Enumeration of virtual libraries of combinatorial modular macrocyclic (Bracelet, Necklace) architectures and their linear counterparts

Journal of Chemical Information and Modeling

Volumn 53, Issue 9, 2013, Pages 2203-2216

  Taniguchi, Masahiko ^a   Du, Hai ^a   Lindsey, Jonathan S ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; CROWN ETHERS; DIGITAL LIBRARIES; ISOMERS; MONOMERS; PEPTIDES;

CYCLIC PEPTIDES; GENERATIVE ALGORITHMS; MATHEMATICAL FORMULAS; MOLECULAR ARCHITECTURE; PHOTOSYNTHETIC LIGHT; PRODUCT DISTRIBUTIONS; SOFTWARE PROGRAM; VIRTUAL LIBRARIES;

DATA MINING;

MACROCYCLIC COMPOUND;

ALGORITHM; CHEMISTRY; COMBINATORIAL CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; INFORMATION SCIENCE; ISOMERISM; PROCEDURES; ARTICLE; METHODOLOGY;

ALGORITHMS; COMBINATORIAL CHEMISTRY TECHNIQUES; INFORMATICS; ISOMERISM; MACROCYCLIC COMPOUNDS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84883274376     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400175f     Document Type: Article

References (90)

1. Bohacek, R. S.; McMartin, C.; Guida, W. C. The Art and Practice of Structure-Based Drug Design: A Molecular Modeling Perspective Med. Res. Rev. 1996, 16, 3-50
2. Weininger, D. Combinatorics of Small Molecular Structures. In Encyclopedia of Computational Chemistry; Schleyer, P. v. R.; Schreiner, P. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P.; Schaefer, H. F., III, Eds.; John Wiley & Sons, Ltd.: Chichester, 1998; Vol. 1, pp 425-430.
3. Ertl, P. Cheminformatics Analysis of Organic Substituents: Identification of the Most Common Substituents, Calculation of Substituent Properties, and Automatic Identification of Drug-like Bioisosteric Groups J. Chem. Inf. Comput. Sci. 2003, 43, 374-380
4. Dobson, C. M. Chemical Space and Biology Nature 2004, 432, 824-828
5. Fink, T.; Bruggesser, H.; Reymond, J.-L. Virtual Exploration of the Small-Molecule Chemical Universe below 160 Da Angew. Chem., Int. Ed. Engl. 2005, 44, 1504-1508
6. Kerber, A.; Laue, R.; Meringer, M.; Rücker, C. Molecules in Silico: Potential Versus Known Organic Compounds MATCH-Commun. Math. Comp. Chem. 2005, 54, 301-312
7. Gorse, A.-D. Diversity in Medicinal Chemistry Space Curr. Top. Med. Chem. 2006, 6, 3-18
8. Pitt, W. R.; Parry, D. M.; Perry, B. G.; Groom, C. R. Heteroaromatic Rings of the Future J. Med. Chem. 2009, 52, 2952-2963
9. Reymond, J.-L.; van Deursen, R.; Blum, L. C.; Ruddigkeit, L. Chemical Space as a Source for New Drugs Med. Chem. Commun. 2010, 1, 30-38
10. Varnek, A.; Baskin, I. I. Cheminformatics as a Theoretical Chemistry Discipline Mol. Inf. 2011, 30, 20-32
11. Ruddigkeit, L.; van Deursen, R.; Blum, L. C.; Reymond, J.-L. Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17 J. Chem. Inf. Model. 2012, 52, 2864-2875
12. Taniguchi, M.; Du, H.; Lindsey, J. S. Virtual Libraries of Tetrapyrrole Macrocycles. Combinatorics, Isomers, Product Distributions, and Data Mining J. Chem. Inf. Model. 2011, 51, 2233-2247
13. Taniguchi, M.; Lindsey, J. S. Diversity, Isomer Composition, and Design of Combinatorial Libraries of Tetrapyrrole Macrocycles J. Porphyrins Phthalocyanines 2012, 16, 1-13
14. Taniguchi, M.; Lindsey, J. S. Enumeration of Isomers of Substituted Tetrapyrrole Macrocycles: From Classical Problems in Biology to Modern Combinatorial Libraries. In Handbook of Porphyrin Science; Kadish, K. M.; Smith, K. M.; Guilard, R., Eds.; World Scientific: Singapore, 2012, Vol. 23, pp 1-80.
15. Lin, H.; Fischbach, M. A.; Liu, D. R.; Walsh, C. T. In Vitro Characterization of Salmochelin and Enterobactin Trilactone Hydrolases IroD, IroE, and Fes J. Am. Chem. Soc. 2005, 127, 11075-11084
16. Luz, Z.; Poupko, R.; Wachtel, E. J.; Zheng, H.; Friedman, N.; Cao, X.; Freedman, T. B.; Nafie, L. A.; Zimmermann, H. Structural and Optical Isomers of Nonamethoxy Cyclotriveratrylene: Separation and Physical Characterization J. Phys. Chem. A 2007, 111, 10507-10516
17. Hardie, M. J. Recent Advances in the Chemistry of Cyclotriveratrylene Chem. Soc. Rev. 2010, 39, 516-527
18. Bruce, J. I.; Dickins, R. S.; Govenlock, L. J.; Gunnlaugsson, T.; Lopinski, S.; Lowe, M. P.; Parker, D.; Peacock, R. D.; Perry, J. J. B.; Aime, S.; Botta, M. The Selectivity of Reversible Oxy-Anion Binding in Aqueous Solution at a Chiral Europium and Terbium Center: Signaling of Carbonate Chelation by Changes in the Form and Circular Polarization of Luminescence Emission J. Am. Chem. Soc. 2000, 122, 9674-9684
19. Yoo, J.; Reichert, D. E.; Welch, M. J. Comparative in Vivo Behavior Studies of Cyclen-Based Copper-64 Complexes: Regioselective Synthesis, X-ray Structure, Radiochemistry, log P, and Biodistribution J. Med. Chem. 2004, 47, 6625-6637
20. Ikeda, A.; Shinkai, S. Novel Cavity Design Using Calix[ n ]arene Skeletons: Toward Molecular Recognition and Metal Binding Chem. Rev. 1997, 97, 1713-1734
21. Coquière, D.; Le Gac, S.; Darbost, U.; Sénèque, O.; Jabin, I.; Reinaud, O. Biomimetic and Self-Assembled Calix[6]arene-based Receptors for Neutral Molecules Org. Biomol. Chem. 2009, 7, 2485-2500
22. Morohashi, N.; Narumi, F.; Iki, N.; Hattori, T.; Miyano, S. Thiacalixarenes Chem. Rev. 2006, 106, 5291-5316
23. Engeldinger, E.; Armspach, D.; Matt, D. Capped Cyclodextrins Chem. Rev. 2003, 103, 4147-4173
24. Krakowiak, K. E.; Bradshaw, J. S.; Zamecka-Krakowiak, D. J. Synthesis of Aza-Crown Ethers Chem. Rev. 1989, 89, 929-972
25. Gokel, G. W.; Leevy, W. M.; Weber, M. E. Crown Ethers: Sensors for Ions and Molecular Scaffolds for Materials and Biological Models Chem. Rev. 2004, 104, 2723-2750
26. Isobe, H.; Sato, S.; Nakamura, E. Synthesis of Disubstituted Cucurbit[6]uril and Its Rotaxane Derivative Org. Lett. 2002, 4, 1287-1289
27. Day, A. I.; Arnold, A. P.; Blanch, R. J. A Method for Synthesizing Partially Substituted Cucurbit[ n ]uril Molecules 2003, 8, 74-84
28. Spitler, E. L.; Johnson, C. A., II; Haley, M. M. Renaissance of Annulene Chemistry Chem. Rev. 2006, 106, 5344-5386
29. Krivokapic, A.; Anderson, H. L. Synthesis and Crystal Structure of a meso -Trialkynyl [28]hexaphyrin Org. Biomol. Chem. 2003, 1, 3639-3641
30. Sankar, J.; Mori, S.; Saito, S.; Rath, H.; Suzuki, M.; Inokuma, Y.; Shinokubo, H.; Kim, K. S.; Yoon, Z. S.; Shin, J.-Y.; Lim, J. M.; Matsuzaki, Y.; Matsushita, O.; Muranaka, A.; Kobayashi, N.; Kim, D.; Osuka, A. Unambiguous Identification of Möbius Aromaticity for meso -Aryl-Substituted [28]Hexaphyrins(1.1.1.1.1.1) J. Am. Chem. Soc. 2008, 130, 13568-13579
31. Misra, R.; Chandrashekar, T. K. Structural Diversity in Expanded Porphyrins Acc. Chem. Res. 2008, 41, 265-279
32. 3-Peptide Nanotubes as Artificial Transmembrane Ion Channels J. Am. Chem. Soc. 1998, 120, 651-656
33. Davies, J. S. The Cyclization of Peptides and Depsipeptides J. Peptide Sci. 2003, 9, 471-501
34. Kofoed, J.; Reymond, J.-L. A General Method for Designing Combinatorial Peptide Libraries Decodable by Amino Acid Analysis J. Comb. Chem. 2007, 9, 1046-1052
35. Fluxa, V. S.; Reymond, J.-L. On-Bead Cyclization in a Combinatorial Library of 15,625 Octapeptides Bioorg. Med. Chem. 2009, 17, 1018-1025
36. Hwang, H.; Schatz, G. C.; Ratner, M. A. Coarse-Grained Molecular Dynamics Study of Cyclic Peptide Nanotube Insertion into a Lipid Bilayer J. Phys. Chem. A 2009, 113, 4780-4787
37. Choi, S.-J.; Jeong, W.-J.; Kang, S.-K.; Lee, M.; Kim, E.; Ryu, D. Y.; Lim, Y.-B. Differential Self-Assembly Behaviors of Cyclic and Linear Peptides Biomacromolecules 2012, 13, 1991-1995
38. Onoda, A.; Takahashi, A.; Oohora, K.; Onuma, Y.; Hayashi, T. Fibrous Supramolecular Hemoprotein Assemblies Connected with Synthetic Heme Dimer and Apohemoprotein Dimer Chem. Biodivers. 2012, 9, 1684-1692
39. Nakanishi, T.; Naito, M.; Takeoka, Y.; Matsuura, K. Versatile Self-assembled Hybrid Systems with Exotic Structures and Unique Functions Curr. Opin. Colloid Interface Sci. 2011, 16, 482-490
40. Schulz, G. E. The Structures of General Porins. In Bacterial and Eukaryotic Porins; Benz, R., Ed.; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, 2004, pp 25-40.
41. Reedy, C. J.; Gibney, B. R. Heme Protein Assemblies Chem. Rev. 2004, 104, 617-649
42. Carlson, J. C. T.; Jena, S. S.; Flenniken, M.; Chou, T.-F.; Siegel, R. A.; Wagner, C. R. Chemically Controlled Self-Assembly of Protein Nanorings J. Am. Chem. Soc. 2006, 128, 7630-7638
43. Grabow, W. W.; Zakrevsky, P.; Afonin, K. A.; Chworos, A.; Shapiro, B. A.; Jaeger, L. Self-Assembling RNA Nanorings Based on RNAI/II Inverse Kissing Complexes Nano Lett. 2011, 11, 878-887
44. Poulsen, S.-A.; Gates, P. J.; Cousins, G. R. L.; Sanders, J. K. M. Electrospray Ionisation Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry of Dynamic Combinatorial Libraries Rapid Commun. Mass Spectrom. 2000, 14, 44-48
45. Otto, S.; Furlan, R. L. E.; Sanders, J. K. M. Dynamic Combinatorial Libraries of Macrocyclic Disulfides in Water J. Am. Chem. Soc. 2000, 122, 12063-12064
46. Saur, I.; Scopelliti, R.; Severin, K. Utilization of Self-Sorting Processes To Generate Dynamic Combinatorial Libraries with New Network Topologies Chem.-Eur. J. 2006, 12, 1058-1066
47. Roy, L.; Case, M. A. Recursively Enriched Dynamic Combinatorial Libraries for the Self-Selection of Optimally Stable Proteins J. Phys. Chem. B 2011, 115, 2454-2464
48. Chakrabarty, R.; Mukherjee, P. S.; Stang, P. J. Supramolecular Coordination: Self-Assembly of Finite Two-and Three-Dimensional Ensembles Chem. Rev. 2011, 111, 6810-6918
49. Laurent, B. A.; Grayson, S. M. Synthetic Approaches for the Preparation of Cyclic Polymers Chem. Soc. Rev. 2009, 38, 2202-2213
50. Endo, K. Synthesis and Properties of Cyclic Polymers Adv. Polym. Sci. 2008, 217, 121-183
51. Bullough, P. A.; Qian, P.; Hunter, C. N. Reaction Center-Light Harvesting Core Complexes of Purple Bacteria. In The Purple Phototrophic Bacteria; Hunter, C. N.; Daldal, F.; Thurnauer, M. C.; Beatty, J. T., Eds.; Advances in Photosynthesis and Respiration, Vol. 28; Springer: Dordrecht, The Netherlands, 2009; pp 155-179.
52. Gabrielsen, M.; Gardiner, A. T.; Cogdell, R. J. Peripheral Complexes of Purple Bacteria. In The Purple Phototrophic Bacteria; Hunter, C. N.; Daldal, F.; Thurnauer, M. C.; Beatty, J. T., Eds.; Advances in Photosynthesis and Respiration, Vol. 28; Springer: Dordrecht, The Netherlands, 2009; pp 135-153.
53. Westerhuis, W. H. J.; Sturgis, J. N.; Ratcliffe, E. C.; Hunter, C. N.; Niederman, R. A. Isolation, Size Estimates, and Spectral Heterogeneity of an Oligomeric Series of Light-Harvesting 1 Complexes from Rhodobacter sphaeroides Biochemistry 2002, 41, 8698-8707
54. McDermott, G.; Prince, S. M.; Freer, A. A.; Hawthornthwaite-Lawless, A. M.; Papiz, M. Z.; Cogdell, R. J.; Isaacs, N. W. Crystal Structure of an Integral Membrane Light-Harvesting Complex from Photosynthetic Bacteria Nature 1995, 374, 517-521
55. Koepke, J.; Hu, X.; Muenke, C.; Schulten, K.; Michel, H. The Crystal Structure of the Light-Harvesting Complex II (B800-850) from Rhodospirillum molischianum Structure 1996, 4, 581-597
56. Jamieson, S. J.; Wang, P.; Qian, P.; Kirkland, J. Y.; Conroy, M. J.; Hunter, C. N.; Bullough, P. A. Projection Structure of the Photosynthetic Reaction Centre-Antenna Complex of Rhodospirrilum rubrum at 8.5 Å Resolution EMBO J. 2002, 21, 3927-3935
57. Roszak, A. W.; Howard, T. D.; Southall, J.; Gardiner, A. T.; Law, C. J.; Isaacs, N. W.; Cogdell, R. J. Crystal Structure of the RC-LH1 Core Complex from Rhodopseudomonas palustris Science 2003, 302, 1969-1972
58. Papiz, M. Z.; Prince, S. M.; Howard, T.; Cogdell, R. J.; Isaacs, N. W. The Structure and Thermal Motion of the B800-850 LH2 Complex from Rps. acidophila at 2.0 Å Resolution and 100K: New Structural Features and Functionally Relevant Motions J. Mol. Biol. 2003, 326, 1523-1538
59. Niedzwiedzki, D. M.; Bina, D.; Picken, N.; Honkanen, N.; Blankenship, R. E.; Holten, D.; Cogdell, R. J. Spectroscopic Studies of Two Spectral Variants of Light-Harvesting Complex 2 (LH2) from the Photosynthetic Purple Sulfur Bacterium Allochromatium vinosum Biochim. Biophys. Acta 2012, 1817, 1576-1587
60. Brotosudarmo, T. H. P.; Collins, A. M.; Gall, A.; Roszak, A. W.; Gardiner, A. T.; Blankenship, R. E.; Cogdell, R. J. The Light Intensity under which Cells Are Grown Controls the Type of Peripheral Light-Harvesting Complexes that Are Assembled in a Purple Photosynthetic Bacterium Biochem. J. 2011, 440, 51-61
61. Springer, J. W.; Parkes-Loach, P. S.; Reddy, K. R.; Krayer, M.; Jiao, J.; Lee, G. M.; Niedzwiedzki, D. M.; Harris, M. A.; Kirmaier, C.; Bocian, D. F.; Lindsey, J. S.; Holten, D.; Loach, P. A. Biohybrid Photosynthetic Antenna Complexes for Enhanced Light-Harvesting J. Am. Chem. Soc. 2012, 134, 4589-4599
62. Reddy, K. R.; Jiang, J.; Krayer, M.; Harris, M. A.; Springer, J. W.; Yang, E.; Jiao, J.; Niedzwiedzki, D. M.; Pandithavidana, D.; Parkes-Loach, P. S.; Kirmaier, C.; Loach, P. A.; Bocian, D. F.; Holten, D.; Lindsey, J. S. Palette of Lipophilic Bioconjugatable Bacteriochlorins for Construction of Biohybrid Light-Harvesting Architectures Chem. Sci. 2013, 4, 2036-2053
63. Faulon, J.-L.; Visco, Jr., D. P.; Roe, D. Enumerating Molecules. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Larter, R.; Cundari, T. R., Eds.; John Wiley and Sons, Inc.: Hoboken, NJ, 2005, Vol. 21, pp 209-286.
64. Cotton, F. A. Chemical Applications of Group Theory; John Wiley & Sons: New York, 1990.
65. Berlin, K.; Jain, R. K.; Richert, C. Are Porphyrin Mixtures Favorable Photodynamic Anticancer Drugs? A Model Study with Combinatorial Libraries of Tetraphenylporphyrins Biotechnol. Bioeng. (Comb. Chem.) 1998, 61, 107-118
66. Drain, C. M.; Gong, X.; Ruta, V.; Soll, C. E.; Chicoineau, P. F. Combinatorial Synthesis and Modification of Functional Porphyrin Libraries: Identification of New, Amphipathic Motifs for Biomolecule Binding J. Comb. Chem. 1999, 1, 286-290
67. Demirev, P. A.; Zubarev, R. A. Probing Combinatorial Library Diversity by Mass Spectrometry Anal. Chem. 1997, 69, 2893-2900
68. Nefedov, A. V.; Sadygov, R. G. A Parallel Method for Enumerating Amino Acid Compositions and Masses of All Theoretical Peptides. BMC Informatics [Online] 2011, 12, Article 432; http://www.biomedcentral.com/1471-2105/12/432.
69. He, F.; Emmett, M. R.; HaÌŠkansson, K.; Hendrickson, C. L.; Marshall, A. G. Theoretical and Experimental Prospects for Protein Identification Based Solely on Accurate Mass Measurement J. Proteome Res. 2004, 3, 61-67
70. Roberts, J. D.; Caserio, M. C. Basic Principles of Organic Chemistry, 2 nd ed.; W. A. Benjamin, Inc.: Menlo Park, CA, 1977, p 32.
71. Mazur, D. R. Combinatorics. A Guided Tour; The Mathematical Association of America: Washington, DC, 2010; pp 187-224.
72. Nefedov, A. V.; Mitra, I.; Brasier, A. R.; Sadygov, R. G. Examining Troughs in the Mass Distribution of All Theoretically Possible Tryptic Peptides J. Proteome Res. 2011, 10, 4150-4157
73. Edelberg, M. Solutions to Problems in Introduction to Combinatorial Mathematics; McGraw Hill Book Co.: New York, 1968; p 103.
74. Davis, T. Pólya's Counting Theory. http://www.geometer.org/ mathcircles (accessed November 10, 2012).
75. Pólya, G.; Tarjan, R. E.; Woods, D. R. Notes on Introductory Combinatorics; Birkhäuser: Boston, 1983.
76. Dineva, R. The Euler Totient, the Mobius and the Divisor Functions; Mount Holyoke College: South Hadley, MA, 2005; pp 1-22; http://www.mtholyoke.edu/ ∼robinson/reu/reu05/rdineva1.pdf.
77. Nieman, J. Symmetries, Coloring, and Polyanumeration. M. S. Thesis, School of Mathematical Sciences, Rochester Institute of Technology, 2007.
78. Bjørge, A. N. Counting and Coloring with Symmetry. A Presentation of Polya's Enumeration Theorem with Applications. M. S. Thesis, Department of Mathematical Sciences, Norwegian University of Science and Technology, 2009.
79. Badar, M.; Iqbal, A. Polya's Enumeration Theorem. M. S. Thesis, School of Computer Science, Physics and Mathematics, Linnaeus University, 2010.
80. Kennedy, B. A.; McQuarrie, D. A.; Brubaker, C. H., Jr. Group Theory and Isomerism Inorg. Chem. 1964, 3, 265-268
81. Freudenstein, F. The Basic Concepts of Polya's Theory of Enumeration, with Application to the Structural Classification of Mechanisms J. Mechan. 1967, 3, 275-290
82. Riordan, J. An Introduction to Combinatorial Analysis; Princeton University Press: Princeton, NJ, 1980; pp 147-151.
83. Economou, A. The Symmetry of the Equal Temperament Scale. In Mathematics & Design 98, Proceedings of the Second International Conference; Barrallo, J., Ed.; The University of Basque Country: Spain, 1998; pp 557-566.
84. Baraldi, I.; Fiori, C.; Vanossi, D. On the Cycle Index of Point Groups J. Math. Chem. 1999, 25, 23-30
85. Tucker, A. C. Burnside/Pólya Counting Formula. In Handbook of Discrete and Combinatorial Mathematics; Rosen, K. H.; Michaels, J. G.; Gross, J. L.; Grossman, W. J.; Shier, D. R., Eds.; CRC Press: New York, 2000; pp 120-127.
86. Mossinghoff, M. J. Enumerating Isodiametric and Isoperimetric Polygons J. Combin. Theory Ser. A 2011, 118, 1801-1815
87. Maclean, D.; Baldwin, J. J.; Ivanov, V. T.; Kato, Y.; Shaw, A.; Schneider, P.; Gordon, E. M. Glossary of Terms Used in Combinatorial Chemistry Pure Appl. Chem. 1999, 71, 2349-2365
88. Escalante, M.; Zhao, Y.; Ludden, M. J. W.; Vermeij, R.; Olsen, J. D.; Berenschot, E.; Hunter, C. N.; Huskens, J.; Subramanian, V.; Otto, C. Nanometer Arrays of Functional Light Harvesting Antenna Complexes by Nanoimprint Lithography and Host-Guest Interactions J. Am. Chem. Soc. 2008, 130, 8892-8893
89. Böhm, P. S.; Southall, J.; Cogdell, R. J.; Köhler, J. Single-Molecule Spectroscopy on RC-LH1 Complexes of Rhodopseudomonas acidophila Strain 10050 J. Phys. Chem. B 2013, 117, 3120-3126
90. Van Patten, P. G.; Shreve, A. P.; Lindsey, J. S.; Donohoe, R. J. Energy-Transfer Modeling for the Rational Design of Multiporphyrin Light-Harvesting Arrays J. Phys. Chem. B 1998, 102, 4209-4216