengths. Here, we address the relationship between the structure and its inflammatory function of this virulence factor using single synthetic MA isomers, differing in oxygenation class and cis- versus α-methyl-trans proximal cyclopropane orientation. Analysis of bronchoalveolar inflammation, lung histopathology and alveolar macrophage transcription revealed a strong dependence on these meromycolic chemistries of mouse pulmonary inflammation in response to intratracheal treatments with MAs. Whereas α-MA was inert, oxygenated methoxy- and keto-MA with cis-cyclopropane stereochemistry elicited solid to mild inflammatory responses respectively. In trans-cyclopropane orientation, methoxy-MA partially lost its inflammatory activity and keto-MA exerted anti-inflammatory alternative activation of alveolar macrophages and counteracted cis-methoxy-MA induced airway inflammation. The differential innate immune activities of MAs demonstrated here, dependent on oxygenation class and cis versus α-methyl-trans cyclopropane chemistry, identify a novel means for M. tuberculosis to steer host immune responses during infection.
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Affiliation(s)
- Seppe Vander Beken
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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Beukes M, Lemmer Y, Deysel M, Al Dulayymi JR, Baird MS, Koza G, Iglesias MM, Rowles RR, Theunissen C, Grooten J, Toschi G, Roberts VV, Pilcher L, Van Wyngaardt S, Mathebula N, Balogun M, Stoltz AC, Verschoor JA. Structure-function relationships of the antigenicity of mycolic acids in tuberculosis patients. Chem Phys Lipids 2010; 163:800-8. [PMID: 20875402 PMCID: PMC3025329 DOI: 10.1016/j.chemphyslip.2010.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/14/2010] [Accepted: 09/17/2010] [Indexed: 11/17/2022]
Abstract
Cell wall mycolic acids (MA) from Mycobacterium tuberculosis (M.tb) are CD1b presented antigens that can be used to detect antibodies as surrogate markers of active TB, even in HIV coinfected patients. The use of the complex mixtures of natural MA is complicated by an apparent antibody cross-reactivity with cholesterol. Here firstly we report three recombinant monoclonal scFv antibody fragments in the chicken germ-line antibody repertoire, which demonstrate the possibilities for cross-reactivity: the first recognized both cholesterol and mycolic acids, the second mycolic acids but not cholesterol, and the third cholesterol but not mycolic acids. Secondly, MA structure is experimentally interrogated to try to understand the cross-reactivity. Unique synthetic mycolic acids representative of the three main functional classes show varying antigenicity against human TB patient sera, depending on the functional groups present and on their stereochemistry. Oxygenated (methoxy- and keto-) mycolic acid was found to be more antigenic than alpha-mycolic acids. Synthetic methoxy-mycolic acids were the most antigenic, one containing a trans-cyclopropane apparently being somewhat more antigenic than the natural mixture. Trans-cyclopropane-containing keto- and hydroxy-mycolic acids were also found to be the most antigenic among each of these classes. However, none of the individual synthetic mycolic acids significantly and reproducibly distinguished the pooled serum of TB positive patients from that of TB negative patients better than the natural mixture of MA. This argues against the potential to improve the specificity of serodiagnosis of TB with a defined single synthetic mycolic acid antigen from this set, although sensitivity may be facilitated by using a synthetic methoxy-mycolic acid.
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Affiliation(s)
- Mervyn Beukes
- Department of Biochemistry, University of Pretoria, South Africa
| | - Yolandy Lemmer
- Department of Biochemistry, University of Pretoria, South Africa
| | - Madrey Deysel
- Department of Biochemistry, University of Pretoria, South Africa
| | | | - Mark S. Baird
- School of Chemistry, University of Wales, Bangor, United Kingdom
| | - Gani Koza
- School of Chemistry, University of Wales, Bangor, United Kingdom
| | | | | | | | - Johan Grooten
- Department of Molecular Biomedical Research, Molecular Immunology Unit, Gent University, Belgium
| | - Gianna Toschi
- Department of Biochemistry, University of Pretoria, South Africa
| | | | - Lynne Pilcher
- Department of Chemistry, University of Pretoria, South Africa
| | | | - Nsovo Mathebula
- Department of Chemistry, University of Pretoria, South Africa
| | | | - Anton C. Stoltz
- Department of Infectious Diseases, University of Pretoria, South Africa
| | - Jan A. Verschoor
- Department of Biochemistry, University of Pretoria, South Africa
- Corresponding author. Tel.: +27 124202477; fax: +27 123625302.
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Koza G, Rowles R, Theunissen C, Al-Dulayymi JR, Baird MS. The synthesis of single enantiomers of trans-alkene-containing mycolic acids. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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The synthesis of single enantiomers of mycobacterial ketomycolic acids containing cis-cyclopropanes. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.09.099] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Sherrill WM, Rubin M. Rhodium-Catalyzed Hydroformylation of Cyclopropenes. J Am Chem Soc 2008; 130:13804-9. [DOI: 10.1021/ja805059f] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- William M. Sherrill
- Department of Chemistry, University of Kansas and Center for Environmentally Beneficial Catalysis, 1251 Wescoe Hall Drive, Malott Hall, Lawrence, Kansas 66045-7582
| | - Michael Rubin
- Department of Chemistry, University of Kansas and Center for Environmentally Beneficial Catalysis, 1251 Wescoe Hall Drive, Malott Hall, Lawrence, Kansas 66045-7582
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Al Dulayymi JR, Baird MS, Roberts E, Deysel M, Verschoor J. The first syntheses of single enantiomers of the major methoxymycolic acid of Mycobacterium tuberculosis. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Sekanka G, Baird M, innikin D, Grooten J. Mycolic acids for the control of tuberculosis. Expert Opin Ther Pat 2007. [DOI: 10.1517/13543776.17.3.315] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Al Dulayymi JR, Baird MS, Roberts E, Minnikin DE. The synthesis of single enantiomers of meromycolic acids from mycobacterial wax esters. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.09.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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